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At least 757 records · Page 42Linked to original sources
PubMed1999

Prevalence and significance of naturally occurring mutations in the surface and polymerase genes of hepatitis B virus.

The prevalence and clinical significance of naturally occurring mutations in the full-length surface and overlapping polymerase genes of hepatitis B virus (HBV) were analyzed in 42 patients with chronic hepatitis. Mutations were observed in 10 patients (24%) in the a determinant region, which is the neutralizing epitope within the major hydrophilic region of the surface gene. A high proportion of these mutations (17/18; 94%) occurred in the first loop, unlike mutations induced by immunization. The presence of serum antibody to hepatitis B surface antigen was significantly associated with these mutations. No other region of the surface gene contained any cluster of mutations. These results suggest that escape mutations commonly contribute to persistency in the natural course of HBV infection. In contrast, mutations affecting the major catalytic domains of the polymerase gene, which could alter susceptibility to antiviral nucleoside analogues, were not detected at all.

Adult↗
PubMed1990

Sendai virus P gene produces multiple proteins from overlapping open reading frames.

The Sendai virus P gene contains overlapping open reading frames (ORFs), and several unusual mechanisms are used to produce multiple proteins from all three ORFs of this gene. These include the use of a non-AUG start codon, leaky ribosomal scanning, what appears to be scanning-independent ribosomal initiation and/or ribosomal jumping, and a form of mRNA editing.

DNA-Directed RNA Polymerases↗
PubMed1999

The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene.

Several lines of evidence indicate that the adaxial leaf domain possesses a unique competence to form shoot apical meristems. Factors required for this competence are expected to cause a defect in shoot apical meristem formation when inactivated and to be expressed or active preferentially in the adaxial leaf domain. PINHEAD, a member of a family of proteins that includes the translation factor eIF2C, is required for reliable formation of primary and axillary shoot apical meristems. In addition to high-level expression in the vasculature, we find that low-level PINHEAD expression defines a novel domain of positional identity in the plant. This domain consists of adaxial leaf primordia and the meristem. These findings suggest that the PINHEAD gene product may be a component of a hypothetical meristem forming competence factor. We also describe defects in floral organ number and shape, as well as aberrant embryo and ovule development associated with pinhead mutants, thus elaborating on the role of PINHEAD in Arabidopsis development. In addition, we find that embryos doubly mutant for PINHEAD and ARGONAUTE1, a related, ubiquitously expressed family member, fail to progress to bilateral symmetry and do not accumulate the SHOOT MERISTEMLESS protein. Therefore PINHEAD and ARGONAUTE1 together act to allow wild-type growth and gene expression patterns during embryogenesis.

Alleles↗
PubMed1989

Analysis of maternal effect mutant combinations elucidates regulation and function of the overlap of hunchback and Krüppel gene expression in the Drosophila blastoderm embryo.

The metameric organisation of the Drosophila embryo is generated early during development, due to the action of maternal effect and zygotic segmentation and homeotic genes. The gap genes participate in the complex process of pattern formation by providing a link between the maternal and the zygotic gene activities. Under the influence of maternal gene products they become expressed in distinct domains along the anteroposterior axis of the embryo; negative interactions between neighboring gap genes are thought to be involved in establishing the expression domains. The gap gene activities in turn are required for the correct patterning of the pair-rule genes; little is known, however, about the underlying mechanisms. We have monitored the distribution of gap and pair-rule genes in wild-type embryos and in embryos in which the anteroposterior body pattern is greatly simplified due to combinations of maternal effect mutations (staufen exuperantia, vasa exuperantia, vasa exuperantia, bicoid oskar, bicoid oskar torsolike, vasa torso exuperantia). We show that the domains of protein distribution of the gap genes hunchback and Krüppel overlap in wild-type embryos. Based on the analysis of the maternal mutant combinations, we suggest an explanation of how this overlap is generated. Furthermore, our data show that different constellations of gap gene activities provide different input for the pair-rule genes, and thus strongly suggest that the overlap of hunchback and Krüppel in wild-type is functional in the formation of the patterns of pair-rule genes.

Animals↗
PubMed1985

The nucleotide sequence of the Pieris brassicae granulosis virus granulin gene.

Two overlapping restriction fragments containing the Pieris brassicae granulosis virus (GV) granulin gene were cloned into plasmids. The regions containing the coding region and the 5' and 3' flanking regions were subcloned into M13 and sequenced. The nucleotide sequence data were compared to those for the granulin gene from the Trichoplusia ni GV and the polyhedrin gene from the Autographa californica nuclear polyhedrosis virus (AcMNPV). The amino acid sequences derived from these DNA sequences indicated that the two GV proteins are more closely related to each other (77% amino acid homology) than either is to the AcMNPV (about 53% amino acid homology for either GV). The N-terminal region shows the greatest degree of variation between these proteins. Highly conserved amino acid sequences were identified between the two GVs and were also found between NPVs. Certain of these conserved regions are shared between GVs and NPVs while others are not.

Amino Acid Sequence↗
PubMed2002

Three classes of proteinase inhibitor gene have distinct but overlapping patterns of expression in Pisum sativum plants.

Genes representative of three gene classes encoding proteinase inhibitor proteins, with distinct spatial expression patterns, were isolated and characterized from Pisum. Under standard plant growth conditions, one class is expressed exclusively in seeds, whereas the other two make minor contributions to seed inhibitor proteins but are also expressed in other organs, predominantly in root endodermal and floral reproductive tissues. Two of the gene classes contain few genes and are genetically linked at the Tri locus, whereas the third class displays complex hybridization patterns to genomic DNA and maps to diverse genetic loci. Expression analysis of this last class suggests that only a small number of these genes are expressed. The quantitative effect of the Tri locus on root and floral inhibitor gene expression was examined in near-isogenic lines of pea. The proteins encoded by the three classes are all members of the same family (Bowman-Birk) of enzyme inhibitors but are distinct in terms of overall sequence, active site sequences and inhibitor function.

Amino Acid Sequence↗
PubMed2006

Novel overlapping coding sequences in Chlamydia trachomatis.

Chlamydia trachomatis is the aetiological agent of trachoma and sexually transmitted infections. The C. trachomatis genome sequence revealed an organism adapted to the intracellular habitat with a high coding ratio and a small genome consisting of 1.042-kilobase (kb) with 895 annotated protein coding genes. Here, we repredict the protein-coding genes of the C. trachomatis genome using the gene-finder EasyGene that was trained specifically for C. trachomatis, and compare it with the primary C. trachomatis annotation. Our work predicts 15 genes not listed in the primary annotation and 853 that are in agreement with the primary annotation. Forty two genes from the primary annotation are not predicted by EasyGene. The majority of these genes are listed as hypothetical in the primary annotation. The 15 novel predicted genes all overlap with genes on the complementary strand. We find homologues of several of the novel genes in C. trachomatis Serovar A and Chlamydia muridarum. Several of the genes have typical gene-like and protein-like features. Furthermore, we confirm transcriptional activity from 10 of the putative genes. The combined evidence suggests that at least seven of the 15 are protein coding genes. The data suggest the presence of overlapping active genes in C. trachomatis.

Chlamydia trachomatis↗
PubMed2006

A high-resolution map of transcription in the yeast genome.

There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3' and 5' UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.

5' Untranslated Regions↗
PubMed2002

Binding of C/EBP and RBP (CBF1) to overlapping sites regulates interleukin-6 gene expression.

The ILRE (interleukin response element) contained within the promoter of the interleukin-6 (IL-6) gene is defined as the site recognized by the p65 NF-kappaB transcriptional activator and is crucial for activation of the IL-6 gene. The region of the promoter containing the ILRE is complex containing a CCAAT enhancer-binding protein (C/EBP) site immediately upstream of the ILRE, which is required for optimal activation of the IL-6 gene. Additionally, the ILRE overlaps a site that is recognized by the mammalian transcriptional repressor RBP (CBF-1), and RBP binding within the ILRE region represses activated IL-6 expression. In this study, the complexity of this region is further revealed by the identification of a second nested C/EBP site, which overlaps that of RBP and therefore also the ILRE. Optimal activation requires both the upstream and newly identified C/EBP sites in conjunction with the p65 NF-kappaB binding site. We previously reported that RBP represses IL-6 activation but does not target p65. We extend these analyses here to show that RBP binding does not occlude p65 from binding but instead directly overlaps the newly identified downstream C/EBP site, thereby impeding p65-C/EBP-mediated co-activation. This result suggests a role for RBP in the repression of other genes containing a C/EBP site that exhibits sequence overlap with the RBP site.

Animals↗
PubMed1994

High variability of the gag/pol transframe region among HIV-1 isolates.

The overlapping region of gag and pol genes of human immunodeficiency virus type 1 (HIV-1) also called transframe region, contains the frameshift locus from gag to pol. This region encodes both the protein p6, the function of which remains unclear, and a putative transframe protein covently linked to the N-terminus of the viral protease within Gag/Pol protein precursor. We have investigated the variability of the transframe region among nine HIV-1 isolates obtained from Congolese AIDS patients. Nucleotide sequences were determined using the polymerase chain reaction and the direct sequencing of amplified products. The sequences of Congolese isolates markedly differed from one another and from other reference HIV-1 strains by both insertion-deletion events and numerous base substitutions. Several putative cleavage sites of precursor polypeptides were modified. When compared to consensus ones the amino acid sequences of p6 protein were very different among divergent HIV-1 isolates, except for a limited group of 10 conserved amino acids.

Amino Acid Sequence↗
PubMed2006

Mutations in surface and polymerase gene of chronic hepatitis B patients with coexisting HBsAg and anti-HBs.

AIM: To investigate the clinical significance and presence of mutations in the surface (S) and overlapping polymerase gene of hepatitis B patients with coexisting HBsAg and anti-HBs. METHODS: Twenty-three patients with chronic hepatitis B were studied. Of the 23 patients, 11 were both positive for hepatitis B virus (HBV) surface antigen (HBsAg) and antibody to HBV surface antigen (anti-HBs), 12 were negative for anti-HBs while positive for HBsAg. DNA was extracted from 200 muL serum of the patients. Nucleotide of the surface and overlapping polymerase gene from HBV-infected patients was amplified by PCR, and the PCR products were sequenced. RESULTS: Forty-one mutations were found within the surface gene protein of HBV in 15 patients (10 with coexisting HBsAg and anti-HBs). Six (14.6%) out of 41 mutations were located at "alpha " determinant region in 5 patients (4 positive for HBsAg and anti-HBs). Eleven mutations (26.8%) occurred in the downstream or upstream of "alpha " determinant region. Lamivudine (LMV)-selected mutations were found in three patients who developed anti-HBs, which occurred in amino acid positions (196, 198, 199) of the surface protein and in YMDD motif (M204I/V) of the polymerase protein simultaneously. Presence of these mutations did not relate to changes in ALT and HBV DNA levels. CONCLUSION: Besides mutations in the "alpha " deter-minant region, mutations at downstream or upstream of the "alpha " determinant region may contribute to the development of anti-HBs. These mutations do not block the replicating competency of HBV in the presence of high titer of anti-HBs.

Adult↗
PubMed1989

Ig VH, DH, and JH germ-line gene segments linked by overlapping cosmid clones of rabbit DNA.

Overlapping cosmid clones of rabbit germ-line DNA containing VH, DH and JH gene segments were isolated. The map of this cluster of cosmid clones indicated that the rabbit VH and JH regions were separated by 63 kb. Hybridization of Southern blots of these cosmid clones with two different DH segment probes identified a total of six DH segments within the region between the VH and JH regions. The nucleotide sequences of the JH region and one of the DH segments have been determined. The DH segment has conserved heptamer and nonamer sequences separated by 12 and 11 bp at the 3' and 5' sides, respectively, of the coding region and hence, appears to be a functional gene. The nucleotide sequence of the JH region revealed four functional JH gene segments and one JH pseudogene. Inasmuch as the JH region had previously been linked by contiguous overlapping clones with C mu, C gamma, C epsilon, and one C alpha gene, this VH-DH-JH cluster and the clones containing the Ig H chain C region genes represent 190 kb of contiguous germ-line DNA of the Ig H chain locus.

Amino Acid Sequence↗
PubMed1989

The morphogenetic and regulatory functions of the Drosophila Abdominal-B gene are encoded in overlapping RNAs transcribed from separate promoters.

The Abdominal-B (Abd-B) gene of the Drosophila bithorax complex is a homeotic gene with two subfunctions: the morphogenetic element required for specifying the identity of parasegments (PS) 10-13 and the regulatory element that represses the expression of other homeotic genes in PS14. Here, we provide evidence that four classes of overlapping transcripts are generated from the Abd-B gene and characterize three of the transcripts in detail. We determined the transcription initiation sites for the 4.6- and 3.4-kb RNAs and show that they are generated from separate promoters. Both of these transcripts are present throughout the period during which the Abd-B subfunctions are required. A mutation that inactivates the morphogenetic function is associated with a 411-bp deletion of the initiation site for the 4.6-kb RNA. The regulatory function mutations disrupt the transcription unit for the 3.4-, but not the 4.6-kb, RNA. These results support the assignment of the morphogenetic function to the 4.6-kb RNA and the regulatory function to the 3.4-kb RNA. A 7.8-kb RNA expressed during embryogenesis may also contribute to the regulatory function. Sequence analysis of cDNAs indicates that the 4.6-kb RNA encodes a 55-kD protein (the m protein), whereas the 3.4-kb RNA encodes a 30-kD protein (the r protein). The m and r proteins share a carboxy-terminal sequence that includes the homeo domain, but the r protein lacks a glutamine-rich amino-terminal domain found in the m protein.

Abdomen↗
PubMed2006

Effect of data normalization on fuzzy clustering of DNA microarray data.

BACKGROUND: Microarray technology has made it possible to simultaneously measure the expression levels of large numbers of genes in a short time. Gene expression data is information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. Clustering is an important tool for finding groups of genes with similar expression patterns in microarray data analysis. However, hard clustering methods, which assign each gene exactly to one cluster, are poorly suited to the analysis of microarray datasets because in such datasets the clusters of genes frequently overlap. RESULTS: In this study we applied the fuzzy partitional clustering method known as Fuzzy C-Means (FCM) to overcome the limitations of hard clustering. To identify the effect of data normalization, we used three normalization methods, the two common scale and location transformations and Lowess normalization methods, to normalize three microarray datasets and three simulated datasets. First we determined the optimal parameters for FCM clustering. We found that the optimal fuzzification parameter in the FCM analysis of a microarray dataset depended on the normalization method applied to the dataset during preprocessing. We additionally evaluated the effect of normalization of noisy datasets on the results obtained when hard clustering or FCM clustering was applied to those datasets. The effects of normalization were evaluated using both simulated datasets and microarray datasets. A comparative analysis showed that the clustering results depended on the normalization method used and the noisiness of the data. In particular, the selection of the fuzzification parameter value for the FCM method was sensitive to the normalization method used for datasets with large variations across samples. CONCLUSION: Lowess normalization is more robust for clustering of genes from general microarray data than the two common scale and location adjustment methods when samples have varying expression patterns or are noisy. In particular, the FCM method slightly outperformed the hard clustering methods when the expression patterns of genes overlapped and was advantageous in finding co-regulated genes. Thus, the FCM approach offers a convenient method for finding subsets of genes that are strongly associated to a given cluster.

Algorithms↗
PubMed1995

An inverted repeat motif stabilizes binding of E2F and enhances transcription of the dihydrofolate reductase gene.

An overlapping inverted repeat sequence that binds the eukaryotic transcription factor E2F is 100% conserved near the major transcription start sites in the promoters of three mammalian genes encoding dihydrofolate reductase, and is also found in the promoters of several other important cellular and viral genes. This element, 5'-TTTCGCGCCAAA-3', is comprised of two overlapping, oppositely oriented sites which match the consensus E2F site (5'-TTT(C/G)(C/G)CGC-3'). Recent work has shown that E2F binding activity is composed of at least six related cellular polypeptides which are capable of forming DNA-binding homo- and heterodimers. We have investigated the binding of cellular E2F activity and of homo- and heterodimers of cloned E2F proteins to the inverted repeat E2F element. We have demonstrated that mutations in this element that abolish its inverted repeat nature, while preserving a single consensus E2F site, significantly decrease the binding stability of all of the forms of E2F tested. The rate of association of E2F-1/DP-1 heterodimers with the inverted repeat wild type site was not significantly different from those with the two single site mutated probes. Furthermore, the mutations decrease in vitro transcription and transient reporter gene expression 2-5-fold, an effect equivalent to that of abolishing E2F binding altogether. These data suggest a functional role that may explain the conservation of inverted repeat E2F elements among the DHFR promoters and several other cellular and viral promoters.

3T3 Cells↗
PubMed1997

Human 4-hydroxyphenylpyruvate dioxygenase gene (HPD).

Overlapping DNA fragments spanning approximately 21 kb of genomic DNA and encompassing the human 4-hydroxyphenylpyruvate dioxygenase gene (HPD) have been cloned by screening a human leukocyte genomic library and by PCR amplification of human fibroblastic DNA. A continuous gene sequence of 20,890 nucleotides was established, including 1957 bp of the 5'-flanking region. The 4-hydroxyphenylpyruvate dioxygenase gene is composed of 14 exons interrupted by 13 introns, all exhibiting conventional vertebrate splicing. Computer analysis of the DNA sequence revealed 12 complete repetitive Alu elements, 1 in the 5'-flanking region and 11 in the intervening segments of the gene. The transcriptional initiation site was mapped to a position 35 nt upstream of the translational start point. The computer analysis also identified several potential transcription regulatory elements, including one CRE site, two AP-2 sites, and two Sp1 sites, in the sequence upstream of the transcription initiation site. Functional analysis of promoter activity by transient transfection of chloramphenicolacetyl transferase reporter plasmids revealed a possible involvement of cyclic adenosine monophosphate in the regulation of transcription. The highest level of expression of 4-hydroxyphenylpyruvate dioxygenase was found in human liver tissue as demonstrated by Northern blot analysis.

4-Hydroxyphenylpyruvate Dioxygenase↗
PubMed1996

Mutational analysis of the Escherichia coli spoT gene identifies distinct but overlapping regions involved in ppGpp synthesis and degradation.

The spoT gene of Escherichia coli encodes a guanosine 3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (ppGppase) as well as an apparent guanosine 3',5'-bis(diphosphate) synthetase (designated PSII). To determine the regions of the SpoT protein that are required for these two competing activities, we analysed plasmid-borne deletion mutations for their ability to complement chromosomal mutations defective in each activity. We found that a region containing the first 203 amino acids of the 702-amino-acid SpoT protein was sufficient for ppGppase activity while an overlapping region containing residues 67-374 was sufficient for PSII activity. These data indicate that the catalytic sites involved in the two activities are separate but closely linked in the primary sequence of the SpoT protein. A ppGppase-defective delta 1-58 deletion mutant strain failed to synthesize ppGpp in response to nutrient limitation, also supporting the notion that PSII activity from wild-type SpoT does not increase in response to nutrient limitation. Using a strain lacking PSII activity but retaining ppGppase activity, we determined the contribution of the RelA protein (ppGpp synthetase I, PSI) to ppGpp synthesis following glucose starvation. We found that the RelA protein activity accounts for the initial burst of ppGpp synthesis at the onset of glucose starvation but that this source of synthesis is absent when amino acids are present during glucose starvation.

Base Sequence↗
PubMed1989

The conserved open reading frame overlapping the thymidine kinase gene of different herpesviruses exists also in bovine herpesvirus 1.

Similar open reading frames (ORF) overlapping the thymidine kinase (TK) gene on the opposite strand or being close to it have been identified in 8 herpesviruses (Jacobson et al., 1989). Study of the DNA sequence of BHV-1 TK gene published by Mittal and Field (1989) and Kit and Kit (1986) revealed the existence of a similar ORF in this virus genome, too.

Amino Acid Sequence↗