bluuebunny/crossref_metadata_2025 huggingface dataset:
Progressively restricted expression of a homeo box gene within the aboral ectoderm of developing sea urchin embryos.
Authors: Angerer L M , Dolecki G J , Gagnon M L , Lum R , Wang G , Yang Q , Humphreys T , Angerer R C
Published: June 2007

A homeo box-containing gene, Hbox1 is expressed in an unusual and highly conserved spatial pattern in embryos of two different species of sea urchin, Tripneustes gratilla and Strongylocentrotus purpuratus. Hybridization in situ shows that this mRNA accumulates initially throughout the aboral ectoderm; however, between blastula and pluteus stages, the region containing Hbox1 mRNA retracts gradually until only a small area around the vertex is labeled in pluteus larvae. Aboral ectoderm appears cytologically uniform and also accumulates uniform levels of other tissue-specific mRNAs. Therefore, the Hbox1 pattern reveals a previously unsuspected heterogeneity of aboral ectoderm cells and a polarity within this tissue. In S. purpuratus, the Hbox1 gene product probably is not involved in initial specification of cell fate, as this message does not achieve a significant fraction of its peak abundance until almost hatching blastula stage, well after the time aboral ectoderm cells have initiated a tissue-specific program of gene expression. RNA blot and RNase protection analyses revealed low levels of Hbox1 mRNA in all adult tissues examined. However, this message was not detectable in mature eggs, suggesting that the Hbox1 gene does not have a maternal function. In addition to highly conserved spatial and temporal patterns of expression, the homeo box genes of these two urchin species also are conserved highly in sequences outside the homeo domain, despite the divergence of these two species (30-45 my). Two notable features of the protein shared with several vertebrate homeo proteins are a short conserved sequence encoded by an exon upstream of that encoding the homeo domain and a large region of high serine and proline content.
Transcriptional control of Drosophila fushi tarazu zebra stripe expression.
Authors: Dearolf C R , Topol J , Parker C S
Published: June 2007

The Drosophila segmentation gene fushi tarazu (ftz) is expressed in a characteristic pattern of seven stripes during early embryogenesis. We have used ftz-lacZ fusion genes to determine the effects of deleting relatively small segments of the ftz promoter region necessary for this expression. We find that this regulatory region contains multiple activator and repressor elements. The deletion of one particular activator element results in a preferential loss of expression in the posterior stripes, whereas the deletion of other activator elements causes a general reduction in expression throughout the germ band. The removal of repressor elements results in a loss of repression in the odd-numbered parasegments. We also find that the ftz upstream enhancer element functions primarily in epidermal cells. Our results indicate that ftz transcription is activated in each parasegment through the 'zebra stripe' promoter region and is then inhibited selectively in the odd-numbered parasegments by repressors that bind directly to elements within this promoter region.
A nucleoprotein complex mediates the integration of retroviral DNA.
Authors: Bowerman B , Brown P O , Bishop J M , Varmus H E
Published: June 2007

The integration of viral DNA into the host genome is an essential step in the retrovirus life cycle. To understand this process better, we have examined the native state of viral DNA in cells acutely infected by murine leukemia virus (MLV), using both a physical assay for viral DNA and a functional assay for integration activity (Brown et al. 1987). The viral DNA and integration activity copurify during velocity sedimentation, gel filtration, and density equilibrium centrifugation, indicating that viral DNA is in a large (approximately 160S) nucleoprotein complex that includes all functions required for integration activity in vitro. Analysis by immunoprecipitation shows that the viral capsid protein is part of the active nucleoprotein complex, but recognition of the complex by only a subset of anti-capsid sera implies that the protein is constrained conformationally. The viral DNA within this structure is accessible to nucleases; the effects of nucleases on the integrity of the complex suggest that the integration-competent particle is derived from and similar to the core of extracellular virions.
Identification and characterization of an RNA molecule that copurifies with RNase P activity from HeLa cells.
Authors: Bartkiewicz M , Gold H , Altman S
Published: June 2007

An RNA molecule, 340 nucleotides in length and designated H1 RNA, copurifies with RNase P activity from extracts of HeLa cells or isolated HeLa cell nuclei. When the genomic DNA of various organisms is probed with H1 cDNA in Southern hybridization assays, only mammalian DNA gives a positive signal. The gene coding for H1 RNA in human cells is present in one to three copies per cell. The nucleotide sequence of H1 RNA, which shows little homology to the known sequences of its analogs from prokaryotes and yeast, can be drawn as a two-dimensional, hydrogen-bonded structure that resembles similar structures proposed for the RNA subunit of RNase P from these other sources. Part of the hypothetical structure is virtually identical to structures that can be drawn for analogous RNAs from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and S. octosporus.
Nuclear factor E2F mediates basic transcription and trans-activation by E1a of the human MYC promoter.
Authors: Thalmeier K , Synovzik H , Mertz R , Winnacker E L , Lipp M
Published: June 2007

Transcription from one of the two initiation sites, P1 and P2, of the dual human MYC promoter seems to be essential in all proliferating cells. To identify proteins and target structures for MYC regulation, a DNA region was analyzed that is critical for P2 promoter activity. Here, we show that a nuclear factor binds to a DNA element within P2, which is conserved perfectly between mouse and man and displays a striking homology to the E1a-inducible E2 promoter of adenovirus type 5 (Ad5). We demonstrate that the same transcription factor, defined recently as E2F, which plays an essential role in the activation of adenovirus early promoters and enhancers, also interacts as a dominant nuclear factor with the MYC promoter. The presence of an intact E2F binding site is required for basic expression and for trans-activation of the P2 promoter by E1a proteins. The human MYC promoter is the first cellular target described for E2F. The results suggest that expression of MYC might be regulated via modulation of E2F by cellular 'E1a-like' factors.
Postnatal repression of the alpha-fetoprotein gene is enhancer independent.
Authors: Camper S A , Tilghman S M
Published: June 2007

The mammalian liver undergoes a number of dramatic changes in gene expression during development. One of these is typified by the alpha-fetoprotein (AFP) gene, which is activated in the fetal liver but undergoes a transcriptional decline at birth. In contrast, although activated at the same time during fetal development, albumin gene transcription is maintained at high levels in adult animals. To determine whether the postnatal decline in AFP gene transcription is mediated through its distal enhancers or through more proximal elements surrounding the promoter or structural gene, chimeric genes bearing substitutions of albumin gene cis-acting elements for the equivalent AFP gene elements were introduced into the germ line of mice. The expression of the transgenes was then analyzed at various stages of development. Our results indicate that the AFP gene enhancers are not involved in the postnatal decline in AFP transcription. Rather, a region within the first kilobase of DNA upstream of the AFP gene, including its promoter, and/or portions of the structural gene is sufficient to direct postnatal repression of the gene.
A bacterial environmental sensor that functions as a protein kinase and stimulates transcriptional activation.
Authors: Igo M M , Ninfa A J , Silhavy T J
Published: June 2007

Transcription of the genes that encode the major outer membrane porin proteins OmpF and OmpC of Escherichia coli is regulated in response to changes in medium osmolarity by EnvZ and OmpR. EnvZ functions to sense environmental conditions and to relay this information to the DNA-binding protein OmpR. We have used a truncated EnvZ protein (EnvZ115), which is defective in sensory function but able to communicate with OmpR, to study the biochemical interactions between these two proteins and their effects on transcription from the ompF promoter. We show that purified EnvZ115 can phosphorylate OmpR in the presence of ATP. In addition, EnvZ115 stimulates the ability of OmpR to activate ompF transcription in vitro. Using antibodies specific for EnvZ, we have purified the wild-type protein and have shown that it is also an OmpR kinase. These results provide a prokaryotic example of a transmembrane sensory protein that functions as a protein kinase and suggest a mechanism by which EnvZ communicates with OmpR in signal transduction.
A gene with homology to the myc similarity region of MyoD1 is expressed during myogenesis and is sufficient to activate the muscle differentiation program.
Authors: Edmondson D G , Olson E N
Published: June 2007

MyoD1 is a nuclear phosphoprotein that is expressed in skeletal muscle in vivo and in certain muscle cell lines in vitro; it has been shown to convert fibroblasts to myoblasts through a mechanism requiring a domain with homology to the myc family of proteins. The BC3H1 muscle cell line expresses skeletal muscle-specific genes upon exposure to mitogen-deficient medium, but does not express MyoD1 at detectable levels. To determine whether BC3H1 cells may express regulatory genes functionally related to MyoD1, a cDNA library prepared from differentiated BC3H1 myocytes, was screened at reduced stringency with the region of the MyoD1 cDNA that shares homology with c-myc. From this screen, a cDNA was identified that encodes a major open reading frame with 72% homology to the myc domain and basic region of MyoD1. The mRNA encoded by this MyoD1-related gene is expressed in skeletal muscle in vivo and in differentiated skeletal myocytes in vitro and is undetectable in cardiac or smooth muscle, nonmuscle tissues, or nonmyogenic cell types. During myogenesis, the MyoD1-related mRNA accumulates several hours prior to other muscle-specific mRNAs and therefore represents an early molecular marker for entry of myoblasts into the differentiation pathway. Transient transfection of 10T1/2 or 3T3 cells with the MyoD1-related cDNA is sufficient to induce myosin heavy-chain expression and to activate a reporter gene under transcriptional control of the muscle creatine kinase 5' enhancer, which functions only in differentiated myocytes. Expression of this cDNA in stably transfected 10T1/2 cells also leads to fusion and muscle-specific gene expression upon exposure to mitogen-deficient medium. Thus, the product of this MyoD1-related gene is sufficient to activate the muscle differentiation program and may substitute for MyoD1 in certain developmental situations. Together, these results suggest the existence of a family of myogenic regulatory genes that share a conserved motif with c-myc.
A neuron-specific enhancer of the Drosophila dopa decarboxylase gene.
Authors: Johnson W A , McCormick C A , Bray S J , Hirsh J
Published: June 2007

At least two cis-regulatory elements are necessary for correct neuron-specific expression of the Drosophila melanogaster dopa decarboxylase gene, Ddc. In addition to a previously described proximal element located approximately 60 bp upstream of the mRNA start site, we have now characterized a distal approximately 600-bp DNA fragment, extending from -1019 to -1623 bp, which possesses enhancer-like properties and is essential for normal neuron-specific expression. Immunofluorescent labeling of neurons expressing deleted Ddc genes indicates that this region contains both general neuronal regulatory elements and cell-specific elements that selectively affect Ddc expression in either dopaminergic or serotonergic neurons. These selective effects can be correlated with the removal of sequence elements that are protected from DNase digestion by factors present in embryonic nuclear extracts. Several of these elements are also homologous to sequences located upstream of the evolutionarily diverged Ddc gene of Drosophila virilis. These results suggest that the neuron-specific expression of Ddc results from the combined action of several factors binding within this distal enhancer region.
The Drosophila female-specific sex-determination gene, Sex-lethal, has stage-, tissue-, and sex-specific RNAs suggesting multiple modes of regulation.
Authors: Salz H K , Maine E M , Keyes L N , Samuels M E , Cline T W , Schedl P
Published: June 2007

For proper sexual development of females, the Sex-lethal (Sxl) gene must be activated early in development and remain on during the rest of the life cycle. Conversely, in males, Sxl must remain functionally off through development. Here, we show that the Sxl transcription unit spans a DNA segment of greater than 20 kb and encodes at least 10 distinct, but overlapping, RNA species. These RNAs range in size from 4.4 to 1.7 kb and exhibit sex, stage, and tissue specificity. Six RNAs, three female specific and three male specific, are first detected by midembryogenesis and persist through the adult stage: Their expression reflects the on/off regulation of Sxl's activity at the level of sex-specific alternate splicing. Four Sxl RNAs are found in adult females. Two of these RNAs are dependent on the presence of a functional germ line and may be relevant to Sxl's role in adult germ-line development. All four are present in unfertilized eggs. Finally, three Sxl RNAs are found only transiently during very early embryogenesis; we suggest that the expression of these RNAs may reflect an early regulation of Sxl at the level of transcription and that these transcripts are involved in the initial selection of the Sxl activity state in response to the primary sex-determination signal, the X/A ratio.
Co-localization of elements required for phorbol ester stimulation and glucocorticoid repression of proliferin gene expression.
Authors: Mordacq J C , Linzer D I
Published: June 2007

Proliferin (PLF) gene expression provides a model of growth-related transcriptional activation in mouse cells. Transcription from a cloned PLF promoter is inducible by phorbol esters, and this induction involves a region of 31 bp that includes an AP-1 site and a cluster of sites similar to the simian virus 40 (SV40) SphI element. The mutation of either the AP-1 or the SphI sites abolishes phorbol ester induction, and the transfer of this 31-bp sequence to a site upstream of a minimal promoter is sufficient to confer phorbol-ester responsiveness. In contrast to phorbol esters, glucocorticoids repress PLF transcription, which results in a reduced accumulation of PLF mRNA in serum-stimulated cells. Repression is dependent on the glucocorticoid receptor, which binds to the PLF promoter in a region that includes the AP-1 site, and the 31-bp phorbol ester 12-O-tetra decanoylphorbol-13-acetate (TPA)-inducible region is sufficient to mediate glucocorticoid repression. In addition, extracts from glucocorticoid-treated and untreated mouse cells are found to differ in the nature of the protein complexes that interact with the AP-1 site.
Fos-Jun interaction: mutational analysis of the leucine zipper domain of both proteins.
Authors: Ransone L J , Visvader J , Sassone-Corsi P , Verma I M
Published: June 2007

Jun and Fos oncoproteins form a complex that regulates transcription from promoters containing AP-1 binding sites. The 'leucine zipper' domain of both Fos and Jun is necessary for the formation of the heterodimer, but the role of specific leucine residues is unclear. We have used site-specific mutagenesis to examine the contribution of individual leucine residues to the formation of a stable Fos-Jun protein complex and the binding of this complex to the AP-1 site. Mutation of a single leucine in either Fos or Jun had no effect on protein complex formation. Furthermore, mutations of two consecutive leucines in Jun did not interfere with heterodimer formation; however, in the case of Fos, two consecutive mutations resulted in an inability to form a heterodimer. Although mutagenesis of the first leucine of the heptad repeat had no effect on protein complex formation, this mutation in either Fos or Jun drastically reduced the affinity of the complex for DNA. Thus, both Fos and Jun contribute directly to the DNA-binding potential of the heterodimer.
Protamine 3'-untranslated sequences regulate temporal translational control and subcellular localization of growth hormone in spermatids of transgenic mice.
Authors: Braun R E , Peschon J J , Behringer R R , Brinster R L , Palmiter R D
Published: June 2007

Although the mouse protamine 1 gene (mP1) is first transcribed in round spermatids, its mRNA is not translated until about 1 week later in elongating spermatids. To determine what mP1 sequences are important for its transcriptional and translational regulation, we have constructed fusions between mP1 and the human growth hormone (hGH) structural gene and analyzed their expression in transgenic mice. We show that mP1 sequences 5' to the start of transcription are sufficient to confer spermatid-specific expression on the hGH gene. We also show that 156 nucleotides of mP1 3'-untranslated sequence is sufficient to confer mP1-like translational regulation on the hGH mRNA. Interestingly, the subcellular localization of hGH was dependent on the time during spermiogenesis that it was made. Synthesis of hGH in early round spermatids resulted in localization in the acrosome, whereas synthesis in late elongating spermatids resulted in intracellular, but not acrosomal, localization.
Expression of c-kit gene products in known cellular targets of W mutations in normal and W mutant mice--evidence for an impaired c-kit kinase in mutant mice.
Authors: Nocka K , Majumder S , Chabot B , Ray P , Cervone M , Bernstein A , Besmer P
Published: June 2007

The proto-oncogene c-kit, a transmembrane tyrosine protein kinase receptor for an unknown ligand, was shown recently to map to the dominant white spotting locus (W) of the mouse. Mutations at the W locus affect various aspects of hematopoiesis, as well as the proliferation and/or migration of primordial germ cells and melanoblasts during development. Here, we show that c-kit is expressed in tissues known to be affected by W mutations in fetal and adult erythropoietic tissues, mast cells, and neural-crest-derived melanocytes. We demonstrate that the c-kit associated tyrosine-specific protein kinase is functionally impaired in W/WV mast cells, thus providing a molecular basis for understanding the developmental defects that result from these mutations.
The role of segment polarity genes during Drosophila neurogenesis.
Authors: Patel N H , Schafer B , Goodman C S , Holmgren R
Published: June 2007

Segment polarity genes in Drosophila are required for the proper formation of epidermal pattern within each segment. Here we show that certain segment polarity genes are also critical for the determination of specific neuronal identities in the developing central nervous system (CNS) of the Drosophila embryo. For several mutants, however, the pattern defects do not simply parallel their cuticular phenotypes. In fused, armadillo, and cubitus interruptus Dominant mutants, much of the CNS appears relatively normal. In hedgehog mutants, the CNS is highly disorganized, but this disruption may occur secondary to the initial events of neurogenesis. The specific cellular defects in patched mutants suggests that this gene specifies a subset of neuroblasts and neural progeny underlying the region of epidermal pattern defect. gooseberry mutants display a complex series of alterations in neuronal identity both underlying and outside of the region of epidermal modification. Neuronal identities of a set of cells along the midline appear to be changed in Cell mutants. The phenotype of wingless mutants is the most restricted and may be due to improper communication between sibling neurons. Thus, in addition to their functions in epidermal pattern formation, at least four of the segment polarity genes (gooseberry, patched, Cell, and wingless) appear to have specific roles in the control of cell fates during neurogenesis.
A cellular protein that binds to the 5'-noncoding region of poliovirus RNA: implications for internal translation initiation.
Authors: Meerovitch K , Pelletier J , Sonenberg N
Published: June 2007

Initiation of translation on poliovirus mRNA occurs by internal binding of ribosomes to a region within the 5'-noncoding portion of the mRNA. The mechanistic details and trans-acting factors involved in this event are not understood fully. We used a mobility-shift electrophoresis assay to identify a specific RNA-protein complex, which can form between an RNA fragment that contains nucleotides 559-624 of the poliovirus 5' UTR (untranslated region) and a component or components of a HeLa cell extract. Complex formation was reduced greatly in a reticulocyte lysate or a wheat-germ extract. A 52-kD polypeptide (p52) has been identified as part of the protein-RNA complex by use of an UV cross-linking assay. This polypeptide apparently is not a known translation initiation or elongation factor. The possible involvement of p52 in translation initiation of poliovirus protein synthesis is discussed.
New suppressors of signal-sequence mutations, prlG, are linked tightly to the secE gene of Escherichia coli.
Authors: Stader J , Gansheroff L J , Silhavy T J
Published: June 2007

Analysis of more than 100 extragenic suppressors of the lamB14D signal-sequence mutation (changes Val in the hydrophobic core region at position 14 to Asp) has revealed alterations that appear to lie at prlA (secY) and secA (prlD), two loci known to be mutable to suppressor alleles, and a new suppressor termed prlG. One allele of the new suppressor class, prlG1, has been characterized in some detail. This suppressor counteracts, to some degree, the export defect conferred by a variety of signal-sequence mutations in two different genes, lamB and malE. Genetic analysis shows that the dominant suppressor mutations are linked tightly to, and probably allelic with, the gene secE. This result, coupled with data obtained with conditional-lethal alleles of secE, argues strongly that SecE is an important component of the cellular protein export machinery in Escherichia coli.
V(D)J recombination: a functional definition of the joining signals.
Authors: Hesse J E , Lieber M R , Mizuuchi K , Gellert M
Published: June 2007

Two conserved DNA sequences serve as joining signals in the assembly of immunoglobulins and T-cell receptors from V-, (D)-, and J-coding segments during lymphoid differentiation. We have examined V(D)J recombination as a function of joining signal sequence. Plasmid substrates with mutations in one or both of the heptamer-spacer-nonamer sequences were tested for recombination in a pre-B-cell line active in V(D)J recombination. No signal variant recombines more efficiently than the consensus forms of the joining signals. We find the heptamer sequence to be the most important; specifically, the three bases closest to the recombination crossover site are critical. The nonamer is not as rigidly defined, and it is not important to maintain the five consecutive As that distinguish the consensus nonamer sequence. Both types of signals display very similar sequence requirements and have in common an intolerance for changes in spacer length greater than 1 bp. Although the two signal types share sequence motifs, we find no evidence of a role in recombination for homology between the signals, suggesting that they serve primarily as protein recognition and binding sites.
An adenovirus early region 4 gene product is required for induction of the infection-specific form of cellular E2F activity.
Authors: Hardy S , Engel D A , Shenk T
Published: June 2007

E2F is a cellular, sequence-specific DNA-binding factor that binds to pairs of sites that occur upstream of the E1A and E2 early mRNA cap sites. During adenovirus infection, there is induction of a form of E2F that binds cooperatively to the pair of sites in the E2 control region. Production of the infection-specific E2F activity is dependent on early region 4 (E4), as extracts of cells infected with a mutant that lacks E4 did not contain this activity. Instead, two new forms of E2F were seen with the E4 mutant. Infection with mutant viruses unable to make E1A gene products produced the wild-type infection-specific E2F activity after a delay. Mutations in the E1B-55 kD-, E1B-21 kD-, E2-72 kD-, and E3-coding regions had no effect on production of infection-specific E2F. Analysis of cell lines confirmed the results obtained with mutant viruses. Cells that expressed E1A but not E4 genes (e.g., 293 cells) did not contain infection-specific E2F. Cell lines that expressed the E4 gene contained the activity. These observations demonstrate that E4 participates in the infection-induced change in E2F-binding activity. The data are consistent with E1A playing an indirect role in the process by mediating the efficient expression of E4 gene products which, in turn, induce the alteration in E2F activity.
Expression of achaete and scute genes in Drosophila imaginal discs and their function in sensory organ development.
Authors: Romani S , Campuzano S , Macagno E R , Modolell J
Published: June 2007

Several kinds of sensory organs (SOs) appear in stereotyped positions on the adult Drosophila cuticle. The generation of these SOs requires the activity of the achaete (ac) and scute (sc) genes. To investigate whether ac and sc also provide spatial information for the positioning of SOs, we have analyzed the patterns of expression of these genes in the wing imaginal disc around the time that SO precursors are being specified. We find that expression coincides with and is restricted to areas of the disc where these precursors are known to be located. In the loss-of-function sc mutant, sc RNA is depleted in a single area located in the region where the precursor for the suppressed macrochaeta should be found. Moreover, some, and probably all, SOs require expression of these genes to reach the earliest detectable differentiated state. These and other results presented here, together with the finding that expansion of the areas of ac and/or sc expression causes the development of ectopic SOs, indicate that ac and sc promote the determination of SO precursors and delimit the regions of the imaginal discs where they can develop.
Notch is required for successive cell decisions in the developing Drosophila retina.
Authors: Cagan R L , Ready D F
Published: June 2007

Mutations in the Notch locus affect a variety of developmental decisions in Drosophila. In this paper, we examine the role of Notch in the developing retina. We reduced Notch activity at successive intervals during development of the retina, and then examined the effect on individual cells. When Notch activity was reduced, cells responded by selecting inappropriate developmental pathways. We found that all cell types appear to require Notch when establishing their fate. To examine further Notch's role in eye development, we examined two alleles of Notch--split and facet-glossy. split flies show defects in the initial clustering of photoreceptors, whereas the defects in facet-glossy flies are due to the misrouting of presumptive primary pigment cells into the secondary pigment cell pathway. Our results suggest that Notch plays a permissive role in the cell-cell interactions used to assemble the eye.
Accurate, TATA box-dependent polymerase III transcription from promoters of the c-myc gene in injected Xenopus oocytes.
Authors: Bentley D L , Brown W L , Groudine M
Published: June 2007

We have investigated the factors that permit a gene normally transcribed by RNA polymerase II to be transcribed by RNA polymerase III. It was shown previously that the human c-myc gene could be transcribed in vitro and in Xenopus oocytes by both alpha-amanitin-sensitive and alpha-amanitin-resistant polymerases, probably corresponding to polymerase II and polymerase III. We confirmed this observation in microinjected oocytes and showed that the alpha-amanitin-resistant transcription of c-myc was competed by known polymerase III genes. Polymerase III transcription of c-myc was very inefficient compared to other polymerase III genes, however, and was observed only when large amounts of template DNA were injected. At lower DNA concentrations the gene was transcribed, exclusively by polymerase II. In contrast, the adenovirus major late promoter was not transcribed by polymerase III. The 5' ends of polymerase III RNAs were almost indistinguishable from those of polymerase II RNAs initiating at the P1 and P2 promoters of the human and mouse c-myc genes. Furthermore, point mutations in the TATA box of the human P2 promoter greatly reduced polymerase III activity. At this promoter, therefore, polymerase II and polymerase III recognize a common element, the TATA box, which probably plays an important role in specifying the start site of transcription for both polymerases. We suggest that the highly accurate though inefficient mimicry of polymerase II by polymerase III at the c-myc promoters reflects the common evolutionary origin of these two enzymes.
The growth hormone-binding protein in rat serum is an alternatively spliced form of the rat growth hormone receptor.
Authors: Baumbach W R , Horner D L , Logan J S
Published: June 2007

A cDNA clone isolated from rat liver was demonstrated to encode a soluble, secreted growth hormone (GH)-binding protein consistent with the properties of the newly discovered serum GH-binding protein. The protein coding region of this cDNA was identical in sequence to the extracellular domain of the rat liver GH receptor up to three amino acids before the putative transmembrane domain. At this point, an additional 17 amino acids were encoded in the GH-binding protein before a stop codon was encountered. This cDNA clone was shown to be representative of the structure of the mRNA present in rat liver. These results suggest that the mechanism for production of the rat serum GH-binding protein is by alternative splicing of the gene for the rat GH receptor.
Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae.
Authors: Vijayraghavan U , Company M , Abelson J
Published: June 2007

In this study we report the isolation of temperature-sensitive mutants that affect pre-mRNA splicing. A bank of approximately 1000 temperature-sensitive Saccharomyces cerevisiae strains was generated and screened on RNA gel blots by hybridization with an actin intron probe. We isolated 16 mutants defining 11 new complementation groups prp(rna)17-prp(rna)27 with four phenotypic classes of mutants and 21 mutants in the prp2-prp11 complementation groups (formerly rna2-rna11). The majority of the complementation groups share a phenotype of pre-mRNA accumulation, seen in all of the prp(rna)2-prp(rna)11 mutants. Three novel classes of mutants were isolated in this study. One class, consisting of two complementation groups, exhibits an accumulation of the lariat intermediate of splicing, with no change in the levels of pre-mRNA. The second class, also represented by two complementation groups, shows an accumulation of the intron released after splicing. The third novel class, comprising one complementation group, accumulates both pre-mRNA and the released intron. All mutants isolated were recessive for the splicing phenotype. Only 2 of the 11 complementation groups, although recessive, were not temperature sensitive. This study, together with previous isolation of the prp(rna)2-prp(rna)11 groups and the spliceosomal snRNAs, puts at least 26 gene products involved directly or indirectly in pre-mRNA splicing.
Induction of a heat shock-like response by unfolded protein in Escherichia coli: dependence on protein level not protein degradation.
Authors: Parsell D A , Sauer R T
Published: June 2007

To test the idea that unfolded protein might act as an intracellular signal for induction of the heat shock response in Escherichia coli, we examined the synthesis of several heat shock proteins after expression of an unfolded variant of the amino-terminal domain of lambda repressor. These experiments show that expression of a single mutant protein, and not its wild-type counterpart, is sufficient to induce a heat shock-like response. In addition, by measuring the abilities of unfolded variants of differing proteolytic susceptibilities to induce heat shock protein synthesis and by monitoring heat shock protein synthesis as a function of the amount of a single unfolded protein, we show that it is the concentration of unfolded protein in the cell, and not its degradation, that is important for inducing the heat shock-like response.
P-element-mediated enhancer detection: an efficient method for isolating and characterizing developmentally regulated genes in Drosophila.
Authors: Wilson C , Pearson R K , Bellen H J , O'Kane C J , Grossniklaus U , Gehring W J
Published: June 2007

We describe a new approach for identifying and studying genes involved in Drosophila development. Single copies of an enhancer detector transposon, P[1ArB], have been introduced into flies at many different genomic locations. The beta-galactosidase reporter gene in this construct is influenced by a wide range of genomic transcriptional regulatory elements in its vicinity. Our results suggest that a significant proportion of these regulatory sequences are control elements of nearby Drosophila genes. These genes need not be disrupted for their regulatory elements to be identified by P[1ArB]. The P[1ArB] transposon has been designed to facilitate both rapid cloning and deletion analysis of genomic sequences into which it inserts. Therefore, the enhancer detection system is an efficient method of screening for genes primarily on the basis of their expression pattern and then rapidly analyzing those of particular interest at the molecular and genetic levels.
CCAAT/enhancer binding protein activates the promoter of the serum albumin gene in cultured hepatoma cells.
Authors: Friedman A D , Landschulz W H , McKnight S L
Published: June 2007

An expression vector capable of encoding full-length CCAAT/enhancer-binding protein (C/EBP) has been constructed and tested in transient transfection assays for its capacity to activate transcription from the promoter of the serum albumin gene. When tested in cultured hepatoma cells, the C/EBP expression vector achieved potent trans-activation of the albumin promoter. Less substantial activation was observed when the same experiment was conducted using cultured mouse fibroblasts. Expression vectors that encoded defective forms of C/EBP failed to activate the albumin promoter. Moreover, mutated variants of the albumin promoter that lack the C/EBP-binding site failed to be trans-activated. The data are consistent with the interpretation that C/EBP is a bona fide transcription factor. During the course of these experiments it was noted also that C/EBP is more than an order of magnitude less concentrated in cultured hepatoma cells than it is in adult liver cells. Given these findings, we speculate that C/EBP may play a general role in establishing and maintaining the differentiated, nonproliferative state.
Loss of Ras activity in Saccharomyces cerevisiae is suppressed by disruptions of a new kinase gene, YAKI, whose product may act downstream of the cAMP-dependent protein kinase.
Authors: Garrett S , Broach J
Published: June 2007

The yeast Saccharomyces cerevisiae contains two functionally redundant genes RAS1 and RAS2, which are homologous to the mammalian ras gene family and are required for vegetative growth. We isolated and characterized five temperature-sensitive alleles of RAS2. In a ras1 strain, these alleles cause growth arrest at the G1 stage of the cell cycle. Revertants capable of growth at the nonpermissive temperature define four recessive, extragenic complementation groups. Suppressors in one complementation group (designated yak1) are particularly intriguing because they appear to alleviate only the growth defect of the temperature-sensitive ras mutants and do not show any of the phenotypes, such as heat shock sensitivity or starvation sensitivity, associated with increased production of cAMP. The YAK1 gene has been cloned, and disruptions generated in vitro reveal that it is not essential for growth and that its loss confers growth to a strain deleted for tpk1, tpk2, and tpk3, the structural genes for the catalytic subunit of the cAMP-dependent protein kinase. These results place Yak1 downstream from, or on a parallel pathway to, the kinase step in the Ras/cAMP pathway. Finally, the coding region predicts a protein with significant homology to the family of protein kinases, suggesting that loss of cAMP-dependent protein kinase function can be suppressed by the loss of a second protein kinase.
STE12, a protein involved in cell-type-specific transcription and signal transduction in yeast, is part of protein-DNA complexes.
Authors: Errede B , Ammerer G
Published: June 2007

The STE12 gene of Saccharomyces cerevisiae is essential for the expression of genes required for mating, such as those involved in pheromone response, and for genes unrelated to mating but regulated by the presence of an adjacent copy of the transposable element Ty1. We show that the STE12 protein is a component of specific DNA-protein complexes that form with transcriptional control elements from Ty1 and the alpha-pheromone receptor gene STE2. Although a sequence involved in pheromone-dependent transcriptional activation is protected in both complexes, competition experiments indicate that the complexes are intrinsically different from each other. We show that another factor involved in cell-type-specific transcription, PRTF/GRM, is a component of the complex with the STE2 fragment but not the Ty1 fragment. We propose that the STE12 product interacts with different transcription factors in different sequence contexts and that PRTF/GRM is one of these factors.
The mab-9 gene controls the fate of B, the major male-specific blast cell in the tail region of Caenorhabditis elegans.
Authors: Chisholm A D , Hodgkin J
Published: June 2007

The internal structures of the tail of male Caenorhabditis elegans nematodes are made by the descendants of four cells (B, Y, F, and U) which divide only in males. These cells are also present in hermaphrodites, where they have minor structural roles in the rectum. Here we show that the gene mab-9 is required for the correct development of two of these male-specific blast cells, B and F. In mutant males, the lineages of B and F resemble those of Y and U, respectively. These abnormal lineages lead to grossly defective male tails. We suggest that in mab-9 males the identities of B and F are transformed into Y and U, their respective anterior neighbors. The case for the F-to-U transformation is less strong than for the B-to-Y transformation because the wild-type lineages of F and U are very similar. Some mab-9 hermaphrodites are constipated as a result of abnormal rectal structure. This may be the result of an analogous fate transformation. mab-9 worms of both sexes are slightly uncoordinated. We propose that the fates of the four rectal cells are initially specified as two pairs (B and Y, F and U) and that the function of mab-9 in both sexes is to differentiate the posterior member of each pair from its anterior neighbor.
The molecular genetics of the bithorax complex of Drosophila: characterization of the products of the Abdominal-B domain.
Authors: Celniker S E , Keelan D J , Lewis E B
Published: June 2007

In Drosophila the Abdominal-B (Abd-B) domain of the bithorax complex specifies the identities of several posterior abdominal segments, comprises homeo-protein-coding regions and cis-regulatory regions, and extends from infra-abdominal-5 (iab-5) to iab-8, inclusive. Mutations that eliminate the Abd-B domain act as late embryonic lethals and result in transformations of posterior abdominal segments toward more anterior ones. The Abd-B domain gives rise to a minimum of five homeo-box-containing transcripts, 7.8, 4.7, 4.3, 3.7, and 3.3 kb in length. We examined the structure of the Abd-B domain by sequencing two Abd-B cDNA clones derived from the 4.3- and the 4.7-kb transcripts and the corresponding genomic DNA. The domain spans approximately 100 kb and contains at least eight exons. The 4.7- and 4.3-kb transcripts contain an open reading frame capable of encoding a 54-kD protein. A portion of the deduced protein-coding sequence common to all of the Abd-B transcripts was cloned into an expression vector. The resultant fusion protein then was used to derive a monoclonal antibody specific to Abd-B. By use of that antibody, we identified two embryonic Abd-B proteins, 54 and 36 kD and determined the sum of their segmental distribution by immunohistochemical analysis of whole-mounted embryos and immunofluorescent analysis of dissected embryonic nervous systems. The proteins are distributed in the fourth to the ninth abdominal segments [parasegments (PS) 10-15] inclusive. Embryos homozygous for Polycomb (Pc) show labeling over almost the entire embryo, whereas embryos deficient for the Abd-B domain show no detectable labeling.
DNA regions that regulate the ovarian transcriptional specificity of Drosophila yolk protein genes.
Authors: Logan S K , Garabedian M J , Wensink P C
Published: June 2007

Yolk protein genes 1 and 2 (yp1 and yp2) of Drosophila melanogaster are divergently transcribed neighboring genes. Both are transcribed in only two tissues, the ovarian follicle cells and the fat bodies of adult females. Previous work has identified a yolk protein enhancer between the genes that is sufficient to direct transcription in one of the tissues, female fat bodies. Using germ-line transformation methods, we identify two cis-acting regions with positive effects on transcription in ovaries. One, a 301-bp region located between the genes, influences both genes and is an enhancer determining the stage and cell type specificity of ovarian transcription. The other, a 105-bp region located in the first exon of yp2, acts across the yp2 promoter region to stimulate yp1 transcription in ovaries. Additional observations suggest how a single enhancer influences both promoters.
The E2 trans-activator can act as a repressor by interfering with a cellular transcription factor.
Authors: Stenlund A , Botchan M R
Published: June 2007

The E2 open reading frame (ORF) of the bovine papillomavirus (BPV-1) encodes a family of site-specific DNA-binding proteins. The full-length protein is a transcriptional activator, whereas the polypeptides that contain only the carboxy-terminal domain are repressors. Here we show that the trans-activator can work as a repressor of transcription for one of the BPV-1 promoters by binding to a DNA sequence required for basal activity of the promoter. This operator site is defined as a 12-bp sequence that lies immediately downstream of the cap site. The operator DNA contains sequences that are defined genetically and biochemically as being important for basal level promoter activity. Furthermore, this site has been shown to be protected in a DNase footprint assay using fractionated HeLa cell extracts. The repression does not simply result from E2 blocking RNA polymerase initiation or elongation, because a strong E2-binding site placed at the operator has no repressive effect on transcription when the basal target sequence is placed independently upstream of the promoter. Thus, this is an interesting parallel to a theme well known in prokaryotes, where some site-specific DNA-binding proteins can work as either activators or repressors. In this system, as well as in the prokaryotic systems, the precise position of the binding site relative to other cis signals at the promoter determines the nature of the effects.
A DNA-binding protein containing two widely separated zinc finger motifs that recognize the same DNA sequence.
Authors: Fan C M , Maniatis T
Published: June 2007

We have isolated a full-length cDNA clone encoding a protein (PRDII-BF1) that binds specifically to a positive regulatory domain (PRDII) of the human IFN-beta gene promoter, and to a similar sequence present in a number of other promoters and enhancers. The sequence of this protein reveals two novel structural features. First, it is the largest sequence-specific DNA-binding protein reported to date (298 kD). Second, it contains two widely separated sets of C2-H2-type zinc fingers. Remarkably, each set of zinc fingers binds to the same DNA sequence motif with similar affinities and methylation interference patterns. Thus, this protein may act by binding simultaneously to reiterated copies of the same recognition sequence. Although the function of PRDII-BF1 is not known, the level of its mRNA is inducible by serum and virus, albeit with different kinetics.
The two candidate testis-determining Y genes (Zfy-1 and Zfy-2) are differentially expressed in fetal and adult mouse tissues.
Authors: Nagamine C M , Chan K , Hake L E , Lau Y F
Published: June 2007

The candidate testis-determining Y genes of the mouse Zfy-1 and Zfy-2, encode proteins containing an acidic amino terminus and a carboxyl terminus composed of 13 zinc fingers. The zinc finger domain is conserved among human and mouse zinc finger X and Y genes. We report a 6-amino-acid deletion in the Zfy-2 zinc finger domain of laboratory mice possessing musculus Y chromosomes. The effect of this deletion on the function of Zfy-2 is not known. The reverse transcriptase-polymerase chain reaction (RT-PCR) and Northern blot techniques were used to study expression of Zfy in adults and fetuses. In adults, the data suggest that Zfy-1 and Zfy-2 transcription is linked to spermatogenesis, that transcription increases with the initiation of meiosis, and that high levels of these mRNAs are found in postmeiotic round spermatid cells. The data also suggest that differential expression of these two genes is present with expression of Zfy-2 being slightly greater than Zfy-1. In fetuses, Zfy transcripts were detected in several tissues, including the testes. In contrast to the situation in adults, the data suggest that expression of Zfy-1 is greater than that of Zfy-2. The data suggesting that Zfy-1 expression is present in fetal testes support the hypothesis that this gene plays a role in testis differentiation. However, because the Zfy genes are apparently also expressed during spermatogenesis and in fetal organs other than testes, they may serve additional functions besides their postulated role in testis determination.
Activation of M-phase-specific histone H1 kinase by modification of the phosphorylation of its p34cdc2 and cyclin components.
Authors: Pondaven P , Meijer L , Beach D
Published: June 2007

An M-phase-specific histone H1 kinase (H1K) has been described in a wide variety of eukaryotic cell types undergoing the G2/M transition in the cell division cycle. We have used p13suc1-Sepharose affinity chromatography to purify H1K to near homogeneity from matured starfish oocytes. A yield of 67% was obtained. Active H1K behaves as a 90- to 100-kD protein and appears to be constituted of equimolar amounts of cyclin and p34cdc2. The p34cdc2 subunit becomes tyrosine-dephosphorylated as the H1K is activated during entry of the oocytes into M phase, whereas the cyclin subunit is reciprocally phosphorylated. Acid phosphatase treatment of inactive p34cdc2/cyclin complex induces p34cdc2 dephosphorylation and three- to eightfold stimulation of the enzyme activity. These results suggest that active M-phase-specific H1K is constituted of both dephosphorylated p34cdc2 and phosphorylated cyclin.