bluuebunny/crossref_metadata_2025 huggingface dataset:
Ecdysone coordinates the timing and amounts of E74A and E74B transcription in Drosophila.
Authors: Karim F D , Thummel C S
Published: June 2007

Pulses of the steroid hormone ecdysone function as temporal signals to coordinate the development of both larval and adult tissues in Drosophila. Ecdysone acts by triggering a genetic regulatory hierarchy that can be visualized as puffs in the larval polytene chromosomes. In an effort to understand how the ecdysone signal is transduced to result in sequential gene activation, we are studying the transcriptional control of E74, an early gene that appears to play a regulatory role in the hierarchy. Northern blot analysis of RNA isolated from staged animals or cultured organs was used to characterize the effects of ecdysone on E74 transcription. Ecdysone directly activates both E74A and E74B promoters. E74B mRNA precedes that of E74A, each mRNA appearing with delay times that agree with their primary transcript lengths and our previous transcription elongation rate measurement of approximately 1.1 kb/min. The earlier appearance of E74B transcripts is enhanced by its activation at an approximately 25-fold lower ecdysone concentration than E74A. E74B is further distinguished from E74A by its repression at a significantly higher ecdysone concentration than that required for its induction, close to the concentration required for E74A activation. These regulatory properties lead to an ecdysone-induced switch in E74 expression, with an initial burst of E74B transcription followed by a burst of E74A transcription. We also show that the patterns of ecdysone-induced E74A and E74B transcription vary in four ecdysone target tissues. These studies provide a means to translate the profile of a hormone pulse into different amounts and times of regulatory gene expression that, in turn, could direct different developmental responses in a temporally and spatially regulated manner.
Complex pattern of immunoglobulin mu gene expression in normal and transgenic mice: nonoverlapping regulatory sequences govern distinct tissue specificities.
Authors: Jenuwein T , Grosschedl R
Published: June 2007

Analysis of normal mice and transgenic mice carrying a rearranged immunoglobulin mu gene revealed a more complex tissue-specific pattern of mu gene expression than anticipated from previous observations. Expression of the endogenous mu locus and the mu transgene was detected both in lymphoid tissues and in skeletal muscle. Analysis of the expression pattern of mu transgenes containing intragenic deletions or point mutations in binding sites for Oct transcription factors (OCTA sites) indicated that distinct regulatory sequences control lymphoid- and muscle-specific mu gene expression. Consistent with previous transfection experiments, mu gene expression in lymphoid tissues is dependent on the intragenic enhancer and the OCTA site in the promoter. However, neither of these regulatory sequences is required for mu gene expression in skeletal muscle that is governed by a muscle-specific control region located 3' of the enhancer. An "off-state" of the mu transgene was observed only in liver and embryonal fibroblasts, whereas enhancer-dependent mu transgene expression was detected at low levels in other nonlymphoid tissues. From these data we suggest a model for the regulation of tissue-specific mu gene expression in which a "ubiquitous" competence for basal transcription is up-regulated in lymphoid and muscle tissues by distinct cell type-specific regulatory sequences and down-regulated in liver and fibroblastic cells by putative negative sequence elements.
Transformation of sensory organ identity by ectopic expression of Cut in Drosophila.
Authors: Blochlinger K , Jan L Y , Jan Y N
Published: June 2007

The loss of cut activity results in a change in neural identity in the peripheral nervous system so that the neurons and support cells of external sensory (es) organs are transformed into those of internal chordotonal (ch) organs, cut encodes a large nuclear homeo domain protein (Cut) that is expressed in the differentiated cells of es organs and their precursors but not in the cells of ch organs. We now analyze the effects of ectopic Cut expression in transformant lines of flies containing the Cut-coding sequences under inducible regulatory control. We demonstrate that ubiquitous Cut expression in embryos results specifically in the morphologic and antigenic transformation of ch organs into es organs. This effect appears to involve positive autoregulation of Cut expression. We conclude that Cut is not only necessary but sufficient for the specification of es organ identify in sensory organ precursor cells and their progeny. The specificity of Cut function to sensory organ cells involves the proneural loci daughterless and the achaete-scute complex.
Characterization of cDNAs encoding the polypyrimidine tract-binding protein.
Authors: Gil A , Sharp P A , Jamison S F , Garcia-Blanco M A
Published: June 2007

The polypyrimidine tract of mammalian introns is recognized by a 62-kD protein (pPTB). Mutations in the polypyrimidine tract that reduce the binding of pPTB also reduce the efficiency of formation of the pre-spliceosome complex containing U2 snRNP. The PTB protein was purified to homogeneity by affinity chromatography on a matrix containing poly(U), and peptide sequence was used to isolate several cDNAs. Because a variety of cell types express mRNA complementary to these cDNAs, PTB may be a ubiquitous splicing factor. Three classes of cDNAs were identified, on the basis of the presence of additional sequences at an internal position. This variation in sequence probably reflects alternative splicing of the PTB pre-mRNA and produces mRNAs encoding the prototype PTB protein, a form of PTB protein containing 19 additional residues, and a truncated form of PTB protein with a novel carboxyl terminus. A murine homolog of pPTB has been characterized previously as a DNA-binding protein. Sequence comparisons indicate that pPTB is distantly related to the hnRNP L protein and that these two proteins should be considered as members of a novel family of RNA-binding proteins.
Nuclear RNase MRP processes RNA at multiple discrete sites: interaction with an upstream G box is required for subsequent downstream cleavages.
Authors: Karwan R , Bennett J L , Clayton D A
Published: June 2007

RNase MRP is a site-specific endoribonuclease that processes primer RNA from the leading-strand origin of mammalian mitochondrial DNA replication. It is present in active form as isolated from the nucleus, suggesting a bipartite cellular location and function. The relatively high abundance of nucleus-localized RNase MRP has permitted its purification to near homogeneity and, in turn, has led to the identification of protein components of this ribonucleoprotein. Analysis of the mode of RNA cleavage by nuclear RNase MRP revealed the surprising and unprecedented ability of the endonuclease to process RNA at multiple discrete locations. Substrate cleavage is dependent on the presence of a previously described G-rich sequence element adjacent to the primary site of RNA processing. Downstream cleavage occur in a distance- and sequence-specific manner.
Effect of RNA secondary structure on polyadenylation site selection.
Authors: Brown P H , Tiley L S , Cullen B R
Published: June 2007

Functional polyadenylation [poly(A)] sites consist of two sequence elements, the AAUAAA and G/U box signals, that closely flank the site of mRNA 3'-end formation. In agreement with previous results, random sequence insertions between the AAUAAA and G/U box signals were observed to inhibit poly(A) site function. However, sequence insertions of similar size that were predicted to form RNA stem-loop structures were found to have little effect on the efficiency of polyadenylation and instead induced a 3' shift in the site of polyadenylation that was equal to the length of the inserted stem-loop. The in vivo utilization of a poly(A) site bearing an internal RNA stem-loop structure was inhibited by mutations that destabilized the predicted stem but was restored by compensatory mutations. These results strongly support the hypothesis that the appropriate spacing of the AAUAAA and G/U box signals is critical for poly(A) site function. Sequence insertions that are able to form RNA secondary structures that maintain the correct spacing of these two RNA target sequences are well tolerated, whereas sequence insertions that disturb this spacing inhibit poly(A) site recognition. It is proposed that the effect of sequence insertions on poly(A) site function may be sufficiently predictable to allow the development of an assay for in vivo RNA secondary structure that uses poly(A) site selection as a readout.
Expression of a retinoic acid response element-hsplacZ transgene defines specific domains of transcriptional activity during mouse embryogenesis.
Authors: Rossant J , Zirngibl R , Cado D , Shago M , Giguère V
Published: June 2007

Treatment with retinoic acid (RA) is known to produce complex teratogenic effects in vertebrates, and its presence in the developing embryo as an endogenous substance has led to the suggestion that RA might be a natural morphogenetic agent. Although our understanding of the molecular mechanism of RA action has improved considerably with the identification of nuclear receptors for RA (RARs) and RA-responsive genes, the exact relationship between the proposed morphogenetic activity of RA and its teratogenic effects remains to be characterized. Here, we show that a RA response element (RARE) present in the RAR beta gene can direct specific spatial and temporal expression of an hsplacZ transgene during mouse embryogenesis. In the early embryo, the transgene is expressed in a specific anterior-posterior domain that is completely obliterated by treatment of pregnant mice with teratogenic doses of RA. The expression of the transgene becomes more restricted as organogenesis progresses and mimics closely the reported expression of the RAR beta gene. These results suggest that, in vivo, some of the morphogenetic effects of RA could be mediated through localized transcriptional activity controlled by the various RARs. The specific pattern of expression of the RAREhsplacZ transgene does not correlate with the proposed sites of action of RA as defined by its teratogenic effects but does support a role for RA in early anterior-posterior patterning along the body axis.
T-lymphocyte development in scid mice is arrested shortly after the initiation of T-cell receptor delta gene recombination.
Authors: Carroll A M , Bosma M J
Published: June 2007

Scid mice lack functional lymphocytes because they carry a mutation that impairs rearrangement of immunoglobulin and T-cell receptor (TCR) genes. Rearrangement of TCR delta, but not gamma and beta genes, was routinely observed in DNA of scid thymocytes and thymocyte hybridomas. TCR delta gene rearrangements appeared to involve D delta 1, D delta 2, and J delta 1 elements only; rearrangement of elements upstream of D delta 1 (e.g., V delta 1) was not observed, and transcripts corresponding to fully assembled TCR delta genes (VDJ delta or VDDJ delta) were not detected in RNA from scid thymocytes. These findings suggest that D delta 1, D delta 2, and J delta 1 may be among the first TCR gene elements to undergo recombination and that scid T-lineage cells are developmentally arrested during or shortly after this stage of differentiation. One class of TCR delta recombination fragments (D delta 2-J delta 1) was amplified by the polymerase chain reaction (PCR) and cloned, and the recombination junctions were sequenced. Most fragments showed normal coding joints. Interestingly, five of seven coding joints that lacked N insertions showed evidence of recombination between short stretches (2-3 bp) of homologous sequence. As discussed, the general absence of V delta-, J gamma-, and J beta-associated rearrangements, despite the occurrence of normal D delta 2-J delta 1 rearrangements, raises the possibility that the scid mutation may cause premature cessation of TCR gene recombination and thereby arrest early T-cell development.
Muscle-specific transcriptional activation by MyoD.
Authors: Weintraub H , Dwarki V J , Verma I , Davis R , Hollenberg S , Snider L , Lassar A , Tapscott S J
Published: June 2007

We focus on the mechanism by which MyoD activates transcription. Previous experiments showed that when the 13-amino-acid basic region of E12 replaced the corresponding basic region of MyoD, the resulting MyoD-E12Basic chimeric protein could bind specifically to muscle-specific enhancers in vitro and form dimers with E12, but could not activate a cotransfected reporter gene or convert 10T1/2 cells to muscle. Here we show that back mutation of this chimeric protein (with the corresponding residues in MyoD) re-establishes activation, and we identify a specific alanine involved in increasing DNA binding and a specific threonine required for activation. Using a reporter gene containing MyoD-binding sites located downstream from the transcription start site, we show that MyoD-E12Basic can bind in vivo and thereby inhibit expression of the reporter. In vivo binding is also supported by the fact that the addition of the "constitutive" VP16 activation domain to MyoD-E12Basic restores full trans-activation potential. The normal MyoD-activation domain maps within the amino-terminal 53 residues and can be functionally replaced by the activation domain of VP16. The activity of the MyoD-activation domain is dramatically elevated when deletions are made almost anywhere in the rest of the MyoD molecule, suggesting that the activation domain in MyoD is usually masked. Surprisingly, MyoD-E12Basic can activate transcription in CV1 and B78 cells (but not in 10T1/2 or 3T3 cells), suggesting that the activation function of the basic domain requires a specific factor present in CV1 and B78 cells. We propose that to function, the masked MyoD-activation domain requires the participation of a second factor that recognizes the basic region. We refer to such a factor as a recognition factor.
Multiple trans-splicing events are required to produce a mature nad1 transcript in a plant mitochondrion.
Authors: Conklin P L , Wilson R K , Hanson M R
Published: June 2007

The mitochondrial gene encoding NADH dehydrogenase subunit 1 (nad1) in Petunia hybrida is split into five exons, a, b, c, d, and e. With the use of a complete restriction map of the 443-kb Petunia mitochondrial genome, we have cloned these exons and mapped their location. Exon a is located 130 kb away from and in the opposite orientation from exons b and c. Exon d maps 95 kb away and in the opposite orientation from exons b and c. Exons d and e are separated by 190 kb. By performing the polymerase chain reaction on Petunia cDNAs, we have shown that transcripts from these five exons are joined via a series of cis- and trans-splicing events to create a mature nad1 transcript. In addition, we have found 23 C----U RNA edit sites in Petunia nad1. RNA editing changes 19 of the amino acids predicted by the genomic sequence.
U1 snRNP can influence 3'-splice site selection as well as 5'-splice site selection.
Authors: Goguel V , Liao X L , Rymond B C , Rosbash M
Published: June 2007

To address the mechanisms that underlie splice site selection and splice site partner assignment, we analyzed the splicing of yeast (Saccharomyces cerevisiae) transcripts containing splice site region duplications. When the 5'-splice site region was duplicated, both sites were utilized to the same extent, indicating little or no influence of proximity on 5'-splice site choice. However, the effect of a 5'-mutant site was greatly enhanced by the presence of an adjacent wild-type site, and this effect was reversed by the restoration of base-pairing with U1 snRNA. 3'-Splice site choice was apparently influenced by proximity, as the site closest to the 5'-splice site was greatly preferred. Studies with strains carrying some U1 snRNA mutations showed an increase in the use of the distal 3'-splice site, indicating a role for U1 snRNP in 3'-splice site selection. The data are compared with those from mammalian splice site choice experiments and suggest mechanisms that influence differential splice site choice as well as exon skipping.
The cloned RNA polymerase II transcription factor IID selects RNA polymerase III to transcribe the human U6 gene in vitro.
Authors: Lobo S M , Lister J , Sullivan M L , Hernandez N
Published: June 2007

Although the human U2 and U6 snRNA genes are transcribed by different RNA polymerases (i.e., RNA polymerases II and III, respectively), their promoters are very similar in structure. Both contain a proximal sequence element (PSE) and an octamer motif-containing enhancer, and these elements are interchangeable between the two promoters. The RNA polymerase III specificity of the U6 promoter is conferred by a single A/T-rich element located around position -25. Mutation of the A/T-rich region converts the U6 promoter into an RNA polymerase II promoter, whereas insertion of the A/T-rich region into the U2 promoter converts that promoter into an RNA polymerase III promoter. We show that this A/T-rich element can be replaced by a number of TATA boxes derived from mRNA promoters transcribed by RNA polymerase II with little effect on RNA polymerase III transcription. Furthermore, the cloned RNA polymerase II transcription factor TFIID both binds to the U6 A/T-rich region and directs accurate RNA polymerase III transcription in vitro. Mutations in the U6 A/T-rich region that convert the U6 promoter into an RNA polymerase II promoter also abolish TFIID binding. Together, these observations suggest that in the human snRNA promoters, unlike in mRNA promoters, binding of TFIID directs the assembly of RNA polymerase III transcription complexes, whereas the lack of TFIID binding results in the assembly of RNA polymerase II snRNA transcription complexes.
Promoter traps in embryonic stem cells: a genetic screen to identify and mutate developmental genes in mice.
Authors: Friedrich G , Soriano P
Published: June 2007

A general strategy for selecting insertion mutations in mice has been devised. Constructs lacking a promoter and including a beta-galactosidase gene, or a reporter gene encoding a protein with both beta-galactosidase and neomycin phosphotransferase activity, were designed so that activation of the reporter gene depends on its insertion within an active transcription unit. Such insertion events create a mutation in the tagged gene and allow its expression to be followed by beta-galactosidase activity. Introduction of promoter trap constructs into embryonic stem (ES) cells by electroporation or retroviral infection has led to the derivation of transgenic lines that show a variety of beta-galactosidase expression patterns. Intercrossing of heterozygotes from 24 strains that express beta-galactosidase identified 9 strains in which homozygosity leads to an embryonic lethality. Because no overt phenotype was detected in the remaining strains, these results suggest that a substantial proportion of mammalian genes identified by this approach are not essential for development.
A family of C/EBP-related proteins capable of forming covalently linked leucine zipper dimers in vitro.
Authors: Williams S C , Cantwell C A , Johnson P F
Published: June 2007

Mouse and rat genomic DNA libraries were screened by reduced stringency hybridization with the DNA-binding domain of the c/ebp gene as a probe. Three genes were isolated that encode bZIP DNA-binding proteins (designated CRP1, CRP2, and CRP3) with strong amino acid sequence similarities to the C/EBP-binding domain. CRP2 is identical to the protein described recently by other groups as NF-IL6, LAP, IL-6DBP, and AGP/EBP, whereas CRP1 and CRP3 represent novel proteins. Several lines of evidence indicate that these three proteins, along with C/EBP, comprise a functional family. Each bacterially expressed polypeptide binds to DNA as a dimer with recognition properties that are virtually identical to those of C/EBP. Every member also bears a conserved cysteine residue at or near the carboxyl terminus, immediately following the leucine zipper, that at least in vitro allows efficient disulfide cross-linking between paired zipper helices. We developed a gel assay for covalent dimers to assess leucine zipper specificities among the family members. The results demonstrate that all pairwise combinations of dimer interactions are possible. To the extent that we have examined them, the same heterodimeric complexes can be detected intracellularly following cotransfection of the appropriate pair of genes into recipient cells. All members are also capable of activating in vivo transcription from promoters that contain a C/EBP-binding site. Our findings indicate that a set of potentially interacting C/EBP-like proteins exists, whose complexity is comparable to that of other bZIP protein subfamilies such as Jun, Fos, and ATF/CREB.
twist and snail as positive and negative regulators during Drosophila mesoderm development.
Authors: Leptin M
Published: June 2007

twist and snail are members of the helix-loop-helix and zinc-finger protein families, respectively, and determine the development of the mesoderm in Drosophila. This paper analyzes their role in mesoderm development by examining how they affect the expression of downstream genes. twist and snail act by regulating gene expression in the mesoderm and in neighboring regions, and have distinct roles in this process. snail prevents expression in the mesoderm of genes that are destined to be active only in more lateral or dorsal regions. twist is required for the activation of downstream mesodermal genes. twist is also required for the full expression of snail and for the maintenance of its own expression. Only the absence of both twist and snail results in the complete loss of all mesodermal characteristics.
Neuroectoderm in Drosophila embryos is dependent on the mesoderm for positioning but not for formation.
Authors: Rao Y , Vaessin H , Jan L Y , Jan Y N
Published: June 2007

By studying neuroectoderm formation in the absence of mesoderm and mesectoderm in mutants of the zygotic genes snail and twist, we have found that the number of neuroblasts is not reduced in these mutants, suggesting that mesoderm and mesectoderm are not essential for the initiation of neural development. The position of the neuroectoderm, however, is ventrally shifted: Neuroectoderm takes over the presumptive peripheral mesoderm domain in single mutants, whereas the entire presumptive mesoderm domain in double mutants takes on the neuroectodermal fate. The shifted neuroectoderm still requires the proneural genes and the neurogenic genes. This shift is unlikely to be due to any shift in the nuclear localization gradient of the maternally supplied dorsal protein. A model for cell fate determination of the neuroectoderm, mesectoderm, and mesoderm will be discussed.
Alignment of recombination sites in Hin-mediated site-specific DNA recombination.
Authors: Moskowitz I P , Heichman K A , Johnson R C
Published: June 2007

The Hin site-specific recombination system normally promotes inversion of DNA between two recombination sites in inverted orientation. We show that the rate of deletion of DNA between two directly repeated recombination sites is 10-300 times slower than inversion between sites in their native configuration as measured in vivo and in vitro, respectively. In vitro studies have shown that the deletion reaction has the same requirement for Fis, a recombinational enhancer, and DNA supercoiling as the inversion reaction. These requirements, together with the finding that the deletion products are interlinked once suggest that the deletion synaptic complex is similar to the invertasome intermediate that generates inversion. The inefficiency of the deletion reaction is not a function of a reduced ability to recognize or synapse recombination sites in direct orientation. Not only do these substrates support an efficient knotting reaction, but directly repeated recombination sites with symmetric core sequences also invert efficiently. These findings demonstrate that the recombination sites are preferentially assembled into the invertasome structure with the sites aligned in the configuration for inversion regardless of their starting orientation. We propose that the dynamics of a supercoiled DNA molecule biases the geometric assembly of specific intermediates. In the case of Hin-mediated recombination, inversion is overwhelmingly preferred over deletion because DNA supercoiling favors a specific alignment of DNA strands in the synaptic complex.
Developmental function of Elf-1: an essential transcription factor during embryogenesis in Drosophila.
Authors: Bray S J , Kafatos F C
Published: June 2007

The Drosophila transcription factor Elf-1 binds to a cis-acting element that is essential for neuronal expression of the Dopa decarboxylase gene (Ddc). Elf-1 also stimulates transcription from the Ddc and Ultrabithorax promoters in vitro. To investigate the function of this factor in vivo we have screened for mutations and identified the Elf-1 gene as grainyhead (grh), a previously known embryonic lethal locus. Elf-1/grh mutations cause late embryonic lethality accompanied by multiple defects in the cuticle and head skeleton. Using Ddc-lacZ gene fusions, we show that these mutations affect Ddc expression in the embryo. Surprisingly, however, epidermal expression is disrupted, whereas neuronal expression remains unaffected. Analysis of the mutant phenotype indicates that Elf-1 coordinately regulates multiple genes involved in the differentiation of epidermal structures. The results highlight the importance of genetic analysis in the study of proteins required for developmental regulation of gene expression.
Functional dissection of the paired segmentation gene in Drosophila embryos.
Authors: Morrissey D , Askew D , Raj L , Weir M
Published: June 2007

An ectopic expression assay in Drosophila embryos was used to investigate the roles of pair-rule segmentation genes in the spatial regulation of the segment-polarity gene, engrailed (en). It is hypothesized that the regions of overlap in expression of two genes, paired (prd) and even-skipped (eve), define the odd-numbered en expression stripes. Consistent with this combinatorial model, ectopic expression of prd caused these en stripes to be expanded posteriorly. Surprisingly, however, ectopic expression of a prd gene with a deletion of the conserved paired box resulted in loss of these odd-numbered en stripes. This dominant negative effect is a phenocopy of en expression in prd embryos and suggests that the paired box is necessary for normal prd- function. A similar deletion of odd-numbered en stripes was also observed after ectopic expression of a chimeric fushi tarazu (ftz) gene containing a substituted prd gene homeo box; in addition, in these embryos, the even-numbered en stripes were expanded anteriorly, as observed when the unaltered ftz gene is ectopically expressed. These effects suggest that the chimeric protein may have DNA or protein targets of both the normal Ftz and Prd proteins.
A 5'-terminal stem-loop structure can stabilize mRNA in Escherichia coli.
Authors: Emory S A , Bouvet P , Belasco J G
Published: June 2007

The 5'-untranslated region of the long-lived Escherichia coli ompA transcript functions as an mRNA stabilizer capable of prolonging the lifetime in E. coli of a number of heterologous messages to which it is fused. To elucidate the structural basis of differential mRNA stability in bacteria, the domains of the ompA 5'-untranslated region that allow it to protect mRNA from degradation have been identified by mutational analysis. The presence of a stem-loop no more than 2-4 nucleotides from the extreme 5' terminus of this RNA segment is crucial to its stabilizing influence, whereas the sequence of the stem-loop is relatively unimportant. The potential to form a hairpin very close to the 5' end is a feature common to a number of stable prokaryotic messages. Moreover, the lifetime of a normally labile message (bla mRNA) can be prolonged in E. coli by adding a simple hairpin structure at its 5' terminus. Accelerated degradation of ompA mRNA in the absence of a 5'-terminal stem-loop appears to start downstream of the 5' end. We propose that E. coli messages beginning with a single-stranded RNA segment of significant length are preferentially targeted by a degradative ribonuclease that interacts with the mRNA 5' terminus before cleaving internally at one or more distal sites.
Analysis of G alpha 4, a G-protein subunit required for multicellular development in Dictyostelium.
Authors: Hadwiger J A , Firtel R A
Published: June 2007

The Dictyostelium G alpha 4 gene encodes a G-protein alpha subunit that is primarily expressed during the multicellular stages of development. g alpha 4 null mutants, created by gene disruption, show aberrant morphological differentiation, reduced levels of prespore gene expression, and a loss of the ability to produce spores. These developmental phenotypes can be rescued by complementation with the wild-type gene. Cells that overexpress the G alpha 4 gene (G alpha 4HC) also show reduced spore production but display an aberrant morphological phenotype distinct from that of g alpha 4 cells. The g alpha 4 phenotype can be partially rescued by the presence of wild-type or G alpha 4HC cells in chimeric organisms, suggesting that G alpha 4-expressing cells produce an intercellular signal that is essential for multicellular development.
Myc and Max associate in vivo.
Authors: Blackwood E M , Lüscher B , Eisenman R N
Published: June 2007

Max is a helix-loop-helix zipper protein that associates in vitro with Myc family proteins to form a sequence-specific DNA-binding complex. We show here, by means of a coimmunoprecipitation assay with anti-Myc and anti-Max antibodies, that Myc and Max are associated in vivo and essentially all of the newly synthesized Myc can be detected in a complex with Max. This complex possesses specific DNA-binding activity for CACGTG-containing oligonucleotides. Although Max itself is a highly stable protein, Myc is rapidly degraded during or after its association with Max. In vivo Max is shown to be a nuclear protein phosphorylated by casein kinase II, and alternatively spliced forms of Max are expressed in cells. Furthermore, the levels of Max expression are equivalent in quiescent, mitogen-stimulated, and cycling cells. We conclude that the highly regulated rate of Myc biosynthesis is likely to be a limiting step in the formation of Myc:Max complexes.
Parallel pathways of gene regulation: homologous regulators SWI5 and ACE2 differentially control transcription of HO and chitinase.
Authors: Dohrmann P R , Butler G , Tamai K , Dorland S , Greene J R , Thiele D J , Stillman D J
Published: June 2007

Two independent pathways of transcriptional regulation that show functional homology have been identified in yeast. It has been demonstrated previously that SWI5 encodes a zinc finger DNA-binding protein whose transcription and cellular localization both are cell cycle regulated. We show that ACE2, whose zinc finger region is nearly identical to that of SWI5, shows patterns of cell cycle-regulated transcription and nuclear localization similar to those seen previously for SWI5. Despite their similarities, SWI5 and ACE2 function in separate pathways of transcriptional regulation. SWI5 is a transcriptional activator of the HO endonuclease gene, whereas ACE2 is not. In contrast, ACE2 is a transcriptional activator of the CTS1 gene (which encodes chitinase), whereas SWI5 is not. An additional parallel between the SWI5/HO pathway and the ACE2/CTS1 pathway is that HO and CTS1 both are cell cycle regulated in the same way, and HO and CTS1 both require the SWI4 and SWI6 transcriptional activators. Overproduction of either SWI5 or ACE2 permits transcriptional activation of the target gene from the other pathway, suggesting that the DNA-binding proteins are capable of binding in vivo to promoters that they do not usually activate. Chimeric SWI5/ACE2 protein fusion experiments suggest that promoter specificity resides in a domain distinct from the zinc finger domain.
Multiple domains of the RNA polymerase I activator hUBF interact with the TATA-binding protein complex hSL1 to mediate transcription.
Authors: Jantzen H M , Chow A M , King D S , Tjian R
Published: June 2007

Recent evidence suggests that transcription initiation by all three eukaryotic RNA polymerases involves a complex of the TATA-binding protein (TBP) and multiple TBP-associated factors (TAFs). Here, we map the functional domains of the nucleolar HMG box protein hUBF, which binds to the human rRNA promoter and stimulates transcription by RNA polymerase I through cooperative interactions with a distinct TBP-TAF complex, hSL1. DNase I footprint analysis of mutant hUBF proteins and of a synthetic peptide of 84 amino acids reveals that HMG box 1 is necessary and sufficient for DNA sequence specificity, whereas other HMG boxes and the amino terminus modulate the binding efficiency. hUBF contains multiple activation domains that include the acidic carboxyl terminus and three HMG boxes. HMG boxes 3 and 4 and the acidic tail contribute significantly to an extended footprinting pattern in the presence of hSL1, suggestive of specific protein-protein interactions. Moreover, the inability of xUBF from Xenopus laevis to form an initiation complex with hSL1 can be overcome by hybrid proteins containing human HMG box 4 and the acidic carboxyl terminus. These results strongly suggest an important role of transcription activation domains of hUBF in mediating interactions with the TBP-TAF complex hSL1.
HAP1 positive control mutants specific for one of two binding sites.
Authors: Turcotte B , Guarente L
Published: June 2007

The expression of the yeast CYC1 and CYC7 genes is controlled by the HAP1 activator. A GAL4-like zinc finger (residues 1-148) specifies binding to the dissimilar sites UAS1 (of CYC1) and CYC7, and an acidic domain (residues 1307-1483) is essential for activation of transcription. To analyze how HAP1 binds to UAS1 and CYC7, we performed saturation mutagenesis of the DNA-binding domain and recovered mutants with altered activity. Class 1 mutants had a reduced activity at both UAS1 and CYC7, and class 2 mutants selectively eliminated activity at CYC7. Surprisingly, several mutants of both classes exhibited wild-type DNA binding, indicating that they were specifically defective in activation. These positive control (PC) mutants alter residues that bracket the zinc finger. We explain these mutants in a model involving cofactor proteins that bind UAS1 and CYC7 along with HAP1. The existence of PC mutants that only affect activity at CYC7 raises the possibility that different cofactors may exist for UAS1 and CYC7.
Cyclin-B homologs in Saccharomyces cerevisiae function in S phase and in G2.
Authors: Richardson H , Lew D J , Henze M , Sugimoto K , Reed S I
Published: June 2007

We have cloned four cyclin-B homologs from Saccharomyces cerevisiae, CLB1-CLB4, using the polymerase chain reaction and low stringency hybridization approaches. These genes form two classes based on sequence relatedness: CLB1 and CLB2 show highest homology to the Schizosaccharomyces pombe cyclin-B homolog cdc13 involved in the initiation of mitosis, whereas CLB3 and CLB4 are more highly related to the S. pombe cyclin-B homolog cig1, which appears to play a role in G1 or S phase. CLB1 and CLB2 mRNA levels peak late in the cell cycle, whereas CLB3 and CLB4 are expressed earlier in the cell cycle but peak later than the G1-specific cyclin, CLN1. Analysis of null mutations suggested that the CLB genes exhibit some degree of redundancy, but clb1,2 and clb2,3 cells were inviable. Using clb1,2,3,4 cells rescued by conditional overproduction of CLB1, we showed that the CLB genes perform an essential role at the G2/M-phase transition, and also a role in S phase. CLB genes also appear to share a role in the assembly and maintenance of the mitotic spindle. Taken together, these analyses suggest that CLB1 and CLB2 are crucial for mitotic induction, whereas CLB3 and CLB4 might participate additionally in DNA replication and spindle assembly.
3'-UTR-dependent deadenylation by the yeast poly(A) nuclease.
Authors: Lowell J E , Rudner D Z , Sachs A B
Published: June 2007

Poly(A) tail removal is the first step in the degradation pathway for some mRNAs. The purified poly(A)-binding protein (PAB)-dependent poly(A) nuclease (PAN) from yeast removes mRNA poly(A) tails in vitro by a process similar to that observed in vivo. The exonucleolytic PAN degrades poly(A) and RNA bound by PAB, and can be activated by spermidine to degrade poly(A) in the absence of PAB. The shortening of the poly(A) tail down to 10-25 nucleotides and the terminal deadenylation of this short adenine tract are kinetically distinct reactions. Poly(A) shortening rates are stimulated by the yeast a-mating factor (MFA2) RNA 3' UTR sequence, and this occurs by switching PAN from a distributive to a more processive enzyme. Terminal deadenylation rates are also stimulated to different extents by various RNAs. Inversion of the MFA2 3' UTR sequence completely inhibits the terminal deadenylation reaction owing to the presence of an inhibitory element 70 nucleotides from the poly(A) tail. Other sequence elements inserted at a similar distance from the poly(A) tail also interfere with the reaction. These data suggest that the two phases of poly(A) degradation can be regulated by mRNA sequences, and they provide a mechanistic description of how this regulation could occur in vivo.
Allelic diversity of the maize B regulatory gene: different leader and promoter sequences of two B alleles determine distinct tissue specificities of anthocyanin production.
Authors: Radicella J P , Brown D , Tolar L A , Chandler V L
Published: June 2007

The B gene encodes a transcription factor of the basic helix-loop-helix class, which controls the synthesis of the anthocyanin pigments in maize. This gene, as well as the highly homologous R gene family, displays extensive allelic variation in that different alleles cause distinct distributions of anthocyanin pigments in different tissues and at different developmental times. The analysis of the expression of two B alleles, with distinct tissue-specific patterns of anthocyanin synthesis in plant and seed tissues, demonstrates that the amount of B transcripts correlates with the accumulation of anthocyanins in the various tissues. The comparison of the genomic clones for the two alleles reveals high sequence identity in the coding and 3'-flanking regions (98% and approximately 90%, respectively). In contrast, the most 5' region of their mRNAs and the 5'-flanking sequences share no significant sequence identity. This result suggests that the alleles diverged from each other by complex genome rearrangements rather than by simple base pair substitutions. We have used the high velocity microprojectile transformation assay to demonstrate that the differential expression of the two alleles in the seed is determined by their 5' variant sequences. Thus, the variation in tissue-specific anthocyanin synthesis in plants with these different B alleles is controlled at the level of B gene expression.
Synergistic activation of the insulin gene by a LIM-homeo domain protein and a basic helix-loop-helix protein: building a functional insulin minienhancer complex.
Authors: German M S , Wang J , Chadwick R B , Rutter W J
Published: June 2007

The distal portion of the rat insulin I gene 5'-flanking DNA contains two sequence elements, the Far and FLAT elements, that can function in combination, but not separately, as a beta-cell-specific transcriptional enhancer. We have isolated several cDNAs encoding proteins that bind to the FLAT element. Two of these cDNAs, cdx-3 and lmx-1, represent homeo box containing mRNAs with restricted patterns of expression. The protein encoded by lmx-1 also contains two amino-terminal cysteine/histidine-rich "LIM" domains. Both cdx-3 and lmx-1 can activate transcription of a Far/FLAT-linked gene when expressed in a normally non-insulin-producing fibroblast cell line. Furthermore, in fibroblasts expressing transfected beta-cell lmx-1, the addition of the Far-binding, basic helix-loop-helix protein shPan-1 (the hamster equivalent of human E47) causes a dramatic synergistic activation. ShPan-1 causes no activation in fibroblasts expressing transfected cdx-3 or the related LIM-homeodomain protein isl-1. Deletion of one or both of the LIM domains from the 5' end of the lmx-1 cDNA removes this synergistic interaction with shPan-1 without any loss of basal transcriptional activation. We conclude that beta-cell lmx-1 functions by binding to the FLAT element and interacting through the LIM-containing amino terminus with shPan-1 bound at the Far element. These proteins form the minimal components for a functional minienhancer complex.
Promoter melting and TFIID complexes on Drosophila genes in vivo.
Authors: Giardina C , Pérez-Riba M , Lis J T
Published: June 2007

In vivo UV cross-linking and nuclear transcriptional run-on experiments have shown that a number of Drosophila genes possess an elongationally paused RNA polymerase on their 5' ends. Here, we examine in vivo promoters that do and do not possess paused polymerases using the single-stranded DNA-probing reagent KMnO4. Melted DNA helices are found associated with the pause site of the uninduced hsp70 and hsp26 heat shock genes and the constitutively expressed beta-1 tubulin gene. The histone H1 and H2B genes, which lack a paused polymerase, have no comparable region of melted DNA. Melting at the pause site persists upon heat shock induction of the hsp70 and hsp26 genes, indicating that pausing continues after gene activation. Interestingly, activation triggers additional melting, both at the start site (in the region where open complexes would be expected to form) and downstream of the uninduced pause site. In the course of our studies, we discovered that some T residues of the TATA box were protected from KMnO4 modification in both induced and uninduced cells. This protection appears to be a consequence of TFIID binding, as a similar protection pattern could be produced in vitro with purified protein.
Casein kinase II inhibits the DNA-binding activity of Max homodimers but not Myc/Max heterodimers.
Authors: Berberich S J , Cole M D
Published: June 2007

Max is a heterodimeric partner of the Myc oncoprotein with sequence-specific DNA-binding activity. We found that the DNA-binding activity of bacterially expressed Max homodimers was inhibited in an ATP-dependent reaction by phosphorylation in vitro with purified bovine casein kinase II (CKII). In contrast, phosphorylation of Max and/or Myc by CKII had no inhibitory or stimulatory effect on the DNA-binding activity of Myc/Max heterodimers. By deletion analysis and site-directed mutagenesis, the inhibitory domain was localized to a CKII phosphorylation site in the amino terminus of Max. Finally, extracts prepared from NIH-3T3 cell lines that overexpress Max contained a phosphorylated Max protein which, following phosphatase treatment or heterodimerization with Myc, was capable of sequence-specific DNA-binding activity. Immunoprecipitation experiments confirmed that Max was also phosphorylated in NIH-3T3 cells, demonstrating that Max phosphorylation may have an important physiological function.
Association of U6 snRNA with the 5'-splice site region of pre-mRNA in the spliceosome.
Authors: Sawa H , Shimura Y
Published: June 2007

U6 snRNA is one of the five RNA species required for splicing of nuclear pre-mRNAs. High conservation of its sequence has led to the hypothesis that U6 snRNA plays a catalytic role in splicing. If this is the case, U6 snRNA should be localized close to sites where the splicing reaction occurs. However, this has never been demonstrated. Here, we have shown that U6 snRNA is cross-linked to the 5'-splice site region of pre-mRNA by UV irradiation during the in vitro splicing reaction. We have also detected the cross-link of U6 snRNA and the region around the branchpoint of the intron lariat. The results show that U6 snRNA is present near the splice sites in the splicing reaction and support the idea that U6 snRNA is a catalytic element in the spliceosome.
DNA sequence requirements for generating paused polymerase at the start of hsp70.
Authors: Lee H , Kraus K W , Wolfner M F , Lis J T
Published: June 2007

RNA polymerase II is transcriptionally engaged but paused approximately 25 nucleotides from the start site of the hsp70 gene of Drosophila melanogaster in uninduced (non-heat-shocked) flies. Here, we identify regions of the hsp70 promoter that are required for formation of this paused polymerase. Various hsp70 promoter sequences are substituted for promoter sequences of a yolk protein gene, yp1, which, in males, is normally not expressed and has no paused polymerase. Run-on assays with nuclei of male transgenic flies are used to measure the level of paused polymerase on the hybrid genes. Sequences that reside upstream of the hsp70 TATA element, when fused upstream of the yp1 TATA element, specify the formation of a paused polymerase on the 5' end of this hybrid gene. Within this region are multiple copies of the GAGA element, which is known to bind a constitutively expressed factor. This element appears to play a role in generating the pause. Also, in the absence of much of this upstream region, hsp70 sequences in the vicinity of the transcriptional start and pause site participate in specifying the pause. Deletions of the pause site reduce the level of paused polymerase but do not lead to constitutive transcription. However, a connection between transcription and pausing is seen. The level of paused polymerase on the various hybrid hsp70-yp1 promoters correlates with the promoter's potential to direct heat-induced transcription.
Yeast and human TFIIDs are interchangeable for the response to acidic transcriptional activators in vitro.
Authors: Kelleher R J , Flanagan P M , Chasman D I , Ponticelli A S , Struhl K , Kornberg R D
Published: June 2007

Previous work showed that human TFIID fails to support yeast cell growth, although it is nearly identical to yeast TFIID in a carboxy-terminal region of the molecule that suffices for basal, TATA-element-dependent transcription in vitro. These and other findings raised the possibility that TFIID participates in species-specific interactions, possibly with mediator factors, required for activated transcription. Here, we report that human TFIID and amino-terminally truncated derivatives of yeast TFIID are fully functional in support of both basal transcription and the response to acidic activator proteins in a yeast in vitro transcription system. Conversely, and in contrast to previously published results, yeast TFIID supports both basal and activated transcription in reactions reconstituted with human components. This functional interchangeability of yeast and human TFIIDs argues strongly against species specificity with regard to TFIID function in basal transcription and the response to acidic activator proteins. In addition, our results suggest that any intermediary factors between acidic activators and TFIID are conserved from yeast to man.