Abstract:
An algorithm has been developed to identify four DNA sequences of 20 bases or more that form a structure called a connectron. Two sequences C1 and C2 are adjacent to each other. These sequences are expressed as RNA in the 3′UTR of some genes in many prokaryotic, archea and eukaryotic genomes. The other half of a connectron is two DNA sequences T1 and T2 that are on the same chromosome and range in distance from each other by about 1 kb to 105 kb. The C1 sequence is identical to the T1 sequence and the C2 sequence is identical to the T2 sequence. C1/C2 and T1-T2 can be on different chromosomes. The C1/C2 RNA sequence of the gene transcript finds the two double-stranded DNA sequences T1 and T2. The single-stranded RNA and double-stranded DNA then form a triple-stranded Hoogsteen helix of the RNA/DNA/DNA variety. Because the C1 sequence is adjacent to the C2 sequence, the T1 sequence is made spatially adjacent to the T2 sequence in a compact X-shaped structure. Chromatin particles form as compact 30 nm assemblies in the DNA between T1 and T2 thus eliminating the intervening genes from promotion and expression. Connectrons remove sets of genes from expression and thus modulate the behavior of many types of cells.

Description:
REFERENCE TO RELATED APPLICATION  
       [0001]    The present application is the subject of Provisional Application Ser. No. 60/208,650 filed Jun. 2, 2000 entitled ALGORITHMIC DETERMINATION OF CONNECTRONS FOR THE HIGH LEVEL REGULATION OF GENE EXPRESSION. 
     
    
     
       INTRODUCTION  
         [0002]    RNA introduced into a cell by a virus is now known to trigger a cellular defense mechanism known as post-transcriptional gene silencing (PTGS). If the viral RNA sequence matches a sequence within the cell&#39;s genome the associated genes are turned off or silenced. This phenomenon is also called ‘RNA interference’ or RNAi. A single-stranded RNA can interact with another single-stranded RNA (known as antisense RNA). The single-stranded RNA can also form a triple-stranded complex with double-stranded DNA. This triple-stranded complex is known as a Hoogsteen helix. This patent application shows how two specific adjacent RNA single-stranded sequences (called C1 and C2—for Control Sequence 1 and Control Sequence 2) interact with two distant double-stranded DNA sequences (called T1 and T2—for Target Sequence 1 and Target Sequence 2) to form a tetradic relationship which is called a “connectron”. The two distant DNA double-stranded sequences (T1 and T2) must be on the same chromosome in a genome and they must be between about 1 kb and 105 kb of each other. The adjacent single-stranded RNA sequences (C1/C2) can be on the same or different chromosome as the T1 and T2 sequences. The C1 sequence is identical to the T1 sequence and the C2 sequence is identical to the T2 sequence. The connectron acts to stabilize the double-stranded DNA by allowing 30 nm chromatin particles to form. Genes that lie between the T1 and T2 sequences when wrapped up in 30 nm chromatin particles are not open to promotion and expression. The connectron (i.e. the tetradic relationship between the T1-T2 sequences and C1/C2 sequences) provides a general explanation for PTGS. A connectron can implemented by RNA sequences, PNA (Peptide Nucleic Acid) sequences or by a zinc-finger DNA Binding Protein (DBP) specific to the T1 and T2 sequences.  
           [0003]    Characteristically the adjacent C1/C2 sequences lie in the 3′UTR of a gene. The T1 and T2 sequences do not lie within the translated region of any gene. These sequences “surround” one or more genes. There are, however, T1 and T2 sequence pairs that surround one or more C1/C2 sequences that are not 3′UTR to any gene. These are called “geneless connectrons”. There may be promoter sequences that cause the transcription of these 3′UTR sequences.  
           [0004]    A computer-based algorithm that is similar to the algorithm used in the U.S. Pat. No. 6,205,404 has been developed to determine the connectron structure of any genome. This algorithm determines the existence of all the connectrons in the genomic DNA. Connectrons exist in prokaryotes, archea, single-celled eukaryotes, multi-celled eukaryotes, plants and higher animals. Connectron relationships exist between prokaryotes and their plasmids. The geneless connectrons provide a possible mechanism for forming a hierarchy of gene expression control that will produce an understanding of cell differentiation and tissue development.  
           [0005]    Each connectron is a unique tetrad of sequences. Each connectron changes the expression of the genes between the T1 and T2 sequences. The C1 sequence (which is equivalent to the T1 sequence) and the C2 sequence (which is equivalent to the T2 sequence) are determined by the invention described in this patent application. In general, the tetrad of connectron sequences can be patented because the structure of matter is known and the function of specific gene expression modulation is also known. Gene expression modification can be produced by introducing antisense RNA or PNA to interact C1/C2 RNA sequences or zinc-finger DBPs to interact with the T1 and T2 sequences. Using connectrons it will be possible to modify cellular and tissue behavior in a very general manner.  
           [0006]    Examples will be given from different genomes to illustrate that the connectron is a perfectly general and universal concept.  
           [0007]    Definitions  
           [0008]    Double stranded DNA—Watson and Crick showed in 1953 that DNA naturally forms a double-stranded helix. A typical double stranded sequence is  
                       5′-TAGAGGAGTACCAC-3′               3′-ATCTCCTCATGGTG-5′          
 
           [0009]    Hydrogen Bond—The force between a hydrogen atom and another heavier atom such as Oxygen (O), Nitrogen (N), Phosphorus (P), or Sulfur (S).  
           [0010]    Positive strand—The positive strand is normally represented 5′ to 3′ running left to right as in  
           [0011]    5′-TAGAGGAGTACCAC-3′ 
           [0012]    Negative strand—The negative strand is normally represented 5′ to 3′ running right to left as in  
           [0013]    3′-ATCTCCTCATGGTG-5′ 
           [0014]    Single stranded RNA—Either the positive or the negative strand of the double-stranded DNA can be transcribed by the polymerase. In RNA U replaces T.  
                                           RNA of positive strand sequence   5′-UAGAGGAGUACCAC-3′                           RNA of negative strand sequence   5′-GUGGUACUCCUCUA-3′          
 
           [0015]    Antisense RNA—The antisense strand of any RNA sequence is the compliment sequence  
                           RNA sequence   5′-UAGAGGAGUACCAC-3′               Antisense RNA sequence   3′-AUCUCCUCAUGGUG-5′          
 
           [0016]    Triple Strand Helix—The RNA sequence of a RNA/DNA triple-strand complex is the same as the positive strand of the DNA  
                           DNA positive strand   5′-TAGAGGAGTACCAC-3′               DNA negative strand   3′-ATCTCCTCATGGTG-5′               RNA strand   5′-UAGAGGAGUACCAC-3′          
 
           [0017]    Promoter—Any region of DNA, that binds proteins which engage the polymerase transcription mechanism.  
           [0018]    TATA Box—A region near the 3′ end of a promoter with the sequence TATA.  
           [0019]    mRNA—The RNA produced from the DNA by the polymerase as a result of transcription  
           [0020]    Start of transcription—The 3′ end of a promoter where the polymerase mechanism begins to transcribe DNA into mRNA.  
           [0021]    Exon—Any region of mRNA which is used to code for proteins  
           [0022]    Intron—Any region of mRNA lying between two exons which is not used to code for proteins. The introns are edited out of the initial RNA transcript to form the mature mRNA.  
           [0023]    3′ UTR—The untranslated 3′ end of an mRNA is beyond the end of the last exon. A stop codon in the mRNA causes the ribosome to stop the translation of mRNA into protein.  
           [0024]    End of translation—The 3′ end of the 3′-most exon.  
           [0025]    Translated region—Any collection of exons and introns.  
           [0026]    Gene—Any DNA region that codes for a protein. Introns do not occur in prokaryotic genes and they sometime fail to occur in eukaryotic genes. A typical model of a gene is  
                         
 
           [0027]    Positive strand gene—Any gene in which the features run 5′ to 3′ on the positive strand  
           [0028]    Negative strand gene—Any gene in which the features run 5′ to 3′ on the negative strand  
           [0029]    C1 sequence—Any positive or negative strand DNA sequence of 20 bases or more.  
           [0030]    The C2 sequence must occur in the same chromosome as the C1 sequence.  
           [0031]    C2 sequence—Any positive or negative strand DNA sequence of 20 bases or more. The C1 sequence must occur in the same chromosome as the C2 sequence.  
           [0032]    C1/C2—Any positive or negative strand DNA sequence of 40 or more bases such that the C1 sequence is adjacent to the C2 sequence  
           [0033]    T1 sequence—Any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence. The T1 and T2 sequences must be between about 1 kb and 105 kb apart.  
           [0034]    T2 sequence—Any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence. The T2 and T1 sequences must be between about 1 kb and 105 kb apart.  
           [0035]    Last exon gap or Gap-Distance—The number of bases between the end of transcription and the beginning of the C1/C2 sequence. In prokaryotes and single-celled eukaryotes this gap can range from no bases to 500 bases. In multi-celled eukaryotes the gap can be as large as 10,000 bases.  
           [0036]    Poly-adenylation signal—A number of Adenosine (A) bases are added to the mRNA at the end of the 3′UTR.  
           [0037]    Possible Connectron—Any set of T1, T2 and C1/C2 sequences such that the C1 sequence is identical to the T1 sequence and the C2 sequence is identical to the T2 sequence. The promoter of some gene causes the mRNA of the gene to be expressed. The mRNA is edited to eliminate the introns. The whole mRNA including the 3′UTR can move about in the cell or the nucleus of the cell. The C1/C2 RNA that is part of the 3′UTR moves to the T1 and T2 DNA sequences. A triple-stranded complex of the DNA and the RNA forms such that the C1 sequence forms hydrogen bonds with the T1 sequence and the C2 sequence forms hydrogen bonds with the T2 sequence.  
           [0038]    Because the C1 sequence is adjacent to the C2 sequence, the T1 sequence is brought physically close to the T2 sequence. This produces a loop of between about 1 kb and 105 kb in the DNA. Histone proteins reduce the length of the DNA by binding 200 bases. Histone/DNA complexes form six-fold symmetry chromatin assemblies. The diameter of the chromatin assemblies is approximately 30 nm.  
           [0039]    Real Connectron—Any Possible Connectron which is within the Gap-Distance of some gene  
           [0040]    Homologous connectron—The T1 sequence and the T2 sequence are on the same chromosome as the C1/C2 sequence  
           [0041]    Heterologous connectron—The T1 sequence and the T2 sequence are on a chromosome different from chromosome of the C1/C2 sequence  
           [0042]    Permanent connectron—Any C1/C2 sequence, which is 3′ UTR to some gene that is not surrounded by any T1 and T2 sequence pairs  
           [0043]    Transient connectron—Any C1/C2 sequence, which is 3′ UTR to some gene that is surrounded by one or more T1 and T2 sequence pairs  
           [0044]    Self-limiting connectron—Any C1/C2 sequence which is 3′UTR to some gene that is surrounded by the T1 and T2 sequences such that C1=T1 and C2=T2  
           [0045]    Geneless connectron—Any C1/C2 sequence which is not 3′UTR to some gene but is surrounded by some T1 and T2. A promoter may lie 5′ to the C1/C2 sequence.  
           [0046]    Bidirectionality of Connectron Excitation—A C1/C2 short loop on one strand selects a T1-T2 long loop pair on the same or the opposite strand. The C1/C2 short loop has a complementary C1′/C2′ sequence on the opposite strand. Similarly the T1-T2 long loop pair has a complementary long loop pair T1′-T2′. Wherever a C1/C2, T1-T2 tetrad exists there is a complementary C1′/C2′, T1′-T2′ tetrad. The C1/C2 short loop can be transcribed as a 3′UTR to a gene on the same strand. The C1′/C2′ short loop which is on the strand opposite to the C1/C2 short loop can also can be transcribed as a 3′UTR to a gene on the same strand. There are four possible models of action  
                                                  T1         T2      gene− C1/C2               + strand ---------------------------------------------           − strand ---------------------------------------------                                  T1         T2           + strand ---------------------------------------------           − strand ---------------------------------------------                                              C2/C1 − gene                       + strand ---------------------------------------------           − strand ---------------------------------------------                         T2′        T1′         C2′/C1′− gene                                                 gene − C1′/C2′           + strand ---------------------------------------------           − strand ---------------------------------------------                   T2′           T1′          
 
           [0047]    Of course, the short loops and the long loops do not have to be on the same chromosome.  
           [0048]    Hierarchy of connectron action—When a C1/C2 is expressed it forms a T1-T2 loop by forming a connectron. The C1/C2 sequence does not have to be on the same chromosome as the T1 and T2 sequences. This provides a way of causing interaction between chromosomes. When the T1-T2 loop forms, any genes in that loop region which had been expressing C1/C2 sequences in their 3′UTRs, now cease expressing the C1/C2 sequences. The connectrons formed by these C1/C2 sequences will cease to exist after some time thus opening up the genes inside the respective T1-T2 loops to expression. The hierarchy of connectron action is alternates between repression and expression. The connectron hierarchies can be of any depth.  
           [0049]    One-to-Many connectron action—One C1/C2 sequence can form connectrons in many different places on many different chromosomes. The only requirement is that C1=T1 and C2=T2. This makes it possible for one expression event to control the expression of many genes on different chromosomes.  
           [0050]    Many-to-One connectron action—C1/C2s that come from many different places on many different chromosomes can form a connectron for a specific T1-T2 sequence pair. The only requirement is that C1=T1 and C2=T2. This makes it possible for many different expression events to control the expression of one set of genes on a particular chromosome.  
           [0051]    Many-to-Many connectron action—The arrangement of C1/C2s and T1-T2s across chromosomes can form a complex web of gene expression control relationships.  
           [0052]    Percentage of the Genome Regulated by Connectrons—Since the connectrons for a sequenced genome can be calculated, the percentage of the genome that is open to connectron regulation can be known.  
           [0053]    Emergent Property—The network of connectrons in any genome emerges from a knowledge of the complete DNA sequence of the genome. Because both the C1/C2 sequences and the T1-T2 sequences can be any place in the genome, the whole genomic sequence must be known before all the connectrons can be determined.  
           [0054]    Paradigm Shift—For the past fifty years since the discovery by Watson and Crick of the double-helical nature of DNA, the reigning paradigm for scientific discovery has been the study of one gene and its effects on the behavior of a cell. The advent of genomic sequencing and this invention of connectrons that emerge from the whole genome will produce a shift in the way scientists view biological systems and the way they formulate and execute experiments. The many-to-many relationships between the connectrons means that there are many ways in which the expression of a set of genes can be modulated. The multiplicity of control pathways means produces a system stability that makes it possible for biological systems to be stable for long periods of evolutionary time. The thinking that goes into formulating scientific experiments will have to change to accommodate the changes in understanding that will be induced by the application and extension of this patent application.  
           [0055]    Hierarchy of DNA Structuring—The DNA of a cell&#39;s genome is structured in a hierarchy of six levels. FIGS. 1, 2 and  3  have been adapted from The Molecular Biology of the Cell by Alberts, Bray, Lewis, Raff, Roberts and Watson [third edition pages 354, 345 and 348]. As shown in FIG. 1, the double stranded DNA is level 1. The double-stranded DNA is wrapped around histone proteins to form a chromatin particle that is level 2 of the hierarchy. Level 2 is described as “beads-on-a-string” in FIG. 1. The chromatin particles are packed in a six-fold symmetry as shown in FIG. 2 a  and FIG. 2 b . These six-fold assemblies have a diameter of 30 nm. Each 30 nm assembly contains from 18 (i.e. 6*3) to 30 (i.e. 6*5) chromatin particles. The 30 nm assemblies aggregate into large loops which range in length from 5,000 bases to 100,000 bases of DNA. The size of these large loops as shown in FIG. 1 is approximately 300 nm. These large loops constitute level 4 of the structuring hierarchy. As shown in FIG. 1, level 5 of the DNA structuring hierarchy many large loops are condensed to form a structure which is approximately 700 nm in diameter. The complete chromosome that constitutes level 6 of the hierarchy is composed of two very long sections of level 5 DNA.  
           [0056]    Model of Chromatin Structure—The level 4 structure of DNA as shown in FIG. 1 ranges in length from 5,000 to 105,000 bases of DNA. FIG. 3 shows that proteins are thought to connect portions of the long loops formed by the 30 nm particles to form a chromosome axis. These condensed long loops are described as chromomeres in The Molecular Biology of the Cell.  
         PRIOR ART  
         [0057]    The chromomere model of DNA structuring was presented by N. A Resnik, et al.[1] and is based on electron microscopic data. There are more recent papers studying a variety of genomes with electron microscopy but no equivalent study of chromomeres has been done on a fully sequenced genome.  
           [0058]    A recent News Feature in Nature by T. Gura [2] described the discovery of post-transcriptional gene silencing in which viral RNA interacts with the transcribed RNA of the cell to silence the expression of genes. This article describes experiments in  C. elegans  and  D. megalomaster  in which RNA that is complementary to mRNA introduced into a cell. This “antisense” RNA has the effect of turning off the expression of one or more genes. The introduced complementary RNA produces an “RNA interference” called RNAi.  
           [0059]    Thomas Werner and his colleagues at Genomatix in Munich, Germany have developed an approach to understanding what they call “Matrix Attachment Region” (MAR). FIG. 5 shows their interpretation of the structure of DNA surrounding a gene. The following description of the MAR is copied from the Genomatrix web site  
           [0060]    “Matrix Attachment Regions (MARs) MARs are sequence regions that are responsible for the attachment of genomic DNA to the nuclear matrix or scaffold. Transcription absolutely requires anchorage of genomic DNA to the nuclear matrix.  
           [0061]    Functional features of MARs:  
           [0062]    Anchoring of regulatory elements like promoters and enhancers to the nuclear matrix.  
           [0063]    Ensuring long term activity of promoters and enhancers in chromatin.  
           [0064]    Insulation, rendering a functional domain insensitive to position effects.  
           [0065]    Genomatix is conducting a research project to define and detect MARs by computer-analysis.” 
         BRIEF DESCRIPTION OF THE OBJECTS OF THE INVENTION  
         [0066]    An object of the invention is to provide a method of identifying DNA sequences that control the expression of different collections of genes in a genome comprising, detecting selected DNA sequences adjacent to some genes excluding exons and introns.  
           [0067]    An object of the invention is to provide a method of identifying DNA sequences that control the expression of different collections of genes comprising, detecting, by computer, one or more pairs of non-adjacent DNA sequences to which are bound to two RNA sequences.  
           [0068]    An object of the invention is to provide a method of identifying DNA sequences that control the expression of different collections of genes in a genome comprising detecting changes in connectron behavior in the genome.  
           [0069]    An object of the invention is to provide a method of modifying the expression of different gene collections in a genome, comprising detecting changes in connectron behavior as a result of an exogenous stimulus.  
           [0070]    An object of the invention is to provide a method of detecting where and when new genes are being integrated into a host genome comprising detecting the connectrons in said host genome.  
           [0071]    An object of the invention is to provide a method of detecting the expression effect of different gene collections in a given body comprising detecting the back and forth flow of connectrons between the chromosomes thereof.  
           [0072]    An object of the invention is to provide a method of modifying a given body comprising modifying the connectron organization therein.  
           [0073]    An object of the invention is to provide a method of detecting connectron control and target sequences in a given genome comprising:  
           [0074]    determining the base composition of said genome,  
           [0075]    determining one or more sites of control sequence organization, and/or  
           [0076]    determining one or more sites of target application.  
           [0077]    An object of the invention is to provide a method of determining the response of a cell in any tissue to changes in the cell&#39;s environment and/or genetic composition comprising providing a complete genomic DNA sequence for the organism and determining the effect of changes in connectrons due to application of a given exogenous stimulus to the gnome.  
           [0078]    An object of the invention is to provide a method of determining in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the tetradic relationship T1=C1 and T2=C2 where T1 and T2 are DNA sequences 20 or more bases in length, where the C1 sequence is adjacent to the C2 sequence, where the T1 and T2 sequences are on the same chromosome, and where the C1/C2 sequences are on the same chromosome as T1 and T2 or where the C1/C2 sequences are on a chromosome different from T1 and T2, wherein:  
           [0079]    C1 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the C1 sequence,  
           [0080]    C2 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C1 sequence must occur in the same chromosome as the C2 sequence,  
           [0081]    C1/C2—any positive or negative strand DNA sequence of 40 or more bases such that the C1 sequence is adjacent to the C2 sequence,  
           [0082]    T1 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the T1 and T2 sequences must be between about 1 kb and 105 kb apart, and  
           [0083]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, the T2 or T1 sequences must be between about 1 kb and 105 kb apart.  
           [0084]    An object of the invention is to provide a method of determining in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the connectron relationship that permits many different C1/C2 short loops to control the existence of a T1-T2 long loop and wherein said C1/C2 short lops can be on the same chromosome or on different chromosomes from the T1-T2 long loop, wherein:  
           [0085]    C1 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the C1 sequence,  
           [0086]    C2 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C1 sequence must occur in the same chromosome as the C2 sequence,  
           [0087]    C1/C2—any positive or negative strand DNA sequence of 40 or more bases such that the C1 sequence is adjacent to the C2 sequence,  
           [0088]    T1 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the T1 and T2 sequences must be between about 1 kb and 105 kb apart, and  
           [0089]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, the T2 or T1 sequences must be between about 1 kb and 105 kb apart.  
           [0090]    An object of the invention is to provide a method of determining in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the connectron relationship that permits one C1/C2 short loop to control the existence of many T1-T2 long loops, the C1/C2 short loop can be on the same chromosome or on different chromosomes from the T1-T2 long loops, wherein:  
           [0091]    C1 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the C1 sequence,  
           [0092]    C2 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C1 sequence must occur in the same chromosome as the C2 sequence,  
           [0093]    C1/C2—any positive or negative strand DNA sequence of 40 or more bases such that the C1 sequence is adjacent to the C2 sequence,  
           [0094]    T1 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the T1 and T2 sequences must be between about 1 kb and 105 kb apart, and  
           [0095]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, the T2 or T1 sequences must be between about 1 kb and 105 kb apart.  
           [0096]    An object of the invention is to provide a method of determining in the connectron relationships between prokaryotes and their plasmids wherein said connectrons implement a control mechanism between the two genomes that makes it possible from them to form a symbiotic relationship, and in the case of  D. radiodurans  the relationship is not symmetric, and the  D. radiodurans  genome sends C1/C2 short loops to the MP1 plasmid, wherein:  
           [0097]    C1 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the C1 sequence,  
           [0098]    C2 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C1 sequence must occur in the same chromosome as the C2 sequence,  
           [0099]    C1/C2—any positive or negative strand DNA sequence of 40 or more bases such that the C1 sequence is adjacent to the C2 sequence,  
           [0100]    T1 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the T1 and T2 sequences must be between about 1 kb and 105 kb apart, and  
           [0101]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, the T2 or T1 sequences must be between about 1 kb and 105 kb apart.  
           [0102]    An object of the invention is to provide a method of determining that connectron relationships that exist in plant and higher animals.  
           [0103]    An object of the invention is to provide a method of determining in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the connectron relationship that permits one C1/C2 short loop to control the existence of one or more T1-T2 long loops without being subject to any expression controls other than those of the gene to which the C1/C2 is 3′UTR, wherein:  
           [0104]    C1 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the C1 sequence,  
           [0105]    C2 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C1 sequence must occur in the same chromosome as the C2 sequence,  
           [0106]    C1/C2—any positive or negative strand DNA sequence of 540 or more bases such that the C1 sequence is adjacent to the C2 sequence,  
           [0107]    T1 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the T1 and T2 sequences must be between about 1 kb and 105 kb apart,  
           [0108]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, the T2 or T1 sequences must be between about 1 kb and 105 kb apart, and  
           [0109]    3′UTR—untranslated 3′ end of an mRNA is beyond the end of the last exon, a stop codon in the mRNA causes the ribosome to stop the translation of mRNA into protein.  
           [0110]    An object of the invention is to provide a method of determining in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the connectron relationship that permits one C1/C2 short loop to control the existence of one or more T1-T2 long loops such that this C1/C2 short loop is itself subject to expression control by another T1-T2 long loop which surrounds it, wherein:  
           [0111]    C1 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the C1 sequence,  
           [0112]    C2 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C1 sequence must occur in the same chromosome as the C2 sequence,  
           [0113]    C1/C2—any positive or negative strand DNA sequence of 540 or more bases such that the C1 sequence is adjacent to the C2 sequence,  
           [0114]    T1 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the T1 and T2 sequences must be between about 1 kb and 105 kb apart, and  
           [0115]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, the T2 or T1 sequences must be between about 1 kb and 105 kb apart.  
           [0116]    An object of the invention is to provide a method of determining in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the connectron relationship that permits one C1/C2 short loop to control the existence of the T1-T2 long loop that surrounds it, wherein:  
           [0117]    C1 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the C1 sequence,  
           [0118]    C2 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C1 sequence must occur in the same chromosome as the C2 sequence,  
           [0119]    C1/C2—any positive or negative strand DNA sequence of 40 or more bases such that the C1 sequence is adjacent to the C2 sequence,  
           [0120]    T1 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the T1 and T2 sequences must be between about 1 kb and 105 kb apart, and  
           [0121]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, the T2 or T1 sequences must be between about 1 kb and 105 kb apart.  
           [0122]    An object of the invention is to provide a method of determining the connectron relationships that do not have any genes within the T1-T2 long loop, wherein:  
           [0123]    T1 sequence is any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, and  
           [0124]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, and the T2 or T1 sequences must be between about 1 kb and 105 kb apart.  
           [0125]    An object of the invention is to provide a method of determining the geneless connectron relationship where one C1/C2 short loop controls the existence of many geneless T1-T2 long loops, wherein:  
           [0126]    C1 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the C1 sequence,  
           [0127]    C2 sequence—any positive or negative strand DNA sequence of 20 bases or more, the C1 sequence must occur in the same chromosome as the C2 sequence,  
           [0128]    C1/C2—any positive or negative strand DNA sequence of 40 or more bases such that the C1 sequence is adjacent to the C2 sequence,  
           [0129]    T1 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the T1 and T2 sequences must be between about 1 kb and 105 kb apart, and  
           [0130]    T2 sequence—any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T1 sequence, the T2 or T1 sequences must be between about 1 kb and 105 kb apart.  
       
    
    
     DESCRIPTION OF THE DRAWINGS AND TABLES  
       [0131]    The above and other objects, advantages and features of the invention will become more apparent when considered with the following specification and accompanying drawings and tables wherein:  
         [0132]    [0132]FIG. 1 DNA is structured in six levels of increasing condensation. Double stranded DNA is level 1. Two turns of DNA are wrapped about each chromatin particle at level 2. The chromatin particles which each containing 200 base pairs form into 30 nm particles at level 3. The 30 nm particles form into large loops with an approximate dimension of 300 nm at level 4. Metaphase chromosomes form a condensed structure with an approximate dimension of 700 nm at level 5. An entire metaphase chromosome has a width of approximately 1400 nm at level 6. The large loops at level 4 of the DNA structuring are thought to have between 20,000 (20 kb) and 100,000 (100 kb) base pairs.  
         [0133]     The Molecular Biology of the Cell by Alberts, Bray, Lewis, Raff, Roberts and Watson, 3rd. ed., Garland Publishing, Inc., New York, 1994, p. 354  
         [0134]    [0134]FIG. 2 (a) Chromatin DNA forms into a six-fold symmetry 30 nm particles.  
         [0135]     (b) The six-fold symmetry 30 nm particles form a linear chain with a varying number of repeat units.  
         [0136]     The Molecular Biology of the Cell by Alberts, Bray, Lewis, Raff, Roberts and Watson, 3rd. ed., Garland Publishing, Inc., New York, 1994, p. 345  
         [0137]    [0137]FIG. 3 Long loops of 30 nm particles are thought to be closed at the bottom of the loop by proteins.  
         [0138]     The Molecular Biology of the Cell by Alberts, Bray, Lewis, Raff, Roberts and Watson, 3rd. ed., Garland Publishing, Inc., New York, 1994, p. 348  
         [0139]    [0139]FIG. 4 (a) Transcription and Editing. (b) Movement of the RNA through the Nucleus. (c) Connectron Formation  
         [0140]    [0140]FIG. 5 Overview of schematic organization of a typical transcriptionally active chromosomal loop.  
         [0141]     From http://genomatix.gsf.de/funcgenomics/functional_genomics.html  
         [0142]    Table 1 Connectron Properties for Prokaryotic, Archea and Eukaryotic Genomes  
         [0143]    Table 2 Yeast Inter-Chromosomal Connectron Distribution  
         [0144]    [0144]FIG. 6 Genome size plotted as a log-log function of the Number of Connectrons  
         [0145]    [0145]FIG. 7 Number of Sequence Instances plotted as a function of the Number of Fragments  
         [0146]    [0146]FIG. 8 Level 0—The overall view of the algorithm  
         [0147]    [0147]FIG. 9 Level 1—Process Flow of the Algorithm  
         [0148]    [0148]FIG. 10 Level 2a—two pages—Process Genome into Blocking Fragment File  
         [0149]    [0149]FIG. 11 Level 2b—two pages—Compute the Connectrons for a Genome  
         [0150]    [0150]FIG. 12 Level 2c—two pages—Analyze Possible Connectrons  
         [0151]    [0151]FIG. 13 Level 3a—Setup Genome Usage Memory  
         [0152]    [0152]FIG. 14 Level 3b—Find DBP-Size Blocking File for T1-Window  
         [0153]    [0153]FIG. 15 Level 1—Find DBP-Size Blocking File for T2-Window  
         [0154]    [0154]FIG. 16 Level 2a—two pages—Find C1/C2 Entries  
         [0155]    [0155]FIG. 17 Level 2b—two pages—Scan Genome Usage Memory for Potential Connectrons  
     
    
     DESCRIPTION OF THE INVENTION  
       [0156]    A connectron is a relationship among four DNA sequences. Each sequence must be at least 20 bases long. There is a report by Sharp and Zamore [3] that RNA sequences of “about length 25” are important as sources of RNAi. 27 bases were actually used as the minimum length of each of the sequences. The T1 sequence is on one strand of some chromosome in a genome. The T2 sequence is on the same strand of the same chromosome as the T1 sequence. The T1 and T2 sequences (which are each at least 20 bases in length) must be at least 5,000 bases distant from each other but they can not be more than 105,000 bases distant from each other. The C1 sequence and the C2 sequence (which are each at least 20 bases in length) are adjacent to each other on some strand of some chromosome in the genome. The C1/C2 sequences—called the “short loop”—can be on the same strand as the T1 and T2 sequences or they can be on the opposite strand. The C1/C2 sequences of the short loop can be on the same chromosome as the T1 and T2 sequences but they can also be on a different chromosome in the genome. When a genome has only one chromosome, then the point is moot. Many genomes, of course, have several chromosomes. The C1 sequence is identical to the T1 sequence and the C2 sequence is identical to the T2 sequence.  
         [0157]    The C1/C2 sequence must be on the same strand as a gene, either be directly adjacent to the gene (i.e. a gap of 0 bases) for prokaryotic genomes or at this time be within 10,000 bases for eukaryotic genomes. The size of the gap between the end of the gene and the beginning of the C1/C2 sequence is a variable. The C1/C2 short loop is expressed as the 3′UTR (Un-Translated Region) of the gene. In the case of prokaryotic genes that do not normally have introns, the whole mRNA becomes the active species for connectron formation. In the case of eukaryotic genes, the whole transcript is the active species for connectron formation upon editing of the transcript to eliminate the introns. The whole transcript then can move about in the cytoplasm of prokaryotic cells or the nucleus of eukaryotic cells. Since the C1 sequence is equivalent to the T1 sequence and the C2 sequence is equivalent to the T2 sequence, the C1 RNA can form a Hoogsteen triple-stranded RNA/DNA/DNA helix with the double-stranded T1 sequence. Similarly the C2 RNA can form a Hoogsteen triple-stranded RNA/DNA/DNA helix with the double-stranded T2 sequence. Because the C1 sequence and the C2 sequence are adjacent to each other, the C1/T2 RNA/DNA/DNA Hoogsteen triple helix is brought into physical adjacency to the C2/T2 RNA/DNA/DNA Hoogsteen triple helix. RNA/DNA/DNA hybrid helices are the most stable form of triple helix. RNA double helices, DNA double helices, RNA triple helices and DNA triple helices are all significantly less stable than a RNA/double-stranded DNA triple helix. The stable physical adjacency of the two triple-stranded Hoogsteen helices ensures that the long loop of double-stranded DNA between the T1 sequence and the T2 sequence can then be structured into 30 nm chromatin particles as shown in level 4 of FIG. 1. The genes on either strand of the DNA between the T1 sequence and the T2 sequence when they are structured into the 30 nm chromatin particles are not open to promotion and expression.  
         [0158]    The tetradic relationship between the T1 and T2 sequences that form the long loop and the C1/C2 sequences that form the short loop are called a connectron. The name “connectron” was suggested by J. David Rawn Ph.D. of Towson University. A connectron is possible if the T1, T2, C1 and C2 sequences exist. A connectron is real if the C1/C2 short loop sequence is adjacent to an expressible gene. If the expression of the adjacent gene is inside one or more T1 —T2 long loops then this connectron is said to be transient. If the adjacent gene is not inside any possible T1-T2 long loop then the connectron is said to be permanent. If a connectron is inside of a T1-T2 long loop that has the same sequences (i.e. T1 is really equal to C1 and T2 is really equal to C2) then the connectron is said to be self-limiting. This is true because once the C1/C2 sequence is expressed it forms the T1-T2 long loop that then shuts off the expression of the gene adjacent to the C1/C2 sequence. Self-limiting conectrons can also be called “spike” connectrons since they generate a short-duration spike of the C1/C2 short loop sequence. If a T1-T2 long loop does not contain any genes but it contains C1/C2 short loop sequences then this type of connectrons is said to be geneless. The C1/C2 short loops within a geneless T1-T2 long loop can, of course, control the expression of genes.  
         [0159]    The physical existence and lifetimes of the connectrons must be proved by molecular biological experimentation. This physical experimental process, however, is logically quite separate from the computational experimentation that have been conducted from June of 1999 to May of 2001. The computational search for the existence of connectrons has been extremely positive. These computations have shown that connectrons exist in prokaryotes, in archea, between prokaryotes and their plasmids, in single-celled eukaryotes, in multi-celled eukaryotes, in plants, in higher animals and in humans. All of these features and properties are described in the claims section that follows.  
         [0160]    The connectron invention is very powerful. It depends only on sequence equivalency. The minimum length of the four sequences seems to be about 20 bases. In the calculations shown in this patent application, 27 bases have been used as a minimum. The Nature News Feature [1] says that other scientists have found RNA sequences of length about 25 that have interesting gene silencing properties. The Nature article does not give any mechanism. Because of my algorithm and its use on a variety of genomes, this patent application provides the computational proof that a particular mechanism is highly probable. The connectron invention provides an explanation for how communication occurs with a chromosome as well as between chromosomes in genomes that have more than one chromosome. Since each T1-T2 long loop can contain one or more genes, the connectron invention provides a mechanism for turning on and turning off sets of genes simultaneously. In time, the connectron invention will provide an explanation for how differentiation of how one cell&#39;s behavior differs from the behavior of another adjacent cell. It is already clear from the computational experiments that have been made on  S. cervesiae, C. elegans  and  D. megalomaster  that the number of geneless connectrons increases dramatically as evolution proceeds from single-celled eukaryotes (i.e.  S. cervesiae ) to 1,000 cell eukaryotes (i.e.  C. elegans ) to visible creatures (i.e.  D. megalomaster ). The extension of this evolutionary progress to plants (i.e.  A. thaliania ) for which only three chromosomes are sequenced and humans (i.e.  H. sapiens ) for which only one chromosome is completely sequenced. Although the complete human genome was published in Nature and Science in February of 2001, the NIH-sponsored genomic sequencing results are available for about ⅓ of the bases in the whole genome. The human genomic sequence determined by Celera Genomics, Inc. is available only by subscription. Table 1 shows how the genome size, the number of genes, the number of gene-containing and geneless connectrons and the percentage of genes controlled are related in many different genomes.  
         [0161]    The C1/C2 short loops originate on one chromosome. The T1-T2 long loops can be on the same or different chromosomes. Table 2 which is for yeast ( S. cervesiae ) is a square matrix of how many C1/C2 short loops on a given chromosome are sent to form T1-T2 long loops on other chromosomes. The diagonal of this matrix shows that many chromosomes send connectrons to themselves. The striking feature of this particular table is that chromosome 6 only sends connectrons to chromosome 12 but that it receives connectrons from chromosomes 4,5,7,10,12,13,15 and 16.  
         [0162]    Any tetrad of connectron sequences (i.e. the T1, T2, C1 and C2 sequences) as well as the fact of the adjacency of the C1/C2 short loop sequence to the transcribing gene can be patented because the content of matter and the utility can be exactly described. The utility of a connectron is that the T1-T2 long loop shuts off the expression of the genes that lie between the T1 sequence and the T2 sequence. In the case of geneless connectrons, the utility is of a higher level in that the C1/C2 short loops contained in the higher-level geneless T1-T2 long loop, eventually form other lower-level T1-T2 long loops around a set of genes.  
         [0163]    The invention of connectrons comes at a particularly important time in biological discovery. The geneless connectrons make a many-to-many hierarchical control mechanism possible. It is already clear from the determination of the conectrons for  C. elegans  and  D. megalomaster  that there are as many or more geneless connectrons than there are genes. It has been clear for some time that the number of genes in a genome is not particularly correlated with the size of the genome. FIG. 6 shows that the size of a genome is roughly linearly correlated with the number of connectrons.  
         [0164]    The connectron invention can be used to generate a model of behavior in any cell. The simulation of connectron behavior in different genomes will be the subject of another patent application.  
         [0165]    The connectron invention provides for a rational exploitation of the information contained in the raw genomic DNA sequence by forming a hierarchy of relationships between geneless connectrons, transient connectrons, permanent connectrons, self-limiting connectrons and the expression of genes.  
       DETAILED DESCRIPTION OF THE INVENTION  
       [0166]    The algorithm for the determination of connectrons in any genome or any genome fragment is represented in the following flow diagrams. The Level 0 diagram in FIG. 8 shows the general relationships in a digital computer. The central processor of the digital computer uses the computer program to take genome descriptors, the genomic DNA sequences and the tables of gene features to produce a file of blocking fragments and a file of the optimal connectrons for the genome. The printer serves to make hard copies of the files and this patent application. The level 1 diagram in FIG. 9 shows the three essential steps in the determination of connectrons. The genome is first processed into a blocking fragment file. Then the blocking fragments are used to compute the connectrons for the genome. Finally the potential connectrons are analyzed to determine if the C1/C2 sequences are in the 3′UTR of a gene. The level 2a diagram in FIG. 10 shows the steps required for the processing of the genome into a file of blocking fragments. The genomic DNA sequence is decomposed into 27-base frames for both the positive and negative strands. These fragments are written to the unsorted fragment file. The fragment file is then sorted is then read and formed into groups of equivalent sequences. The (.blk) file contains the sequence and a pointer to the (.gptr) file which contains the pointers to the position of the fragments in the genomes. The position in the genome includes the chromosome number, the position in the chromosome and the strand (i.e. positive and negative). A sample of these files follows  
         [0167]    Sample of the (.blk) file for  S. cervesiae   
                                                           Sample of the (.blk) file for  S. cervesiae                  Number   Pointer       27-base fragment   of instances   to (.gptr) file                    111111111111111111111111111   0   1       111111123244233313332443414   1   2       111111141113443133314333341   2   4       111111232442333133324434141   1   5       111111323311133323144423444   2   7       111111332213331341414443413   2   9       111111333444112343412323243   1   10       111111333444113343412323243   9   19       111111411134431333143333414   2   21       111111443223134142124434124   2   23       111112223234344444443144442   2   25       111112244123441122214421213   8   33       111112311241114344334134431   2   35       111112324423331333244341414   1   36       111112344232231344242234342   1   37       111112433444244421144134211   1   38       111112444311313442332142224   1   39       111113131241131114424413231   1   40       111113143332344311113133411   1   41       111113233111333231444234441   2   43                          
 
         [0168]    In fragments above 1=G, 2=C, 3=A, 4=T  
         [0169]    Sample of the (.gptr) file for  S. cervesiae    
         [0170]    There are 16 chromosomes in  S. cervesiae   
                                                                           Sample of the (.gptr) file for  S. cervesiae         There are 16 chromosomes in  S. cervesiae                          Position               Item   Chromosome   in Chromosome   Direction                            1   0   0   0           2   4   11137   1           3   12   467619   1           4   12   458482   1           5   4   11138   1           6   12   465759   2           7   12   456622   1           8   1   219366   1           9   8   539978   1           10   14   522451   1           11   4   1099073   1           12   4   1210003   1           13   7   539068   1           14   12   654136   1           15   12   596455   1           16   15   121016   1           17   15   598127   2           18   16   847724   1           19   16   59765   1           20   12   467620   1           21   12   458483   1           22   12   461657   1           23   12   452520   1           24   13   838006   1           25   15   288270   1           26   4   83593   1           27   4   992867   1           28   6   162265   1           29   7   845687   1           30   10   531560   2           31   15   282208   1           32   16   860418   1           33   16   572308   1           34   12   465992   1           35   12   456855   1           36   4   11139   1           37   8   89343   1           38   4   10302   1           39   1   19894   2           40   16   9311   1           41   10   735203   1           42   12   465760   1           43   12   456623   1                                  
 
         [0171]    In direction column above 1=positive strand, 2=negative strand  
         [0172]    The level 2b diagram in FIG. 11 shows the computation of the connectrons. The genome descriptors consist of the number and length of the chromosomes. The algorithm uses an array that represents several facts about each base position in the genome. The level 3a diagram in FIG. 13 shows the setup of the Genome-Usage memory. The gene features are used to prevent the region of the genome that codes for proteins from being used for the connectron sequences (i.e. the T1s, the T2s, the C1s and the C2s). In the level 2a diagram of FIG. 10, the algorithm steps through each chromosome and within each chromosome through each base position looking for acceptable T1-windows of 27 bases. A T1-window can be used to form a connectron relationship if there are two or more instances of this fragment in the blocking fragment file. The computation in the level 3b diagram of FIG. 14 determines if the T1-window is acceptable of not. Once an acceptable T1-window is found, the algorithm (in the level 2a diagram of FIG. 10) looks for acceptable T2-window positions that lie between 5,000 and 105,000 bases from the T1-window. The computation for determining acceptable T2-window positions is done in the level 3c diagram of FIG. 15. Once a pair of T1 and T2 window positions are found, the algorithm looks among the instances of these T1 and T2 sequences for a pair of sequences C1 and C2 that lie within 200 bases of each other on the same chromosome. The computation for determining acceptable C1/C2 windows is shown in the level 3d diagram in FIG. 16. In the level 3e diagram of FIG. 17 the Genome-Usage memory is scanned for the Possible-Connectrons. In the level 2c diagram of FIG. 12 the Possible-Connectrons are scanned to determine if the C1/C2 sequences are within the Gap-Distance of a gene on either the positive or the negative strands. The Real-Connectrons are then written out in several different files including the descriptions in the claims section.  
       EXAMPLES  
       [0173]    The algorithm for the determination of optimal connectrons has been applied to a number of different publicly available genomes. The connectron is a tetradic relationship between four sequence elements—T1, T2, C1 and C2. The claims presented in this section are written by the program NearGene that implements the flow diagram Level 2c of FIG. 12. The examples are written a uniform type of English. Each example contains some or all of the following elements  
         [0174]    Name of genome  
         [0175]    Description of T1  
         [0176]    Length of T1 -T2 loop  
         [0177]    The chromosome on which the T1-T2 loop exists  
         [0178]    The identifier number within the genome of the T1 sequence  
         [0179]    The T1 sequence  
         [0180]    Description of T2  
         [0181]    The identifier number within the genome of the T2 sequence  
         [0182]    The T2 sequence  
         [0183]    A list of genes whose expression is controlled by the T1-T2 loop  
         [0184]    The common names of the genes as obtained from the NCBI gene feature file (.ptt)  
         [0185]    A list of C1/C2 short loops whose expression if controlled by the T1-T2 loop  
         [0186]    The chromosome on which the C1/C2 short loop exists  
         [0187]    The common name of the gene which expresses the C1/C2 short loop as an RNA  
         [0188]    The sequence of the C1/C2 short loop  
         [0189]    A list of C1/C2 short loops that control the formation of the T1-T2 loop  
         [0190]    The chromosome on which the C1/C2 short loop exists  
         [0191]    The common name of the gene which expresses the C1/C2 short loop as an RNA  
         [0192]    The sequence of the C1/C2 short loop  
         [0193]    The match between the C1/C2 sequence and the T1 sequence  
         [0194]    The match between the C1/C2 sequence and the T2 sequence  
         [0195]    The uniform descriptions make it possible to rapidly comprehend the specifics in each example.  
         [0196]    When a sequence element is very long a series of four dots has been inserted between the beginning and ending sequence groups. A variable number of bases have been deleted.  
         [0197]    Index of Pages for Connectron Samples  
         [0198]    Page 39  
         [0199]    1. Connectrons occur in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0200]    Page 57  
         [0201]    2. Many Connectrons control the expression of one set of genes in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0202]    Page 83  
         [0203]    3. One connectron controls the expression of many sets of genes in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0204]    Page 107  
         [0205]    4. Connectrons occur between prokaryotes and their plasmids.  
         [0206]    Page 117  
         [0207]    5. Connectrons occur in plants and higher animals  
         [0208]    Page 126  
         [0209]    6. Permanent connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0210]    Page 135  
         [0211]    7. Transient connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0212]    Page 152  
         [0213]    8. Self-limiting connectrons occur in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes  
         [0214]    Page 164  
         [0215]    9. Geneless connectrons exist in single-celled and multi-celled eukaryotes  
         [0216]    Page 174  
         [0217]    10. One connectron controls many geneless connectrons in single-celled and multi-celled eukaryotes  
         [0218]    1. Connectrons Occur in Prokaryotes, Archea, Single-celled Eukaryotes and Multi-celled Eukaryotes.  
         [0219]    Connectrons exist as tetradic relationships where the sequence T1 is equivalent to the sequence C1 (written T1=C1) and where the sequence T2 equals the sequence C2 (written T2=C2) where T1 and T2 are DNA sequences 20 or more bases in length, where the C1 sequence is adjacent to the C2 sequence, where the T1 and T2 sequences are on the same chromosome, and where the C1/C2 sequences are on the same chromosome as T1 and T2 or where the C1/C2 sequences are on a chromosome different from T1 and T2. The connectron relationship has been found to exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0220]    Example of a Prokaryote Connectron— E. coli    
         [0221]    In this example the existence of the T1-T2 (3197-3308) long loop is controlled by three C1/C2 short loops (3307, 3432 and 2218). The T1-T2 long loop controls the expression of 64 genes on chromosome 1 in addition to six C1/C2 (3204, 3206, 3223, 3228, 3301 and 3327) short loops. The C1/C2 short loop 3327 lies outside the range of the T1-T2 long loop (3197-3308) but this C1/C2 is expressed as a 3′UTR to the gene hemG that is within the range of the T1-T2 long loop.  
                                           3307 Chromosome 1                           3432 Chromosome 1                       2218 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 1            |       3197                             3308       |            3204  3206           |       |            3224  3228           |       |            3301  3327           |       --------------------------------------------------------          
 
         [0222]    Connectron Control Elements for Chromosome 1 of the  E. coli  Genome  
         [0223]    A double stranded DNA loop of length 93.542 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3197. This T1 control element has the DNA sequence  
                       AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG               AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG               CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA               ATAAATGCTTGACTCTGTAGCGGGAA          
 
         [0224]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3308. This T2 control element has the DNA sequence  
                       TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG               ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG               AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG               GCGTATTATGCACACCCCGCGCCGCT          
 
         [0225]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           rrsC   gltU   rrlC   rrfC   aspT   trpT   yifA   yifE   yifB                   ilvL   ilvG_1   ilvM   ilvE   ilvD   ilvA   ilvY   ilvC   ppiC               b3776   rep   gppA   rhlB   trxA   rhoL   rho   rfe   wzzE               wecB   rffH   weeD   wecE   wzxE   yifM_2   wecG   yifK               argX   hisR   leuT   proM   aslB   aslA   hemY   hemX               hemD   cyaA   cyaY   b3808   dapF   uvrD   b38l4   corA               yigF   yigG   rarD   yigI   pldA   recQ   yigJ   yigK   pldB               yigL   yigM   metR   metE   ysgA   udp   yigN   ubiE   yigP               b3836   yigU   yigW_1   rfaH   yigC   ubiB   fadA   fadB               pepQ   trkH   hemG          
 
         [0226]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0227]    A C1/C2 short loop on chromosome 1 whose identifier is 3204 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrsC and has the DNA sequence  
                       GATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGG               CGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAG               ACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATG               GGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAA          
 
         [0228]    A C1/C2 short loop on chromosome 1 whose identifier is 3206 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrsC and has the DNA sequence  
                       GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG               GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTC               ACCTGCCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTG               CTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAA          
 
         [0229]    A C1/C2 short loop on chromosome 1 whose identifier is 3223 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrlC and has the DNA sequence  
                       GCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGC               GAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGG               CGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGG               ACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCA          
 
         [0230]    A C1/C2 short loop on chromosome 1 whose identifier is 3225 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrlC and has the DNA sequence  
                       AAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCAT               GCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTC               CCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAAGCAGTA          
 
         [0231]    A C1/C2 short loop on chromosome 1 whose identifier is 3228 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrfC and has the DNA sequence  
                       GGTCATAAAACCGGTGGTTGTAAAAGAATTCGGTGGAGCGGTAGTTCAGT               CGGTTAGAATACCTGCCTGTCACGCAGGGGGTCGCGGGTTCGAGTCCCGT               CCGTTCCGCCAC          
 
         [0232]    A C1/C2 short loop on chromosome 1 whose identifier is 3301 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ubiB and has the DNA sequence  
                       TTATCGTGCCTACAAATAGTCCGAACCGTAGGCCGGATAAGGCGTTTACG               CCGCATC          
 
         [0233]    A C1/C2 short loop on chromosome 1 whose identifier is 3307 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene fadA and has the DNA sequence  
                       TGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGTTCGGACTATTTGT               AGGCA          
 
         [0234]    A C1/C2 short loop on chromosome 1 whose identifier is 3327 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene hemG and has the DNA sequence  
                                       AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG                           AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG                       CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA                       ATAAATGCTTGACTCTGTAGCGGGAAGGCGTATTATG...CCCGTCACACCA                       TGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCT                       TACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTA                       GGGGAACCTGCGGTTGGATCACCTCCTTACCTTAAAGAAGCGTTCTTTG          
 
         [0235]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0236]    A C1/C2 short loop on chromosome 1 whose identifier is 3307 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene hemG and has the DNA sequence  
                                       AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG                           AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG                       CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA                       ATAAATGCTTGACTCTGTAGCGGGAAGGCGTATTATG...CCCGTCACACCA                       TGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCT                       TACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTA                       GGGGAACCTGCGGTTGGATCACCTCCTTACCTTAAAGAAGCGTTCTTTG          
 
         [0237]    The match between the T1 sequence and the C1/C2 sequence is  
                       AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG               AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG               CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA               ATAAATGCTTGACTCTGTAGCGGGAA          
 
         [0238]    The match between the T2 sequence and the C1/C2 sequence is  
                       TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG               ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG               AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG               GCGTATTATGCACACCCCGCGCCGCT          
 
         [0239]    A C1/C2 short loop on chromosome 1 whose identifier is 3432 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene btuB and has the DNA sequence  
                                       TGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACT                           CCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGG                       GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATG                       CTTGACTCTGTAGCGGGAAGGCGTATTATGCACACC...ACACCATGGGAGT                       GGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACT                       TTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAAC                       CTGCGGTTGGATCACCTCCTTACCTTAAAGAAGCGT          
 
         [0240]    The match between the T1 sequence and the C1/C2 sequence is  
                       TGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACT               CCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGG               GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATG               CTTGACTCTGTAGCGGGAA          
 
         [0241]    The match between the T2 sequence and the C1/C2 sequence is  
                       TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG               ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG               AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG               GCGTATTATGCACACCCCGCGCCGCT          
 
         [0242]    A C1/C2 short loop on chromosome 1 whose identifier is 2218 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene clpB and has the DNA sequence  
                       CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC               AACGGCAAACACGCCGCCGGGC          
 
         [0243]    The match between the T1 sequence and the C1/C2 sequence is  
                       CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC               AACGGCAAACACGCCGCCGGGC          
 
         [0244]    The match between the T2 sequence and the C1/C2 sequence is  
                       CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC               AACGGCAAACACGCCGCCGGGTC          
 
         [0245]    Example of an Archea Connectron— H. pylori    
         [0246]    In this example the existence of the T1-T2 (812-882) long loop is controlled by three C1/C2 short loops (881, 813 and 1214). The T1-T2 long loop controls the expression of 54 genes on chromosome 1 in addition to one C1/C2 (843) short loop.  
                                           881 Chromosome 1                           813 Chromosome 1                       1241 Chromosome 1                       |       *------------------*------------------*       |             Chromosome 1           |       812                           882       |               842          |       --------------------------------------------------------          
 
         [0247]    Connectron control elements for chromosome 1 of  H. pylori  genome  
         [0248]    A double stranded DNA loop of length 96.385 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 812. This T1 control element has the DNA sequence  
         [0249]    TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA  
         [0250]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 882. This T2 control element has the DNA sequence  
         [0251]    TAGCGGAACTAAAGCATTCATCCCAAACACTAAAGATATTTGG  
         [0252]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           HP0999   HP1000   HP1001   HP1002   HP1003   HP1005   HP1006       HP1008   HP1009   HPtRNA-Pro   HP1010   HP1011   HP1013   HP1015       HP1017   HP1018   HP1020   HP1021   HP1022   HP1023   HP1024       HP1025   HP1027   HP1028   HP1030   HP1031   HP1033   HP1034       HP1038   HP1039   HP1040   HP1041   HP1042   HP1043   HP1044       HP1045   HP1046   HP1051   HP1052   HP1055   HP1056   HP1058       HP1060   HP1065   HPtRNA-Ser   HP1066   HP1067   HP1069   HP1070       HP1074   HP1075   HP1076   HP1077   HP1078   HP1079   HP1080       HP1081   HP1083   HP1084   HP1085   HP1088   HP1091   HP1092       HP1093   HP1094   HP1095   HP1096                  
 
         [0253]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0254]    A C1/C2 short loop on chromosome 1 whose identifier is 813 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene HP0998 and has the DNA sequence  
                       TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC               AAACACTAAAGATATTTGG          
 
         [0255]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0256]    A C1/C2 short loop on chromosome 1 whose identifier is 881 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene HP1096 and has the DNA sequence  
                       TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC               AAACACTAAAGATATTTGG          
 
         [0257]    The match between the T1 sequence and the C1/C2 sequence is  
         [0258]    TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA  
         [0259]    The match between the T2 sequence and the C1/C2 sequence is  
         [0260]    TAGCGGAACTAAAGCATTCATCCCAAACACTAAAGATATTTGG  
         [0261]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0262]    A C1/C2 short loop on chromosome 1 whose identifier is 813 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene HP0998 and has the DNA sequence  
                       TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC               AAACACTAAAGATATTTGG          
 
         [0263]    A C1/C2 short loop on chromosome 1 whose identifier is 881 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene HP1096 and has the DNA sequence  
                       TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC               AAACACTAAAGATATTTGG          
 
         [0264]    The match between the T1 sequence and the C1/C2 sequence is  
         [0265]    TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA  
         [0266]    The match between the T2 sequence and the C1/C2 sequence is  
         [0267]    TAGCGGAACTAAAGCATTCATCCCAAACACTAAAGATATTTGG  
         [0268]    A C1/C2 short loop on chromosome 1 whose identifier is 1241 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene HP1535 and has the DNA sequence  
                       TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC               AAACA          
 
         [0269]    The match between the T1 sequence and the C1/C2 sequence is  
         [0270]    TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA  
         [0271]    The match between the T2 sequence and the C1/C2 sequence is  
         [0272]    TAGCGGAACTAAAGCATTCATCCCAAACA  
         [0273]    Example of Single-celled Connectron— S. cervesiae    
         [0274]    In this example the existence of the T1-T2 (1352-1416) long loop on chromosome 4 is controlled by one C1/C2 short loop (4213) on chromosome 10. The T1-T2 long loop controls the expression of 34 genes on chromosome 4 in addition to one C1/C2 (1356) short loop.  
                                            4213 Chromosome 10                            |       *------------------*------------------*       |            Chromosome 4            |       1352                             1416       |              1356             |       --------------------------------------------------------          
 
         [0275]    Connectron Control Elements for Chromosome 1 of  S. cervesiae  Genome  
         [0276]    A double stranded DNA loop of length 68.908 kilo-bases on chromosome 4 is bounded on the left by a T1 sequence whose identifier is 1352. This T1 control element has the DNA sequence  
         [0277]    TTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAA  
         [0278]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1416. This T2 control element has the DNA sequence  
                       ATTAGATCTATTACATTATGGGTGGTATGTTGGAATAAAAATCAACTATCA               TCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGTTAGA               AGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCTGAA               ACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAAAAC               GATGATAATAATATTTATAGAATTGTGTAGAATTGCAGATTCCCTTTTATG               GATTCCTAAATCCTTGAGGAGAACTTCTAGTATATCTACATACCTAATATT               ATAGCCTTAATCACAATGGAATCCCAACAATTACATCAAAATCCACATTC               TCTACAGTA          
 
         [0279]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                       YDR170W-A YDR171W YDR172W YDR173C YDR174W YDR175C               YDR176W YDR177W YDR178W YDR179C YDR179W-A YDR180W               YDR181C YDR182W YDR183W YDR184C YDR185C YDR186C               YDR187C YDR188W YDR189W YDR190C YDR191W YDR192C               YDR193W YDR194C YDR195W YDR196C YDR197W YDR198C               YDR199W YDR200C YDR201W YDR202C YDR203W YDR204W               YDR205W YDR206W YDR207C YDR208W YDR209C YDR210W          
 
         [0280]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0281]    A C1/C2 short loop on chromosome 4 whose identifier is 1356 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YDR170W-A and has the DNA sequence  
                       AATCACACTAATCATTCTGATGATGAACTCCCTGGACACCTCCTTCTCGAT               TCAGGAGCATCACGAACCCTTATAAGATCTGCTCATCACATACACTCAGC               ATCATCTAATCCTGACATAAACGTAGTTTGATGCTCAAAAAAGAAATATAC               CAATTAACGCTATTGGTGACCTACAATTCACTTCCAGGACAACACCAAA               ACATCAATAAAGGTATTGCACACTCCTAACATAGCCTATGACTTACTCAGT               TTGAATGAATTGGCTGCAGTAGATATCACAGCATGCTTTACCAAAAACGT               CTTAGAACG          
 
         [0282]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0283]    A C1/C2 short loop on chromosome 10 whose identifier is 4213 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YJR029W and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATCCACTATCGTCTAT               CAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGATGAT               GACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAACGC               AAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGA               ATGAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGA               GGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATA               TTATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACAT          
 
         [0284]    The match between the T1 sequence and the C1/C2 sequence is  
         [0285]    TTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAA  
         [0286]    The match between the T2 sequence and the C1/C2 sequence is  
         [0287]    ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATC  
         [0288]    Example of a Multi-celled Connectron— C. elegans    
         [0289]    In this example the existence of the T1-T2 (9-138) long loop on chromosome 1 is controlled by three C1/C2 short loops on chromosome 5 (21719, 21949 and 21655). The T1-T2 long loop controls the expression of four genes on chromosome 1 in addition to seven C1/C2 (119, 122, 125, 130, 132, 134 and 136) short loops.  
                                           21719 Chromosome 5                           21949 Chromosome 5                       21655 Chromosome 5                       |       *------------------*------------------*       |            Chromosome 1            |       95                            138       |             119 122           |       |             125 130           |       |             132 134           |       |             136             |       --------------------------------------------------------          
 
         [0290]    A double stranded DNA loop of length 41.978 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 95. This T1 control element has the DNA sequence  
                       CAGCACGTTCTTAACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTC               CCGC          
 
         [0291]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 138. This T2 control element has the DNA sequence  
         [0292]    ACTCTGCGTCTCTTCTCCCGCATTTTTTGTAGATCA  
         [0293]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0294]    Y73A3A.1 Y73A3A.1 ZC123.3 ZC123.2  
         [0295]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0296]    A C1/C2 short loop on chromosome 1 whose identifier is 119 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC123.3 and has the DNA sequence  
                       TTGAGAACTCTGCGTCTCAACTCCCGCATTTTTTGTAGATCTACGTAGATC               AAACCGAAATGGGACACT          
 
         [0297]    A C1/C2 short loop on chromosome 1 whose identifier is 122 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC123.3 and has the DNA sequence  
                       GCACGGGGTTCTGGCCTTCCTCATTGAATTTTTCGCGCTCCATTGACAATC               GCCTGCCGGACAACGCGTGGGAAAGTCGTGTACTCCAC          
 
         [0298]    A C1/C2 short loop on chromosome 1 whose identifier is 125 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC123.3 and has the DNA sequence  
                       ACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATGGCCTAGTTTC               GGCAAACTCTTTCATTTCAATTTATGAGGGAAGCCAGAA          
 
         [0299]    A C1/C2 short loop on chromosome 1 whose identifier is 130 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC123.2 and has the DNA sequence  
                       CTCCCGCATTTTTTGTAGATCTACGTAGATCAAACCGAAATGAGGCACTTT               CTGAATCCACGAGCTAGGCTTAAGCTTAGGCTTAAGCTTAGGCCTTTTCTC               AGGCTTAGGCTTAGGCTTA          
 
         [0300]    A C1/C2 short loop on chromosome 1 whose identifier is 132 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC123.2 and has the DNA sequence  
                       GCTTATGCTTGGGCTTAGGCTTAGGCGTAGGCTTAGGCTTAGGCTTAGGCT               TATGCTTAGACTTAGTCTCACTATCAGTCTTAGGCTTAGGCTTAGACTTAG               GCTTAAGCTTAGGCTTAAGCTTAGACTTAGGCTTAGGCTTAGGCTTAGGCT               TAGGCTTAGGTTTGGGCTTAGGCTTAGGCTTAACCTC          
 
         [0301]    A C1/C2 short loop on chromosome 1 whose identifier is 134 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC123.2 and has the DNA sequence  
                       TCTGCGTCTTTTCTCCCGCATTTTTTGTAGATCTACGTAGATCAAACCGAA               ATGAGGCACTTTCTGAATCCACGAGCTAGGCTTAAGCTTAGGCTTAAGCTT               AGGCCTTTTCTCAGGCTTAGGCTTAGGCTTA          
 
         [0302]    A C1/C2 short loop on chromosome 1 whose identifier is 136 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC 123.2 and has the DNA sequence  
                       GCTTATGCTTGGGCTTAGGCTTAGGCGTAGGCTTAGGCTTAGGCTTAGGCT               TATGCTTAGACTTAGTCTCACTATCAGTCTTAGGCTTAGGCTTAGACTTAG               GCTTAAGCTTAGGCTTAAGCTTAGACTTAGGCTTAGGCTTAGGCTTAGGCT               TAGGCTTAGGTTTGGGCTTAGGCTTAGGCTTAACCTC          
 
         [0303]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0304]    A C1/C2 short loop on chromosome 5 whose identifier is 21719 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene C39F7.5 and has the DNA sequence  
                       ACGTTCTTAACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGC               ATTTTTTGTAGATC          
 
         [0305]    The match between the T1 sequence and the C1/C2 sequence is  
         [0306]    ACGTTCTTAACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGC  
         [0307]    The match between the T2 sequence and the C1/C2 sequence is  
         [0308]    ACTCTGCGTCTCTTCTCCCGCATTTTTTGTAGATC  
         [0309]    A C1/C2 short loop on chromosome 5 whose identifier is 21949 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene F136B4.4 and has the DNA sequence  
                       ACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGCATTTTTTGT               AGATCTACGTAGATCAAGCCGAAATGAGACACTCTGACACCACG          
 
         [0310]    The match between the T1 sequence and the C1/C2 sequence is  
         [0311]    ACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGC  
         [0312]    The match between the T2 sequence and the C1/C2 sequence is  
         [0313]    ACTCTGCGTCTCTTCTCCCGCATTTTTTGTAGATC  
         [0314]    A C1/C2 short loop on chromosome 5 whose identifier is 21655 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene C39F7.3 and has the DNA sequence  
                       AACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGCATTTTTTG               TAGATCTACG          
 
         [0315]    The match between the T1 sequence and the C1/C2 sequence is  
         [0316]    AACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGC  
         [0317]    The match between the T2 sequence and the C1/C2 sequence is  
         [0318]    ACTCTGCGTCTCTTCTCCCGCATTTTTTGTAGATC  
         [0319]    2. Many Connectrons Control the Expression of one Set of Genes in Prokaryotes, Archea, Single-celled Eukaryotes and Multi-celled Eukaryotes.  
         [0320]    Many different C1/C2 short loops can control the existence of one T1-T2 long loop. The C1/C2 short loops can be on the same chromosome or on different chromosomes from the T1-T2 long loop. This relationship is described as “many-to-one”. This relationship exists in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes  
         [0321]    Example of a Many-to-one Connectron in Prokaryotes— E. coli    
         [0322]    In this example the existence of the T1-T2 (3197-3308) long loop is controlled by three C1/C2 short loops (3307, 3432 and 2218).  
                                           3307 Chromosome 1                           3432 Chromosome 1                       2218 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 1            |       3197                             3308       --------------------------------------------------------          
 
         [0323]    A double stranded DNA loop of length 93.542 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3197. This T1 control element has the DNA sequence  
                       AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG               AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG               CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA               ATAAATGCTTGACTCTGTAGCGGGAA          
 
         [0324]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3308. This T2 control element has the DNA sequence  
                       TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG               ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG               AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG               GCGTATTATGCACACCCCGCGCCGCT          
 
         [0325]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                                                                                                                                             rrsC   gltU   rrlC   rrfC   aspT   trpT   yifA   yifE   yifB       ilvL   ilvG_1   ilvM   ilvE   ilvD   ilvA   ilvY   ilvC   ppiC       b3776   rep   gppA   rhlB   trxA   rhoL   rho   rfe   wzzE            wecB   rffH   wecD   wecE   wzxE   yifM_2   wecG   yifK       argX   hisR   leuT   proM   aslB   aslA   hemY   hemX       hemD   cyaA   cyaY   b3808   dapF   uvrD   b3814   corA            yigF   yigG   rarD   yigI   pldA   recQ   yigJ   yigK   pldB       yigL   yigM   metR   metE   ysgA   udp   yigN   ubiE   yigP            b3836   yigU   yigW_1   rfaH   yigC   ubiB   fadA   fadB       pepQ   trkH   hemG                  
 
         [0326]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0327]    A C1/C2 short loop on chromosome 1 whose identifier is 3307 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene hemG and has the DNA sequence  
                                       AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG                           AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG                       CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA                       ATAAATGCTTGACTCTGTAGCGGGAAGGCGTATTATG...GGAGTCTGCAAC                       TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACG                       GTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGT                       GGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACT                       TTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAAC                       CTGCGGTTGGATCACCTCCTTACCTTAAAGAAGCGTTCTTTG          
 
         [0328]    The match between the T1 sequence and the C1/C2 sequence is  
                       AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG               AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG               CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA               ATAAATGCTTGACTCTGTAGCGGGAA          
 
         [0329]    The match between the T2 sequence and the C1/C2 sequence is  
                       TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG               ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG               AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG               GCGTATTATGCACACCCCGCGCCGCT          
 
         [0330]    A C1/C2 short loop on chromosome 1 whose identifier is 3432 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene btuB and has the DNA sequence  
                                       TGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACT                           CCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGG                       GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATG                       CTTGACTCTGTAGCGGGAAGGCGTATTATGCACACC...ACACCATGGGAGT                       GGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACT                       TTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAAC                       CTGCGGTTGGATCACCTCCTTACCTTAAAGAAGCGT          
 
         [0331]    The match between the T1 sequence and the C1/C2 sequence is  
                       TGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACT               CCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGG               GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATG               CTTGACTCTGTAGCGGGAA          
 
         [0332]    The match between the T2 sequence and the C1/C2 sequence is  
                       TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG               ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG               AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG               GCGTATTATGCACACCCCGCGCCGCT          
 
         [0333]    A C1/C2 short loop on chromosome 1 whose identifier is 2218 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene clpB and has the DNA sequence  
                       CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC               AACGGCAAACACGCCGCCGGGC          
 
         [0334]    The match between the T1 sequence and the C1/C2 sequence is  
                       CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC               AACGGCAAACACGCCGCCGGGC          
 
         [0335]    The match between the T2 sequence and the C1/C2 sequence is  
                       CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC               AACGGCAAACACGCCGCCGGGC          
 
         [0336]    Example of a Many-to-one Connectron in Archea— M. jannaschii    
         [0337]    In this example the existence of the T1-T2 (1630-1643) long loop is controlled by four C1/C2 short loops (1629, 1642, 124 and 1533).  
                                           1629 Chromosome 1                           1642 Chromosome 1                       124 Chromosome 1                       1533 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 1            |       1630                             1643       --------------------------------------------------------          
 
         [0338]    A double stranded DNA loop of length 4.998 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 1630. This T1 control element has the DNA sequence  
                                       TTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTT                           GATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA                       AGATTAATTAGGAAAGGAAATAAGATTTCTCTAACAGACAAGTTAAATTT                       TTGGATTTAAAAAGATAAAAAT          
 
         [0339]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1643. This T2 control element has the DNA sequence  
                                       TTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTATTG                           AATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAAAT                       TTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACTCT                       GTTTTATTATGGAAAGAAAGAT          
 
         [0340]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0341]    MJ1597 MJ1598 MJ1599 MJ1600 MJ1601 MJ1602  
         [0342]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0343]    A C1/C2 short loop on chromosome 1 whose identifier is 1629 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1597 and has the DNA sequence  
                                       ATATGTTTGAAATTTGAAAATAAGAGTATTTAGAAGTTATTAATTAGTTCA                           AAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATAT                       TTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA          
 
         [0344]    The match between the T1 sequence and the C1/C2 sequence is  
                       TTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTT               GATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA          
 
         [0345]    The match between the T2 sequence and the C1/C2 sequence is  
                                       GCTGGTTTGATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTA                           AAAATTA          
 
         [0346]    A C1/C2 short loop on chromosome 1 whose identifier is 1642 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3 ′UTR to the gene MJ1602 and has the DNA sequence  
                                       ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAA                       ATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACT                       CTGTTTTATTATGGAAAGAAAGAT          
 
         [0347]    The match between the T1 sequence and the C1/C2 sequence is  
                                       GCTGGTTTGATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTA                           AAAATTA          
 
         [0348]    The match between the T2 sequence and the C1/C2 sequence is  
                                       TTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTATTG                           AATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAAAT                       TTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACTCT                       GTTTTATTATGGAAAGAAAGAT          
 
         [0349]    A C1/C2 short loop on chromosome 1 whose identifier is 124 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ0112 and has the DNA sequence  
                                       ATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAT          
 
         [0350]    The match between the T1 sequence and the C1/C2 sequence is  
                                       ATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAT          
 
         [0351]    The match between the T2 sequence and the C1/C2 sequence is  
                                       GCTGGTTTGATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTA                           AAAAT          
 
         [0352]    A C1/C2 short loop on chromosome 1 whose identifier is 1533 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1486 and has the DNA sequence  
                                       TTTTTATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATATTTGAG                           TTTATT          
 
         [0353]    The match between the T1 sequence and the C1/C2 sequence is  
                                       TTTTTATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATATTTGAG                           TTTATT          
 
         [0354]    The match between the T2 sequence and the C1/C2 sequence is  
         [0355]    GCTGGTTTGATTATTTAGAATATTTGAGTTTATT  
         [0356]    Example of a Many-to-one Connectron in Single-cell Eukaryotes— S. cervesiae    
         [0357]    In this example the existence of the T1-T2 (5515-5533) long loop on chromosome 12 is controlled by seventeen C1/C2 short loops (5516, 5532, 1939, 2323, 1942, 3286, 3649, 4764, 4751, 5536, 6102, 8023, 7356, 3293, 3291, 3289 and 146).  
                                           5516 Chromosome 12                           5532 Chromosome 12                       1939 Chromosome 4                       2323 Chromosome 5                       1942 Chromosome 5                       3286 Chromosome 7                       3649 Chromosome 8                       4764 Chromosome 12                       4751 Chromosome 12                       5536 Chromosome 13                       6102 Chromosome 14                       8023 Chromosome 16                       7356 Chromosome 16                       3293 Chromosome 8                       3291 Chromosome 8                       3289 Chromosome 8                       146 Chromosome 2                       |       *------------------*------------------*       |            Chromosome 12            |       3197                              3308       --------------------------------------------------------          
 
         [0358]    A double stranded DNA loop of length 6.466 kilo-bases on chromosome 12 is bounded on the left by a T1 sequence whose identifier is 5515. This T1 control element has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0359]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 5533. This T2 control element has the DNA sequence  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0360]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0361]    YLR467W  
         [0362]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0363]    A C1/C2 short loop on chromosome 12 whose identifier is 5516 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YLR464W and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0364]    A C1/C2 short loop on chromosome 12 whose identifier is 5532 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YLR467W and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0365]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0366]    A C1/C2 short loop on chromosome 4 whose identifier is 1939 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YDR545W and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGG          
 
         [0367]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGG          
 
         [0368]    The match between the T2 sequence and the C1/C2 sequence is  
                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA               ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC               ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC               TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGG          
 
         [0369]    A C1/C2 short loop on chromosome 5 whose identifier is 2323 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YER189W and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0370]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0371]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTA                       AGAGACAACAGGGCT          
 
         [0372]    A C1/C2 short loop on chromosome 5 whose identifier is 1942 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YEL077C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0373]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0374]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTA                       AGAGACAACAGGGCT          
 
         [0375]    A C1/C2 short loop on chromosome 7 whose identifier is 3286 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YGR296W and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0376]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0377]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0378]    A C1/C2 short loop on chromosome 8 whose identifier is 3649 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YHR219W and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0379]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0380]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0381]    A C1/C2 short loop on chromosome 12 whose identifier is 4764 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YLL066C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0382]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0383]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0384]    A C1/C2 short loop on chromosome 12 whose identifier is 4751 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YLL067C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0385]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0386]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0387]    A C1/C2 short loop on chromosome 13 whose identifier is 5536 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YML133C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0388]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0389]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0390]    A C1/C2 short loop on chromosome 14 whose identifier is 6102 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YNL339C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0391]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0392]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0393]    A C1/C2 short loop on chromosome 16 whose identifier is 8023 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YPR204W and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0394]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0395]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0396]    A C1/C2 short loop on chromosome 16 whose identifier is 7356 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YPL283C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0397]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0398]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0399]    A C1/C2 short loop on chromosome 8 whose identifier is 3293 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YHL050C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTT          
 
         [0400]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTT          
 
         [0401]    The match between the T2 sequence and the C1/C2 sequence is  
                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA               ATATGCGTTTT          
 
         [0402]    A C1/C2 short loop on chromosome 8 whose identifier is 3291 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YHL050C and has the DNA sequence  
                       ATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGC               GAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAA          
 
         [0403]    The match between the T1 sequence and the C1/C2 sequence is  
                       ATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGC               GAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAA          
 
         [0404]    The match between the T2 sequence and the C1/C2 sequence is  
                       ATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGC               GAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAA          
 
         [0405]    A C1/C2 short loop on chromosome 2 whose identifier is 145 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YBL113C and has the DNA sequence  
                       CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAAC               ATCCGGGTAAGAGACAACAGGCT          
 
         [0406]    The match between the T1 sequence and the C1/C2 sequence is  
         [0407]    CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTG  
         [0408]    The match between the T2 sequence and the C1/C2 sequence is  
                       CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAAC               ATCCGGGTAAGAGACAACAGGCT          
 
         [0409]    A C1/C2 short loop on chromosome 8 whose identifier is 3289 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YHL050C and has the DNA sequence  
                       CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAAC               ATCCGGGTAAGAGACAACAGGCT          
 
         [0410]    The match between the T1 sequence and the C1/C2 sequence is  
         [0411]    CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTG  
         [0412]    The match between the T2 sequence and the C1/C2 sequence is  
                       CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAAC               ATCCGGGTAAGAGACAACAGGCT          
 
         [0413]    A C1/C2 short loop on chromosome 2 whose identifier is 146 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YBL113C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAA          
 
         [0414]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAA          
 
         [0415]    The match between the T2 sequence and the C1/C2 sequence is  
         [0416]    ATTATGTATTGTGTAGTATAGTATATTGTAAGAAA  
         [0417]    Example of a Many-to-one Connectron in Multi-cell Eukaryotes— C. elegans    
         [0418]    In this example the existence of the T1-T2 (3197-3308) long loop on chromosome 5 is controlled by three C1/C2 short loops (4382, 4375 and 28633).  
                                            4382 Chromosome 1                            4375 Chromosome 1                        28633 Chromosome 5                        |       *-------------------*-------------------*       |             Chromosome 5             |       28632                               28697       --------------------------------------------------------          
 
         [0419]    A double stranded DNA loop of length 58.451 kilo-bases on chromosome 5 is bounded on the left by a T1 sequence whose identifier is 28632. This T1 control element has the DNA sequence  
                       GCAAAAATTGACTGAAAATTTGAATTTCCCGCAAAAAATTGACTGAAAAT               TTGAATTTCCCGCCAAAAATTGACTGAAAATTTGAA          
 
         [0420]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 28697. This T2 control element has the DNA sequence  
                       CAAAAAATTGACTGAAAATTTGAATTTCCCTCCAAAAATTGACTGAAAAT               TTGAATTTCCCGCCAAAAATTGACTGAAAATTTGAATATCCCGCCAAAAA               TTGACTGAAAATTTGAATTTCCCGCCGAAAATTAAATGAAAAATGGAATT               TCTCGCCGAA          
 
         [0421]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0422]    M162.8 M162.4 M162.3 M162.6 M162.2 M162.1 M162.7  
         [0423]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0424]    A C1/C2 short loop on chromosome 1 whose identifier is 4382 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene Y43F8B.10 and has the DNA sequence  
                       ATTATAGAAAATTTAAATTTCCCTCCAAAAAATTGACTGAAAATTTGAATT               TCCCTCCAAAAATTGACTGAAAATTTGAATTTCCCGCCAAAAATTGACTG               AAAATTTGAATATCCCGCCAAAAATTGACTGAAAATTTGAATTTCCCGCC               GAAAATTAAATGAAAAATGGAATTTCTCGCCGAAAAATTCAGTAAAAATT               TGAATTTCCTGCCAAAAATTGACTGAAAATTTGAATTTCTTGCCAAAAAA               GTGACTGGGAATTTGAATTTCCCTCCAAAAATTGACTGAAATTTTGAATTT               CCCGCTAAAAGTTGACT          
 
         [0425]    The match between the T1 sequence and the C1/C2 sequence is  
         [0426]    CAAAAATTGACTGAAAATTTGAATTTCCCGC  
         [0427]    The match between the T2 sequence and the C1/C2 sequence is  
                       CAAAAAATTGACTGAAAATTTGAATTTCCCTCCAAAAATTGACTGAAAAT               TTGAATTTCCCGCCAAAAATTGACTGAAAATTTGAATATCCCGCCAAAAA               TTGACTGAAAATTTGAATTTCCCGCCGAAAATTAAATGAAAAATGGAATT               TCTCGCCGAA          
 
         [0428]    A C1/C2 short loop on chromosome 1 whose identifier is 4375 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene Y43F8B.10 and has the DNA sequence  
                       ATTATAGAAAATTTAAATTTCCCTCCAAAAAATTGACTGAAAATTTGAATT               TCCCTCCAAAAATTGACTGAAAATTTGAATTTCCCGCCAAAAATTGACTG               AAAATTTGAATATCCCGCCAAAAATTGACTGAAAATTTGAATTTCCCGCC               GAAAATTAAATGAAAAATGGAATTTCTCGCCGAAAAATTCAGTAAAAATT               TGAATTTCCTGCCAAAATTGACTGAAAATTTGAATTTCTTGCCAAAAAA               GTGACTGGGAATTTGAATTTCCCTCCAAAAATTGACTGAAATTTTGAATTT               CCCGCTAAAAGTTGACT          
 
         [0429]    The match between the T1 sequence and the C1/C2 sequence is  
         [0430]    CAAAAATTGACTGAAAATTTGAATTTCCCGC  
         [0431]    The match between the T2 sequence and the C1/C2 sequence is  
                       CAAAAAATTGACTGAAAATTTGAATTTCCCTCCAAAAATTGACTGAAAAT               TTGAATTTCCCGCCAAAAATTGACTGAAAATTTGAATATCCCGCCAAAAA               TTGACTGAAAATTTGAATTTCCCGCCGAAAATTAAATGAAAAATGGAATT               TCTCGCCGAA          
 
         [0432]    A C1/C2 short loop on chromosome 5 whose identifier is 28633 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene M162.5 and has the DNA sequence  
                       CAAAAATTGACTGAAAATTTGAATTTCCCGCAAAAAATTGACTGAAAATT               TGAATTTCCCGCCAAAAATTGACTGAAAATTTGAA          
 
         [0433]    The match between the T1 sequence and the C1/C2 sequence is  
                       CAAAAATTGACTGAAAATTTGAATTTCCCGCAAAAAATTGACTGAAAATT               TGAATTTCCCGCCAAAAATTGACTGAAAATTTGAA          
 
         [0434]    The match between the T2 sequence and the C1/C2 sequence is  
                                   CAAAAAATTGACTGAAAATTTGAATTTCCC          
 
         [0435]    3. One Connectron Controls the Expression of Many Sets of Genes in Prokaryotes, Archea, Single-celled Eukaryotes and Multi-celled Eukaryotes.  
         [0436]    One C1/C2 short loop can control the existence of a many T1-T2 long loops. The C1/C2 short loop can be on the same chromosome or on different chromosomes from the T1-T2 long loops. This relationship is described as “one-to-many”. This relationship exists in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0437]    Example of a One-to-many Connectron in Prokaryotes— E. coli    
         [0438]    In this example the existence of T1-T2 (3208-3315, 3436-3476, 3439-3478 and 3441-3479) long loops are controlled by one C1/C2 short loop (3206).  
                                           3206 Chromosome 1                           |       *------------------*------------------*       |            Chromosome 1            |       3208                             3315                               3206 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 1            |       3436                             3476                               3206 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 1            |       3439                             3478                               3206 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 1            |       3441                             3479       --------------------------------------------------------          
 
         [0439]    A double stranded DNA loop of length 93.377 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3208. This T1 control element has the DNA sequence  
                                       ACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCA                           AGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAA                       ATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGG                       TTAAGCGACTAAGCGTACACGGTGGATGCCCTGGC...AGTGTGTTTCGACA                       CACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTG                       AAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTA                       GCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGT          
 
         [0440]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3315. This T2 control element has the DNA sequence  
                       TTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAAC               GAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACTCTGAAGTGAAACATC               TTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCA               GTCAGAGGCGATGAAGGACGTGCTAATCTGCGATA...GGTTAATGAGGCG               AACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACC               GAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGA               ATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAA          
 
         [0441]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                                   rrlC   rrfC   aspT   trpT   yifA   yifE   yifB   ilvL   ilvG_1       ilvM   ilvE   ilvD   ilvA   ilvY   ilvC   ppiC   b3776   rep       gppA   rhlB   trxA   rhoL   rho   rfe   wzzE   wecB   rffH       wecD   wecE   wzxE   yifM_2   wecG   yifK   argX   hisR       leuT   proM   aslB   aslA   hemY   hemX   hemD   cyaA       cyaY   b3808   dapF   uvrD   b3814   corA   yigF   yigG   rarD       yigI   pldA   recQ   yigJ   yigK   pldB   yigL   yigM   metR       metE   ysgA   udp   yigN   ubiE   yigP   b3836   yigU       yigW_1   rfaH   yigC   ubiB   fadA   fadB   pepQ   trkH       hemG   rrsA   ileT                  
 
         [0442]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0443]    A C1/C2 short loop on chromosome 1 whose identifier is 3206 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrsC and has the DNA sequence  
                                       GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG                           GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTC                       ACCTGCCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTG                       CTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAA...ACCGGCGATTTCCG                       AATGGGGAAACCCAGTGTGTTTCGACACACTATCATTTAACTGAATCCATA                       GGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGA                       AAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCA                       GCCCAGAGCCTGAATCAGT          
 
         [0444]    The match between the T1 sequence and the C1/C2 sequence is  
                                       ACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCA                           AGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAA                       ATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGG                       TTAAGCGACTAAGCGTACACGGTGGATGCCCTGGC...AGTGTGTTTCGACA                       CACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTG                       AAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTA                       GCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGT          
 
         [0445]    The match between the T2 sequence and the C1/C2 sequence is  
                       TTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAAC               GAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAAC          
 
         [0446]    A double stranded DNA loop of length 41.279 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3436. This T1 control element has the DNA sequence  
                       ACGCAACGCGTGATAAGCAATTTTCGTGTCCCCTTCGTCTAGAGGCCCAG               GACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACG               CCACTTGCTGGTT          
 
         [0447]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3476. This T2 control element has the DNA sequence  
                       AGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCT               AGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCC               CTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTCACCTGCCTTAATA          
 
         [0448]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                                   gltT   rrlB   rrfB   murB   coaA   b3975   tyrU   thrT   tufB       secE   nusG   rplK   rplA   rplJ   rplL   rpoB   rpoC   htrC       thiH   thiF   thiE   yjaE   yjaD   hemE   nfi   yjaG   hupA       yjaH   yjaI   hydH   purD   purH                  
 
         [0449]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0450]    A C1/C2 short loop on chromosome 1 whose identifier is 3206 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrsC and has the DNA sequence  
                       GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG               GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTC               ACCTGCCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTG               CTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAA               GTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGA               AACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGATGCC               CTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGT               AAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAG               TGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAA               CCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGA               GATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAAT               CAGT          
 
         [0451]    The match between the T1 sequence and the C1/C2 sequence is  
                       GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG               GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTT          
 
         [0452]    The match between the T2 sequence and the C1/C2 sequence is  
                       GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG               GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTC               ACCTGCCTTAATA          
 
         [0453]    A double stranded DNA loop of length 41.336 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3439. This T1 control element has the DNA sequence  
                                       CCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTT                           AAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGA          
 
         [0454]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3478. This T2 control element has the DNA sequence  
                       GTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTG               AAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTT          
 
         [0455]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                                   rrlB   rrfB   murB   coaA   b3975   tyrU   thrT   tufB   secE       nusG   rplK   rplA   rplJ   rplL   rpoB   rpoC   htrC   thiH       thiF   thiE   yjaE   yjaD   hemE   nfi   yjaG   hupA   yjaH       yjaI   hydH   purD   purH   gltV                  
 
         [0456]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0457]    A C1/C2 short loop on chromosome 1 whose identifier is 3206 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the generrsC and has the DNA sequence  
                                       GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG                           GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTC                       ACCTGCCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTG                       CTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAA...ACCGGCGATTTCCG                       AATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATA                       GGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGA                       AAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCA                       GCCCAGAGCCTGAATCAGT          
 
         [0458]    The match between the T1 sequence and the C1/C2 sequence is  
                                       CCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTT                           AAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGA          
 
         [0459]    The match between the T2 sequence and the C1/C2 sequence is  
                       GTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTG               AAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTT          
 
         [0460]    A double stranded DNA loop of length 38.285 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3441. This T1 control element has the DNA sequence  
                       AATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAG               GTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATG               AAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTA               TAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGT...GATGAGAGAAGA               TTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATAAAA               CAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCC               GAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCC               ATGCGAG          
 
         [0461]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3479. This T2 control element has the DNA sequence  
                                       AAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGA                           TGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGT                       CGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAAC                       CCAGTGTGTTTCGACACACTATCATTAACTGAATCC...CAGATTAAATCAG                       AACGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGC                       GGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCG                       CCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCA                       TCAAATTA          
 
         [0462]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                                   rrlB   rrfB   murB   coaA   b3975   tyrU   thrT   tufB   secE       nusG   rplK   rplA   rplJ   rplL   rpoB   rpoC   htrC   thiH       thiF   thiE   yjaE   yjaD   hemE   nfi   yjaG   hupA   yjaH       yjaI   hydH   purD   purH   gltV                  
 
         [0463]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0464]    A C1/C2 short loop on chromosome 1 whose identifier is 3206controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrsC and has the DNA sequence  
                                       GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG                           GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTC                       ACCTGCCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTG                       CTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAA...ACCGGCGATTTCCG                       AATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATA                       GGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGA                       AAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCA                       GCCCAGAGCCTGAATCAGT          
 
         [0465]    The match between the T1 sequence and the C1/C2 sequence is  
                       AATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAG               GTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATG               AAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTA               TAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATC               ATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATC               TAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCG               AGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGT          
 
         [0466]    The match between the T2 sequence and the C1/C2 sequence is  
                       AAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGA               TGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGT               CGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAAC               CCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGC               GAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAAC               CGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTG               AATCAGT          
 
         [0467]    Example of a One-to-many Connectron in Archea— M. jannaschii    
         [0468]    In this example the existence of T1-T2 (534-611, 1139-1159, and 1630-1643) long loops are controlled by one C1/C2 short loop (1642).  
                           1642 Chromosome 1                        |       *------------------*------------------*       |          Chromosome 1              |       534                              611                             1642 Chromosome 1                     |       *------------------*------------------*       |            Chromosome 1            |       1139                              1159                            1642 Chromosome 1                    |       *------------------*------------------*       |            Chromosome 1            |       1630                             1643       -------------------------------------------------------          
 
         [0469]    A double stranded DNA loop of length 72.886 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 534. This T1 control element has the DNA sequence  
         [0470]    TAAGTAAATAAAATTTCTCTAACAAATAAGTTAAATT  
         [0471]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 611. This T2 control element has the DNA sequence  
                       TAAATAAAATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATA               AAAATGCT          
 
         [0472]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           MJ0486   MJ0487   MJ0488   MJ0489   MJ0490   MJ0492   MJ0493       MJ0494   MJ0495   MJ0496   MJ0497   MJ0499   MJ0500   MJ0501       MJ0502   MJ0503   MJ0504   MJ0506   MJ0507   MJ0508   MJ0509       MJ0510   MJ0511   MJ0512   MJ0513   MJ0514   MJ0514   MJ0517       MJ0519   MJ0520   MJ0521   MJ0522   MJ0523   MJ0525   MJ0526       MJ0526   MJ0529   MJ0530   MJ0531   MJ0532   MJ0534   MJ0535       MJ0536   MJ0538   MJ0539   MJ0540   MJ0541   MJ0542   MJ0543       MJ0544   MJ0545   MJ0547   MJ0548   MJ0549   MJ0550   MJ0552       MJ0553   MJ0554   MJ0555   MJ0556   MJ0558   MJ0559   MJ0560       MJ0561   MJ0562   MJ0563   MJ0564                  
 
         [0473]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0474]    A C1/C2 short loop on chromosome 1 whose identifier is 1642 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1602 and has the DNA sequence  
                                       ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAA                       ATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACT                       CTGTTTTATTATGGAAAGAAAGAT          
 
         [0475]    The match between the T1 sequence and the C1/C2 sequence is  
         [0476]    AAGTAAATAAAATTTCTCTAACAAATAAGTTAAATT  
         [0477]    The match between the T2 sequence and the C1/C2 sequence is  
                       TAAATAAAATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATA               AAAAT          
 
         [0478]    A double stranded DNA loop of length 14.509 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 1139. This T1 control element has the DNA sequence  
                       ATTTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTAGCTGG               TTTGATTGTTTAAAATATTTGAGTTTA          
 
         [0479]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1159. This T2 control element has the DNA sequence  
                                       ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAATTA          
 
         [0480]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           MJ1096   MJ1097   tRNA-Arg-3   MJ1098   MJ1099   MJ1100   MJ1101       MJ1102   MJ1103   MJ1104   MJ1105   MJ1106   MJ1107   MJ1108                  
 
         [0481]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0482]    A C1/C2 short loop on chromosome 1 whose identifier is 1642 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1602 and has the DNA sequence  
                                       ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAA                       ATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACT                       CTGTTTTATTATGGAAAGAAAGAT          
 
         [0483]    The match between the T1 sequence and the C1/C2 sequence is  
         [0484]    ATTTAATTTCTAAGGGTTAGCTGGTTTGATT  
         [0485]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAATTA          
 
         [0486]    A double stranded DNA loop of length 4.998 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 1630. This T1 control element has the DNA sequence  
                                       TTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTT                           GATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA                       AGATTAATTAGGAAAGGAAATAAGATTTCTCTAACAGACAAGTTAAATTT                       TTGGATTTAAAAAGATAAAAAT          
 
         [0487]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1643. This T2 control element has the DNA sequence  
                                       TTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTATTG                           AATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAAAT                       TTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACTCT                       GTTTTATTATGGAAAGAAAGAT          
 
         [0488]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0489]    MJ1597 MJ1598 MJ1599 MJ1600 MJ1601 MJ1602  
         [0490]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0491]    A C1/C2 short loop on chromosome 1 whose identifier is 1642 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1602 and has the DNA sequence  
                                       ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAA                       ATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACT                       CTGTTTTATTATGGAAAGAAAGAT          
 
         [0492]    The match between the T1 sequence and the C1/C2 sequence is  
                                       GCTGGTTTGATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTA                           AAAATTA          
 
         [0493]    The match between the T2 sequence and the C1/C2 sequence is  
                                       TTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTATTG                           AATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAAAT                       TTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACTCT                       GTTTTATTATGGAAAGAAAGAT          
 
         [0494]    Example of a One-to-many Connectron in Single-cell Eukaryotes— S. cervesiae    
         [0495]    In this example the existence of T1-T2 (158-171, 293-317, 4295-4308 and 5916-5923) long loops are controlled by one C1/C2 short loop (86).  
                           86 Chromosome 1                        |       *------------------*------------------*       |            Chromosome 1            |       158                           171                            86 Chromosome 1                    |       *------------------*-------------------*       |            Chromosome 1            |       293                           317                            86 Chromosome 1                    |       *-------------------*------------------*       |            Chromosome 10           |       4295                             4308                            86 Chromosome 1                    |       *-------------------*------------------*       |            Chromosome 13           |       5916                             5923       ---------------------------------------------------------          
 
         [0496]    A double stranded DNA loop of length 20.391 kilo-bases on chromosome 2 is bounded on the left by a T1 sequence whose identifier is 158. This T1 control element has the DNA sequence  
                       CCAATTGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTT               ACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAGAA               ATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTAAT               AG          
 
         [0497]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 171. This T2 control element has the DNA sequence  
                       ATAATTGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTT               ACTAGTATATTATCATATACGGTGTTAGAAGATGACACAAATGATGAGAA               ATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTAAT               AGGATCAATGAATATTAACATATAAAATGATGATAATAATA          
 
         [0498]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                       YBL107W-A   TL(UAA)B1   YBL107C   YBL106C   YBL105C   YBL104C       YBL103C   YBL102W   YBL101C                  
 
         [0499]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0500]    A C1/C2 short loop on chromosome 1 whose identifier is 86 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YAR009C and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAGAAATCAACTATCATCTAC               TAACTAGTATTTACATTACTAGTATATTATCATATACGGTGTTAGAAGATG               ACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCTGAAACGCA               AGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT               GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGG               ATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATT               ATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCACCCAT               TTCTCAGAA          
 
         [0501]    The match between the T1 sequence and the C1/C2 sequence is  
         [0502]    AAATCAACTATCATCTACTAACTAGTATTTAC  
         [0503]    The match between the T2 sequence and the C1/C2 sequence is  
         [0504]    AAATCAACTATCATCTACTAACTAGTATTTAC  
         [0505]    A double stranded DNA loop of length 38.470 kilo-bases on chromosome 2 is bounded on the left by a T1 sequence whose identifier is 293. This T1 control element has the DNA sequence  
                       GAATTGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTA               TCAATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAA               GCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCAAGGATTGATAATGTAAT               AGGATAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGT               ATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTTGAGGAGAAC               TTCTAGT          
 
         [0506]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 317. This T2 control element has the DNA sequence  
                       AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC               GAGGAGAACTTCTAGTATATTCTGTA          
 
         [0507]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                       YBL005W-B   TS(AGA)B   YBL004W   YBL003C   YBL002W   YBL001C       YBR001C   YBR002C   YBR003W   YBR004C   YBR005W   YBR006W       YBR007C   YBR008C   YBR009C   YBR010W   YBR011C   YBR012C                  
 
         [0508]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0509]    A C1/C2 short loop on chromosome 1 whose identifier is 86 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YAR009C and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAGAAATCAACTATCATCTAC               TAACTAGTATTTACATTACTAGTATATTATCATATACGGTGTTAGAAGATG               ACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCTGAAACGCA               AGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT               GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGG               ATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATT               ATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCACCCAT               TTCTCAGAA          
 
         [0510]    The match between the T1 sequence and the C1/C2 sequence is  
                       AAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAAT               ATAGATTCCATTTTGAGGATTCCTATATCCT          
 
         [0511]    The match between the T2 sequence and the C1/C2 sequence is  
                       AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC               GAGGAGAACTTCTAGTATATTCTGTA          
 
         [0512]    A double stranded DNA loop of length 11.020 kilo-bases on chromosome 10 is bounded on the left by a T1 sequence whose identifier is 4295. This T1 control element has the DNA sequence  
                       AAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAA               ACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCAT               TTTGAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTG          
 
         [0513]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 4308. This T2 control element has the DNA sequence  
                       GGAAGCTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAA               ACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAATAT               AGATTCCATTTTGAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATT               CTGTATACCTAATATTATAGCCTTTATCAA          
 
         [0514]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0515]    YJR027W YJR029W  
         [0516]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0517]    A C1/C2 short loop on chromosome 1 whose identifier is 87 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YAR009C and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAGAAATCAACTATCATCTAC               TAACTAGTATTTACATTACTAGTATATTATCATATACGGTGTTAGAAGATG               ACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCTGAAACGCA               AGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT               GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGC               ATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATT               ATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCACCCAT               TTCTCA          
 
         [0518]    A double stranded DNA loop of length 5.462 kilo-bases on chromosome 13 is bounded on the left by a T1 sequence whose identifier is 5916. This T1 control element has the DNA sequence  
                       AAGCTGAAGTGCAAGGATTGATAATGTAATAGGATAATGAAACATATAA               AACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCA               TTTTGAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTA          
 
         [0519]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 5923. This T2 control element has the DNA sequence  
                       TAATAGGATAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATT               AGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTCGAGGAG               AACTTCTAGTATATTCTGTATACCTAATATTATAGCCTTTATCAA          
 
         [0520]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0521]    YML045W  
         [0522]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0523]    A C1/C2 short loop on chromosome 1 whose identifier is 87 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YAR009C and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAGAAATCAACTATCATCTAC               TAACTAGTATTTACATTACTAGTATATTATCATATACGGTGTTAGAAGATG               ACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCTGAAACGCA               AGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT               GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGG               ATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATT               ATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCACCCAT               TTCTCA          
 
         [0524]    Example of a One-to-many Connectron in Multi-cell Eukaryotes— C. elegans    
         [0525]    In this example the existence of T1-T2 (16554-16661 and 21565-21590) long loops are controlled by one C1/C2 short loop (21591).  
                                         21591 Chromosome 5                         |       *------------------*------------------*       |            Chromosome 4            |       16554                            16661                             21591 Chromosome 5                     |       *------------------*------------------*       |            Chromosome 5            |       21565                            21590       ---------------------------------------------------------          
 
         [0526]    A double stranded DNA loop of length 50.159 kilo-bases on chromosome 4 is bounded on the left by a T1 sequence whose identifier is 16554. This T1 control element has the DNA sequence  
                       TGCCTGAAAAAATTGGCTCCGAGTTAGGACACTTGGGGTGGTCAAAAAT               TTTGTGACTATTGTCAAATGAAAGATCATAGTTGATAACATAAATTCCCAA               AGTTTCATAAAAATCGATACGCAGCGAACAAAGTTATCAATT          
 
         [0527]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 16661. This T2 control element has the DNA sequence  
                       CACTTGGGGTGGTCAAAAAATTTTGTGATTATTGTCAAATGAAAGATCAT               GGTTGATAACATAAATTCCCAAAGTTTCATAAAAATCGATACGCAGCGAA               CAAAGTTATGATTTTTGACCCGGAACTTATTTGGAGACCTA          
 
         [0528]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0529]    C23H5.7 C23H5.8a C23H5.3 C23H5.2 C23H5.9 C23H5.1  
         [0530]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0531]    A C1/C2 short loop on chromosome 5 whose identifier is 21591 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene F25A2.1 and has the DNA sequence  
                       TATTGTCAAATGAAAGATCATGGTTGATAACATAAATTCCCACAATTTCAT               AAAAATCGATACGCAGCGAACAAAGTTATGATTTTTGACCCGGAACTTAT               TTGGAGACCTAATATT          
 
         [0532]    The match between the T1 sequence and the C1/C2 sequence is  
         [0533]    TTTCATAAAAATCGATACGCAGCGAACAAAGTTAT  
         [0534]    The match between the T2 sequence and the C1/C2 sequence is  
         [0535]    TATTGTCAAATGAAAGATCATGGTTGATAACATAAATTCCCA  
         [0536]    A double stranded DNA loop of length 18.142 kilo-bases on chromosome 5 is bounded on the left by a T1 sequence whose identifier is 21565. This T1 control element has the DNA sequence  
                       CTCCGAGTTAGGACACTTGGGGTGGACAAAAAATTTTGTGACTATTGTCA               AATGAAAGATCATGGTTGATAA          
 
         [0537]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 21590. This T2 control element has the DNA sequence  
                       TATTGTCAAATGAAAGATCATGGTTGATAACATAAATTCCCACAATTTCAT               AAAAATCGATACGCAGCGAACAAAGTTATGATTTTTGACCCGGAACTTAT               TTGGAGACCTAATA          
 
         [0538]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0539]    T21H3.2 T21H3.1 F25A2.1  
         [0540]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0541]    A C1/C2 short loop on chromosome 5 whose identifier is 21591 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene F25A2.1 and has the DNA sequence  
                       TATTGTCAAATGAAAGATCATGGTTGATAACATAAATTCCCACAATTTCAT               AAAAATCGATACGCAGCGAACAAAGTTATGATTTTTGACCCGGAACTTAT               TTGGAGACCTAATATT          
 
         [0542]    The match between the T1 sequence and the C1/C2 sequence is  
         [0543]    TATTGTCAAATGAAAGATCATGGTTGATAA  
         [0544]    The match between the T2 sequence and the C1/C2 sequence is  
                       TATTGTCAAATGAAAGATCATGGTTGATAACATAAATTCCCACAATTTCAT               AAAAATCGATACGCAGCGAACAAAGTTATGATTTTTGACCCGGAACTTAT               TTGGAGACCTAATA          
 
         [0545]    4. Connectrons Occur Between Prokaryotes and Their Plasmids.  
         [0546]    Connectron relationships exist between prokaryotes and their plasmids. These connectrons implement a control mechanism between the two genomes that makes it possible for them to form a symbiotic relationship. In the case of  D. radiodurans  the relationship is not symmetric. The  D. radiodurans  genome sends C1/C2 short loops to the MP1 plasmid.  
         [0547]    Example of a Prokaryote/Plasmid Connectron— D. radiodurans    
         [0548]    In this example the existence of T1-T2 (2654-2694 and 2692-2749) long loops in chromosome 3 that is the plasmid MP1 are controlled by one C1/C2 short loop (16) in chromosome 1.  
                                         16 Chromosome 1                         2768 Chromosome 3 (plasmid MP1)                     2653 Chromosome 3 (plasmid MP1)                     |       *------------------*------------------*       |         Chromosome 3 (plasmid MP1)    |       2654                         2694       |             2693            |                             16 Chromosome 1                     2768 Chromosome 3 (plasmid MP1)                     2693 Chromosome 3 (plasmid MP1)                     |       *------------------*------------------*       |         Chromosome 3 (plasmid MP1)    |       2692                        2749       |        2693  2695         |       --------------------------------------------------------          
 
         [0549]    A double stranded DNA loop of length 46.903 kilo-bases on chromosome 3 (plasmid MP1) is bounded on the left by a T1 sequence whose identifier is 2654. This T1 control element has the DNA sequence  
                       CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG               GTATAGCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTG               ACGATGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGACTGTCAGTACA               GCAATCGAGAGTGGGCTGATCAGCCCACTGTGCGTTCTGGCCATCGACGC               CTCTTTTCACCGCAAAGCCGGTCAGCACACCGCACACCTCGGCTCGTTCTG               GAATGGCTGTGCCGCGCGGACC          
 
         [0550]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 2694. This T2 control element has the DNA sequence  
                       GCTGAACGCCCTGAATCTCTCCCGGTATGCAGCCTGCTCGGAGAGTACGA               TTCGTCGTTGGCTGCACCGAAGTGACGATGGGGCCATTCCGTGGGGCGCG               TTACACCAGGCGACTGTCAGTACAGCAATCGAGAGTGGGCTGATCAGCCC               ACTGTGCGTTCTGGCCATCGACGCCTCTTTTCACCGCAAAGCCGGTCAGCA               CACCGCACACCTCGGCTCGTTCTGGAATGGCTGTGCCGCGCGGACCGAAC               GCGGAATCGAGCAATCCTGTTGT          
 
         [0551]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                       DRB0020   DRB0021   DRB0022   DRB0023   DR80024   DRB0025       DRB0027   DRB0030   DRB0032   DRB0033   DRB0034   DRB0035       DRB0037   DRB0038   DRB0039   DRB0041   DRB0042   DRB0043       DRB0044   DRB0045   DRB0047   DRB0051   DRB0052   DRB0054       DRB0055   DRB0057                  
 
         [0552]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0553]    A C1/C2 short loop on chromosome 3 (plasmid MP1) whose identifier is 2693 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DRB0057 and has the DNA sequence  
                       CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC               GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG               AC          
 
         [0554]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0555]    A C1/C2 short loop on chromosome 1 whose identifier is 16 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DR0009 and has the DNA sequence  
                       GCTGTGAAATCACCGCTTCCAATGGGTCTGATGGCCATCCTACAGTACGTT               CTCAGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCT               GCTCAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTC               CCGGTATGCAGCCTGCTCGGAGAGTACGATTCGT          
 
         [0556]    The match between the T1 sequence and the C1/C2 sequence is  
                       CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG               GTATGCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTG               ACGATGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGACTGTCAGTACA               GCAATCGAGAGTGGGCTGATCAGCCCACTGTGCGTTCTGGCCATCGACGC               CTCTTTTCACCGCAAAGCCGGTCAGCACACCGCACACCTCGGCTCGTTCTG               GAATGGCTGTGCCGCGCGGACC          
 
         [0557]    The match between the T2 sequence and the C1/C2 sequence is  
                       GCTGAACGCCCTGAATCTCTCCCGGTATGCAGCCTGCTCGGAGAGTACGA               TTCGTCGTTGGCTGCACCGAAGTGACGATGGGGCCATTCCGTGGGGCGCG               TTACACCAGGCGACTGTCAGTACAGCAATCGAGAGTGGGCTGATCAGCCC               ACTGTGCGTTCTGGCCATCGACGCCTCTTTTCACCGCAAAGCCGGTCAGCA               CACCGCACACCTCGGCTCGTTCTGGAATGGCTGTGCCGCGCGGACCGAAC               GCGGAATCGAGCAATCCTGTTGT          
 
         [0558]    A C1/C2 short loop on chromosome 3 (plasmid MP1) whose identifier is 2768 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DRB0133 and has the DNA sequence  
                       GCTGTGAAATCACCGCTTCCAATGGGTCTGATGGCCATCCTACAGTACGTT               CTCAGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCT               GCTCAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTC               CCGGTATGCAGCCTGCTCGGAGAGTACGATTCGT          
 
         [0559]    The match between the T1 sequence and the C1/C2 sequence is  
                       CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG               GTATGCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTG               ACGATGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGACTGTCAGTACA               GCAATCGAGAGTGGGCTGATCAGCCCACTGTGCGTTCTGGCCATCGACGC               CTCTTTTCACCGCAAAGCCGGTCAGCACACCGCACACCTCGGCTCGTTCTG               GAATGGCTGTGCCGCGCGGACC          
 
         [0560]    The match between the T2 sequence and the C1/C2 sequence is  
                       GCTGAACGCCCTGAATCTCTCCCGGTATGCAGCCTGCTCGGAGAGTACGA               TTCGTCGTTGGCTGCACCGAAGTGACGATGGGGCCATTCCGTGGGGCGCG               TTACACCAGGCGACTGTCAGTACAGCAATCGAGAGTGGGCTGATCAGCCC               ACTGTGCGTTCTGGCCATCGACGCCTCTTTTCACCGCAAAGCCGGTCAGCA               CACCGCACACCTCGGCTCGTTCTGGAATGGCTGTGCCGCGCGGACCGAAC               GCGGAATCGAGCAATCCTGTTGT          
 
         [0561]    A C1/C2 short loop on chromosome 3 (plasmid MP1) whose identifier is 2653 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DRB0017 and has the DNA sequence  
                       CGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCTCAGC               GTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCGGTAT               GCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTGACGA               TGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGA          
 
         [0562]    The match between the T1 sequence and the C1/C2 sequence is  
                       CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG               GTATGCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTG               ACGATGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGACTGTCAGTACA               GCAATCGAGAGTGGGCTGATCAGCCCACTGTGCGTTCTGGCCATCGACGC               CTCTTTTCACCGCAAAGCCGGTCAGCACACCGCACACCTCGGCTCGTTCTG               GAATGGCTGTGCCGCGCGGACC          
 
         [0563]    The match between the T2 sequence and the C1/C2 sequence is  
                       GCTGAACGCCCTGAATCTCTCCCGGTATGCAGCCTGCTCGGAGAGTACGA               TTCGTCGTTGGCTGCACCGAAGTGACGATGGGGCCATTCCGTGGGGCGCG               TTACACCAGGCGACTGTCAGTACAGCAATCGAGAGTGGGCTGATCAGCCC               ACTGTGCGTTCTGGCCATCGACGCCTCTTTTCACCGCAAAGCCGGTCAGCA               CACCGCACACCTCGGCTCGTTCTGGAATGGCTGTGCCGCGCGGACCGAAC               GCGGAATCGAGCAATCCTGTTGT          
 
         [0564]    A double stranded DNA loop of length 68.612 kilo-bases on chromosome 3 (plasmid MP1) is bounded on the left by a T1 sequence whose identifier is 2692. This T1 control element has the DNA sequence  
                       CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC               GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG               AC          
 
         [0565]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 2749. This T2 control element has the DNA sequence  
                       AGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCT               CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG               GT          
 
         [0566]    This long T1/ T2 double stranded DNA loop modulates the expression of the following genes  
                                                       DRB0059   DRB0060   DRB0061   DRB0062   DRB0064   DRB0065       DRB0066   DRB0067   DRB0068   DRB0069   DRB0070   DRB0072       DRB0073   DRB0074   DRB0076   DRB0077   DRB0079   DRB0080       DRB0081   DRB0083   DRB0085   DRB0086   DRB0087   DRB0088       DRB0089   DRB0090   DRB0092   DRB0093   DRB0094   DRB0096       DRB0097   DRB0098   DRB0102   DRB0103   DRB0104   DRB0105       DRB0106   DRB0107   DRB0111   DRB0112                  
 
         [0567]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0568]    A C1/C2 short loop on chromosome 3 (plasmid MP1) whose identifier is 2693 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DRB0057 and has the DNA sequence  
                       CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC               GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG               AC          
 
         [0569]    A C1/C2 short loop on chromosome 3 (plasmid MP1) whose identifier is 2695 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DRB0057 and has the DNA sequence  
                       GCTGAACGCCCTGAATCTCTCCCGGTATGCAGCCTGCTCGGAGAGTACGA               TTCGTCGTTGGCTGCACCGAAGTGACGATGGGGCCATTCCGTGGGGCGCG               TTACACCAGGCGACTGTCAGTACAGCAATCGAGAGTGGGCTGATCAGCCC               ACTGTGCGTTCTGGCCATCGACGCCTCTTTTCACCGCAAAGCCGGTCAGCA               CACCGCACACCTCGGCTCGTTCTGGAATGGCTGTGCCGCGCGGACCGAAC               GCGGAATCGAGCAATCCTGTTGT          
 
         [0570]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0571]    A C1/C2 short loop on chromosome 1 whose identifier is 16 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DR0009 and has the DNA sequence  
                       GCTGTGAAATCACCGCTTCCAATGGGTCTGATGGCCATCCTACAGTACGTT               CTCAGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCT               GCTCAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTC               CCGGTATGCAGCCTGCTCGGAGAGTACGATTCGT          
 
         [0572]    The match between the T1 sequence and the C1/C2 sequence is  
                       CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC               GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG               AC          
 
         [0573]    The match between the T2 sequence and the C1/C2 sequence is  
                       AGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCT               CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG               GT          
 
         [0574]    A C1/C2 short loop on chromosome 3 (plasmid MP1) whose identifier is 2768 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DRB0133 and has the DNA sequence  
                                       GCTGTGAAATCACCGCTTCCAATGGGTCTGATGGCCATCCTACAGTACGTT                           CTCAGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCT                       GCTCAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTC                       CCGGTATGCAGCCTGCTCGGAGAGTACGATTCGT...CGGACCGAACGCGGA                       ATCGAGCAATCCTGTTGTGCCCTCATTGATGTCCAGCACCGGCAGGCCTTG                       ACGGTCGATGTCCGTCAGACCCTGACCGGGTCTGAGGCTCCAACTCGTCT                       GGAACAG          
 
         [0575]    The match between the T1 sequence and the C1/C2 sequence is  
                       CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC               GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG               AC          
 
         [0576]    The match between the T2 sequence and the C1/C2 sequence is  
                       AGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCT               CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG               GT          
 
         [0577]    A C1/C2 short loop on chromosome 3 (plasmid MP1) whose identifier is 2693 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DRB0057 and has the DNA sequence  
                       CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC               GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG               AC          
 
         [0578]    The match between the T1 sequence and the C1/C2 sequence is  
                       CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC               GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG               AC          
 
         [0579]    The match between the T2 sequence and the C1/C2 sequence is  
                       AGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCT               CAGCGTTTTTCTCGCTGTTCCTGGAC          
 
         [0580]    A C1/C2 short loop on chromosome 3 (plasmid MP1) whose identifier is 2653 controls the expression of the genes in this T1T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene DRB0017 and has the DNA sequence  
                       CGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCTCAGC               GTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCGGTAT               GCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTGACGA               TGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGA          
 
         [0581]    The match between the T1 sequence and the C1/C2 sequence is  
                       CGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCTCAGC               GTTTTTCTCGCTGTTCCTGGAC          
 
         [0582]    The match between the T2 sequence and the C1/C2 sequence is  
                       CGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCTCAGC               GTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCGGT          
 
         [0583]    5. Connectrons Occur in Plants and Higher Animals  
         [0584]    Connectron relationships exist in plant and higher animals.  
         [0585]    Example of a Plant Connectron— A. thaliania    
         [0586]    In this example the existence of the T1-T2 (423-469) long loop is controlled by six C1/C2 short loops (972, 21396, 422, 21762, 21813 and 10882). The T1-T2 long loop controls the expression of six genes on chromosome 2 in addition to two C1/C2 (426 and 430) short loops.  
                                        972 Chromosome 2                        21396 Chromosome 4                    422 Chromosome 2                    21762 Chromosome 4                    21813 Chromosome 4                    10882 Chromosome 4                    |       *------------------*------------------*       |            Chromosome 2            |       423                              469       |            426      430       |       -------------------------------------------------------          
 
         [0587]    A double stranded DNA loop of length 42.285 kilo-bases on chromosome 2 is bounded on the left by a T1 sequence whose identifier is 423. This T1 control element has the DNA sequence  
                       TATCTCTTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTA               ATTAAAAAACGAAATA          
 
         [0588]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 469. This T2 control element has the DNA sequence  
                       TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATTATTAATT               TTCAAAAATAATAACC          
 
         [0589]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0590]    At2g02070 At2g02080 At2g02090 At2g02100 At2g02120 At2g02130  
         [0591]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0592]    A C1/C2 short loop on chromosome 2 whose identifier is 426 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene At2g02060 and has the DNA sequence  
                       TTCCAAAAATAATAACCAATCAAAATCAACATATAAGATTTGATATCTAA               ATTTT          
 
         [0593]    A C1/C2 short loop on chromosome 2 whose identifier is 430 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene At2g02060 and has the DNA sequence  
                       TTGCGGAAAAATAATATCATCATTATAAAAAAATAATTAGAGTTTTTTCG               CATAT          
 
         [0594]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0595]    A C1/C2 short loop on chromosome 2 whose identifier is 972 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene At2g04240 and has the DNA sequence  
                       GTATGCCATTAGAAATAAAATTTTAAAAGTAAATTAATTCATCTCTTTAAA               AATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAAAAACG               AAATACATTATTAATTT          
 
         [0596]    The match between the T1 sequence and the C1/C2 sequence is  
                       ATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAAAAACGA               AATA          
 
         [0597]    The match between the T2 sequence and the C1/C2 sequence is  
                       TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATTATTAAT               TT          
 
         [0598]    A C1/C2 short loop on chromosome 4 whose identifier is 21396 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene AT4g15300 and has the DNA sequence  
                       TGCCATTAGAAATAAAATTTTAAAGAGTAAATTAATTTATCTCTTTAAGGA               TTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAAAAACGAA               ATACATTATTAATTTCCAAAA          
 
         [0599]    The match between the T1 sequence and the C1/C2 sequence is  
                       TATCTCTTTAAGGATTAAAAAGTCAAATACTATTTAATTAATTAAATTTA               ATTAAAAAACGAAATA          
 
         [0600]    The match between the T2 sequence and the C1/C2 sequence is  
                       TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATTATTAATT               T          
 
         [0601]    A C1/C2 short loop on chromosome 2 whose identifier is 422 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene At2g02060 and has the DNA sequence  
                       TAACCTTAATTTTTGTAAGTAATTATATAGGTATGCCATTAGAAATAAAAT               TTTAAAGAGTAAATTAATTTATCTCTTTAAGGATTAAAAAGTCAAATACTA               ATTTAATTAATTAAATTTAATTAAAAAACGAAATA          
 
         [0602]    The match between the T1 sequence and the C1/C2 sequence is  
                       TATCTCTTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTA               ATTAAAAAACGAAATA          
 
         [0603]    The match between the T2 sequence and the C1/C2 sequence is  
         [0604]    TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATA  
         [0605]    A C1/C2 short loop on chromosome 4 whose identifier is 21762 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene AT4g17510 and has the DNA sequence  
                       TTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAA               AAACGAAATACATT          
 
         [0606]    The match between the T1 sequence and the C1/C2 sequence is  
                       TTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAA               AAACGAAATA          
 
         [0607]    The match between the T2 sequence and the C1/C2 sequence is  
         [0608]    TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATT  
         [0609]    A C1/C2 short loop on chromosome 4 whose identifier is 21813 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene AT4g17680 and has the DNA sequence  
                       TTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAA               AAACGAAATACATT          
 
         [0610]    The match between the T1 sequence and the C1/C2 sequence is  
                       TTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAA               AAACGAAATA          
 
         [0611]    The match between the T2 sequence and the C1/C2 sequence is  
         [0612]    TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATT  
         [0613]    A C1/C2 short loop on chromosome 2 whose identifier is 10882 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene At2g26540 and has the DNA sequence  
                       TATCTCTTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTA               ATTAA          
 
         [0614]    The match between the T2 sequence and the C1/C2 sequence is  
         [0615]    TACTAATTTAATTAATTAAATTTAATTAA  
         [0616]    Example of a Animal Connectron— D. megalomaster    
         [0617]    A double stranded DNA loop of length 88.159 kilo-bases on chromosome 4 is bounded on the left by a T1 sequence whose identifier is 3340. This T1 control element has the DNA sequence  
                       ACCTAAAAGAAGTACCGTTTTTTACTCCTAATTACCAATTCTAACCATCCA               TATCACTTTTTGACGGACTCCGTGAAAATAATTTTTGGCCAAATTTTCGCA               TTTTTTGTAAGGGGTAACATCATAAAAATT          
 
         [0618]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3372. This T2 control element has the DNA sequence  
                                       AAAAAAGTACCGCGTTTTACTCCTAATTACCAATTCTAACCATCCATATCA                           CTTTTTGACGGACTCCGTGAAAATAATTTTTGGCCAAATTTTCGCATTTTTT                       GTAAGGGGTAACATCATCAAAATTTGCGAAAAA          
 
         [0619]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0620]    [Some of the Following Gene Names have not been Determined.] 
                                                                   —   —   —   —   —           —   CG11207   —   CG2186   CG2157           —   Ork1   —   —   —           —                      
 
         [0621]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0622]    A C1/C2 short loop on chromosome 4 whose identifier is 3362 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene XXX and has the DNA sequence  
                                       AAAAAAGTACCGCGTTTTACTCCTAATTACCAATTCTAACCATCCATATCA                           CTTTTTGACGGACTCCGTTAAAATAATTTTTGACCAAATTTTCGCATTTTTT                       GTAATCAAAATTTGCAAAAAATTGAAAAAAC          
 
         [0623]    A C1/C2 short loop on chromosome 4 whose identifier is 3364 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene XXX and has the DNA sequence  
                       CAAAATTTGAATGCAAATCGATTGGGAATCAAAAAACAAACTCAACGAG               GTATGACATTCCATATTTGGGCCATTATTTCCAA          
 
         [0624]    A C1/C2 short loop on chromosome 4 whose identifier is 3366 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene XXX and has the DNA sequence  
                       TTTTTTCACAAAAATTAGGAAAATGATTTTGGGTAAAAAAATGAATATTT               AAGTTGGGTTTT          
 
         [0625]    A C1/C2 short loop on chromosome 4 whose identifier is 3369 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene XXX and has the DNA sequence  
                       AAATCGATTGGGAATCAAAAAACAAACCTCAACGAGGTATGACATTCCAT               ATCTGGGCCATTATTTCCAATCTTTTGATCAAAATAC          
 
         [0626]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0627]    A C1/C2 short loop on chromosome 4 whose identifier is 3373 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene XXX and has the DNA sequence  
                                       AAAAAAGTACCGCGTTTTACTCCTAATTACCAATTCTAACCATCCATATCA                           CTTTTTGACGGACTCCGTGAAAATAATTTTTGGCCAAATTTTCGCATTTTTT                       GTAAGGGGTAACATCATCAAAATTTGCGAAAAA          
 
         [0628]    The match between the T1 sequence and the C1/C2 sequence is  
                                       TTTTACTCCTAATTACCAATTCTAACCATCCATATCACTTTTTGACGGACTC                           CGTGAAAATAATTTTTGGCCAAATTTTCGCATTTTTTGTAAGGGGTAACAT                       CAT          
 
         [0629]    Example of an Animal Connectron— H. sapiens    
         [0630]    All of the human genome that has been fully sequenced by both the NIH-lead global sequencing project and the Celera Genomics, Inc. project. The gene descriptors for this chromosome do not yet exist. Without the positions and directions of the genes, it is not possible to select from among the possible connectrons to determine the real connectrons.  
         [0631]    Human chromosome 22 has been processed and there 31,000 possible connectrons.  
         [0632]    The gene descriptors for all the chromosomes of the human genome should become available within the year.  
         [0633]    6. Permanent Connectrons Exist in Prokaryotes, Archea, Single-celled Eukaryotes and Multi-celled Eukaryotes.  
         [0634]    C1/C2 short loops are normally expressed as the 3′UTR of some gene. A class of connectron relationships exist that permit one C1/C2 short loop to control the existence of one or more T1-T2 long loops without being subject to any expression controls other than those of the gene to which the C1/C2 is 3′UTR. These connectron relationships are described as “permanent”. Permanent connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0635]    Example of a Prokaryote Permanent Connectron— E. coli    
         [0636]    In this example the existence of the T1-T2 (3200-3210) long loop is controlled by a C1/C2 short loop (3432). The expression of this C1/C2 short loop is controlled only by the gene btuB.  
                                         3432 Chromosome 1                         |       *------------------*------------------*       |            Chromosome 1            |       3200                             3210       --------------------------------------------------------          
 
         [0637]    A double stranded DNA loop of length 93.339 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3200. This T1 control element has the DNA sequence  
                       AAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCG               AAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCA               AGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAACTT               TTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCC               TAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGA               CGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGG               GATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAA               GAGGGGGACCTTCGGGCCTCTTGCCATC          
 
         [0638]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3310. This T2 control element has the DNA sequence  
                       CAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGA               CGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAG               TTTAATTCTTTGAGCGTCAAACTTTTAAATTGAAGAGTTTGATCATGGCTC               AGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACA               GGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTC               TGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAAT               ACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCA               TCGGATGTGCCCAGATGGGATTAGCTAGT          
 
         [0639]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                                   rrsC   gltU   rrlC   rrfC   aspT   trpT   yifA   yifE   yifB       ilvL   ilvG_1   ilvM   ilvE   ilvD   ilvA   ilvY   ilvC   ppiC       b3776   rep   gppA   rhlB   trxA   rhoL   rho   rfe   wzzE       wecB   rffH   wecD   wecE   wzxE   yifM_2   wecG   yifK       argX   hisR   leuT   proM   aslB   aslA   hemY   hemX       hemD   cyaA   cyaY   b3808   dapF   uvrD   b3814   corA       yigF   yigG   rarD   yigI   pldA   recQ   yigJ   yigK   pldB       yigL   yigM   metR   metE   ysgA   udp   yigN   ubiE   yigP       b3836   yigU   yigW_1   rfaH   yigC   ubiB   fadA   fadB       pepQ   trkH   hemG                  
 
         [0640]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0641]    A C1/C2 short loop on chromosome 1 whose identifier is 3432 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene btuB and has the DNA sequence  
                                       TGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACT                           CCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGG                       GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATG                       CTTGACTCTGTAGCGGGAAGGCGTATTATGCACACC...TGCAACTCGACTC                       CATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATA                       CGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGC                       AAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGAT                       TCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGT                       TGGATCACCTCCTTACCTTAAAGAAGCGT          
 
         [0642]    The match between the T1 sequence and the C1/C2 sequence is  
                       AAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCG               AAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCA               AGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGC          
 
         [0643]    The match between the T2 sequence and the C1/C2 sequence is  
                       CAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGA               CGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAG               TTTAATTCTTTGAGCGTCAAACTTTTAAATTGAAGAGTTTGATCATGGCTC               AGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACA               GGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTC               TGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAAT               ACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCA               TCGGATGTGCCCAGATGGGATTAGCTAGT          
 
         [0644]    Example of an Archea Permanent Connectron— H. pylori    
         [0645]    In this example the existence of the T1-T2 (812-882) long loop is controlled by a C1/C2 short loop (1241). The expression of this C1/C2 short loop is controlled only by the gene HP1535.  
                                        1241 Chromosome 1                        |       *------------------*------------------*       |            Chromosome 1            |       812                             882       --------------------------------------------------------          
 
         [0646]    A double stranded DNA loop of length 96.385 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 812. This T1 control element has the DNA sequence  
         [0647]    TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA  
         [0648]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 882. This T2 control element has the DNA sequence  
         [0649]    TAGCGGAACTAAAGCATTCATCCCAAACACTAAAGATATTTGG  
         [0650]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           HP0999   HP1000   HP1001   HP1002   HP1003   HP1005   HP1006       HP1008   HP1009   HPtRNA-Pro   HP1010   HP1011   HP1013   HP1015       HP1017   HP1018   HP1020   HP1021   HP1022   HP1023   HP1024       HP1025   HP1027   HP1028   HP1030   HP1031   HP1033   HP1034       HP1038   HP1039   HP1040   HP1041   HP1042   HP1043   HP1044       HP1045   HP1046   HP1051   HP1052   HP1055   HP1056   HP1058       HP1060   HP1065   HPtRNA-Ser   HP1066   HP1067   HP1069   HP1070       HP1074   HP1075   HP1076   HP1077   HP1078   HP1079   HP1080       HP1081   HP1083   HP1084   HP1085   HP1088   HP1091   HP1092       HP1093   HP1094   HP1095   HP1096                  
 
         [0651]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0652]    A C1/C2 short loop on chromosome 1 whose identifier is 1241 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene HP1535 and has the DNA sequence  
                       TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC               AAACA          
 
         [0653]    The match between the T1 sequence and the C1/C2 sequence is  
         [0654]    TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA  
         [0655]    The match between the T2 sequence and the C1/C2 sequence is  
         [0656]    TAGCGGAACTAAAGCATTCATCCCAAACA  
         [0657]    Example of a Single-celled Permanent Connectron— S. cervesiae    
         [0658]    In this example the existence of the T1-T2 (5515-5533) long loop is controlled by a C1/C2 short loop (6102). The expression of this C1/C2 short loop is controlled only by the gene YNL339C.  
                                        6102 Chromosome 14                        |       *------------------*------------------*       |            Chromosome 12             |       5515                            5533       -------------------------------------------------------          
 
         [0659]    A double stranded DNA loop of length 6.466 kilo-bases on chromosome 12 is bounded on the left by a T1 sequence whose identifier is 5515. This T1 control element has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0660]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 5533. This T2 control element has the DNA sequence  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0661]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0662]    YLR467W  
         [0663]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0664]    A C1/C2 short loop on chromosome 14 whose identifier is 6102 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YNL339C and has the DNA sequence  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT          
 
         [0665]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT               ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT               TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG               GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA               AGGTAGTAAGTAGCTTTTGGTTG          
 
         [0666]    The match between the T2 sequence and the C1/C2 sequence is  
                                       ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA                           ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC                       ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC                       TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA                       TCCGGGTAAGAGACAACAGGGCT          
 
         [0667]    Example of a Multi-celled Permanent Connectron— C. elegans    
         [0668]    In this example the existence of the T1-T2 (5515-5533) long loop is controlled by a C1/C2 short loop (6102). The expression of this C1/C2 short loop is controlled only by the gene YNL339C.  
                                        24442 Chromosome 5                        |       *------------------*------------------*       |            Chromosome 1            |       569                              596       --------------------------------------------------------          
 
         [0669]    A double stranded DNA loop of length 30.606 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 569. This T1 control element has the DNA sequence  
         [0670]    AAATCGAGCCCGTAAATCGACACAAGCGCTACAGTAGTC  
         [0671]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 596. This T2 control element has the DNA sequence  
         [0672]    AGTGCTACAGTAGTCATTTAAAGAATTACTGTAGTTTTCGCT  
         [0673]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0674]    A C1/C2 short loop on chromosome 5 whose identifier is 24442 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene F20D6.4 and has the DNA sequence  
                       GAGCCCGTAAATCGACACAAGCGCTACAGTAGTCATTTAAAGAATTACTG               TAGTTTTC          
 
         [0675]    The match between the T1 sequence and the C1/C2 sequence is  
         [0676]    GAGCCCGTAAATCGACACAAGCGCTACAGTAGTC  
         [0677]    The match between the T2 sequence and the C1/C2 sequence is  
         [0678]    GCTACAGTAGTCATTTAAAGAATTACTGTAGTTTTC  
         [0679]    7. Transient Connectrons Exist in Prokaryotes, Archea, Single-celled Eukaryotes and Multi-celled Eukaryotes.  
         [0680]    A class of connectron relationships exist that permit one C1/C2 short loop to control the existence of one or more T1-T2 long loops such that this C1/C2 short loop is itself subject to expression control by another T1-T2 long loop which surrounds it. These connectron relationships are described as “transient”. Transient connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0681]    Example of a Prokaryote Transient Connectron— E. coli    
         [0682]    In this example the existence of the T1-T2 (3227-3329) long loop is controlled by the C1/C2(3225) short loop. The expression of this C1/C2 short loop is controlled by the existence of the T1-T2 (3216-3224) long loop. The existence of this T1-T2 long loop is itself determined by the expression of the C1/C2 (3223) short loop. The C1/C2 (3225) short loop is the transient connectron.  
                                        3223 Chromosome 1                        |       *------------------*------------------*       |            Chromosome 1            |       3216                          3324       |            3225               |                            3225 Chromosome 1                    |       *------------------*-------------------*       |            Chromosome 1            |       3227                              3329       --------------------------------------------------------          
 
         [0683]    A double stranded DNA loop of length 93.464 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3216. This T1 control element has the DNA sequence  
                       AGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACT               ATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGC               ACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAA               TTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCC               CGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGG               ATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCT               TGAAATACCACCCTTTAATGTTTGATGTTCTAACGT          
 
         [0684]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3324. This T2 control element has the DNA sequence  
                       CCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCC               TTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTG               TCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTA               CCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACT               GAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGA               CGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATG               TTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGT          
 
         [0685]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                                   rrfC   aspT   trpT   yifA   yifE   yifB   ilvL   ilvG_1   ilvM       ilvE   ilvD   ilvA   ilvY   ilvC   ppiC   b3776   rep   gppA       rhlB   trxA   rhoL   rho   rfe   wzzE   wecB   rffH   wecD       wecE   wzxE   yifM_2   wecG   yifK   argX   hisR   leuT       proM   aslB   aslA   hemY   hemX   hemD   cyaA   cyaY       b3808   dapF   uvrD   b3814   corA   yigF   yigG   rarD   yigI       pldA   recQ   yigJ   yigK   pldB   yigL   yigM   metR   metE       ysgA   udp   yigN   ubiE   yigP   b3836   yigU   yigW_1   rfaH       yigC   ubiB   fadA   fadB   pepQ   trkH   hemG   rrsA   ileT       rrlA                  
 
         [0686]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0687]    A C1/C2 short loop on chromosome 1 whose identifier is 3225 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrlC and has the DNA sequence  
                       AAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCAT               GCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTC               CCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTA          
 
         [0688]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0689]    A C1/C2 short loop on chromosome 1 whose identifier is 3323 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrlA and has the DNA sequence  
                       GCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGG               TCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATG               GCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACT               CGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGA...AACAGAATTTGC               CTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAA               GTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTC          
 
         [0690]    The match between the T1 sequence and the C1/C2 sequence is  
                       GCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGG               TCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATG               GCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACT               CGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAA               CCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGT               GGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAAT               ACCACCCTTTAATGTTTGATGTTCTAACGT          
 
         [0691]    The match between the T2 sequence and the C1/C2 sequence is  
                       CCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCC               TTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTG               TCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTA               CCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACT               GAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGA               CGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATG               TTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGT          
 
         [0692]    A double stranded DNA loop of length 93.749 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3227. This T1 control element has the DNA sequence  
                       AGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCA               GG          
 
         [0693]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3329. This T2 control element has the DNA sequence  
                       CATGCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAG               TCG          
 
         [0694]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                                   aspT   trpT   yifA   yifE   yifB   ilvL   ilvG_1   ilvM   ilvE       ilvD   ilvA   ilvY   ilvC   ppiC   b3776   rep   gppA   rhlB       trxA   rhoL   rho   rfe   wzzE   wecB   rffH   wecD   wecE       wzxE   yifM_2   wecG   yifK   argX   hisR   leuT   proM       aslB   aslA   hemY   hemX   hemD   cyaA   cyaY   b3808       dapF   uvrD   b3814   corA   yigF   yigG   rarD   yigI   pldA       recQ   yigJ   yigK   pldB   yigL   yigM   metR   metE   ysgA       udp   yigN   ubiE   yigP   b3836   yigU   yigW_1   rfaH   yigC       ubiB   fadA   fadB   pepQ   trkH   hemG   rrsA   ileT   rrlA       rrfA                  
 
         [0695]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0696]    A C1/C2 short loop on chromosome 1 whose identifier is 3225 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene rrlC and has the DNA sequence  
                       AAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCAT               GCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTC               CCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTA          
 
         [0697]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCA               GG          
 
         [0698]    The match between the T2 sequence and the C1/C2 sequence is  
         [0699]    CATGCGAGAGTAGGGAACTGCCAGGCATCAAAT  
         [0700]    Example of an Archea Transient Connectron— M. jannaschii    
         [0701]    In this example the existence of the T1-T2 (1139-1159) long loop is controlled by the C1/C2 (533) short loop. The expression ofthis C1/C2 short loop is controlled by the existence of the T1-T2 (532-622) long loop. The existence of this T1-T2 long loop is itself determined by the expression of the C1/C2 (1629) short loop. The C1/C2 (533) short loop is the transient connectron.  
                                           1629 Chromosome 1                           |       *------------------*------------------*       |            Chromosome 1            |       532                        622       |              533        |                               533 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 1            |       1139                             1159       --------------------------------------------------------          
 
         [0702]    A double stranded DNA loop of length 78.672 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 532. This T1 control element has the DNA sequence  
         [0703]    ATATGTTTGAAATTTGAAAATAAGAGTATTTAG  
         [0704]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 622. This T2 control element has the DNA sequence  
         [0705]    TTGAAAATAAGAGCATTTAGAAGTTATTAATTAGTTCAAAGGATTTT  
         [0706]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           MJ0486   MJ0487   MJ0488   MJ0489   MJ0490   MJ0492   MJ0493       MJ0494   MJ0495   MJ0496   MJ0497   MJ0499   MJ0500   MJ0501       MJ0502   MJ0503   MJ0504   MJ0506   MJ0507   MJ0508   MJ0509       MJ0510   MJ0511   MJ0512   MJ0513   MJ0514   MJ0514   MJ0517       MJ0519   MJ0520   MJ0521   MJ0522   MJ0523   MJ0525   MJ0526       MJ0526   MJ0529   MJ0530   MJ0531   MJ0532   MJ0534   MJ0535       MJ0536   MJ0538   MJ0539   MJ0540   MJ0541   MJ0542   MJ0543       MJ0544   MJ0545   MJ0547   MJ0548   MJ0549   MJ0550   MJ0552       MJ0553   MJ0554   MJ0555   MJ0556   MJ0557   MJ0558   MJ0559       MJ0560   MJ0561   MJ0562   MJ0563   MJ0564   MJ0565   MJ0566       MJ0568   MJ0569   MJ0570                  
 
         [0707]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0708]    A C1/C2 short loop on chromosome 1 whose identifier is 533 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ0485 and has the DNA sequence  
                       ATTTTTATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTT               GAGTTTATTGAATT          
 
         [0709]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0710]    A C1/C2 short loop on chromosome 1 whose identifier is 1629 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1597 and has the DNA sequence  
                                       ATATGTTTGAAATTTGAAAATAAGAGTATTTAGAAGTTATTAATTAGTTCA                           AAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATAT                       TTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA          
 
         [0711]    The match between the T2 sequence and the C1/C2 sequence is  
         [0712]    ATTTAGAAGTTATTAATTAGTTCAAAGGATTTT  
         [0713]    A double stranded DNA loop of length 14.509 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 1139. This T1 control element has the DNA sequence  
                       ATTTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTAGCTGG               TTTGATTGTTTAAAATATTTGAGTTTA          
 
         [0714]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1159. This T2 control element has the DNA sequence  
                                       ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT                           TGAATTATTCAGATTTTTAAAAATTA          
 
         [0715]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           MJ1096   MJ1097   tRNA-Arg-3   MJ1098   MJ1099   MJ1100   MJ1101       MJ1102   MJ1103   MJ1104   MJ1105   MJ1106   MJ1107   MJ1108                  
 
         [0716]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0717]    A C1/C2 short loop on chromosome 1 whose identifier is 533 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ0485 and has the DNA sequence  
                                       ATTTTTATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGA                           GTTTATTGAATT          
 
         [0718]    The match between the T1 sequence and the C1/C2 sequence is  
         [0719]    ATTTTTATTTAATTTCTAAGGGTTAGCTGGTTTGATT  
         [0720]    The match between the T2 sequence and the C1/C2 sequence is  
                       ATTTAATTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT               TGAATT          
 
         [0721]    Example of a Single-celled Transient Connectron— S. cervesiae    
         [0722]    In this example the existence of the T1-T2 (2840-2859) long loop is controlled by the C1/C2 (298) short loop. The expression of this C1/C2 short loop is controlled by the existence of the T1-T2 (293-320) long loop. The existence of this T1-T2 long loop is itself determined by the expression of the C1/C2 (86) short loop. The C1/C2 (298) short loop is the transient connectron.  
                                           86 Chromosome 1                           |       *------------------*------------------*       |            Chromosome 1            |       293                         320       |               298        |                               298 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 7            |       2840                             2859       --------------------------------------------------------          
 
         [0723]    A double stranded DNA loop of length 38.470 kilo-bases on chromosome 2 is bounded on the left by a T1 sequence whose identifier is 293. This T1 control element has the DNA sequence  
                       GAATTGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTA               TCAATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAA               GCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCAAGGATTGATAATGTAAT               AGGATAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGT               ATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTTGAGGAGAAC               TTCTAGT          
 
         [0724]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 320. This T2 control element has the DNA sequence  
                       AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC               GAGGAGAACTTCTAGTATATTCTGTA          
 
         [0725]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                       YBL005W-B   TS(AGA)B   YBL004W   YBL003C   YBL002W   YBL001C       YBR001C   YBR002C   YBR003W   YBR004C   YBR005W   YBR006W       YBR007C   YBR008C   YBR009C   YBR010W   YBR011C   YBR012C                  
 
         [0726]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0727]    A C1/C2 short loop on chromosome 2 whose identifier is 298 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YBL005W-B and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATCCACTATCGTCTAT               CAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGATGAT               GACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCA               AGGATTGATAATGTAATAGGATAATGAAACATATAAAACGGAATGAGGA               ATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCT               ATATCCTTGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCC               TTTATCAACAATGGAATCCCAACAATTATCTCAACATTC          
 
         [0728]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0729]    A C1/C2 short loop on chromosome 1 whose identifier is 86 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YAR009C and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAGAAATCAACTATCATCTAC               TAACTAGTATTTACATTACTAGTATATTATCATATACGGTGTTAGAAGATG               ACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCTGAAACGCA               AGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT               GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGG               ATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATT               ATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCACCCAT               TTCTCAGAA          
 
         [0730]    The match between the T1 sequence and the C1/C2 sequence is  
                       AAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAAT               ATAGATTCCATTTTGAGGATTCCTATATCCT          
 
         [0731]    The match between the T2 sequence and the C1/C2 sequence is  
                       AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC               GAGGAGAACTTCTAGTATATTCTGTA          
 
         [0732]    A double stranded DNA loop of length 5.302 kilo-bases on chromosome 7 is bounded on the left by a T1 sequence whose identifier is 2840. This T1 control element has the DNA sequence  
                       TCTGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATC               AATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGC               TGTCATCGAAGTTAGAGGAAGCTGAAACGCAAGGATTGATAATGTAATAG               GATCAATGAATATAAACATATAAAACGGAATGAGGAATAATCGTAATATT               AGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTCGAGGAG               AACTTCTAGTATATTCTGTATACCTAAATTATAGCCTTTATCAACAATGGA               ATCCCAACAA          
 
         [0733]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 2859. This T2 control element has the DNA sequence  
                       CTATCAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGA               TGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAA               CGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACG               GAATGAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTT               GAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAA               TATTATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCAC               ATATTTCTCAT          
 
         [0734]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0735]    A C1/C2 short loop on chromosome 2 whose identifier is 298 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YBL005W-B and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATCCACTATCGTCTAT               CAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGATGAT               GACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCA               AGGATTGATAATGTAATAGGATAATGAAACATATAAAACGGAATGAGGA               ATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCT               ATATCCTTGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCC               TTTATCAACAATGGAATCCCAACAATTATCTCAACATTC          
 
         [0736]    The match between the T1 sequence and the C1/C2 sequence is  
                       TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAA               TATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTG               TCATCGAAGTTAGAGGAAGCTGAA          
 
         [0737]    The match between the T2 sequence and the C1/C2 sequence is  
                       CTATCAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGA               TGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAA          
 
         [0738]    Example of a Multi-celled Transient Connectron— C. elegans    
         [0739]    In this example the existence of the T1-T2 (22072-22108) long loop is controlled by the C1/C2 (125) short loop. The expression of this C1/C2 short loop is controlled by the existence of the T1-T2 (110-129) long loop. The existence of this T1-T2 long loop is itself determined by the expression of the C1/C2 (16859) short loop. The C1/C2 (125) short loop is the transient connectron.  
                                          16859 Chromosome 4                          |       *-----------------*-----------------*       |           Chromosome 1           |       110                           129       |             125            |                              125 Chromosome 1                      |       *-----------------*-----------------*       |           Chromosome 5           |       22072                           22108       --------------------------------------------------------          
 
         [0740]    A double stranded DNA loop of length 18.855 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 110. This T1 control element has the DNA sequence  
         [0741]    AGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGC  
         [0742]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 129. This T2 control element has the DNA sequence  
                       TTCTCCCGCATTTTTTGTAGATCTACGTAGATCAAACCGAAATGAGGCACT               TTCTGAATCCACGAGCTAGGCTTAAGCTTAGGCTTAAGCTTAGGCCTTTTC               TCAGGCTTAGGCTTAGGCTTA          
 
         [0743]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0744]    ZC123.3 ZC123.2  
         [0745]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0746]    A C1/C2 short loop on chromosome 1 whose identifier is 125 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC123.3 and has the DNA sequence  
                       ACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATGGCCTAGTTC               GGCAAACTCTTTCATTTCAATTTATGAGGGAAGCCAGAA          
 
         [0747]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0748]    A C1/C2 short loop on chromosome 4 whose identifier is 16859 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene F58E2.7 and has the DNA sequence  
                       CTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTT               AGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAG               GCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCT               TAAGCTTAGACTTA          
 
         [0749]    The match between the T1 sequence and the C1/C2 sequence is  
         [0750]    AGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGC  
         [0751]    The match between the T2 sequence and the C1/C2 sequence is  
         [0752]    TAGGCTTAAGCTTAGGCTTAAGCTTAGGC  
         [0753]    A double stranded DNA loop of length 51.031 kilo-bases on chromosome 5 is bounded on the left by a T1 sequence whose identifier is 22072. This T1 control element has the DNA sequence  
                       CGCAACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATGACCTA               GTTCGGC          
 
         [0754]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 22108. This T2 control element has the DNA sequence  
                       TGACAATCGCCTGCCGGACAACGCGTGGAAAAGTGTCGTGTACTCCACAC               GGACAAATACATTTAGTTTTACAACTAAAATCGAACCGCGACGCGACACG               CAACGCGACGTAAATCTACCCCAGATATGGCCGAGCCAAAATGGCCTAGT               TCGGCAAACTCTTCTATTTC          
 
         [0755]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
         [0756]    F36H9.3 F36H9.4 F36H9.5 F36H9.2 F36H9.1 F36H9.6  
         [0757]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0758]    A C1/C2 short loop on chromosome 1 whose identifier is 125 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZC123.3 and has the DNA sequence  
                       ACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATGGCCTAGTTC               GGCAAACTCTTTCATTTCAATTTATGAGGGAAGCCAGAA          
 
         [0759]    The match between the T1 sequence and the C1/C2 sequence is  
         [0760]    ACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATG  
         [0761]    The match between the T2 sequence and the C1/C2 sequence is  
                       CGTAAATCTACCCCAGATATGGCCGAGCCAAAATGGCCTAGTTCGGCAAA               CTCTT          
 
         [0762]    8. Self-limiting Connectrons Occur in Prokaryotes, Archea, Single-celled Eukaryotes and Multi-celled Eukaryotes  
         [0763]    A class of connectron relationships exist that permit one C1/C2 short loop to control the existence of the T1-T2 long loop that surrounds it. These connectron relationships are described as “self-limiting”. Self-limiting connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes.  
         [0764]    Example of a Prokaryotic Self-limiting Connectrons— E. coli    
         [0765]    In this example the existence of the T1-T2 (1704-1718) long loop is controlled by two C1/C2 (1705 and 1713) short loops. The expression of these C1/C2 short loops is controlled by the existence of the T1-T2 (1704-1718) long loop. The existence of this T1-T2 long loop is itself determined by the expression of the two C1/C2 (1705 and 1713) short loops. The C1/C2 (1705 and 1713) short loops are the self-limiting connectrons.  
                                           1705 Chromosome 1                           1713 Chromosome 1                       |       *------------------*------------------*       |            Chromosome 1            |       1704                             1718       |            1705  1713           |       --------------------------------------------------------          
 
         [0766]    A double stranded DNA loop of length 15.259 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 1704. This T1 control element has the DNA sequence  
                       CGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACT               GTTAATCCGTATGTCACTGGT          
 
         [0767]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1718. This T2 control element has the DNA sequence  
                       TTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTC               CAGTCAGAGGAGCCAAATTC          
 
         [0768]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                               asnT   b1978   b1979   b1980   shiA   amn   b1983   asnW       yeeO   asnU                  
 
         [0769]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0770]    A C1/C2 short loop on chromosome 1 whose identifier is 1705 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene and has the DNA sequence  
                       CGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACT               GTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTC          
 
         [0771]    A C1/C2 short loop on chromosome 1 whose identifier is 1713 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene asnW and has the DNA sequence  
                       CACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTAT               GTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATT          
 
         [0772]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0773]    A C1/C2 short loop on chromosome 1 whose identifier is 1705 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene and has the DNA sequence  
                       CGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACT               GTTAATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATTC          
 
         [0774]    The match between the T1 sequence and the C1/C2 sequence is  
                       CGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACT               GTTAATCCGTATGTCACTGGT          
 
         [0775]    The match between the T2 sequence and the C1/C2 sequence is  
                       TTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTC               CAGTCAGAGGAGCCAAATTC          
 
         [0776]    A C1/C2 short loop on chromosome 1 whose identifier is 1713 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene asnW and has the DNA sequence  
                       CACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTAT               GTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATT          
 
         [0777]    The match between the T1 sequence and the C1/C2 sequence is  
                       CACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTAT               GTCACTGGT          
 
         [0778]    The match between the T2 sequence and the C1/C2 sequence is  
                       TTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTC               CAGTCAGAGGAGCCAAATT          
 
         [0779]    Example of a Archea Self-limiting Connectrons— M. jannaschii    
         [0780]    In this example the existence of the T1-T2 (1447-1471) long loop is controlled by two C1/C2 (1448 and 1470) short loops. The expression of these C1/C2 short loops is controlled by the existence of the T1-T2 (1447-1471) long loop. The existence of this T1-T2 long loop is itself determined by the expression of the two C1/C2 (1705 and 1713) short loops. The C1/C2 (1448 and 1470) short loops are the self-limiting connectrons.  
                                          1448 Chromosome 1                          1470 Chromosome 1                      |       *------------------*------------------*       |            Chromosome 1            |       1447                             1471       |            1448 1470            |       --------------------------------------------------------          
 
         [0781]    A double stranded DNA loop of length 22.675 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 1447. This T1 control element has the DNA sequence  
                       TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA               CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTATGATA          
 
         [0782]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1471. This T2 control element has the DNA sequence  
                       CAACTAACAACCGTATCGAATTTACCATTACTTGGAAATCTATTTAAAACC               TCTTTAATCTTGTGATAATAAATTCTAATCGATTCGTGACTTAT          
 
         [0783]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           MJ1402   MJ1403   MJ1404   MJ1405   MJ1406   MJ1407   MJ1408       MJ1409   MJ1410   MJ1411   MJ1412   MJ1413   MJ1414   MJ1415       MJ1416   MJ1417   MJ1418   MJ1419   MJ1420                  
 
         [0784]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0785]    A C1/C2 short loop on chromosome 1 whose identifier is 1448 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1401 and has the DNA sequence  
                       TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA               CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTATGATAATAAATT               CTAATCGATTCGTGACTTAT          
 
         [0786]    A C1/C2 short loop on chromosome 1 whose identifier is 1470 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1420 and has the DNA sequence  
                       TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA               CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTGTGATAATAAATT               CTAATCGATTCGTG          
 
         [0787]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0788]    A C1/C2 short loop on chromosome 1 whose identifier is 1470 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1420 and has the DNA sequence  
                       TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA               CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTGTGATAATAAATT               CTAATCGATTCGTG          
 
         [0789]    The match between the T1 sequence and the C1/C2 sequence is  
                       TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA               CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTT          
 
         [0790]    The match between the T2 sequence and the C1/C2 sequence is  
                       CAACTAACAACCGTATCGAATTTACCATTACTTGGAAATCTATTTAAAACC               TCTTTAATCTTGTGATAATAAATTCTAATCGATTCGTG          
 
         [0791]    A C1/C2 short loop on chromosome 1 whose identifier is 1448 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene MJ1401 and has the DNA sequence  
                       TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA               CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTATGATAATAAATT               CTAATCGATTCGTGACTTAT          
 
         [0792]    The match between the T1 sequence and the C1/C2 sequence is  
                       TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA               CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTATGATA          
 
         [0793]    The match between the T2 sequence and the C1/C2 sequence is  
                       CAACTAACAACCGTATCGAATTTACCATTACTTGGAAATCTATTTAAAACC               TCTTTAATCTT          
 
         [0794]    Example of a Single-celled Self-limiting Connectron— S. cervesiae    
         [0795]    In this example the existence of the T1-T2 (293-320) long loop is controlled by C1/C2 (298) short loop. The expression of this C1/C2 short loop is controlled by the existence of the T1-T2 (293-320) long loop. The existence of this T1-T2 long loop is itself determined by the expression of the C1/C2 (298) short loop. The C1/C2 (298) short loop is the self-limiting connectron.  
                                           298 Chromosome 2                           |       *------------------*------------------*       |            Chromosome 2            |       293                        320       |              298        |       --------------------------------------------------------          
 
         [0796]    A double stranded DNA loop of length 38.470 kilo-bases on chromosome 2 is bounded on the left by a T1 sequence whose identifier is 293. This T1 control element has the DNA sequence  
                       GAATTGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTA               TCAATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAA               GCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCAAGGATTGATAATGTAAT               AGGATAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGT               ATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTTGAGGAGAAC               TTCTAGT          
 
         [0797]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 320. This T2 control element has the DNA sequence  
                       AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC               GAGGAGAACTTCTAGTATATTCTGTA          
 
         [0798]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                       YBL005W-B   TS(AGA)B   YBL004W   YBL003C   YBL002W   YBL001C       YBR001C   YBR002C   YBR003W   YBR004C   YBR005W   YBR006W       YBR007C   YBR008C   YBR009C   YBR010W   YBR011C   YBR012C                  
 
         [0799]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0800]    A C1/C2 short loop on chromosome 2 whose identifier is 298 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YBL005W-B and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATCCACTATCGTCTAT               CAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGATGAT               GACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCA               AGGATTGATAATGTAATAGGATAATGAAACATATAAAACGGAATGAGGA               ATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCT               ATATCCTTGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCC               TTTATCAACAATGGAATCCCAACAATTATCTCAACATTC          
 
         [0801]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0802]    A C1/C2 short loop on chromosome 2 whose identifier is 298 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YBL005W-B and has the DNA sequence  
                       ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATCCACTATCGTCTAT               CAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGATGAT               GACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCA               AGGATTGATAATGTAATAGGATAATGAAACATATAAAACGGAATGAGGA               ATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCT               ATATCCTTGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCC               TTTATCAACAATGGAATCCCAACAATTATCTCAACATTC          
 
         [0803]    The match between the T1 sequence and the C1/C2 sequence is  
                       TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAA               TATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTG               TCATCGAAGTTAGAGGAAGCTGAAGTGCAAGGATTGATAATGTAATAGGA               TAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTA               GAAATATAGATTCCATTTTGAGGATTCCTATATCCTTGAGGAGAACTTCTA               GT          
 
         [0804]    The match between the T2 sequence and the C1/C2 sequence is  
         [0805]    AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCT  
         [0806]    Example of a Multi-celled Self-limiting Connectron— C. elegans    
         [0807]    In this example the existence of the T1-T2 (293-320) long loop is controlled by C1/C2 (298) short loop. The expression of this C1/C2 short loop is controlled by the existence of the T1-T2 (293-320) long loop. The existence of this T1-T2 long loop is itself determined by the expression of the C1/C2 (298) short loop. The C1/C2 (298) short loop is the self-limiting connectron.  
                                           17155 Chromosome 4                           |       *------------------*------------------*       |            Chromosome 4            |       17154                             17190       |             17155              |       --------------------------------------------------------          
 
         [0808]    A double stranded DNA loop of length 89.919 kilo-bases on chromosome 4 is bounded on the left by a T1 sequence whose identifier is 17154. This T1 control element has the DNA sequence  
         [0809]    AAATTTCCGGCAAATCGGCAAACTGGCAA  
         [0810]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 17190. This T2 control element has the DNA sequence  
         [0811]    AATTTGCCGATTTGCCGAATTTGTCGACA  
         [0812]    This long T1/T2 double stranded DNA loop modulates the expression of the following genes  
                                                           R08C7.11   M01H9.2   M01H9.3   M01H9.4   M01H9.1   ZK180.1   ZK180.2       ZK180.3   ZK180.4   ZK180.5   ZK180.6   ZK185.3   ZK185.2                  
 
         [0813]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0814]    A C1/C2 short loop on chromosome 4 whose identifier is 17155 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene R08C7.1 and has the DNA sequence  
                       AAATTTCCGGCAAATCGGCAAACTGGCAATTTGCCGATTTGCCGAATTTGT               CGACA          
 
         [0815]    A C1/C2 short loop on chromosome 4 whose identifier is 17171 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene ZK180.2 and has the DNA sequence  
                       TGGAAATTTCAGAATTTCAATTTTAATCGGCAAAATTGTACGCATCCTATG               AATTT          
 
         [0816]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0817]    A C1/C2 short loop on chromosome 4 whose identifier is 17155 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene R08C7.1 and has the DNA sequence  
                       AAATTTCCGGCAAATCGGCAAACTGGCAATTTGCCGATTTGCCGAATTTGT               CGACA          
 
         [0818]    The match between the T1 sequence and the C1/C2 sequence is  
         [0819]    AAATTTCCGGCAAATCGGCAAACTGGCAA  
         [0820]    The match between the T2 sequence and the C1/C2 sequence is  
         [0821]    AATTTGCCGATTTGCCGAATTTGTCGACA  
         [0822]    9. Geneless Connectrons Exist in Single-celled and Multi-celled Eukaryotes  
         [0823]    Normally T1-T2 long loops contain genes whose expression is regulated by the existence of the long loop. When a T1-T2 long loop does not contain any genes it is described as being “geneless”. The existence of the T1-T2 long loop is itself controlled by one or more C1/C2 short loops that may be on the same or different chromosomes. The geneless T1-T2 long loops must contain one or more C1/C2 short loops.  
         [0824]    Example of a Single-celled Geneless Connectron— S. cervesiae    
         [0825]    In this example the existence of the T1-T2 (1537-1559) long loop is controlled by three C1/C2 (3789, 5289 and 5753) short loops. The expression of 21 C1/C2 (1538 through 1558) short loops are controlled by the existence of the T1-T2 (1537-1559) long loop.  
                                           3789 Chromosome 9                           5289 Chromosome 12                       5753 Chromosome 13                       |       *------------------*------------------*       |            Chromosome 4            |       1537                             1559       |          1538 through 1558          |       --------------------------------------------------------          
 
         [0826]    A double stranded DNA loop of length 4.825 kilo-bases on chromosome 4 is bounded on the left by a T1 sequence whose identifier is 1537. This T1 control element has the DNA sequence  
                                       ATGAGATATATGTGGGTAATTAGATAATTGTTGGGATTCCATTGTTGATAA                           AGGCTATAATATTAGGTATACAGAATATACTAGAAGTTCTCCTCGAGGAT                       TTAGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTATAAATAT                       TATTATCATCGTTTTATATGTTAATATTCATTGATCCTATTACATTATCAAT                       CCTTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGT                       CATCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATACTAGTTA                       GTAGATGATAGTTGATTTTTATTCCAACATACCACCCATAATGTAATAGAT                       CTAAT          
 
         [0827]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1559. This T2 control element has the DNA sequence  
                                       ATGAGATATATGTGGGTAATTAGATAATTGTTGGGATTCCATTGTTGATAA                           AGGCTATAATATTAGGTATACAGAATATACTAGAAGTTCTCCTCGAGGAT                       TTAGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTATAAATAT                       TATTATCATCGTTTTATATGTTAATATTCATTGATCCTATTACATTATCAAT                       CCTTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGT                       CATCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATACTAGTTA                       GTAGATGATAGTTGATTTTTATTCCAACATACCACCCATAATGTAATAGAT                       CTAAT          
 
         [0828]    There are no genes controlled by this T1/T2 loop.  
         [0829]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0830]    A C1/C2 short loop on chromosome 4 whose identifier is 1538 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                                       ATGAGATATATGTGGGTAATTAGATAATTGTTGGGATTCCATTGTTGATAA                           AGGCTATAATATTAGGTATACAGAATATACTAGAAGTTCTCCTCGAGGAT                       TTAGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTATAAATAT                       TATTATCATCGTTTTATATGTTAATATTCATTGATCCTATTACATTATCAAT                       CCTTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGT                       CATCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATACTAGTTA                       GTAGATGATAGTTGATTTTTATTCCAACATACCACCCATAATGTAATAGAT                       CTAATGAATCCATTTGTTTGTTAATAGTTT          
 
         [0831]    This T1-T2 loop also modulates the C1/C2 short loops numbered 1539 to 1557  
         [0832]    A C1/C2 short loop on chromosome 4 whose identifier is 1558 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                                       AGCTTCTCATAACTTATGTCATCATCTTAACACCGTATATGATAATATATT                           GATAATATAACTTGTTGGAATAAAAATCAACTATCATCTACTAACTAGTAT                       TTACGTTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATG                       ATGAGAAATAGTCATCTAAATTAGTGGAAGCTGA...GTCTATCTGGCGAAT                       ATAAATTTTTACGCTACACACGTCATCGACATCTAAATATGACAGTCGCTG                       AACTGTTCTTAGATATCCATGCTATTTATGAAGAACAACAGGGATCGAGA                       AACAG          
 
         [0833]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0834]    A C1/C2 short loop on chromosome 9 whose identifier is 3789 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YIL059C and has the DNA sequence  
                                       TTTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCA                           GCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACA                       CCGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAG                       TTGATTTTTATTCCAACAGTAT          
 
         [0835]    The match between the T1 sequence and the C1/C2 sequence is  
                                       TTTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCA                           GCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACA                       CCGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAG                       TTGATTTTTATTCCAACA          
 
         [0836]    The match between the T2 sequence and the C1/C2 sequence is  
                                       TTTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCA                           GCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACA                       CCGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAG                       TTGATTTTTATTCCAACA          
 
         [0837]    A C1/C2 short loop on chromosome 12 whose identifier is 5289 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YLR301W and has the DNA sequence  
                                       GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA                           TTAGGTATGTAGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCAT                       AAAAGGGAATCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTT                       TTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAG                       CTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACAC                       CGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGT                       TGATTTTTATTCCAACAC          
 
         [0838]    The match between the T1 sequence and the C1/C2 sequence is  
                                       AGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAA                           TCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTTTTATATGTTA                       ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA                       TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT                       AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT                       CCAACA          
 
         [0839]    The match between the T2 sequence and the C1/C2 sequence is  
                                       AGGATTTAGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTATA                           AATATTATTATCATCGTTTTATATGTTAATATTCATTGATCCTATTACATTA                       TCAATCCTTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCATT                       TGCGTCATCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATACT                       AGTTAGTAGATGATAGTTGATTTTTATTCCAACA          
 
         [0840]    A C1/C2 short loop on chromosome 13 whose identifier is 5753 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YMR044W and has the DNA sequence  
                                       TTGAGAAATGGGGGAATGTTGAGATAATTGTTGGGATTCCATTGTTGATA                           AAGGCTATAATATTAGGTATACAGAATATACTAGAAGTTCTCCTCAAGGA                       TATAGGAATCCTCAAAATGGAATCTATATTTCTACATACTAATATTACGAT                       TATTCCTCATTCCGTTTTATATGTTTCATTATCCTATTACATTATCAATCCT                       TGCACTTCAGCTTCCTCTAACTTCGATGACAGCTTCTCATAACTTATGTCA                       TCATCTTAACACCGTATATGATAATATATTGATAATATAACTATTAGTTGA                       TAGACGATAGTGGATTTTTATTCCAACAT          
 
         [0841]    The match between the T1 sequence and the C1/C2 sequence is  
                       AGATAATTGTTGGGATTCCATTGTTGATAAAGGCTATAATATTAGGTATAC               AGAATATACTAGAAGTTCTCCTC          
 
         [0842]    The match between the T2 sequence and the C1/C2 sequence is  
                       TTGTTGGGATTCCATTGTTGATAAAGGCTATAATATTAGGTATACAGAATA               TACTAGAAGTTCTCCTCAAGGAT          
 
         [0843]    Two Examples of Multi-celled Geneless Connectrons— C. elegans    
         [0844]    In the first example the existence of the T1-T2 (2342-2344) long loop is controlled by the C1/C2 (24114) short loop. The expression of one C1/C2 (2343) short loop is controlled by the existence of the T1-T2 (2342-2344) long loop.  
                                           24114 Chromosome 5                           |       *------------------*------------------*       |            Chromosome 1            |       2342                             2344       |              2343             |       --------------------------------------------------------          
 
         [0845]    In the second example the existence of the T1-T2 (29221-29262) long loop is controlled by the C1/C2 (24114) short loop. The expression of one C1/C2 (2343) short loop is controlled by the existence of the T1-T2 (2342-2344) long loop.  
                                           4291 Chromosome 1                           |       *------------------*------------------*       |            Chromosome 5            |       29221                             29262       |          29222 through 29261         |       --------------------------------------------------------          
 
         [0846]    A double stranded DNA loop of length 67.059 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 2342. This T1 control element has the DNA sequence  
         [0847]    TGAAAACTACAGTAATTCTTTAAATGACTACTGTAGC  
         [0848]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 2344. This T2 control element has the DNA sequence  
         [0849]    CTACTGTAGCGCTTGTGTCGATTTACGGGCTCGATTT  
         [0850]    There are no genes controlled by this T1/T2 loop.  
         [0851]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0852]    A C1/C2 short loop on chromosome 1 whose identifier is 2343 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       TCGACACAAGCGCTACAGTAGCTATTTAAAGAATTACTGTAGTTTTCGCTA               CGAGATATTT          
 
         [0853]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0854]    A C1/C2 short loop on chromosome 5 whose identifier is 24114 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene C13F10.5 and has the DNA sequence  
                       GCGAAAACTACAGTAATTCTTTAAATGACTACTGTAGCGCTTGTGTCGATT               TACGGGCTCGATTTTCG          
 
         [0855]    The match between the T1 sequence and the C1/C2 sequence is  
         [0856]    GAAAACTACAGTAATTCTTTAAATGACTACTGTAGC  
         [0857]    The match between the T2 sequence and the C1/C2 sequence is  
         [0858]    CTACTGTAGCGCTTGTGTCGATTTACGGGCTCGATTT  
         [0859]    A double stranded DNA loop of length 41.297 kilo-bases on chromosome 5 is bounded on the left by a T1 sequence whose identifier is 29221. This T1 control element has the DNA sequence  
                       TTTAAATTTCCCGCCAAAAATTGACTGAAAATTTGGATTTTCTTTCCAAAA               ATTGACAGAAA          
 
         [0860]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 29262. This T2 control element has the DNA sequence  
         [0861]    TGAAAATTTGAATTTCCCGCCAAAAATTAAC  
         [0862]    There are no genes controlled by this T1/T2 loop.  
         [0863]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0864]    A C1/C2 short loop on chromosome 5 whose identifier is 29222 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       AATTTCCCGCCAAAAATTGACTGAAAATTTGGATTTTCTTTCCAAAAATTG               ACAGAAA          
 
         [0865]    This T1-T2 loop also modulates the C1/C2 short loops numbered 29223 to 29260  
         [0866]    A C1/C2 short loop on chromosome 5 whose identifier is 29261 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       AAAATTGACTGAAAATTTGAATTTCCAGCCAAAAATTGACTGAAAATTTG               AATT          
 
         [0867]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0868]    A C1/C2 short loop on chromosome 1 whose identifier is 4291 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene Y43F8C.5 and has the DNA sequence  
                                       AAAATTAACTGAAAATTTGAATTTCCCGCCAAAAATTGACTGAAAATTTG                           AATTTCCCGCCAAAAAAAATTGACTGAAAATTTGAATTTCCCGCCAAAAA                       TTGACTGAAAATTTGAATTTCCCGCCAAAAATTAATTGAAAATTTGAATTT                       CCCGCCAAAAATTAATTGAAACTTTGAATTTTCAA...ATTTCCCGCCAAAA                       ATTAATTGAAACTTTGAATTTTCAAATTTCCCGCCAAAAATTGACTGAAAA                       TTTGAATTTCCCGCCAAAAATTAATTGAAAATTTGAATTTTTGAATTTCCC                       GCCAAAAATGACTGA          
 
         [0869]    The match between the T1 sequence and the C1/C2 sequence is  
         [0870]    TTTAAATTTCCCGCCAAAAATTGACTGAAAATTTG  
         [0871]    The match between the T2 sequence and the C1/C2 sequence is  
         [0872]    AAAAAAATTGACTGAAAATTTGAATTTCCCGCCAAAAATTGA  
         [0873]    10. One Connectron Controls many Geneless Connectrons in Single-Celled and Multi-celled Eukaryotes  
         [0874]    One C1/C2 short loop can control the existence of many geneless T1-T2 long loops.  
         [0875]    Example of a Single-celled Geneless Connectron— S. cervesiae    
         [0876]    In this example the existence of the three T1-T2 (1142-1156, 1242-1272 and 7102-7117) long loops is controlled by the C1/C2 (5289) short loop.  
                                         5289 Chromosome 12                         |       *------------------*------------------*       |            Chromosome 4             |       1142                             1156       |         1143 through 1155           |                             5289 Chromosome 12                     |       *------------------*------------------*       |            Chromosome 4             |       1243                             1272       |         1244 through 1271           |                             5289 Chromosome 12                     |       *------------------*------------------*       |            Chromosome 5             |       7102                             7117       |         7103 through 7116           |       --------------------------------------------------------          
 
         [0877]    A double stranded DNA loop of length 5.337 kilo-bases on chromosome 4 is bounded on the left by a T1 sequence whose identifier is 1142. This T1 control element has the DNA sequence  
                                       ATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATATTAGG                           TATGTAGATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAG                       GGAATCTGCAATTCTACACAATTCTATAAATATTATTATCATCATTTTATA                       TGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCC                       ACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTAT                       ATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTT                       TTATTCCAACA          
 
         [0878]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1156. This T2 control element has the DNA sequence  
                                       TTTTAATAAGGCAATAATATTAGGTATGTAGATATACTAGAAGTTCTCCTC                           CAGGATTTAGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTAT                       AAATATTATTATCATCATTTTATATGTTAATATTCATTGATCCTATTACATT                       ATCAATCCTTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCAT                       TTGCGTCATCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATAC                       TAGTTAGTAGATGATAGTTGATTTTTATTCCAACAAGAA          
 
         [0879]    There are no genes controlled by this T1/T2 loop.  
         [0880]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0881]    A C1/C2 short loop on chromosome 4 whose identifier is 1143 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                                       ATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATATTAGG                           TATGTAGATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAG                       GGAATCTGCAATTCTACACAATTCTATAAATATTATTATCATCATTTTATA                       TGTTAATATTCATTGATCCTATTACATTATCAAT...CTCTAAGTCTCATTGCC                       TTTGTGCCAAAAAATCTGTTTCTAAATTTCTCTTCATTTGTAGACTTAATTA                       TACTGATCGTTGATCTACTATCAGTAAGTAAGCCTTTAATAATTGGTTTCT                       TGTTAAGTTCTTGCACAAGGTGACTGAGGTTATTCAATAGCGG          
 
         [0882]    This T1-T2 loop also modulates the C1/C2 short loops numbered 1144 to 1154  
         [0883]    A C1/C2 short loop on chromosome 4 whose identifier is 1155 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       GAGGAGAACTTCTAGTATATCTACATACCTAATATTATTGCCTTATTAAAA               ATGGAATCCCAACAATTA          
 
         [0884]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0885]    A C1/C2 short loop on chromosome 12 whose identifier is 5289 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YLR301W and has the DNA sequence  
                                       GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA                           TTAGGTATGTAGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCAT                       AAAAGGGAATCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTT                       TTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAG                       CTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACAC                       CGTATATGATAATATACTAGTACGTAAATACTAGTTAGTAGATGATAGTT                       GATTTTTATTCCAACAC          
 
         [0886]    The match between the T1 sequence and the C1/C2 sequence is  
                       ATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATATTAGG               TATGTAGA          
 
         [0887]    The match between the T2 sequence and the C1/C2 sequence is  
         [0888]    TTTTAATAAGGCAATAATATTAGGTATGTAGA  
         [0889]    A double stranded DNA loop of length 5.251 kilo-bases on chromosome 4 is bounded on the left by a T1 sequence whose identifier is 1243. This T1 control element has the DNA sequence  
                                       CGTGTTTTATCTCATGTTGTTCGTTTTGTTATTGAGATATATGTGGGTAATT                           AGATAATTGTTGGGATTCCATTGTTGATAAAGGCTATAATATTAGGTATAC                       AGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAA                       TCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTTTTATATGTTA                       ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA                       TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT                       AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT                       CCAACA          
 
         [0890]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 1272. This T2 control element has the DNA sequence  
                                       TGAGATATATGTGGGTAATTAGATAATTGTTGGGATTCCATTGTTGATAAA                           GGCTATAATATTAGGTATACAGAATATACTAGAAGTTCTCCTCGAGGATTT                       AGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTATAAATATTA                       TTATCATCGTTTTATATGTTAATATTCATTGATC...TATACTAGTAACGTAA                       ATACTAGTTAGTAGATGATAGTTGATTTTTATTCCAACAGTTATAAGGTTG                       TTTCATATGTGTTTTATGAA          
 
         [0891]    There are no genes controlled by this T1/T2 loop.  
         [0892]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0893]    A C1/C2 short loop on chromosome 4 whose identifier is 1244 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                                       TTTATCTCATGTTGTTCGTTTTGTTATTGAGATATATGTGGGTAATTAGATA                           ATTGTTGGGATTCCATTGTTGATAAAGGCTATAATATTAGGTATACAGAAT                       ATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAATCTGC                       AATTCTACACAATTCTATAAATATTATTATCAT...GTCTCGATGTAGTATAC                       GTATAAATTATTACCTGATACTTCATCTCTAAGTCTCATTGCCTTTGTGCCA                       AAAAATCTGTTTCTAAATTTCTCTTCATTTGTAGACTTAATTATACTGATCG                       TTGATCTACTATCAGTAAGT          
 
         [0894]    This T1-T2 loop also modulates the C1/C2 short loops numbered 1245 to 1270  
         [0895]    A C1/C2 short loop on chromosome 4 whose identifier is 1271 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       TGTTGTATCTCAAAATGAGATATGTCAGTATGACAATACGTCATCCTAAAC               GTTCATAAAACACATATGAAACAACCTTATAACTGTTGGAATAAAAATCA               ACTATCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGG               TGTTAGAAGATGACGCAAATGATGAGAAATAGTC...CAACAATGGAATCC               CAACAATTATCTAATTACCCACATATATCTCATGGTAGCGCCTGTGCTTCG               GTTACTTCTAAGGAAGTCGACAGAAATCAAGATCCGTTAGACGTTTCAGC               TTCCAAAA          
 
         [0896]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0897]    A C1/C2 short loop on chromosome 12 whose identifier is 5289 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YLR301W and has the DNA sequence  
                                       GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA                           TTAGGTATGTAGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCAT                       AAAAGGGAATCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTT                       TTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAG                       CTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACAC                       CGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGT                       TGATTTTTATTCCAACAC          
 
         [0898]    The match between the T1 sequence and the C1/C2 sequence is  
                                       AGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAA                           TCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTTTTATATGTTA                       ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA                       TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT                       AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT                       CCAACA          
 
         [0899]    The match between the T2 sequence and the C1/C2 sequence is  
                                       AGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAA                           TCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTTTTATATGTTA                       ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA                       TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT                       AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT                       CCAACA          
 
         [0900]    A double stranded DNA loop of length 5.296 kilo-bases on chromosome 15 is bounded on the left by a T1 sequence whose identifier is 7102. This T1 control element has the DNA sequence  
                                       CATGATTAATATGACCAATCGGCGTGTGTTTTTGAAAAGTGGGTGAATTTT                           GAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATATTAGGTATGT                       AGAATGTACTAGAAGTTCTCCTCAAGGATTTAGGAATCCATGAAAGGGAA                       TCTGCAATTCTACACAATTCTATAAATATTATTATCATCATTTTATATGTTA                       ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA                       TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT                       AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT                       CCAACA          
 
         [0901]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 7117. This T2 control element has the DNA sequence  
                                       TGAAAAGTGGGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAG                           GCAATAATATTAGGTATGTAGAATGTACTAGAAGTTCTCCTCAAGGATTT                       AGGAATCCATGAAAGGGAATCTGCAATTCTACACAATTCTATAAATATTA                       TTATCATCATTTTATATGTTAATATTCATTGATCCTATTACATTATCAATCC                       TTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCA                       TCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATACTAGTTAGT                       AGATGATAGTTGATTTTTATTCCAACAGTTTTATATACCTCTCTTATTTAGT                       ATAAGAA          
 
         [0902]    There are no genes controlled by this T1/T2 loop.  
         [0903]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0904]    A C1/C2 short loop on chromosome 15 whose identifier is 7103 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       AAGAACATTGCTGATGTGATGACAAAACCTCTTCCGATAAAAACATTTAA               ACTATTAACTAACAAATGGATTCATTAGATCTATTACATTATGGGTGGTAT               GTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTTACTAGT               ATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTC               ATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTAATAGGATC               AATGAATATTAACATATAAAATGATGATAATAATATTTATAGAATTGTGT               AGAATTGCAGATTCCCTTTCATGGATTCCTAAATCCTTGAGGAGAACTTCT               AGTA          
 
         [0905]    This T1-T2 loop also modulates the C1/C2 short loops numbered 7104 to 7115  
         [0906]    A C1/C2 short loop on chromosome 15 whose identifier is 7116 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       CCATTCTGTGGAGGTGGTACTGAAGCAGGTTGAGGAGAGACATGATGATG               GTTCTCTGGAACAGCT          
 
         [0907]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0908]    A C1/C2 short loop on chromosome 12 whose identifier is 5289 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene YLR301W and has the DNA sequence  
                                       GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA                           TTAGGTATGTAGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCAT                       AAAAGGGAATCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTT                       TTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAG                       CTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACAC                       CGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGT                       TGATTTTTATTCCAACAC          
 
         [0909]    The match between the T1 sequence and the C1/C2 sequence is  
                       GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA               TTAGGTATGTAGAAT          
 
         [0910]    The match between the T2 sequence and the C1/C2 sequence is  
                       GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA               TTAGGTATGTAGAAT          
 
         [0911]    Example of a Multi-celled Geneless Connectron— C. elegans    
         [0912]    In this example the existence of the three T1-T2 (1142-1156, 14840-15042 and 15365-15627) long loops is controlled by the C1/C2 (16760) short loop.  
                                           16760 Chromosome 4                           |       *------------------*------------------*       |            Chromosome 4             |       1142                             1156       |           3103 through 3119         |                               16760 Chromosome 4                       |       *------------------*------------------*       |            Chromosome 4             |       14840                             15042       |          14841 through 15401        |                               16760 Chromosome 4                       |       *------------------*------------------*       |            Chromosome 5             |       15365                             15627       |          15366 through 15625          |       --------------------------------------------------------          
 
         [0913]    A double stranded DNA loop of length 15.894 kilo-bases on chromosome 1 is bounded on the left by a T1 sequence whose identifier is 3101. This T1 control element has the DNA sequence  
         [0914]    CAAATCGGCAAATTGCCGGAATTGAACATTTCC  
         [0915]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 3120. This T2 control element has the DNA sequence  
                       AAACGATTTTTCCGGCAAATCGGCAAATTGCCGGAATTGTAATTTCCGGC               AAAT          
 
         [0916]    There are no genes controlled by this T1/T2 loop.  
         [0917]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0918]    A C1/C2 short loop on chromosome 1 whose identifier is 3103 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       TTAAAATTTCCGGCAAATCGGCAAATTGGCAGAAATGAAACTCACGGCAA               ATCGG          
 
         [0919]    This T1-T2 loop also modulates the C1/C2 short loops numbered 3104 to 3118  
         [0920]    A C1/C2 short loop on chromosome 1 whose identifier is 3119 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       CCCGCATTTTTTGTAGATCAAACCGTAATGGGACGGCCTGGCAACACGTG               ATTTTCCAAAT          
 
         [0921]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0922]    A C1/C2 short loop on chromosome 4 whose identifier is 16760 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene T23E1.2 and has the DNA sequence  
                       GGCAAATTGCCGAAATTGAACATTTCCGGCAAATCGGCAAATTGCCGGAA               TTGAACATTTCCGGCAAATCGGCAAATTGCCGGAATTGAACATTTCCGGC               AAATCGGCAAATTGCCGGAATTGA          
 
         [0923]    The match between the T1 sequence and the C1/C2 sequence is  
         [0924]    CAAATCGGCAAATTGCCGGAATTGAACATTTCC  
         [0925]    The match between the T2 sequence and the C1/C2 sequence is  
         [0926]    TTTCCGGCAAATCGGCAAATTGCCGGAATTG  
         [0927]    A double stranded DNA loop of length 86.977 kilo-bases on chromosome 3 is bounded on the left by a T1 sequence whose identifier is 14840. This T1 control element has the DNA sequence  
                       AAAAATTTCCGGCAAGTCGGCAATTTTCCGAAAATGAAAATTTCCGGCAA               ATCGGCAAATTGCCGGAATTGAAAATTCCTGGCAAATCAGCAAATTTGCG               GCAAATCGGCAATTTGCCGAAAATGAAAATTTCCGGCAAAT          
 
         [0928]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 15042. This T2 control element has the DNA sequence  
                       CAAATCGGTAGGTAAATTGGCCAAACTTGAAAATTTCCGGCAAATCGGCA               AATTCCGCGAACTGAACATTTCCGGCAAATCGGCAAATTGCTCGAACT          
 
         [0929]    There are no genes controlled by this T1/T2 loop.  
         [0930]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0931]    A C1/C2 short loop on chromosome 3 whose identifier is 14841 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       AAAAATTTCCGGCAAGTCGGCAATTTTCCGAAAATGAAAATTTCCGGGAA               ATCGGCAAATTGCCGGAATTGAAAATTCCTGGCAAATCAGCAAATTTGCG               GCAAATCGGCAATTTGCCGAAAATGAAAATTTCCGGCAAAT          
 
         [0932]    This T1-T2 loop also modulates the C1/C2 short loops numbered 14842 to 15040  
         [0933]    A C1/C2 short loop on chromosome 3 whose identifier is 15041 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       CGGCAATTGCCGTTCGGCAATTTGCCAATTTGCCGGAAATTTTCAATTCCG               GCAA          
 
         [0934]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0935]    A C1/C2 short loop on chromosome 4 whose identifier is 16760 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene T23E1.2 and has the DNA sequence  
                       GGCAAATTGCCGAAATTGAACATTTCCGGCAAATCGGCAAATTGCCGGAA               TTGAACATTTCCGGCAAATCGGCAAATTGCCGGAATTGAACATTTCCGGC               AAATCGGCAAATTGCCGGAATTGA          
 
         [0936]    The match between the T1 sequence and the C1/C2 sequence is  
         [0937]    ATTTCCGGCAAATCGGCAAATTGCCGGAATTGAA  
         [0938]    The match between the T2 sequence and the C1/C2 sequence is  
         [0939]    TGAACATTTCCGGCAAATCGGCAAATTGC  
         [0940]    A double stranded DNA loop of length 98.488 kilo-bases on chromosome 3 is bounded on the left by a T1 sequence whose identifier is 15365. This T1 control element has the DNA sequence  
                                       AAAATTTCCGGCAAATCGGCAATTTGCCAAAAATTGAAATTTCCGGCAAA                           TCGGCAATTTGTCAAAAATGAAAATTTCCGGCAAATCGGCAAATTGCCGA                       AAATGAAAATTTCCGGCAAATCGGCAAACTTCCGGAACTGAAAATTTCCG                       GCAAATCGGCAATTTGCCATAAATGAACATTTCCGG...GGCGAAAATTAAA                       ATTTCCGCCATATCGGCAATTTGCCAAAAAATTAAAATTTCCGGCAAATC                       GGCAAATTGCCGGAATTCAAAATTTCCGGCAAACCGGCAAATTGCCGGAA                       CTCAAAATTCCCGGCAAATCAGCAAATTGCCGGAATT          
 
         [0941]    This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 15627. This T2 control element has the DNA sequence  
                       TGGCAAACCGGCAAATTGCCGGAATTGAACATTTCCGGCAAATCGGCAAT               TTGCCGGAATTGAAATTT          
 
         [0942]    There are no genes controlled by this T1/T2 loop.  
         [0943]    This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops  
         [0944]    A C1/C2 short loop on chromosome 3 whose identifier is 15366 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       TGCCGATTTGCCGGAAATTTTCATTTTCGGCAATTTGCCGATTTGCCGGAA               ATTTTCATT          
 
         [0945]    This T1-T2 loop also modulates the C1/C2 short loops numbered 15366 to 15624  
         [0946]    A C1/C2 short loop on chromosome 3 whose identifier is 15625 controls the expression of the genes of one or more other T1/T2 long loops. This C1/C2 short loop has the DNA sequence  
                       TCAAGCAAATTGTCAAATTCGCGGAACTAAACATTTCCGGCAAATCGGCA               AATT          
 
         [0947]    The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops.  
         [0948]    A C1/C2 short loop on chromosome 4 whose identifier is 16760 controls the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single strand that is 3′UTR to the gene T23E1.2 and has the DNA sequence  
                       GGCAAATTGCCGAAATTGAACATTTCCGGCAAATCGGCAAATTGCCGGAA               TTGAACATTTCCGGCAAATCGGCAAATTGCCGGAATTGAACATTTCCGGC               AAATCGGCAAATTGCCGGAATTGA          
 
         [0949]    The match between the T1 sequence and the C1/C2 sequence is  
         [0950]    ATTTCCGGCAAATCGGCAAATTGCCGGAATT  
         [0951]    The match between the T2 sequence and the C1/C2 sequence is  
         [0952]    CGGCAAATTGCCGGAATTGAACATTTCCGGCAAATCGGCAA