ALGORITHMIC DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN PROKARYOTIC, ARCHEA AND EUKARYOTIC GENOMES

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 1kb to 105kb. 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 30nm 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: ALGORITHMIC DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN PROKARYOTIC, ARCHEA AND EUKARYOTIC GENOMES Reference to Related Application The present application is the subject of Provisional Application Serial No. 60/208,650 filed June 2, 2000 entitled ALGORITHMIC DETERMINATION OF CONNECTRONS FOR THE HIGH LEVEL REGULATION OF GENE EXPRESSION. Introduction 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'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 Cl and C2 - for Control Sequence 1 and Control Sequence 2) interact with two distant double-stranded DNA sequences (called Tl 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 (Tl and T2) must be on the same chromosome in a genome and they must be between about lkb and 105kb of each other. The adjacent single-stranded RNA sequences (C1/C2) can be on the same or different chromosome as the Tl and T2 sequences. The Cl sequence is identical to the Tl sequence and the C2 sequence is identical to the T2 sequence. The connectron acts to stabilize the double-stranded DNA by allowing 30nm chromatin particles to form. Genes that lie between the Tl and T2 sequences when wrapped up in 30nm 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 Tl and T2 sequences. Characteristically the adjacent C1/C2 sequences lie in the 3'UTR of a gene. The Tl and T2 sequences do not lie within the translated region of any gene. These sequences "surround" one or more genes. There are, however, Tl 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. A computer-based algorithm that is similar to the algorithm used in the US Patent 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. Each connectron is a unique tetrad of sequences. Each connectron changes the expression of the genes between the Tl and T2 sequences. The Cl sequence (which is equivalent to the Tl 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 Tl and T2 sequences. Using connectrons it will be possible to modify cellular and tissue behavior in a very general manner. Examples will be given from different genomes to illustrate that the connectron is a perfectly general and universal concept. Definitions 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 ' Hydrogen Bond - The force between a hydrogen atom and another heavier atom such as Oxygen (O), Nitrogen (N), Phosphorus (P), or Sulfur (S). Positive strand - The positive strand is normally represented 5' to 3' running left to right as in 5'-TAGAGGAGTACCAC-3' Negative strand - The negative strand is normally represented 5' to 3' running right to left as in 3'-ATCTCCTCATGGTG-5' 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' Antisense RNA - The antisense strand of any RNA sequence is the compliment sequence RNA sequence 5 '-UAGAGGAGUACCAC-3 ' Antisense RNA sequence 3'-AUCUCCUCAUGGUG-5' Triple Strand Helix - The RNA sequence of a RNA DNA triple-strand complex is the same as the positive strand of the DNA p. DNA positive strand 5'-TAGAGGAGTACCAC-3 ' DNA negative strand 3 '-ATCTCCTCATGGTG-5 ' RNA strand 5 '-UAGAGGAGUACCAC-3 ' Promoter - Any region of DNA, that binds proteins which engage the polymerase transcription mechanism. TATA Box - A region near the 3' end of a promoter with the sequence TATA. mRNA - The RNA produced from the DNA by the polymerase as a result of transcription Start of transcription - The 3' end of a promoter where the polymerase mechanism begins to transcribe DNA into mRNA. Exon - Any region of mRNA which is used to code for proteins 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. 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. End of translation - The 3 ' end of the 3 ' -most exon. Translated region - Any collection of exons and introns. 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 |< Promoter >| |<-TATA Box->| )<-Beginning of Translation j <- Translated Region >| End of Translation->| |<-Exon->|<-Intron->|<-Exon->|<-Intron->|<-Exon->|<-3'UTR->| + strand - strand -Gene- -> Positive strand gene - Any gene in which the features run 5' to 3' on the positive strand Negative strand gene - Any gene in which the features run 5' to 3' on the negative strand C I sequence - Any positive or negative strand DNA sequence of 20 bases or more. The C2 sequence must occur in the same chromosome as the Cl sequence. C2 sequence - Any positive or negative strand DNA sequence of 20 bases or more. The Cl sequence must occur in the same chromosome as the C2 sequence. C1/C2 - Any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence Tl sequence - Any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence. The Tl and T2 sequences must be between about lkb and 105kb apart. T2 sequence - Any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence. The T2 and Tl sequences must be between about lkb and 105kb apart. 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. Poly-adenylation signal - A number of Adenosine (A) bases are added to the mRNA at the end of the 3 'UTR. Possible Connectron - Any set of Tl, T2 and C1/C2 sequences such that the Cl sequence is identical to the Tl 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 Tl and T2 DNA sequences. A triple-stranded complex of the DNA and the RNA forms such that the Cl sequence forms hydrogen bonds with the Tl sequence and the C2 sequence forms hydrogen bonds with the T2 sequence. Because the Cl sequence is adjacent to the C2 sequence, the Tl sequence is brought physically close to the T2 sequence. This produces a loop of between about lkb and 105kb 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 30nm. Real Connectron - Any Possible Connectron which is within the Gap-Distance of some gene Homologous connectron - The Tl sequence and the T2 sequence are on the same chromosome as the C1/C2 sequence Heterologous connectron - The Tl sequence and the T2 sequence are on a chromosome different from chromosome of the C1/C2 sequence Permanent connectron - Any C1/C2 sequence, which is 3' UTR to some gene that is not surrounded by any Tl and T2 sequence pairs Transient connection - Any C1/C2 sequence, which is 3' UTR to some gene that is surrounded by one or more Tl and T2 sequence pairs Self-limiting connectron - Any C1/C2 sequence which is 3 'UTR to some gene that is surrounded by the Tl and T2 sequences such that C1=T1 and C2=T2 Geneless connectron - Any C1/C2 sequence which is not 3 'UTR to some gene but is surrounded by some Tl and T2. A promoter may lie 5' to the C1/C2 sequence. 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 C17C2' sequence on the opposite strand. Similarly the T1-T2 long loop pair has a complementary long loop pair Tl'-T2'. Wherever a C1/C2, T1-T2 tetrad exists there is a complementary Cl 7C2', Tl'-T2' tetrad. The C1/C2 short loop can be transcribed as a 3 'UTR to a gene on the same strand. The C1VC2' 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 Tl T2 gene - C1/C2 + strand - strand Tl T2 + strand - strand C2/C1 - gene + strand - strand T2' Tl' C27Cl' - gene gene - C17C2' + strand - strand T2' Tl' Of course, the short loops and the long loops do not have to be on the same chromosome. 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 Tl 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. One-to-Many connectron action - One C1/C2 sequence can foπn 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. Many-to-One connectron action - Cl/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. Many-to-Many connectron action - The arrangement of Cl/C2s and Tl-T2s across chromosomes can form a complex web of gene expression control relationships. Percentage of the Genome Regulated by Connectrons - Since the connections for a sequenced genome can be calculated, the percentage of the genome that is open to connectron regulation can be known. 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. 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 connections 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. Hierarchy of DNA Structuring - The DNA of a cell's genome is structured in a hierarchy of six levels. Figures 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 figure 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 figure 1. The chromatin particles are packed in a six-fold symmetry as shown in figure 2a and figure 2b. 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 figure 1 is approximately 300 nm. These large loops constitute level 4 of the structuring hierarchy. As shown in figure 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. Model of Chromatin Structure - The level 4 structure of DNA as shown in figure 1 ranges in length from 5,000 to 105,000 bases of DNA. Figure 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 The chromomere model of DNA structuring was presented by N. A Resnik, et al.[l] 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. 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. Thomas Werner and his colleagues at Genomatix in Munich, Germany have developed an approach to understanding what they call "Matrix Attachment Region" (MAR). Figure 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 "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. Functional features of MARs: Anchoring of regulatory elements like promoters and enhancers to the nuclear matrix. Ensuring long term activity of promoters and enhancers in chromatin. Insulation, rendering a functional domain insensitive to position effects. Genomatix is conducting a research project to define and detect MARs by computer- analysis." Brief Description of the Objects of the Invention 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. 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. 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. 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. 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. 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. An object of the invention is to provide a method of modifying a given body comprising modifying the connectron organization therein. An object of the invention is to provide a method of detecting connecti-on control and target sequences in a given genome comprising: determining the base composition of said genome, determining one or more sites of control sequence organization, and/or determining one or more sites of target application. 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'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. 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 Tl and T2 are DNA sequences 20 or more bases in length, where the Cl sequence is adjacent to the C2 sequence, where the Tl and T2 sequences are on the same chromosome, and where the C1/C2 sequences are on the same chromosome as Tl and T2 or where the C1/C2 sequences are on a chromosome different from Tl and T2, wherein: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. An object of the invention is to provide a method of determining in prokaiyotes, archea, single-celled eukaiyotes 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. An object of the invention is to provide a method of determining in the connectron relationships between prokaryotes and their plasmids wherein said connectiOns 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. An object of the invention is to provide a method of determining that connection relationships that exist in plant and higher animals. 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 540 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart, and 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. 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 confrol 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 540 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. 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: Tl 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 T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, and the T2 or Tl sequences must be between about lkb and 105kb apart. 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. Description of the Drawings and Tables 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: Figure 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. The Molecular Biology of the Cell by Alberts, Bray, Lewis, Raff, Roberts and Watson, 3rd. ed. , Garland Publishing, Inc., New York, 1994, p. 354 Figure 2 (a) Chromatin DNA forms into a six-fold symmetry 30nm particles. (b) The six-fold symmetry 30nm particles form a linear chain with a varying number of repeat units. The Molecular Biology of the Cell by Alberts, Bray, Lewis, Raff, Roberts and Watson , 3rd. ed. , Garland Publishing, Inc., New York, 1994, p. 345 Figure 3 Long loops of 30nm particles are thought to be closed at the bottom of the loop by proteins. The Molecular Biology of the Cell by Alberts, Bray, Lewis, Raff, Roberts and Watson, 3rd. ed. , Garland Publishing, Inc., New York, 1994, p. 348 Figure 4 (a) Transcription and Editing, (b) Movement of the RNA through the Nucleus, (c) Connectron Formation Figure 5 Overview of schematic organization of a typical transcriptionally active chromosomal loop. From http://genomatix.gsf.de/func_genomics/ functional_genomics.html Table 1 Connectron Properties for Prokaryotic, Archea and Eukaryotic Genomes Table 2 Yeast Inter-Chromosomal Connectron Distribution Figure 6 Genome size plotted as a log-log function of the Number of Connectrons Figure 7 Number of Sequence Instances plotted as a function of the Number of Fragments Figure 8 Level 0 - The overall view of the algorithm Figure 9 Level 1 - Process Flow of the Algorithm Figure 10 Level 2a - two pages - Process Genome into Blocking Fragment File Figure 11 Level 2b - two pages - Compute the Connectrons for a Genome Figure 12 Level 2c - two pages - Analyze Possible Connectrons Figure 13 Level 3a - Setup Genome Usage Memory Figure 14 Level 3b - Find DBP-Size Blocking File for Tl -Window Figure 15 Level 1 - Find DBP-Size Blocking File for T2-Window Figure 16 Level 2a - two pages - Find C 1 /C2 Entries Figure 17 Level 2b - two pages - Scan Genome Usage Memory for Potential Connectrons Description of the Invention 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 Tl 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 Tl sequence. The Tl 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 Cl 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 Tl 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 Tl 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 Cl sequence is identical to the Tl sequence and the C2 sequence is identical to the T2 sequence. 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 Cl sequence is equivalent to the Tl sequence and the C2 sequence is equivalent to the T2 sequence, the Cl RNA can form a Hoogsteen triple-stranded RNA/DNA/DNA helix with the double-stranded Tl sequence. Similarly the C2 RNA can form a Hoogsteen triple- stranded RNA/DNA/DNA helix with the double-stranded T2 sequence. Because the Cl 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 Tl sequence and the T2 sequence can then be structured into 30 nm chromatin particles as shown in level 4 of figure 1. The genes on either strand of the DNA between the Tl sequence and the T2 sequence when they are structured into the 30 nm chromatin particles are not open to promotion and expression. The tetradic relationship between the Tl 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 Tl, T2, Cl 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 Tl - T2 long loops then this connection 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. Tl is really equal to Cl 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, confrol the expression of genes. 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. 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'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 eukaiyotes (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 1/3 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. 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. Any tetrad of connectron sequences (i.e. the Tl, T2, Cl 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 Tl 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. 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. Figure 6 shows that the size of a genome is roughly linearly correlated with the number of connectrons. 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. 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 connectiOns, permanent connectrons, self- limiting connectrons and the expression of genes. Detailed Description of the Invention 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 figure 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 connections for the genome. The printer serves to make hard copies of the files and this patent application. The level 1 diagram in figure 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 figure 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 Sample of the (.blk) file for S. cervesiae 27-base fragment Number Pointer 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 36 111112344232231344242234342 37 111112433444244421144134211 38 111112444311313442332142224 39 111113131241131114424413231 40 111113143332344311113133411 41 111113233111333231444234441 43 In fragments above 1=G, 2=C, 3=A, 4=T Sample of the (.gptr) file for S. cervesiae There are 16 chromosomes in S. cervesiae Item Chromosome Position Direction in Chromosome 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 In direction column above l=positive strand, 2=negative strand The level 2b diagram in figure 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 figure 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 Tls, the T2s, the Cis and the C2s). In the level 2a diagram of figure 10, the algorithm steps through each chromosome and within each chromosome through each base position looking for acceptable Tl-windows of 27 bases. A Tl-window can be used to form a connection relationship if there are two or more instances of this fragment in the blocking fragment file. The computation in the level 3b diagram of figure 14 determines if the Tl-window is acceptable of not. Once an acceptable Tl-window is found, the algorithm (in the level 2a diagram of figure 10) looks for acceptable T2- window positions that lie between 5,000 and 105,000 bases from the Tl-window. The computation for determining acceptable T2-window positions is done in the level 3c diagram of figure 15. Once a pair of Tl and T2 window positions are found, the algorithm looks among the instances of these Tl and T2 sequences for a pair of sequences Cl 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 figure 16. In the level 3e diagram of figure 17 the Genome- Usage memory is scanned for the Possible-Connectrons. In the level 2c diagram of figure 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 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 - Tl, T2, Cl and C2. The claims presented in this section are written by the program NearGene that implements the flow diagram Level 2c of figure 12. The examples are written a uniform type of English. Each example contains some or all of the following elements Name of genome Description of Tl Length of T1-T2 loop The chromosome on which the T1-T2 loop exists The identifier number within the genome of the Tl sequence The Tl sequence Description of T2 The identifier number within the genome of the T2 sequence The T2 sequence A list of genes whose expression is controlled by the T1-T2 loop The common names of the genes as obtained from the NCBI gene feature file (.ptt) A list of C1/C2 short loops whose expression if controlled by the T1-T2 loop The chromosome on which the C1/C2 short loop exists The common name of the gene which expresses the C1/C2 short loop as an RNA The sequence of the C1/C2 short loop A list of C1/C2 short loops that control the formation of the T1-T2 loop The chromosome on which the C1/C2 short loop exists The common name of the gene which expresses the C1/C2 short loop as an RNA The sequence of the C1/C2 short loop The match between the C1/C2 sequence and the Tl sequence The match between the C1/C2 sequence and the T2 sequence The uniform descriptions make it possible to rapidly comprehend the specifics in each example. 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. Index of Pages for Connection Samples Page 39 Connectrons occur in prokaryotes, archea, single-celled eukaryotes and multi- celled eukaryotes. Page 57 Many Connectrons control the expression of one set of genes in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. Page 83 One connectron controls the expression of many sets of genes in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. Page 107 Connectrons occur between prokaryotes and their plasmids. Page 117 Connectrons occur in plants and higher animals Page 126 Permanent connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. Page 135 Transient connections exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. Page 152 Self-limiting connectrons occur in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes Page 164 Geneless connectrons exist in single-celled and multi-celled eukaryotes Page 174 One connectron controls many geneless connectrons in single-celled and multi-celled eukaryotes 1. Connectrons occur in prokaryotes, archea, single-celled eukaryotes and multi- celled eukaryotes. Connectrons exist as tetradic relationships where the sequence Tl is equivalent to the sequence Cl (written T1=C1) and where the sequence T2 equals the sequence C2 (written T2=C2) where Tl and T2 are DNA sequences 20 or more bases in length, where the Cl sequence is adjacent to the C2 sequence, where the Tl and T2 sequences are on the same chromosome, and where the C1/C2 sequences are on the same chromosome as Tl and T2 or where the C1/C2 sequences are on a chromosome different from Tl and T2. The connectron relationship has been found to exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. Example of a prokaryote connectron - E. coli 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 Connectron control elements for chromosome 1 of the E. coli genome A double stranded DNA loop of length 93.542 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3197. This Tl control element has the DNA sequence AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA ATAAATGCTTGACTCTGTAGCGGGAA 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 This long T1/T2 double stianded DNA loop modulates the expression of the following genes rrsC gltU rrlC rrfC aspT trpT yifA yiffi yifB ilvL ilvG_l ilvM ilvE ilvD ilvA ilvY ilvC ppiC b3776 rep gPP 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 yi F yigG rarD yigl pldA recQ yigJ y K pldB yigL yigM metR metE ysgA udp yigN ubiE yigP b3836 yigU yigW_l rfaH yigC ubiB fadA fadB pepQ trkH hemG This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 A C1/C2 short loop on chromosome 1 whose identifier is 3206 contiols 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 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 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 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 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 A C1/C2 short loop on chromosome 1 whose identifier is 3307 contiols 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 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGC AAACACG CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA ATAAATGCTTGACTCTGTAGCGGGAAGGCGTATTATG...CCCGTCACACCA TGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCT TACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTA GGGGAACCTGCGGTTGGATCACCTCCTTACCTTAAAGAAGCGTTCTTTG The match between the Tl sequence and the C1/C2 sequence is AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA ATAAATGCTTGACTCTGTAGCGGGAA The match between the T2 sequence and the C1/C2 sequence is TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG GCGTATTATGCACACCCCGCGCCGCT 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 The match between the Tl sequence and the C1/C2 sequence is TGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACT CCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGG GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATG CTTGACTCTGTAGCGGGAA The match between the T2 sequence and the C1/C2 sequence is TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG GCGTATTATGCACACCCCGCGCCGCT 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 The match between the Tl sequence and the C1/C2 sequence is CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC AACGGCAAACACGCCGCCGGGC The match between the T2 sequence and the C1/C2 sequence is CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC AACGGCAAACACGCCGCCGGGTC Example of an archea connectron - H. pylori 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 Connectron control elements for chromosome 1 of H. pylori genome A double stranded DNA loop of length 96.385 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 812. This Tl control element has the DNA sequence TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA 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 TAGCGGAACTAAAGCATTCATCCCAAACACTAAAGATATTTGG 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 HP 1067 HP1069 HP1070 HP1074 HP1075 HP1076 HP1077 HP1078 HP 1079 HP1080 HP1081 HP1083 HP1084 HP1085 HP1088 HP1091 HP1092 HP1093 HP1094 HP1095 HP1096 This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 HP099S and has the DNA sequence TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC AAACACTAAAGATATTTGG The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 HP 1096 and has the DNA sequence TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC AAACACTAAAGATATTTGG The match between the Tl sequence and the C1/C2 sequence is TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA The match between the T2 sequence and the C1/C2 sequence is TAGCGGAACTAAAGCATTCATCCCAAACACTAAAGATATTTGG The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 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 HP 1096 and has the DNA sequence TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC AAACACTAAAGATATTTGG The match between the Tl sequence and the C1/C2 sequence is TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA The match between the T2 sequence and the C1/C2 sequence is TAGCGGAACTAAAGCATTCATCCCAAACACTAAAGATATTTGG 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 The match between the Tl sequence and the C1/C2 sequence is TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA The match between the T2 sequence and the C1/C2 sequence is TAGCGGAACTAAAGCATTCATCCCAAACA Example of single-celled connectron - S. cervesiae 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 confrols the expression of 34 genes on chromosome 4 in addition to one C1/C2 (1356) short loop. 4213 Chromosome 10 I Chromosome 4 | 1352 1416 I 1356 I Connectron control elements for chromosome 1 of S. cervesiae genome A double stranded DNA loop of length 68.908 kilo-bases on chromosome 4 is bounded on the left by a Tl sequence whose identifier is 1352. This Tl control element has the DNA sequence TTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAA 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 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 This long T1 T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 ATCATCTAATCCTGACATAAACGTAGTTGATGCTCAAAAAAGAAATATAC CAATTAACGCTATTGGTGACCTACAATTTCACTTCCAGGACAACACCAAA ACATCAATAAAGGTATTGCACACTCCTAACATAGCCTATGACTTACTCAGT TTGAATGAATTGGCTGCAGTAGATATCACAGCATGCTTTACCAAAAACGT CTTAGAACG The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is TTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAA The match between the T2 sequence and the C1/C2 sequence is ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATC Example of a multi-celled connectron - C. elegans 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 1 * 1 , * _* 1 Chromosome 1 | 95 138 | 119 122 | 1 125 130 j 1 132 134 ' j 1 136 | A double stranded DNA loop of length 41.978 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 95. This Tl control element has the DNA sequence CAGCACGTTCTTAACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTC CCGC 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 ACTCTGCGTCTCTTCTCCCGCATTTTTTGTAGATCA This long T1/T2 double stranded DNA loop modulates the expression of the following genes Y73A3A.1 Y73A3A.1 ZC123.3 ZC123.2 This long T1/T2 double stranded DNA loop modulates the expression of the following C 1/C2 short loops 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 ZC 123.3 and has the DNA sequence TTGAGAACTCTGCGTCTCAACTCCCGCATTTTTTGTAGATCTACGTAGATC AAACCGAAATGGGACACT 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 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 A C1/C2 short loop on chromosome 1 whose identifier is 130 confrols 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 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 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 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 ZC123.2 and has the DNA sequence GCTTATGCTTGGGCTTAGGCTTAGGCGTAGGCTTAGGCTTAGGCTTAGGCT TATGCTTAGACTTAGTCTCACTATCAGTCTTAGGCTTAGGCTTAGACTTAG GCTTAAGCTTAGGCTTAAGCTTAGACTTAGGCTTAGGCTTAGGCTTAGGCT TAGGCTTAGGTTTGGGCTTAGGCTTAGGCTTAACCTC The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is ACGTTCTTAACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGC The match between the T2 sequence and the C1/C2 sequence is ACTCTGCGTCTCTTCTCCCGCATTTTTTGTAGATC 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 F16B4.4 and has the DNA sequence ACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGCATTTTTTGT AGATCTACGTAGATCAAGCCGAAATGAGACACTCTGACACCACG The match between the Tl sequence and the C1/C2 sequence is ACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGC The match between the T2 sequence and the C1/C2 sequence is ACTCTGCGTCTCTTCTCCCGCATTTTTTGTAGATC 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 The match between the Tl sequence and the C1/C2 sequence is AACCATGCAAAATCAGTTGAGAACTCTGCGTCTCTTCTCCCGC The match between the T2 sequence and the C1/C2 sequence is ACTCTGCGTCTCTTCTCCCGCATTTTTTGTAGATC 2. Many Connectrons control the expression of one set of genes in prokaryotes, archea, single-celled eukaiyotes and multi-celled eukaryotes. 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 Example of a many-to-one connectron in prokaryotes - E. coli 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 I Chromosome 1 | 3197 3308 A double sfranded DNA loop of length 93.542 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3197. This Tl confrol element has the DNA sequence AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA ATAAATGCTTGACTCTGTAGCGGGAA 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes rrsC gitu rrlC rrfC aspT trpT yifA yiffi yiffi ilvL ilvG_l ilvM ilvE ilvD ilvA ilvY ilvC ppiC b3776 rep PP 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 yigl pldA recQ yigJ yig pldB yigL yigM metR metE ysgA udp yigN ubiE yigP b3836 yigu yigW_ , 1 rfaH yigC ubiB fadA fadB pepQ trkH hemG The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 'UTR to the gene hemG and has the DNA sequence AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAA ATAAATGCTTGACTCTGTAGCGGGAAGGCGTATTATG...GGAGTCTGCAAC TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACG GTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGT GGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACT TTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAAC CTGCGGTTGGATCACCTCCTTACCTTAAAGAAGCGTTCTTTG The match between the Tl sequence and the C1/C2 sequence is AAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGG AATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACG CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAG AGAAAGC AAAA ATAAATGCTTGACTCTGTAGCGGGAA The match between the T2 sequence and the C1/C2 sequence is TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG GCGTATTATGCACACCCCGCGCCGCT 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 The match between the Tl sequence and the C1/C2 sequence is TGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACT CCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGG GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATG CTTGACTCTGTAGCGGGAA The match between the T2 sequence and the C1/C2 sequence is TAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTG ACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAG AACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAG GCGTATTATGCACACCCCGCGCCGCT A C1/C2 short loop on chromosome 1 whose identifier is 2218 confrols 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 The match between the Tl sequence and the C1/C2 sequence is CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC AACGGCAAACACGCCGCCGGGC The match between the T2 sequence and the C1/C2 sequence is CTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAAC AACGGCAAACACGCCGCCGGGC Example of a many-to-one connectron in archea - M. jannaschii 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 I Chromosome 1 | 1630 1643 A double stranded DNA loop of length 4.998 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 1630. This Tl confrol element has the DNA sequence TTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTT GATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA AGATTAATTAGGAAAGGAAATAAGATTTCTCTAACAGACAAGTTAAATTT TTGGATTTAAAAAGATAAAAAT 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes MJ1597 MJ1598 MJ1599 MJ1600 MJ1601 MJ1602 The expression of genes in this T1 T2 long loop is controlled by the following C1/C2 short loops. 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'UT to the gene MJ1597 and has the DNA sequence ATATGTTTGAAATTTGAAAATAAGAGTATTTAGAAGTTATTAATTAGTTCA AAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATAT TTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA The match between the Tl sequence and the C1/C2 sequence is TTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTT GATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA The match between the T2 sequence and the C1/C2 sequence is AAAATTA 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 M 1 02 and has the DNA sequence ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT TGAATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAA ATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACT CTGTTTTATTATGGAAAGAAAGAT The match between the Tl sequence and the C1/C2 sequence is GCTGGTTTGATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTA AAAATTA The match between the T2 sequence and the C1/C2 sequence is TTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTATTG AATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAAAT TTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACTCT GTTTTATTATGGAAAGAAAGAT 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 3TJTR to the gene MJ0112 and has the DNA sequence ATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATATTTGAGTTTAT TGAATTATTCAGATTTTTAAAAT The match between the Tl sequence and the C1/C2 sequence is ATTΓAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATATΓTGAGTTTAT TGAATTATTCAGATTTTTAAAAT The match between the T2 sequence and the C1/C2 sequence is GCTGGTTTGATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTA AAAAT 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 The match between the Tl sequence and the C1/C2 sequence is TTTTTATTTAATTTCTAAGGGTTTGCTGGTTTGATTATTTAGAATATTTGAG TTTATT The match between the T2 sequence and the C1/C2 sequence is GCTGGTTTGATTATTTAGAATATTTGAGTTTATT Example of a many-to-one connectron in single-cell eukaryotes — S. cervesiae In this example the existence of the T1-T2 (5515-5533) long loop on chromosome 12 is controlled by seventeen C1/C.2 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 I Chromosome 12 3197 3308 A double stranded DNA loop of length 6.466 kilo-bases on chromosome 12 is bounded on the left by a Tl sequence whose identifier is 5515. This Tl control element has the DNA sequence AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG This double sfranded 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes YLR467W This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 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 The expression of genes in this T1 T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is ' AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGG ATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGG The match between the T2 sequence and the C1 C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGG 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTA AGAGACAACAGGGCT 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTA AGAGACAACAGGGCT 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT 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 stiand that is 3'UTR to the gene YHR219W and has the DNA sequence AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC ( TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT 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 stiand that is 3'UTR to the gene YLL066C and has the DNA sequence AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT 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 GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT A C1/C2 short loop on chromosome 16 whose identifier is 8023 conti-ols 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT A C1/C2 short loop on chromosome 16 whose identifier is 7356 conti-ols 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT A.TTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTT The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTT 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 The match between the Tl sequence and the C1/C2 sequence is ATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGC GAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAA The match between the T2 sequence and the C1/C2 sequence is ATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGC GAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAA 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 The match between the Tl sequence and the C1/C2 sequence is CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAAC ATCCGGGTAAGAGACAACAGGCT 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 The match between the Tl sequence and the C1/C2 sequence is CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is CTATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAAC ATCCGGGTAAGAGACAACAGGCT 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 The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAA The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAA Example of a many-to-one connectron in multi-cell eukaryotes - C. elegans 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 *. I Chromosome 5 | 28632 28697 A double stranded DNA loop of length 58.451 kilo-bases on chromosome 5 is bounded on the left by a Tl sequence whose identifier is 28632. This Tl control element has the DNA sequence GCAAAAATTGACTGAAAATTTGAATTTCCCGCAAAAAATTGACTGAAAAT TTGAATTTCCCGCCAAAAATTGACTGAAAATTTGAA This double stranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 28697. This T2 control element has the DNA sequence CAAAAAATTGACTGAAAATTTGAATTTCCCTCCAAAAATTGACTGAAAAT TTGAATTTCCCGCCAAAAATTGACTGAAAATTTGAATATCCCGCCAAAAA TTGACTGAAAATTTGAATTTCCCGCCGAAAATTAAATGAAAAATGGAATT TCTCGCCGAA This long T1/T2 double stranded DNA loop modulates the expression of the following genes M162.8 M162.4 M162.3 M162.6 M162.2 M162.1 M162.7 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is CAAAAATTGACTGAAAATTTGAATTTCCCGC The match between the T2 sequence and the C1/C2 sequence is CAAAAAATTGACTGAAAATTTGAATTTCCCTCCAAAAATTGACTGAAAAT TTGAATTTCCCGCCAAAAATTGACTGAAAATTTGAATATCCCGCCAAAAA TTGACTGAAAATTTGAATTTCCCGCCGAAAATTAAATGAAAAATGGAATT TCTCGCCGAA 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 T U 01/16471 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 The match between the Tl sequence and the C1/C2 sequence is CAAAAATTGACTGAAAATTTGAATTTCCCGC The match between the T2 sequence and the C1/C2 sequence is CAAAAAATTGACTGAAAATTTGAATTTCCCTCCAAAAATTGACTGAAAAT TTGAATTTCCCGCCAAAAATTGACTGAAAATTTGAATATCCCGCCAAAAA TTGACTGAAAATTTGAATTTCCCGCCGAAAATTAAATGAAAAATGGAATT TCTCGCCGAA 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 The match between the Tl sequence and the C1/C2 sequence is CAAAAATTGACTGAAAATTTGAATTTCCCGCAAAAAATTGACTGAAAATT TGAATTTCCCGCCAAAAATTGACTGAAAATTTGAA The match between the T2 sequence and the C1/C2 sequence is CAAAAAATTGACTGAAAATTTGAATTTCCC 3. One connectron controls the expression of many sets of genes in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. 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. Example of a one-to-many connectron in prokaryotes - E. coli 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 * * * I Chromosome 1 | 3208 3315 3206 Chromosome 1 * * 1 I Chromosome 1 | 3436 3476 3206 Chromosome 1 I * * * I Chromosome 1 j 3439 3478 3206 Chromosome 1 * I * * I Chromosome 1 j 3441 3479 A double stranded DNA loop of length 93.377 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3208. This Tl control element has the DNA sequence ACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCA AGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAA ATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGG TTAAGCGACTAAGCGTACACGGTGGATGCCCTGGC...AGTGTGTTTCGACA CACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTG AAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTA GCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGT This double stianded 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes rrlC rrfC aspT trpT yifA yiffi yifB ilvL ilvG_l ilvM ilvE ilvD ilvA ilvY ilvC ppiC b3776 rep Pp 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 yigl pldA recQ yigJ yigK pldB yigL yigM metR metE ysgA udp yigN ubiE yigP b3836 yigU yigW_l rfaH yigC ubiB fadA fadB pepQ trkH hemG rrsA ileT The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 AATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATA GGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGA AAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCA GCCCAGAGCCTGAATCAGT The match between the Tl sequence and the C1/C2 sequence is ACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCA AGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAA ATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGG TTAAGCGACTAAGCGTACACGGTGGATGCCCTGGC...AGTGTGTTTCGACA CACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTG AAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTA GCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGT The match between the T2 sequence and the C1/C2 sequence is TTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAAC GAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAAC A double stranded DNA loop of length 41.279 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3436. This Tl control element has the DNA sequence ACGC AACGCGTGATAAGCAATTTTCGTGTCCCCTTCGTCTAGAGGCCCAG GACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACG CCACTTGCTGGTT 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 This long T1/T2 double sfranded DNA loop modulates the expression of the following genes gltT rrlB rrfB murB coaA b3975 tyrU thrT tuffi secE nusG rplK rplA rplJ rplL rpoB rpoC htrC thiH thiF thiE yjaE yjaD hemE nfi yjaG hupA yjaH yjal hydH purD purH This long T1/T2 double sfranded DNA loop modulates the expression of the following C1/C2 short loops 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 The match between the Tl sequence and the C1/C2 sequence is GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTT The match between the T2 sequence and the C1/C2 sequence is GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTC ACCTGCCTTAATA A double stranded DNA loop of length 41.336 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3439. ' This Tl control element has the DNA sequence CCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTT AAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGA 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 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 stiand that is 3 'UTR to the generrsC and has the DNA sequence GTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAG GGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTC ACCTGCCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTG CTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAA... ACCGGCGATTTCCG AATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATA GGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGA AAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCA GCCCAGAGCCTGAATCAGT The match between the Tl sequence and the C1/C2 sequence is CCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTT AAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGA The match between the T2 sequence and the C1/C2 sequence is GTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTG AAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTT A double stranded DNA loop of length 38.285 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3441. This Tl contiol element has the DNA sequence AATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAG GTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATG AAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTA TAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGT...GATGAGAGAAGA TTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATAAAA CAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCC GAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCC ATGCGAG 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 This long T1/T2 double sfranded DNA loop modulates the expression of the following genes rrlB rrfB murB coaA b3975 tyrU thrT tuffi secE nusG rplK rplA rplJ rplL rpoB rpoC htrC thiH thiF thiE yjaE yjaD hemE nfi yjaG hupA yjaH yjal hydH purD purH gltV The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is AATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAG GTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATG AAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTA TAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATC ATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATC TAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCG AGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGT The match between the T2 sequence and the C 1/C2 sequence is AAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGA TGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGT CGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAAC CCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGC GAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAAC CGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTG AATCAGT Example of a one-to-many connectron in archea - M. jannaschii 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 I Chromosome 1 534 611 1642 Chromosome 1 I Chromosome 1 ] 1139 1159 1642 Chromosome 1 I * * „* I Chromosome 1 | 1630 1643 A double stranded DNA loop of length 72.886 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 534. This Tl control element has the DNA sequence TAAGTAAATAAAATTTCTCTAACAAATAAGTTAAATT This double stianded DNA loop is bounded on the right by a T2 contiol element whose identifier is 611. This T2 control element has the DNA sequence TAAATAAAATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATA AAAATGCT 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is AAGTAAATAAAATTTCTCTAACAAATAAGTTAAATT The match between the T2 sequence and the C1/C2 sequence is TAAATAAAATTTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATA AAAAT A double stranded DNA loop of length 14.509 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 1139. This Tl control element has the DNA sequence ATTTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTAGCTGG TTTGATTGTTTAAAATATTTGAGTTTA 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 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is ATTTAATTTCTAAGGGTTAGCTGGTTTGATT The match between the T2 sequence and the C1/C2 sequence is ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT TGAATTATTCAGATTTTTAAAAATTA A double stranded DNA loop of length 4.998 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 1630. This Tl control element has the DNA sequence TTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTTGCTGGTTT GATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTAAAAATTA AGATTAATTAGGAAAGGAAATAAGATTTCTCTAACAGACAAGTTAAATTT TTGGATTTAAAAAGATAAAAAT This double stianded 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes MJ1597 MJ1598 MJ1599 MJ1600 MJ1601 MJ1602 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 ATTTCTCTA AC AAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACT CTGTTTTATTATGGAAAGAAAGAT The match between the Tl sequence and the C1/C2 sequence is GCTGGTTTGATTATTTAGAATATTTGAGTTTATTGAATTATTCAGATTTTTA AAAATTA The match between the T2 sequence and the C1/C2 sequence is TTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTATTG AATTATTCAGATTTTTAAAAATTAGGATTAATTAGGCAAGTAAATAAAAT TTCTCTAACAAATAAGTTAAATTTTTGGATTTAAAAAGATAAAAATACTCT GTTTTATTATGGAAAGAAAGAT Example of a one-to-many connectron in single-cell eukaryotes - S. cervesiae 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 I Chromosome 1 158 171 86 Chromosome 1 I Chromosome 1 293 317 86 Chromosome 1 I Chromosome 10 4295 4308 86 Chromosome 1 j Chromosome 13 5916 5923 A double stranded DNA loop of length 20.391 kilo-bases on chromosome 2 is bounded on the left by a Tl sequence whose identifier is 158. This Tl conti-ol element has the DNA sequence CCAATTGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTT ACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAGAA ATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTAAT AG This double sfranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 171. This T2 control element has the DNA sequence ATAATTGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTT ACTAGTATATTATCATATACGGTGTTAGAAGATGACACAAATGATGAGAA ATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTAAT AGGATCAATGAATATTAACATATAAAATGATGATAATAATA 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 YBLIOIC The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 1 whose identifier is 86 confrols 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 The match between the Tl sequence and the C1/C2 sequence is AAATCAACTATCATCTACTAACTAGTATTTAC The match between the T2 sequence and the C1/C2 sequence is AAATCAACTATCATCTACTAACTAGTATTTAC A double sfranded DNA loop of length 38.470 kilo-bases on chromosome 2 is bounded on the left by a Tl sequence whose identifier is 293. This Tl control element has the DNA sequence GAATTGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTA TCAATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAA GCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCAAGGATTGATAATGTAAT AGGATAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGT ATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTTGAGGAGAAC TTCTAGT This double stranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 317. This T2 confrol element has the DNA sequence AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC GAGGAGAACTTCTAGTATATTCTGTA This long T1/T2 double sfranded 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 1 whose identifier is 86 conti-ols 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 GAGGAATAATCGTAATATTAGTATGTAG AAATATAGATTCC ATTTTGAGG ATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATT ATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCACCCAT TTCTCAGAA The match between the Tl sequence and the C1/C2 sequence is AAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAAT ATAGATTCCATTTTGAGGATTCCTATATCCT The match between the T2 sequence and the C1/C2 sequence is AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC GAGGAGAACTTCTAGTATATTCTGTA A double stranded DNA loop of length 11.020 kilo-bases on chromosome 10 is bounded on the left by a Tl sequence whose identifier is 4295. This Tl control element has the DNA sequence AAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAA ACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCAT TTTGAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTG • 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 This long T1/T2 double sfranded DNA loop modulates the expression of the following genes YJR027W YJR029W The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 1 whose identifier is 87 confrols 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 A double sfranded DNA loop of length 5.462 kilo-bases on chromosome 13 is bounded on the left by a Tl sequence whose identifier is 5916. This Tl control element has the DNA sequence AAGCTGAAGTGCAAGGATTGATAATGTAATAGGATAATGAAACATATAA AACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCA TTTTGAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTA This double sfranded 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes YML045W The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 1 whose identifier is 87 confrols 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 Example of a one-to-many connectron in multi-cell eukaryotes - C. elegans 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 * * * I Chromosome 4 | 16554 16661 21591 Chromosome 5 I Chromosome 5 | 21565 21590 A. double stranded DNA loop of length 50.159 kilo-bases on chromosome 4 is bounded on the left by a Tl sequence whose identifier is 16554. This Tl control element has the DNA sequence TGCCTGAAAAAATTGGCTCCGAGTTAGGACACTTGGGGTGGTCAAAAAAT TTTGTGACTATTGTCAAATGAAAGATCATAGTTGATAACATAAATTCCCAA AGTTTCATAAAAATCGATACGCAGCGAACAAAGTTATCAATT 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes C23H5.7 C23H5.8a C23H5.3 C23H5.2 C23H5.9 C23H5.1 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is TTTCATAAAAATCGATACGCAGCGAACAAAGTTAT The match between the T2 sequence and the C1/C2 sequence is TATTGTCAAATGAAAGATCATGGTTGATAACATAAATTCCCA A double stranded DNA loop of length 18.142 kilo-bases on chromosome 5 is bounded on the left by a Tl sequence whose identifier is 21565. This Tl control element has the DNA sequence CTCCGAGTTAGGACACTTGGGGTGGACAAAAAATTTTGTGACTATTGTCA AATGAAAGATCATGGTTGATAA This double sfranded 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 This long T1/T2 double sfranded DNA loop modulates the expression of the following genes T21H3.2 T21H3.1 F25A2.1 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is TATTGTCAAATGAAAGATCATGGTTGATAA The match between the T2 sequence and the C1/C2 sequence is TATTGTCAAATGAAAGATCATGGTTGATAACATAAATTCCCACAATTTCAT AAAAATCGATACGCAGCGAACAAAGTTATGATTTTTGACCCGGAACTTAT TTGGAGACCTAATA 4. Connectrons occur between prokaryotes and their plasmids. Connecfron 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 MPl plasmid. Example of a prokaryote/plasmid connectron - D. radiodurans In this example the existence of T1-T2 (2654-2694 and 2692-2749) long loops in chromosome 3 that is the plasmid MPl are controlled by one C1/C2 short loop (16) in chromosome 1. 16 Chromosome 1 2768 Chromosome 3 (plasmid MPl) 2653 Chromosome 3 (plasmid MPl) I * * * 1 Chromosome 3 (plasmid MPl) | 2654 2694 I ' 2693 I 16 Chromosome 1 2768 Chromosome 3 (plasmid MPl) 2693 Chromosome 3 (plasmid MPl) I Chromosome 3 (plasmid MPl) 2692 2749 I 2693 2695 I A double stranded DNA loop of length 46.903 kilo-bases on chromosome 3 (plasmid MPl) is bounded on the left by a Tl sequence whose identifier is 2654. This Tl control element has the DNA sequence CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG GTATGCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTG ACGATGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGACTGTCAGTACA GCAATCGAGAGTGGGCTGATCAGCCCACTGTGCGTTCTGGCCATCGACGC CTCTTTTCACCGCAAAGCCGGTCAGCACACCGCACACCTCGGCTCGTTCTG GAATGGCTGTGCCGCGCGGACC 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes DRB0020 DRB0021 DRB0022 DRB0023 DRB0024 DRB0025 DRB0027 DRB0030 DRB0032 DRB0033 DRB0034 DRB0035 DRB0037 DRB0038 DRB0039 DRB0041 DRB0042 DRB0043 DRB0044 DRB0045 DRB0047 DRB0051 DRB0052 DRB0054 DRB0055 DRB0057 This long T1/T2 double sfranded DNA loop modulates the expression of the following C1/C2 short loops A C1/C2 short loop on chromosome 3 (plasmid MPl) 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG GTATGCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTG ACGATGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGACTGTCAGTACA GCAATCGAGAGTGGGCTGATCAGCCCACTGTGCGTTCTGGCCATCGACGC CTCTTTTCACCGCAAAGCCGGTCAGCACACCGCACACCTCGGCTCGTTCTG GAATGGCTGTGCCGCGCGGACC The match between the T2 sequence and the C1/C2 sequence is GCTGAACGCCCTGAATCTCTCCCGGTATGCAGCCTGCTCGGAGAGTACGA TTCGTCGTTGGCTGCACCGAAGTGACGATGGGGCCATTCCGTGGGGCGCG TTACACCAGGCGACTGTCAGTACAGCAATCGAGAGTGGGCTGATCAGCCC ACTGTGCGTTCTGGCCATCGACGCCTCTTTTCACCGCAAAGCCGGTCAGCA CACCGCACACCTCGGCTCGTTCTGGAATGGCTGTGCCGCGCGGACCGAAC GCGGAATCGAGCAATCCTGTTGT • A C1/C2 short loop on chromosome 3 (plasmid MPl) 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 The match between the Tl sequence and the C1/C2 sequence is CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG GTATGCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTG ACGATGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGACTGTCAGTACA GCAATCGAGAGTGGGCTGATCAGCCCACTGTGCGTTCTGGCCATCGACGC CTCTTTTCACCGCAAAGCCGGTCAGCACACCGCACACCTCGGCTCGTTCTG GAATGGCTGTGCCGCGCGGACC The match between the T2 sequence and the C1/C2 sequence is GCTGAACGCCCTGAATCTCTCCCGGTATGCAGCCTGCTCGGAGAGTACGA TTCGTCGTTGGCTGCACCGAAGTGACGATGGGGCCATTCCGTGGGGCGCG TTACACCAGGCGACTGTCAGTACAGCAATCGAGAGTGGGCTGATCAGCCC ACTGTGCGTTCTGGCCATCGACGCCTCTTTTCACCGCAAAGCCGGTCAGCA CACCGCACACCTCGGCTCGTTCTGGAATGGCTGTGCCGCGCGGACCGAAC GCGGAATCGAGCAATCCTGTTGT A C1/C2 short loop on chromosome 3 (plasmid MPl) 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 CGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCTC AGC GTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCGGTAT GCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTGACGA TGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGA The match between the Tl sequence and the C1/C2 sequence is CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG GTATGCAGCCTGCTCGGAGAGTACGATTCGTCGTTGGCTGCACCGAAGTG ACGATGGGGCCATTCCGTGGGGCGCGTTACACCAGGCGACTGTCAGTACA GCAATCGAGAGTGGGCTGATCAGCCCACTGTGCGTTCTGGCCATCGACGC CTCTTTTCACCGCAAAGCCGGTCAGCACACCGCACACCTCGGCTCGTTCTG GAATGGCTGTGCCGCGCGGACC The match between the T2 sequence and the C1/C2 sequence is GCTGAACGCCCTGAATCTCTCCCGGTATGCAGCCTGCTCGGAGAGTACGA TTCGTCGTTGGCTGCACCGAAGTGACGATGGGGCCATTCCGTGGGGCGCG TTACACCAGGCGACTGTCAGTACAGCAATCGAGAGTGGGCTGATCAGCCC ACTGTGCGTTCTGGCCATCGACGCCTCTTTTCACCGCAAAGCCGGTCAGCA CACCGCACACCTCGGCTCGTTCTGGAATGGCTGTGCCGCGCGGACCGAAC GCGGAATCGAGCAATCCTGTTGT A double stranded DNA loop of length 68.612 kilo-bases on chromosome 3 (plasmid MPl) is bounded on the left by a Tl sequence whose identifier is 2692. This Tl control element has the DNA sequence CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG AC 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 This long TI/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 This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops A C1/C2 short loop on chromosome 3 (plasmid MPl) whose identifier is 2693 confrols 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 A C1/C2 short loop on chromosome 3 (plasmid MPl) whose identifier is 2695 confrols 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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'UT to the gene DR0009 and has the DNA sequence GCTGTGAAATCACCGCTTCCAATGGGTCTGATGGCCATCCTACAGTACGTT CTCAGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCT GCTCAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTC CCGGTATGCAGCCTGCTCGGAGAGTACGATTCGT The match between the Tl sequence and the C1/C2 sequence is CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG AC The match between the T2 sequence and the C1/C2 sequence is AGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCT CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG GT A C1/C2 short loop on chromosome 3 (plasmid MPl) 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 GCTCAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCfc CCGGTATGCAGCCTGCTCGGAGAGTACGATTCGT...CGGACCGAACGCGGA ATCGAGCAATCCTGTTGTGCCCTCATTGATGTCCAGCACCGGCAGGCCTTG ACGGTCGATGTCCGTCAGACCCTGACCGGGTCTGAGGCTCCAACTCGTCT GGAACAG The match between the Tl sequence and the C1/C2 sequence is CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG AC The match between the T2 sequence and the C1/C2 sequence is AGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCT CAGCGTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCG GT A C1/C2 short loop on chromosome 3 (plasmid MPl) whose identifier is 2693 confrols 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 The match between the Tl sequence and the C1/C2 sequence is CTGATGGCCATCCTACAGTACGTTCTCAGCGCGGTCCCGCTGCGCAAGAC GCAGCGGAATTTCCTGACCGTGCTGCTCAGCGTTTTTCTCGCTGTTCCTGG AC The match between the T2 sequence and the C1/C2 sequence is AGCGCGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCT CAGCGTTTTTCTCGCTGTTCCTGGAC A C1/C2 short loop on chromosome 3 (plasmid MPl) whose identifier is 2653 confrols 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 The match between the Tl sequence and the C1/C2 sequence is CGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCTCAGC GTTTTTCTCGCTGTTCCTGGAC The match between the T2 sequence and the C1/C2 sequence is CGGTCCCGCTGCGCAAGACGCAGCGGAATTTCCTGACCGTGCTGCTCAGC GTTTTTCTCGCTGTTCCTGGACGGCTGAACGCCCTGAATCTCTCCCGGT 5. Connectrons occur in plants and higher animals Connectron relationships exist in plant and higher animals. Example of a plant connectron - A. thaliania 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 I Chromosome 2 423 469 I 426 430 1 A double stranded DNA loop of length 42.285 kilo-bases on chromosome 2 is bounded on the left by a Tl sequence whose identifier is 423. This Tl conti-ol element has the DNA sequence TATCTCTTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTA ATTAAAAAACGAAATA 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes At2g02070 At2g02080 At2g02090 At2g02100 At2g02120 At2g02130 This long T1/T2 double stranded DNA loop modulates the expression of the following C 1 /C2 short loops 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 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 TTGCGGAAAAATAATATCATCATTATAAAAAAATAATTAGAGTTTTTTCGC ATAT The expression of genes in this T1 T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is ATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAAAAACGA AATA The match between the T2 sequence and the C1/C2 sequence is TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATTATTAATT T 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 AT4gl5300 and has the DNA sequence TGCCATTAGAAATAAAATTTTAAAGAGTAAATTAATTTATCTCTTTAAGGA TTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAAAAACGAA ATACATTATTAATTTCCAAAA The match between the Tl sequence and the C1/C2 sequence is TATCTCTTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTA ATTAAAAAACGAAATA The match between the T2 sequence and the C1/C2 sequence is TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATTATTAATT T 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 The match between the Tl sequence and the C1/C2 sequence is TATCTCTTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTA ATTAAAAAACGAAATA The match between the T2 sequence and the C1/C2 sequence is TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATA 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 AT4gl7510 and has the DNA sequence TTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAA AAACGAAATACATT The match between the Tl sequence and the C1/C2 sequence is TTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAA AAACGAAATA The match between the T2 sequence and the C1/C2 sequence is TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATT A C1/C2 short loop on chromosome 4 whose identifier is 21813 confrols 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 AT4gl7680 and has the DNA sequence TTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAA AAACGAAATACATT The match between the Tl sequence and the C1/C2 sequence is TTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTAATTAAA AAACGAAATA The match between the T2 sequence and the C1/C2 sequence is TACTAATTTAATTAATTAAATTTAATTAAAAAACGAAATACATT 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 The match between the Tl sequence and the C1/C2 sequence is TATCTCTTTAAGGATTAAAAAGTCAAATACTAATTTAATTAATTAAATTTA ATTAA The match between the T2 sequence and the C1 C2 sequence is TACTAATTTAATTAATTAAATTTAATTAA Example of a animal connecfron - D. megalomaster A double sfranded DNA loop of length 88.159 kilo-bases on chromosome 4 is bounded on the left by a Tl sequence whose identifier is 3340. This Tl confrol element has the DNA sequence ACCTAAAAGAAGTACCGTTTTTTACTCCTAATTACCAATTCTAACCATCCA TATCACTTTTTGACGGACTCCGTGAAAATAATTTTTGGCCAAATTTTCGCA TTTTTTGTAAGGGGTAACATCATAAAAATT 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 This long T1/T2 double sfranded DNA loop modulates the expression of the following genes [Some of the following gene names have not been determined.] CGI 1207 - CG2186 CG2157 Orkl This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 AAAAAAGTACCGCGTTTTACTCCTAATTACC AATTCTAACCATCCATATCA CTTTTTGACGGACTCCGTTAAAATAATTTTTGACCAAATTTTCGCATTTTTT GTAATCAAAATTTGCAAAAAATTGAAAAAAC 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 sfrand that is 3'UTR to the gene XXX and has the DNA sequence CAAAATTTGAATGCAAATCGATTGGGAATCAAAAAACAAACTCAACGAG GTATGACATTCCATATTTGGGCCATTATTTCCAA 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 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1 C2 sequence is TTTTACTCCTAATTACCAATTCTAACCATCCATATCACTTTTTGACGGACTC CGTGAAAATAATTTTTGGCCAAATTTTCGCATTTTTTGTAAGGGGTAACAT CAT The match between the T2 sequence and the C1/C2 sequence is AAAAAAGTACCGCGTTTTACTCCTAATTACCAATTCTAACCATCCATATCA CTTTTTGACGGACTCCGTGAAAATAATTTTTGGCCAAATTTTCGCATTTTTT GTAAGGGGTAACATCATCAAAATTTGCGAAAAA Example of an animal connectron - H. sapiens 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. Human chromosome 22 has been processed and there 31,000 possible connectrons. The gene descriptors for all the chromosomes of the human genome should become available within the year. 6. Permanent connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. C1/C2 short loops are noπnally 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. Example of a prokaryote permanent connectron - E. coli 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 * * =! I Chromosome 1 | 3200 3210 A double sfranded DNA loop of length 93.339 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3200. This Tl control element has the DNA sequence AAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCG AAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCA AGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAACTT TTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCC TAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGA CGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGG GATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAA GAGGGGGACCTTCGGGCCTCTTGCCATC 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 This long T1/T2 double stianded DNA loop modulates the expression of the following genes rrsC gltU rrlC rrfC aspT trpT yifA yiffi yifB ilvL ilvG_l 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 yigl pldA recQ yigJ yigK pldB yϊgL yigM metR metE ysgA udp yigN ubiE yigP b3836 yigU yigW_ 1 rfaH yigC ubiB fadA fadB pepQ trkH hemG The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is AAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCG AAGATACGGATTCTTAACGTCGCAAGACGAAAAATGAATACCAAGTCTCA AGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGC The match between the T2 sequence and the C1/C2 sequence is CAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGA CGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAG TTTAATTCTTTGAGCGTCAAACTTTTAAATTGAAGAGTTTGATCATGGCTC AGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACA GGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTC TGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAAT ACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCA TCGGATGTGCCCAGATGGGATTAGCTAGT Example of an archea permanent connectron - H. pylori 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 A double stranded DNA loop of length 96.385 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 812. This Tl control element has the DNA sequence TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 882. This T2 confrol element has the DNA sequence TAGCGGAACTAAAGCATTCATCCCAAACACTAAAGATATTTGG This long T1/T2 double sfranded 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 1 whose identifier is 1241 confrols the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed, as a RNA single sfrand that is 3'UTR to the gene HP1535 and has the DNA sequence TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCATTCATCCC AAACA The match between the Tl sequence and the C1/C2 sequence is TTTTACTCATAGGGTTTTTATAGTTCCTAGCGGAACTAAAGCA The match between the T2 sequence and the C1/C2 sequence is TAGCGGAACTAAAGCATTCATCCCAAACA Example of a single-celled peπnanent connectron - S. cervesiae 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 1 Chromosome 12 5515 5533 A double stianded DNA loop of length 6.466 kilo-bases on chromosome 12 is bounded on the left by a Tl sequence whose identifier is 5515. This Tl control element has the DNA sequence AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG This double stranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 5533. This T2 control element has the DNA sequence ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT This long T1/T2 double sfranded DNA loop modulates the expression of the following genes YLR467W The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 GGAAAGAGTAGG ATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCT The match between the Tl sequence and the C1/C2 sequence is AGGAAATTGTTGTTACGAAAGTCAGTGATTATGTATTGTGTAGTATAGTAT ATTGTAAGAAATTTTTTTTTCTAGGGAATATGCGTTTTGATGTAGTAGTAT TTCACTGTTTTGATTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTG GGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACATAAAATAA AGGTAGTAAGTAGCTTTTGGTTG The match between the T2 sequence and the C1/C2 sequence is ATTATGTATTGTGTAGTATAGTATATTGTAAGAAATTTTTTTTTCTAGGGA ATATGCGTTTTGATGTAGTAGTATTTCACTGTTTTGATTTAGTGTTTGTTGC ACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATC TATAAAAAGTAAACATAAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACA TCCGGGTAAGAGACAACAGGGCT Example of a multi-celled permanent connectron - C. elegans 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 I Chromosome 1 569 596 A double stranded DNA loop of length 30.606 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 569. This Tl control element has the DNA sequence AAATCGAGCCCGTAAATCGACACAAGCGCTACAGTAGTC This double sfranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 596. This T2 control element has the DNA sequence AGTGCTACAGTAGTCATTTAAAGAATTACTGTAGTTTTCGCT The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 sfrand that is 3'UTR to the gene F20D6.4 and has the DNA sequence GAGCCCGTAAATCGACACAAGCGCTACAGTAGTCATTTAAAGAATTACTG TAGTTTTC The match between the Tl sequence and the C1/C2 sequence is GAGCCCGTAAATCGACACAAGCGCTACAGTAGTC The match between the T2 sequence and the C1/C2 sequence is GCTACAGTAGTCATTTAAAGAATTACTGTAGTTTTC 7. Transient connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. A class of connectron relationships exist that permit one C1/C2 short loop to confrol 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 connecfron relationships are described as "transient". Transient connectrons exist in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes. Example of a prokaryote transient connectron - E. coli 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 * * * I Chromosome 1 | 3216 3324 I 3225 I 3225 Chromosome 1 ] Chromosome 1 | 3227 3329 A double stranded DNA loop of length 93.464 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3216. This Tl control element has the DNA sequence AGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACT ATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGC ACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAA TTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCC CGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGG ATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCT TGAAATACCACCCTTTAATGTTTGATGTTCTAACGT 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes rrfC aspT trpT yifA yiffi yifB ilvL ilvG 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 yi L yigM metR metE ysgA udp yigN ubiE yigP b3836 yi u yigW_l rfaH yigC ubiB fadA fadB pepQ trkH hemG rrsA ileT rrlA This long T1/T2 double sfranded DNA loop modulates the expression of the following C1/C2 short loops 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 stiand that is 3TJTR to the gene rrlA and has the DNA sequence GCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGG TCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATG GCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACT CGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGA...AACAGAATTTGC CTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAA GTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTC The match between the Tl sequence and the C1/C2 sequence is GCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGG TCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATG GCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACT CGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAA CCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGT GGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAAT ACCACCCTTTAATGTTTGATGTTCTAACGT The match between the T2 sequence and the C1/C2 sequence is CCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCC TTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTG TCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTA CCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACT GAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGA CGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATG TTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGT A double sfranded DNA loop of length 93.749 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3227. This Tl control element has the DNA sequence AGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCA GG This double stianded DNA loop is bounded on the right by a T2 control element whose identifier is 3329. This T2 confrol element has the DNA sequence CATGCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAG TCG This long T1/T2 double stranded DNA loop modulates the expression of the following genes aspT trpT yifA yiffi yiffi ilvL ilvG 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_l rfaH yigc ubiB fadA fadB pepQ trkH hemG rrsA ileT rrlA rrfA The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is AGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCA GG The match between the T2 sequence and the C1/C2 sequence is CATGCGAGAGTAGGGAACTGCCAGGCATCAAAT Example of an archea transient connectron - M. jannaschii In this example the existence of the T1-T2 (1139-1159) long loop is conti-olled by the C1/C2 (533) short loop. The expression of this 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 I 533 I 533 Chromosome 1 I Chromosome 1 | 1139 1159 A double stranded DNA loop of length 78.672 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 532. This Tl control element has the DNA sequence ATATGTTTGAAATTTGAAAATAAGAGTATTTAG 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 TTGAAAATAAGAGCATTTAGAAGTTATTAATTAGTTCAAAGGATTTT 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 This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 ATTTTTATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGA GTTTATTGAATT The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 1 whose identifier is 1629 confrols 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 The match between the Tl sequence and the C1/C2 sequence is ATATGTTTGAAATTTGAAAATAAGAGTATTTAG The match between the T2 sequence and the C1/C2 sequence is ATTTAGAAGTTATTAATTAGTTCAAAGGATTTT A double stranded DNA loop of length 14.509 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 1139. This Tl control element has the DNA sequence ATTTATTAATTAGTTCAAAGGATTTTTATTTAATTTCTAAGGGTTAGCTGG TTTGATTGTTTAAAATATTTGAGTTTA This double stranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 1159. This T2 control element has the DNA sequence ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT TGAATTATTCAGATTTTTAAAAATTA 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is ATTTTTATTTAATTTCTAAGGGTTAGCTGGTTTGATT The match between the T2 sequence and the C1/C2 sequence is ATTTAATTTCTAAGGGTTAGCTGGTTTGATTATTTAGAATATTTGAGTTTAT TGAATT Example of a single-celled transient connectron - S. cervesiae 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 I Chromosome 1 293 320 I 298 I 298 Chromosome 1 I Chromosome 7 | 2840 2859 A double sfranded DNA loop of length 38.470 kilo-bases on chromosome 2 is bounded on the left by a Tl sequence whose identifier is 293. This Tl control element has the DNA sequence GAATTGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTA TCAATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAA GCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCAAGGATTGATAATGTAAT AGGATAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGT ATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTTGAGGAGAAC TTCTAGT This double sfranded DNA loop is bounded on the right by a T2 control element whose identifier is 320. This T2 confrol element has the DNA sequence AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC GAGGAGAACTTCTAGTATATTCTGTA This long T1/T2 double sfranded 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 This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 sfrand that is 3 'UTR to the gene YBL005W-B and has the DNA sequence ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATCCACTATCGTCTAT CAACTAATAGTTATATTATCAATATATTATC ATATACGGTGTTAAGATGAT GACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCA AGGATTGATAATGTAATAGGATAATGAAACATATAAAACGGAATGAGGA ATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCT ATATCCTTGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCC TTTATCAACAATGGAATCCCAACAATTATCTCAACATTC The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 1 whose identifier is 86 contiols 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 The match between the Tl sequence and the C1/C2 sequence is AAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAAT ATAGATTCCATTTTGAGGATTCCTATATCCT The match between the T2 sequence and the C1/C2 sequence is AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC GAGGAGAACTTCTAGTATATTCTGTA A double sfranded DNA loop of length 5.302 kilo-bases on chromosome 7 is bounded on the left by a Tl sequence whose identifier is 2840. This Tl control element has the DNA sequence TCTGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATC AATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGC TGTCATCGAAGTTAGAGGAAGCTGAAACGCAAGGATTGATAATGTAATAG GATCAATGAATATAAACATATAAAACGGAATGAGGAATAATCGTAATATT AGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTCGAGGAG AACTTCTAGTATATTCTGTATACCTAAATTATAGCCTTTATCAACAATGGA ATCCCAACAA 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAA TATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTG TCATCGAAGTTAGAGGAAGCTGAA The match between the T2 sequence and the C1/C2 sequence is CTATCAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGA TGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAA Example of a multi-celled transient connectron - C. elegans 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 I Chromosome 1 110 129 I 125 I 125 Chromosome 1 j Chromosome 5 | 22072 22108 A double sfranded DNA loop of length 18.855 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 110. This Tl control element has the DNA sequence AGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGC This double stranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 129. This T2 confrol element has the DNA sequence TTCTCCCGCATTTTTTGTAGATCTACGTAGATCAAACCGAAATGAGGCACT TTCTGAATCCACGAGCTAGGCTTAAGCTTAGGCTTAAGCTTAGGCCTTTTC TCAGGCTTAGGCTTAGGCTTA This long T1/T2 double sfranded DNA loop modulates the expression of the following genes ZC123.3 ZC123.2 This long T1/T2 double sfranded DNA loop modulates the expression of the following C1/C2 short loops A C1/C2 short loop on chromosome 1 whose identifier is 125 confrols 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 sfrand that is 3'UTR to the gene ZC123.3 and has the DNA sequence ACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATGGCCTAGTTC GGCAAACTCTTTCATTTCAATTTATGAGGGAAGCCAGAA The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 sfrand that is 3'UTR to the gene F58E2.7 and has the DNA sequence CTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTT AGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAG GCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGCT TAAGCTTAGACTTA The match between the Tl sequence and the C1/C2 sequence is AGCTTAGGCTTAAGCTTAGGCTTAAGCTTAGGC The match between the T2 sequence and the C1/C2 sequence is TAGGCTTAAGCTTAGGCTTAAGCTTAGGC A double stranded DNA loop of length 51.031 kilo-bases on chromosome 5 is bounded on the left by a Tl sequence whose identifier is 22072. This Tl control element has the DNA sequence CGCAACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATGACCTA GTTCGGC 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes F36H9.3 F36H9.4 F36H9.5 F36H9.2 F36H9.1 F36H9.6 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 1 whose identifier is 125 confrols 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'UTRto the gene ZC123.3 and has the DNA sequence ACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATGGCCTAGTTC GGCAAACTCTTTCATTTCAATTTATGAGGGAAGCCAGAA The match between the Tl sequence and the C1/C2 sequence is ACGCGCCGTAAATCTACCCCAGATATGGCCGAGCCAAAATG The match between the T2 sequence and the C1/C2 sequence is CGTAAATCTACCCCAGATATGGCCGAGCCAAAATGGCCTAGTTCGGCAAA CTCTT 8. Self-limiting connectrons occur in prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes A class of connectron relationships exist that permit one C1/C2 short loop to contiol 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. Example of a prokaryotic self-limiting connectrons - E. coli 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 I Chromosome 1 | 1704 1718 I 1705 1713 I A double stranded DNA loop of length 15.259 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 1704. This Tl control element has the DNA sequence CGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACT GTTAATCCGTATGTCACTGGT This double sfranded 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 This long T1/T2 double stranded DNA loop modulates the expression of the following genes asnT bl978 bl979 bl980 shiA amn bl983 asnW yeeO asnU This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 A C1/C2 short loop on chromosome 1 whose identifier is 1713 contiols 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 GTC ACTGGTTCGAGTCCAGTCAGAGGAGCCAAATT The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is CGCCCCGTTCACACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACT GTTAATCCGTATGTCACTGGT The match between the T2 sequence and the C1/C2 sequence is TTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTC CAGTCAGAGGAGCCAAATTC A C1/C2 short loop on chromosome 1 whose identifier is 1713 confrols the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single sfrand that is 3'UTR to the gene asnW and has the DNA sequence CACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTAT GTCACTGGTTCGAGTCCAGTCAGAGGAGCCAAATT The match between the Tl sequence and the C1/C2 sequence is CACGATTCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTAT GTCACTGGT The match between the T2 sequence and the C1/C2 sequence is TTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGTC CAGTCAGAGGAGCCAAATT Example of a archea self-limiting connectrons - M. jannaschii 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 * * * I Chromosome 1 | 1447 1471 I 1448 1470 I A double sfranded DNA loop of length 22.675 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 1447. This Tl confrol element has the DNA sequence TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTATGATA 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 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 This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 stiand that is 3 'UTR to the gene MJ1401 and has the DNA sequence TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTATGATAATAAATT CTAATCGATTCGTGACTTAT 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 sfrand that is 3 'UTR to the gene MJ1420 and has the DNA sequence TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTGTGATAATAAATT CTAATCGATTCGTG The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 sfrand that is 3'UTR to the gene MJ1420 and has the DNA sequence TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA , CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTGTGATAATAAATT CTAATCGATTCGTG The match between the Tl sequence and the C1/C2 sequence is TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTT The match between the T2 sequence and the C1/C2 sequence is CAACTAACAACCGTATCGAATTTACCATTACTTGGAAATCTATTTAAAACC TCTTTAATCTTGTGATAATAAATTCTAATCGATTCGTG 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 sfrand that is 3'UTR to ' the gene MJ1401 and has the DNA sequence TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTATGATAATAAATT CTAATCGATTCGTGACTTAT The match between the Tl sequence and the C1/C2 sequence is TTATAGAACATTATGAAGCTTTTTACTCAACTAACAACCGTATCGAATTTA CCATTACTTGGAAATCTATTTAAAACCTCTTTAATCTTATGATA The match between the T2 sequence and the C1/C2 sequence is CAACTAACAACCGTATCGAATTTACCATTACTTGGAAATCTATTTAAAACC TCTTTAATCTT Example of a single-celled self-limiting connectron - S. cervesiae In this example the existence of the T1-T2 (293-320) long loop is conti-olled 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 * * I Chromosome 2 293 320 I 298 I A double stranded DNA loop of length 38.470 kilo-bases on chromosome 2 is bounded on the left by a Tl sequence whose identifier is 293. This Tl control element has the DNA sequence GAATTGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTA TCAATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAA GCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCAAGGATTGATAATGTAAT AGGATAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGT ATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTTGAGGAGAAC TTCTAGT This double stranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 320. This T2 control element has the DNA sequence AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTC GAGGAGAACTTCTAGTATATTCTGTA 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 YBROllC YBR012C This long T1 T2 double sfranded DNA loop modulates the expression of the following C1/C2 short loops 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 YBL005 W-B and has the DNA sequence ATCTATTACATTATGGGTGGTATGTTGGAATAAAAATCCACTATCGTCTAT CAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGATGAT GACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAGTGCA AGGATTGATAATGTAATAGGATAATGAAACATATAAAACGGAATGAGGA ATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCT ATATCCTTGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCC TTTATCAACAATGGAATCCCAACAATTATCTCAACATTC The match between the Tl sequence and the C1/C2 sequence is TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAA TATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTG TCATCGAAGTTAGAGGAAGCTGAAGTGCAAGGATTGATAATGTAATAGGA TAATGAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTA GAAATATAGATTCCATTTTGAGGATTCCTATATCCTTGAGGAGAACTTCTA GT The match between the T2 sequence and the C1/C2 sequence is AATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCT Example of a multi-celled self-limiting connectron - C. elegans 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 * __* * 1 Chromosome 4 1 17154 17190 | 17155 A double sfranded DNA loop of length 89.919 kilo-bases on chromosome 4 is bounded on the left by a Tl sequence whose identifier is 17154. This Tl confrol element has the DNA sequence AAATTTCCGGCAAATCGGCAAACTGGCAA This double stranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 17190. This T2 confrol element has the DNA sequence AATTTGCCGATTTGCCGAATTTGTCGACA 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 This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 sfrand that is 3 'UTR to the gene R08C7.1 and has the DNA sequence AAATTTCCGGCAAATCGGCAAACTGGCAATTTGCCGATTTGCCGAATTTGT CGACA 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 ZK 180.2 and has the DNA sequence TGGAAATTTCAGAATTTCAATTTTAATCGGCAAAATTGTACGCATCCTATG AATTT The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 4 whose identifier is 17155 confrols 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 The match between the Tl sequence and the C1/C2 sequence is AAATTTCCGGCAAATCGGCAAACTGGCAA The match between the T2 sequence and the C1/C2 sequence is AATTTGCCGATTTGCCGAATTTGTCGACA 9. Geneless connectrons exist in single-celled and multi-celled eukaryotes 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. Example of a single-celled geneless connectron - S. cervesiae 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 I Chromosome 4 | 1537 1559 I 1538 through 1558 | A double stranded DNA loop of length 4.825 kilo-bases on chromosome 4 is bounded on the left by a Tl sequence whose identifier is 1537. This Tl control element has the DNA sequence ATGAGATATATGTGGGTAATTAGATAATTGTTGGGATTCCATTGTTGATAA AGGCTATAATATTAGGTATACAGAATATACTAGAAGTTCTCCTCGAGGAT TTAGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTATAAATAT TATTATCATCGTTTTATATGTTAATATTCATTGATCCTATTACATTATCAAT CCTTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGT CATCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATACTAGTTA GTAGATGATAGTTGATTTTTATTCCAACATACCACCCATAATGTAATAGAT CTAAT This double sfranded 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 GTAGATG ATAGTTGATTTTTATTCCAACATACCACCCATAATGTAATAGAT CTAAT There are no genes controlled by this T1/T2 loop. This long T1/T2 double sfranded DNA loop modulates the expression of the following C1/C2 short loops 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 This T1-T2 loop also modulates the C1/C2 short loops numbered 1539 to 1557 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 9 whose identifier is 3789 confrols the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single sfrand that is 3'UTR to the gene YIL059C and has the DNA sequence TTTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCA GCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACA CCGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAG TTGATTTTTATTCCAACAGTAT The match between the Tl sequence and the C1/C2 sequence is TTTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCA GCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACA CCGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAG TTGATTTTTATTCCAACA The match between the T2 sequence and the C1/C2 sequence is TTTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCA GCTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACA CCGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAG TTGATTTTTATTCCAACA 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 sfrand that is 3'UTR to the gene YLR301W and has the DNA sequence GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA TTAGGTATGTAGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCAT AAAAGGGAATCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTT TTATATGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAG CTTCCACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACAC CGTATATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGT TGATTTTTATTCCAACAC The match between the Tl sequence and the C1/C2 sequence is AGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAA TCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTTTTATATGTTA ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT CCAACA The match between the T2 sequence and the C1 C2 sequence is AGGATTTAGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTATA AATATTATTATCATCGTTTTATATGTTAATATTCATTGATCCTATTACATTA TCAATCCTTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCATT TGCGTCATCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATACT AGTTAGTAGATGATAGTTGATTTTTATTCCAACA A C1/C2 short loop on chromosome 13 whose identifier is 5753 conti-ols the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single stiand that is 3 'UTR to the gene YMR044W and has the DNA sequence TTGAGAAATGGGGGAATGTTGAGATAATTGTTGGGATTCCATTGTTGATA AAGGCTATAATATTAGGTATACAGAATATACTAGAAGTTCTCCTCAAGGA TATAGGAATCCTCAAAATGGAATCTATATTTCTACATACTAATATTACGAT TATTCCTCATTCCGTTTTATATGTTTCATTATCCTATTACATTATCAATCCT TGCACTTCAGCTTCCTCTAACTTCGATGACAGCTTCTCATAACTTATGTCA TCATCTTAACACCGTATATGATAATATATTGATAATATAACTATTAGTTGA TAGACGATAGTGGATTTTTATTCCAACAT The match between the Tl sequence and the C1/C2 sequence is AGATAATTGTTGGGATTCCATTGTTGATAAAGGCTATAATATTAGGTATAC AGAATATACTAGAAGTTCTCCTC The match between the T2 sequence and the C1/C2 sequence is TTGTTGGGATTCCATTGTTGATAAAGGCTATAATATTAGGTATACAGAATA TACTAGAAGTTCTCCTCAAGGAT Two examples of multi-celled geneless connectrons - C. elegans 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 * * * ■ I Chromosome 1 | 2342 2344 I 2343 I 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 I Chromosome 5 | 29221 29262 I 29222 through 29261 | A double stranded DNA loop of length 67.059 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 2342. This Tl control element has the DNA sequence TGAAAACTACAGTAATTCTTTAAATGACTACTGTAGC 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 CTACTGTAGCGCTTGTGTCGATTTACGGGCTCGATTT There are no genes controlled by this T1/T2 loop. This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops A C1/C2 short loop on chromosome 1 whose identifier is 2343 confrols 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 5 whose identifier is 24114 confrols 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 The match between the Tl sequence and the C1/C2 sequence is GAAAACTACAGTAATTCTTTAAATGACTACTGTAGC The match between the T2 sequence and the C1/C2 sequence is CTACTGTAGCGCTTGTGTCGATTTACGGGCTCGATTT A double sfranded DNA loop of length 41.297 kilo-bases on chromosome 5 is bounded on the left by a Tl sequence whose identifier is 29221. This Tl confrol element has the DNA sequence TTTAAATTTCCCGCCAAAAATTGACTGAAAATTTGGATTTTCTTTCCAAAA ATTGACAGAAA This double stranded DNA loop is bounded on the right by a T2 control element whose identifier is 29262. This T2 confrol element has the DNA sequence TGAAAATTTGAATTTCCCGCCAAAAATTAAC There are no genes controlled by this T1/T2 loop. This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops A C1/C2 short loop on chromosome 5 whose identifier is 29222 confrols 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 This T1-T2 loop also modulates the C1/C2 short loops numbered 29223 to 29260 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is TTTAAATTTCCCGCCAAAAATTGACTGAAAATTTG The match between the T2 sequence and the C1/C2 sequence is AAAAAAATTGACTGAAAATTTGAATTTCCCGCCAAAAATTGA 10. One connectron controls many geneless connectrons in single-celled and multi-celled eukaryotes One C1/C2 short loop can control the existence of many geneless T1-T2 long loops. Example of a single-celled geneless connection - S. cervesiae 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 * I * * J Chromosome 4 | 1142 1156 I 1143 through 1155 ] 5289 Chromosome 12 I * * * I Chromosome 4 | 1243 1272 I 1244 through 1271 | 5289 Chromosome 12 I I Chromosome 5 | 7102 7117 ] 7103 through 7116 | A double stranded DNA loop of length 5.337 kilo-bases on chromosome 4 is bounded on the left by a Tl sequence whose identifier is 1142. This Tl control element has the DNA sequence ATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATATTAGG TATGTAGATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAG GGAATCTGCAATTCTACACAATTCTATAAATATTATTATCATCATTTTATA TGTTAATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCC ACTAATTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTAT ATGATAATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTT TTATTCCAACA 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 TTTTAATAAGGC AATAATATTAGGTATGTAGATATACTAGAAGTTCTCCTC CAGGATTTAGGAATCCATAAAAGGGAATCTGCAATTCTACACAATTCTAT AAATATTATTATCATCATTTTATATGTTAATATTCATTGATCCTATTACATT ATCAATCCTTGCGTTTCAGCTTCCACTAATTTAGATGACTATTTCTCATCAT TTGCGTCATCTTCTAACACCGTATATGATAATATACTAGTAACGTAAATAC TAGTTAGTAGATGATAGTTG ATTTTTATTCC AAC A AGAA There are no genes controlled by this T1/T2 loop. This long T1/T2 double stranded DNA loop modulates the expression of the following C 1/C2 short loops 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 This T1-T2 loop also modulates the C1/C2 short loops numbered 1144 to 1154 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 CGTATATGATAATATACTAGTACGTAAATACTAGTTAGTAGATQATAGTT GATTTTTATTCCAACAC The match between the Tl sequence and the C1/C2 sequence is ATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATATTAGG TATGTAGA The match between the T2 sequence and the C1/C2 sequence is TTTTAATAAGGCAATAATATTAGGTATGTAGA A double stranded DNA loop of length 5.251 kilo-bases on chromosome 4 is bounded on the left by a Tl sequence whose identifier is 1243. This Tl control element has the DNA sequence CGTGTTTTATCTCATGTTGTTCGTTTTGTTATTGAGATATATGTGGGTAATT AGATAATTGTTGGGATTCCATTGTTGATAAAGGCTATAATATTAGGTATAC AGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAA TCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTTTTATATGTTA ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT CCAACA 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 There are no genes controlled by this T1/T2 loop. This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 This T1-T2 loop also modulates the C1/C2 short loops numbered 1245 to 1270 A C1/C2 short loop on chromosome 4 whose identifier is 1271 confrols 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 GTTACTTCTAAGGAAGTCCACACAAATCAAGATCCGTTAGACGTTTCAGC TTCCAAAA The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is AGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAA TCTGCAATTCTACAC AATTCTATAAATATTATTATCATCGTTTTATATGTTA ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT CCAACA The match between the T2 sequence and the C1/C2 sequence is AGAATATACTAGAAGTTCTCCTCGAGGATTTAGGAATCCATAAAAGGGAA TCTGCAATTCTACACAATTCTATAAATATTATTATCATCGTTTTATATGTTA ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT CCAACA „ ^ , PCT/US01/16471 A double stranded DNA loop of length 5.296 kilo-bases on chromosome 15 is bounded on the left by a Tl sequence whose identifier is 7102. This Tl confrol element has the DNA sequence CATGATTAATATGACCAATCGGCGTGTGTTTTTGAAAAGTGGGTGAATTTT GAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATATTAGGTATGT AGAATGTACTAGAAGTTCTCCTCAAGGATTTAGGAATCCATGAAAGGGAA TCTGCAATTCTACACAATTCTATAAATATTATTATCATCATTTTATATGTTA ATATTCATTGATCCTATTACATTATCAATCCTTGCGTTTCAGCTTCCACTAA TTTAGATGACTATTTCTCATCATTTGCGTCATCTTCTAACACCGTATATGAT AATATACTAGTAACGTAAATACTAGTTAGTAGATGATAGTTGATTTTTATT CCAACA 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 There are no genes controlled by this T1/T2 loop. This long T1/T2 double stranded DNA loop modulates the expression of the following C 1/C2 short loops 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 AATGAATATTAAC ATATAAAATGATGATAATAATATTTATAGAATTGTGT AGAATTGCAGATTCCCTTTCATGGATTCCTAAATCCTTGAGGAGAACTTCT AGTA This T1-T2 loop also modulates the C1/C2 short loops numbered 7104 to 7115 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1/C2 sequence is GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA TTAGGTATGTAGAAT The match between the T2 sequence and the C1/C2 sequence is GGTGAATTTTGAGATAATTGTTGGGATTCCATTTTTAATAAGGCAATAATA TTAGGTATGTAGAAT Example of a multi-celled geneless connectron - C. elegans 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 I Chromosome 4 | 1142 1156 I 3103 through 3119 | 16760 Chromosome 4 I Chromosome 4 | 14840 15042 I 14841 through 15041 ] 16760 Chromosome 4 I Chromosome 5 j 15365 15627 I 15366 through 15625 | A double sfranded DNA loop of length 15.894 kilo-bases on chromosome 1 is bounded on the left by a Tl sequence whose identifier is 3101. This Tl control element has the DNA sequence CAAATCGGCAAATTGCCGGAATTGAACATTTCC This double stranded DNA loop is bounded on the right by a T2 control element wfrose identifier is 3120. This T2 confrol element has the DNA sequence AAACGATTTTTCCGGCAAATCGGCAAATTGCCGGAATTGTAATTTCCGGC AAAT There are no genes controlled by this T1/T2 loop. This long T1/T2 double stranded DNA loop modulates the expression of the following C1/C2 short loops 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 This T1-T2 loop also modulates the C1/C2 short loops numbered 3104 to 3118 • A C1/C2 short loop on chromosome 1 whose identifier is 3119 confrols 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. A C1/C2 short loop on chromosome 4 whose identifier is 16760 confrols the expression of the genes in this T1/T2 long loop. This C1/C2 short loop is expressed as a RNA single sfrand that is 3'UTR to the gene T23E1.2 and has the DNA sequence GGCAAATTGCCGAAATTGAACATTTCCGGCAAATCGGCAAATTGCCGGAA TTGAACATTTCCGGCAAATCGGCAAATTGCCGGAATTGAACATTTCCGGC AAATCGGCAAATTGCCGGAATTGA The match between the Tl sequence and the C1/C2 sequence is CAAATCGGCAAATTGCCGGAATTGAACATTTCC The match between the T2 sequence and the C1/C2 sequence is TTTCCGGCAAATCGGCAAATTGCCGGAATTG A double stranded DNA loop of length 86.977 kilo-bases on chromosome 3 is bounded on the left by a Tl sequence whose identifier is 14840. This Tl control element has the DNA sequence AAAAATTTCCGGCAAGTCGGCAATTTTCCGAAAATGAAAATTTCCGGCAA ATCGGCAAATTGCCGGAATTGAAAATTCCTGGCAAATCAGCAAATTTGCG GCAAATCGGCAATTfGCCGAAAATGAAAATTTCCGGCAAAT 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 There are no genes controlled by this T1/T2 loop. This long T1/T2 double stianded DNA loop modulates the expression of the following C 1/C2 short loops 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 AAAAATTTCCGGCAAGTCGGCAATTTTCCGAAAATGAAAATTTCCGGCAA ATCGGCAAATTGCCGGAATTGAAAATTCCTGGCAAATCAGCAAATTTGCG GCAAATCGGCAATTTGCCGAAAATGAAAATTTCCGGCAAAT This T1-T2 loop also modulates the C1/C2 short loops numbered 14842 to 15040 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 The match between the Tl sequence and the C1 C2 sequence is ATTTCCGGCAAATCGGCAAATTGCCGGAATTGAA The match between the T2 sequence and the C1/C2 sequence is TGAACATTTCCGGCAAATCGGCAAATTGC A double stranded DNA loop of length 98.488 kilo-bases on chromosome 3 is bounded on the left by a Tl sequence whose identifier is 15365. This Tl control element has the DNA sequence AAAATTTCCGGCAAATCGGCAATTTGCCAAAAATTGAAATTTCCGGCAAA TCGGCAATTTGTCAAAAATGAAAATTTCCGGCAAATCGGCAAATTGCCGA AAATGAAAATTTCCGGCAAATCGGCAAACTTCCGGAACTGAAAATTTCCG GCAAATCGGCAATTTGCCATAAATGAACATTTCCGG...GGCGAAAATTAAA ATTTCCGCCATATCGGCAATTTGCCAAAAAATTAAAATTTCCGGCAAATC GGCAAATTGCCGGAATTCAAAATTTCCGGCAAACCGGCAAATTGCCGGAA CTCAAAATTCCCGGCAAATCAGCAAATTGCCGGAATT This double stranded DNA loop is bounded on the right by a T2 confrol element whose identifier is 15627. This T2 control element has the DNA sequence TGGCAAACCGGCAAATTGCCGGAATTGAACATTTCCGGCAAATCGGCAAT TTGCCGGAATTGAAATTT There are no genes controlled by this T1/T2 loop. This long T1/T2 double sfranded DNA loop modulates the expression of the following C1/C2 short loops A C1/C2 short loop on chromosome 3 whose identifier is 15366 confrols 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 This T1-T2 loop also modulates the C1/C2 short loops numbered 15366 to 15624 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 The expression of genes in this T1/T2 long loop is controlled by the following C1/C2 short loops. 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 sfrand that is 3 'UTR to the gene T23E1.2 and has the DNA sequence GGCAAATTGCCGAAATTGAACATTTCCGGCAAATCGGCAAATTGCCGGAA TTGAACATTTCCGGCAAATCGGCAAATTGCCGGAATTGAACATTTCCGGC AAATCGGCAAATTGCCGGAATTGA The match between the Tl sequence and the C1/C2 sequence is ATTTCCGGCAAATCGGCAAATTGCCGGAATT The match between the T2 sequence and the C1/C2 sequence is CGGCAAATTGCCGGAATTGAACATTTCCGGCAAATCGGCAA

Claims: Claims What is claimed is: 1. 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. 2. 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. 3. 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. 4. 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. 5. A method of detecting where and when new genes are being integrated into a host genome comprising detecting the connections in said host genome. 6. 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. 7. A method of modifying a given body comprising modifying the connectron organization therein. 8. A method of detecting connectron control and target sequences in a given genome comprising: determining the base composition of said genome, determining one or more sites of confrol sequence organization, and/or determining one or more sites of target application. 9. A method of determining the response of a cell in any tissue to changes in the cell'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. 10. In prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the tetradic relationship T1=C1 and T2=C2 where Tl and T2 are DNA sequences 20 or more bases in length, where the Cl sequence is adjacent to the C2 sequence, where the Tl and T2 sequences are on the same chromosome, and where the C1/C2 sequences are on the same chromosome as Tl and T2 or where the C1/C2 sequences are on a chromosome different from Tl and T2, wherein: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative sfrand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative sfrand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. 11. In prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the connecfron 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative sfrand DNA sequence of 540 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative sfrand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2. sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. . 12. In prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the connecfron relationship that permits one C1/C2 short loop to contiol 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same, chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. ,13. 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 MPl plasmid, wherein: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, I C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative stiand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. 14. The connectron relationships that exist in plant and higher animals. 15. 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1 C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative stiand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, T2 sequence - any positive or negative stiand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart, and 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. 16. In prokaryotes, archea, single-celled eukaryotes and multi-celled eukaryotes, the connecfron 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 confrol by another T1-T2 long loop which surrounds it, wherein: Cl sequence - any positive or negative sfrand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. 17. 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: Cl sequence - any positive or negative strand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative sfrand DNA sequence of 50 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative sfrand DNA sequence of 20bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative sfrand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart. 18. The connectron relationship that do not have any genes within the T1-T2 long loop, wherein: Tl 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 T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, and the T2 or Tl sequences must be between about lkb and 105kb apart. 19. The geneless connectron relationship where one C1/C2 short loop controls the existence of many geneless T1-T2 long loops, wherein: Cl sequence - any positive or negative sfrand DNA sequence of 20 bases or more, the C2 sequence must occur in the same chromosome as the Cl sequence, C2 sequence - any positive or negative strand DNA sequence of 20 bases or more, the Cl sequence must occur in the same chromosome as the C2 sequence, C1/C2 - any positive or negative strand DNA sequence of 40 or more bases such that the Cl sequence is adjacent to the C2 sequence, Tl sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the T2 sequence, the Tl and T2 sequences must be between about lkb and 105kb apart, and T2 sequence - any positive or negative strand DNA sequence of 20 bases or more that is on the same chromosome as the Tl sequence, the T2 or Tl sequences must be between about lkb and 105kb apart.

Inventors: FELDMANN RICHARD J, FELDMANN, RICHARD, J.
Applicants: GLOBAL DETERMINANTS INC, GLOBAL DETERMINANTS, INC.
Application year: 2001
Main classification: C12N
IPC codes: C12N15, C12Q1, G06F19