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At least 793 records · Page 44Linked to original sources
PubMed1989

Transcription of a poxvirus early gene is regulated both by a short promoter element and by a transcriptional termination signal controlling transcriptional interference.

The promoter region of an early gene (38K gene) of cowpox virus has been characterized by deletion and linker scanning mutational analyses. Modified versions of this promoter region were placed into the genome of vaccinia virus, and their transcriptional efficiencies were assessed by quantifying RNAs transcribed from these sequences. These analyses showed that the sequences in the region between 33 and 4 base pairs upstream of the transcriptional start site affect the efficiency of transcription from this promoter. Linker scanning mutations in the -27 to -10 region inhibited transcription. This region contains the sequence 5'-GAAAATATATT-3', which is present in at least two other early genes in the same positions (-21 to -11) relative to the transcriptional start sites of these genes. Elements of this sequence are similarly positioned in the promoter regions of several other poxvirus genes, suggesting that this sequence represents a transcriptional control element of at least a subset of poxvirus genes. The -8 to -2 sequence (5'-TTTTTAT-3') contains a transcriptional termination signal. Mutation of this sequence had two separate effects: (i) it reduced the efficiency of transcription from the promoter by approximately 30%, and (ii) it prevented this sequence from terminating the transcription from upstream genes. When overlapping transcription from upstream genes was not prevented by a termination signal present either within the 38K promoter or upstream of the promoter, transcription from this promoter was reduced by about 30%. This indicates that transcriptional termination has a role in the regulation of viral gene expression by controlling transcriptional interference.

Amino Acid Sequence↗
PubMed1994

Role of transcriptional repressors in transformation by bovine papillomavirus type 1.

Transformation of rodent cells by bovine papillomavirus type 1 (BPV-1) has been shown to require the direct contribution of the viral oncogenes encoded by the E5, E6, and E7 translational open reading frames (ORFs). It is also known that the viral E1 and E2 ORFs contribute indirectly to cellular transformation through their transcriptional modulation of these viral oncogenes. A mutant BPV-1 disrupted in two of the proteins encoded by the E2 ORF, the E2 transcriptional repressors, has a complex transformation phenotype. In this paper, we provide evidence that (i) this phenotype is not attributable to the absence of other viral genes that overlap the E2 repressor genes, (ii) the acquisition of transformation over time in cells harboring the E2 double-repressor mutant correlates with reversions of the mutations that disrupt one of the E2 repressor genes, E8/E2TR, and (iii) the initial transformation defect in the E2 double-repressor mutant can be rescued by disruption of the full-length protein encoded by the E1 ORF, the E1 transcriptional repressor. We propose a model by which the combination of E1 and E2 transcriptional repressors functions to modulate the transforming capacity of the virus.

Animals↗
PubMed2005

Genomic responses in rat cerebral cortex after traumatic brain injury.

BACKGROUND: Traumatic brain injury (TBI) initiates a complex sequence of destructive and neuroprotective cellular responses. The initial mechanical injury is followed by an extended time period of secondary brain damage. Due to the complicated pathological picture a better understanding of the molecular events occurring during this secondary phase of injury is needed. This study was aimed at analysing gene expression patterns following cerebral cortical contusion in rat using high throughput microarray technology with the goal of identifying genes involved in an early and in a more delayed phase of trauma, as genomic responses behind secondary mechanisms likely are time-dependent. RESULTS: Among the upregulated genes 1 day post injury, were transcription factors and genes involved in metabolism, e.g. STAT-3, C/EBP-delta and cytochrome p450. At 4 days post injury we observed increased gene expression of inflammatory factors, proteases and their inhibitors, like cathepsins, alpha-2-macroglobulin and C1q. Notably, genes with biological function clustered to immune response were significantly upregulated 4 days after injury, which was not found following 1 day. Osteopontin and one of its receptors, CD-44, were both upregulated showing a local mRNA- and immunoreactivity pattern in and around the injury site. Fewer genes had decreased expression both 1 and 4 days post injury and included genes implicated in transport, metabolism, signalling, and extra cellular matrix formation, e.g. vitronectin, neuroserpin and angiotensinogen. CONCLUSION: The different patterns of gene expression, with little overlap in genes, 1 and 4 days post injury showed time dependence in genomic responses to trauma. An early induction of factors involved in transcription could lead to the later inflammatory response with strongly upregulated CD-44 and osteopontin expression. An increased knowledge of genes regulating the pathological mechanisms in trauma will help to find future treatment targets. Since trauma is a risk factor for development of neurodegenerative disease, this knowledge may also reduce late negative effects.

Animals↗
PubMed2001

Mice doubly deficient for the Polycomb Group genes Mel18 and Bmi1 reveal synergy and requirement for maintenance but not initiation of Hox gene expression.

Polycomb group genes were identified as a conserved group of genes whose products are required in multimeric complexes to maintain spatially restricted expression of Hox cluster genes. Unlike in Drosophila, in mammals Polycomb group (PcG) genes are represented as highly related gene pairs, indicative of duplication during metazoan evolution. Mel18 and Bmi1 are mammalian homologs of Drosophila Posterior sex combs. Mice deficient for Mel18 or Bmi1 exhibit similar posterior transformations of the axial skeleton and display severe immune deficiency, suggesting that their gene products act on overlapping pathways/target genes. However unique phenotypes upon loss of either Mel18 or Bmi1 are also observed. We show using embryos doubly deficient for Mel18 and Bmi1 that Mel18 and Bmi1 act in synergy and in a dose-dependent and cell type-specific manner to repress Hox cluster genes and mediate cell survival of embryos during development. In addition, we demonstrate that Mel18 and Bmi1, although essential for maintenance of the appropriate expression domains of Hox cluster genes, are not required for the initial establishment of Hox gene expression. Furthermore, we show an unexpected requirement for Mel18 and Bmi1 gene products to maintain stable expression of Hox cluster genes in regions caudal to the prospective anterior expression boundaries during subsequent development.

Animals↗
PubMed1986

Nucleotide sequence and in vivo expression of the ilvY and ilvC genes in Escherichia coli K12. Transcription from divergent overlapping promoters.

The ilvC gene of Escherichia coli K12 encodes acetohydroxy acid isomeroreductase, the second enzyme in the parallel isoleucine-valine biosynthetic pathway. Previous data have shown that transcription of the ilvC gene is induced by the acetohydroxy acid isomeroreductase substrates, acetohydroxybutyrate or acetolactate, and that this substrate induction of ilvC expression is mediated by a positive activator encoded by the ilvY gene. We report here the isolation and complete nucleotide sequence of the ilvY and ilvC genes. The ilvY and ilvC genes encode polypeptides of Mr 33,200 and 54,000, respectively. In vitro transcription-translation of these gene templates results in the synthesis of gene products of these identical molecular weights. The ilvC gene is transcribed in the same direction as the genes of the adjacent ilvGMEDA operon. The ilvY gene is transcribed in a direction opposite to the ilvC and ilvGMEDA genes. The in vivo transcriptional initiation sites of the ilvY and ilvC genes have been determined by S1 nuclease protection experiments. These transcriptional initiation sites are 45 nucleotides apart, and transcription of the ilvY and ilvC genes is initiated via divergent overlapping promoters. The nucleotide sequence of the ilvY and ilvC promoters and 5'-coding regions of Salmonella typhimurium LT2 have been determined. A comparison of these sequences with E. coli K12 suggests regions important in the promotion, regulation, and translation of the ilvY and ilvC genes. A model is presented in which the ilvY-encoded activator binds to an operator site in the overlapping promoter region and reciprocally regulates the transcription of the ilvY and ilvC genes. The carboxyl-terminal amino acid sequence of threonine deaminase encoded by the ilvA gene of the ilv-GMEDA operon of E. coli K12 has been identified by homology with the previously deduced threonine deaminase amino acid sequence encoded by the ilv1 gene of Saccharomyces cerevisiae. Based on the deduced amino acid sequences of the ilvA and ilvY genes, the translational termination codons for both genes are shown to be separated by 52 nucleotides. The proximity of the ilvA and ilvY genes suggests that the 3'-ends of these transcripts overlap.

Alcohol Oxidoreductases↗
PubMed1996

Alternate promoters and alternate splicing of human tenascin-X, a gene with 5' and 3' ends buried in other genes.

Tenascin-X (TN-X) is an extracellular matrix protein encoded by a large gene that overlaps the steroid 21-hydroxylase (P450c21) gene in the HLA locus on chromosome 6p21.3. This may be the most complex locus in the human genome identified to date, containing 13 overlapping transcription units in 160 kb of DNA. Previous studies determined the sequence of 39 TN-X exons, encoding a 12 kb open reading frame, but the promoter(s) of the gene had not been located. We identify the principal TN-X promoter and a previously unknown 5' untranslated exon that lies more than 10 kb upstream from the previously known exons. This promoter, which is substantially different from the promoter for TN-C, initiates transcription in human fetal adrenal and muscle, but expression in human NCI-H295 adrenocortical carcinoma cells is initiated by two other promoters lying further upstream. One of these is the same as the promoter for a recently identified Creb-related protein (Creb-rp), but transcripts initiated form this promoter in human adrenal NCI-H295 tumor cells are spliced differently from Creb-rp, and are largely retained in the nuclei of these cells. By analogy with the other two members of the tenascin family, TN-C and TN-R, it has been predicted that TN-X should undergo alternate splicing in its fibronectin-like domains. RACE cloning and RNase protection experiments reveal no such alternate splicing. The TN-X gene appears to be unique in having both its 5' and 3' ends buried in other genes.

Adrenal Glands↗
PubMed1980

DNA sequence of the int-xis-Pi region of the bacteriophage lambda; overlap of the int and xis genes.

The DNA sequence of the int and xis genes of lambda bacteriophage, as well as that of the PI promoter and a region of unknown function beyond this, was determined by the chain termination procedure. The Pribnow box sequence of the PI promoter lies just within the xis gene, and both possible sites of mRNA initiation from PI are within the xis gene. The end of the xis gene in its turn overlaps the start of the int gene by 23 base pairs, in a different reading frame. This overlap may play a role in ensuring efficient excision of the prophage in response to natural induction signals.

Amino Acid Sequence↗
PubMed1994

Structure of the mouse cholesterol 7 alpha-hydroxylase gene.

Three overlapping cholesterol 7 alpha-hydroxylasecDNAs were cloned from total mouse liver RNA by a combination of the polymerase chain reaction and mouse liver cDNA library screening. One of the cDNA clones was used to screen a mouse genomic library; three genomic clones were isolated and one of them was fully characterized. The mouse cholesterol 7 alpha-hydroxylase gene spans approximately 10 kb. The gene contains six exons including a 1509-bp open reading frame encoding 503 amino acid residues. The predicted amino acid sequence of mouse cholesterol 7 alpha-hydroxylase showed 93 and 82% identity to the rat and human enzymes, respectively. The transcription initiation site is mapped to 64 bases 5' of the translation initiation codon. Several transcription factor binding sequences are identified in the 5' flanking region of the mouse cholesterol 7 alpha-hydroxylase gene.

Amino Acid Sequence↗
PubMed1983

Cloning of a human complement component C4 gene.

Six overlapping cosmid clones having an average insert size of 40 kilobase pairs were identified and isolated from a human genomic library by using a cDNA probe, Alu-7, specific for the amino acid sequence of C4d, a known region of the fourth component of human complement. Analysis of these genomic clones by restriction digestion and Southern blotting shows that all six probably contain the same complete C4 gene. Nucleotide sequence comparison of the genomic clone Cos-A and the cDNA clone Alu-7 shows an identical sequence except for the presence of a 1,500-base-pair intron in the genomic sequence. The amino acid sequence predicted from the nucleotide sequence agrees with the known C4d region amino acid sequence with one exception.

Amino Acid Sequence↗
PubMed1999

Overlapping positive and negative GATA factor binding sites mediate inducible DAL7 gene expression in Saccharomyces cerevisiae.

Allantoin pathway gene expression in Saccharomyces cerevisiae responds to two different environmental stimuli. The expression of these genes is induced in the presence of allantoin or its degradative metabolites and repressed when a good nitrogen source (e. g. asparagine or glutamine) is provided. Three types of cis-acting sites and trans-acting factors are required for allantoin pathway gene transcription as follows: (i) UAS(NTR) element associated with the transcriptional activators Gln3p and Gat1p, (ii) URS(GATA) element associated with the repressor Dal80p, and (iii) UIS(ALL) element associated with the Dal82 and Dal81 proteins required for inducer-dependent transcription. Most of the work leading to the above conclusions has employed inducer-independent allantoin pathway genes (e.g. DAL5 and DAL3). The purpose of this work is to extend our understanding of these elements and their roles to inducible allantoin pathway genes using the DAL7 (encoding malate synthase) as a model. We show that eight distinct cis-acting sites participate in the process as follows: a newly identified GC-rich element, two UAS(NTR), two UIS(ALL), and three URS(GATA) elements. The two GATA-containing UAS(NTR) elements are coincident with two of the three GATA sequences that make up the URS(GATA) elements. The remaining URS(GATA) GATA sequence, however, is not a UAS(NTR) element but appears to function only in repression. The data provide insights into how these cis- and trans-acting factors function together to accomplish the regulated expression of the DAL7 gene that is observed in vivo.

Allantoin↗
PubMed1988

The Abdominal-B gene of Drosophila melanogaster: overlapping transcripts exhibit two different spatial distributions.

The Abdominal-B (Abd-B) gene of Drosophila controls the specification of segment identities in the posterior abdomen. We describe here the spatial and temporal distribution of Abd-B transcripts. At least five RNA species are detected on Northern blots with probes within the region of the Abd-B homeobox. We have identified probes specific for subsets of these transcripts and have used these probes to study the distribution of each subset by in situ hybridization to embryonic tissue sections. The transcripts can be divided into two groups: one group is expressed maximally in parasegment (PS)13 and extends anteriorly to PS10; the other is expressed only in PS14 and 15. These two different patterns of expression correspond to the anatomical domains defined by two classes of mutations in Abd-B. These results help explain the complex genetic interactions and phenotypes of mutations within this gene.

Journal Article↗
PubMed1991

Structure and function of the maize Spm transposable element.

The Spm's primary transcript is alternatively spliced to give at least 4 different transcripts which code for proteins with extensive overlapping domains. Two of these proteins, the tnpA and tnpD gene products, are necessary and sufficient to promote dSpm transposition in tobacco. Moreover, the tnpA gene product is also sufficient to suppress the basal level of expression observed in some dSpm-disrupted genes, and probably to activate the expression of inactive elements and of other dSpm-disrupted genes. The functions of the tnpB and tnpC gene products remain unknown. However, their structure suggests that they act as negative regulators of the Spm transposase function.

DNA Transposable Elements↗
PubMed1994

Cloning of cDNAs and the molecular evolution of a bovine MHC class II DRA gene.

Two overlapping cDNA clones coding for bovine major histocompatibility complex (MHC) class II antigen DRA chain were isolated and characterized. The full-length cDNA clone, MR1, encoded a primary translated product of 253 amino acids, 24 of which were deduced to be a signal peptide and 229 which formed a mature polypeptide. The amino acid sequences deduced from this clone resembled those of class II A molecules from other species in both size and structure, but no potential consensus site of N-linked glycosylation comparable to those in the human, mouse, rat and swine proteins was found in the alpha 2 domain, as well as ovine and equine DRA molecules. Comparison of amino acid sequences encoded by class II A genes among several species and a dendrogram constructed from these data places the DRA gene and the DQA/DYA genes on two distinct branches of a phylogenetic tree, with bovine DRA and ovine DRA being most similar on the DRA branch.

Amino Acid Sequence↗
PubMed2005

Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries.

BACKGROUND: In expressed sequence tag (EST) sequencing, we are often interested in how many genes we can capture in an EST sample of a targeted size. This information provides insights to sequencing efficiency in experimental design, as well as clues to the diversity of expressed genes in the tissue from which the library was constructed. RESULTS: We propose a compound Poisson process model that can accurately predict the gene capture in a future EST sample based on an initial EST sample. It also allows estimation of the number of expressed genes in one cDNA library or co-expressed in two cDNA libraries. The superior performance of the new prediction method over an existing approach is established by a simulation study. Our analysis of four Arabidopsis thaliana EST sets suggests that the number of expressed genes present in four different cDNA libraries of Arabidopsis thaliana varies from 9155 (root) to 12005 (silique). An observed fraction of co-expressed genes in two different EST sets as low as 25% can correspond to an actual overlap fraction greater than 65%. CONCLUSION: The proposed method provides a convenient tool for gene capture prediction and cDNA library property diagnosis in EST sequencing.

Algorithms↗
PubMed1990

Restoration of the yeast LEU2 gene by transcriptionally controlled recombination between tandem repeats.

The LEU2 gene of a his3 strain was inactivated by inserting the HIS3 gene between two overlapping inactive leu2 gene fragments, and mitotic stability of the resulting leu2:HIS3::leu2 sequence was measured under leucine repression and derepression. Both inactive leu2 regions were transcribed under derepressing conditions (growth in low leucine), and the LEU2 gene was completely restored by illegitimate recombination between the overlapping tandem repeats, leading to the loss of the intervening HIS3 gene. In contrast, only the downstream leu2 fragment was transcribed upon leucine repression, and the HIS3 insert in the leu2 region remained intact. The reciprocal experiment (inactivation of the HIS3 gene by inserting the marker gene LEU2) revealed a moderate rate of HIS3 restoration and LEU2 excision, reflecting transcriptional activity of the HIS3 region intermediate between that of LEU2 transcription in the repressed and derepressed state.

Blotting, Northern↗
PubMed1995

Extensive alternate exon usage at the 5' end of the sheep tropoelastin gene.

Several overlapping cDNA clones were isolated from a lambda gt10 cDNA library constructed using poly A+ RNA from neonatal sheep lung. DNA sequence analysis of these cDNA recombinants revealed the complete derived amino acid sequence of sheep tropoelastin. A comparison of DNA sequences from individual sheep tropoelastin cDNA also confirmed the presence of several tropoelastin mRNA isoforms in neonatal lung tissue. Coding domains corresponding to exons 13, 14 and 33 were present in several of the sheep tropoelastin cDNA fragments but absent in others. The relative amount of alternate usage of these exons was quantitated by polymerase chain amplification. In confirmation of previous studies in other mammalian species, extensive alternate usage of exon 33 was observed in total RNA isolated from aorta, nuchal ligament and pulmonary artery from neonatal sheep. In striking contrast to all previous studies, however, exons 13 and 14 were shown to be subject to almost the same level of alternate usage as exon 33 in all three neonatal sheep tissues examined.

Alternative Splicing↗
PubMed1991

Two homologous regulatory genes, lin-12 and glp-1, have overlapping functions.

Two homologous genes, lin-12 and glp-1, encode transmembrane proteins required for regulatory cell interactions during C. elegans development. Based on their single mutant phenotypes, each gene has been thought to govern a distinct set of cell fates. We show here that lin-12 and glp-1 are functionally redundant during embryogenesis: Unlike either single mutant, the lin-12 glp-1 double mutant dies soon after hatching. Numerous cellular defects can be observed in these Lag (for lin-12 and glp-1) double mutants. Furthermore, we have identified two genes, lag-1 and lag-2, that appear to be required for both lin-12 and glp-1-mediated cell interactions. Strong loss-of-function lag mutants are phenotypically indistinguishable from the lin-12 glp-1 double; weak lag mutants have phenotypes typical of lin-12 and glp-1 single mutants. We speculate that the lin-12 and glp-1 proteins are biochemically interchangeable and that their divergent roles in development may rely largely on differences in gene expression.

Animals↗
PubMed2003

Difference between Swedish and Japanese men in the association between AR CAG repeats and prostate cancer suggesting a susceptibility-modifying locus overlapping the androgen receptor gene.

Previous studies have shown that short CAG repeats in the androgen receptor (AR) gene are associated with increased risk of prostate cancer. It is unclear if this association is due to linkage disequilibrium with a susceptibility locus or directly linked to the possible functional impact of the length of the CAG repeats. In this study, the number of the AR CAG repeats was determined in prostate cancer patients, benign prostatic hyperplasia (BPH) patients, and controls in both Swedish and Japanese men. Prostate cancer patients included 59 Swedish hereditary, 59 Swedish sporadic and 33 Japanese sporadic cases. BPH patients included 38 Swedish and 33 Japanese cases. Controls included 98 Swedish healthy men and 43 Japanese men without either prostate cancer or BPH. No significant difference in AR CAG repeats was found in comparison between BPH patients and controls. In contrast, both Swedish hereditary and sporadic prostate cancer patients had shorter AR CAG repeats than Swedish controls, but Japanese prostate cancer patients had longer repeats than controls. These differences between the two populations in the association of prostate cancer and the AR CAG repeats may suggest that the AR CAG repeats are in linkage disequilibrium with a prostate cancer susceptibility locus localized in a small region flanking or overlapping the AR gene at Xq12.1.

Adolescent↗