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At least 775 records · Page 43Linked to original sources
PubMed1985

The rat casein multigene family. Fine structure and evolution of the beta-casein gene.

Eight overlapping phage clones, spanning 34.4 kilobase pairs of genomic DNA, containing the 7.2-kilobase pair rat beta-casein gene have been isolated and characterized. The first 510 base pairs (bp) of 5' flanking, 110 bp of 3' flanking, and all the exon/intron junctions have been sequenced. The beta-casein gene contains 9 exons ranging in size from 21 to 525 bp. We have attempted to identify potential regulatory elements by searching for regions of sequence homology shared between milk protein genes which respond similarly to lactogenic hormones and by searching for previously reported hormone receptor-binding sites. Within the conserved first 200 bp of 5' flanking sequences 3 regions of greater than 70% homology were observed between the rat beta- and gamma-casein genes. One of these contains a region 90% homologous to the chicken progesterone receptor-binding site. The conserved 5' noncoding region, the highly conserved signal peptide, and the hydrophobic carboxyl-terminal region of the protein are each encoded by a separate exon. In contrast the evolutionarily conserved phosphorylation site of beta-casein is formed by an RNA-splicing event. The exons which encode the phosphorylation sites of beta-casein appear to have resulted from an intragenic duplication. Based upon the exon structure of the casein genes, an evolutionary model of intragenic and intergenic exon duplications for this gene family is proposed.

Animals↗
PubMed1986

Control of gene expression in the P2-related template coliphages. III. DNA sequence of the major control region of phage 186.

The PstI fragment (65.5% to 77.4%) of coliphage 186, known genetically to encode the major control genes, has been sequenced, and an analysis performed to assess coding capacity, transcription-translation signals, and to identify any other significant features. Our analysis indicates that the region encodes: seven genes, including the int and cI genes, which overlap, the late control gene B, and two genes, named CP75 and CP76, encoding potential DNA-binding proteins; a promoter pB and terminator tB for the rightward transcription of the B gene, and we predict the existence of this transcript in a lysogen; a promoter pL and terminator tL for leftward transcription that encodes the int and cI genes, and represents the presumed lysogenic transcript; a promoter pR for rightward transcription to give the presumed (early) lytic transcript that is overlapping and convergent with the lysogenic transcript; and finally, a potential operator site for repressor binding in the region of the pR promoter. Preliminary evidence is presented to support this analysis.

Base Sequence↗
PubMed1999

Fused and overlapping rpoB and rpoC genes in Helicobacters, Campylobacters, and related bacteria.

The genes coding for the beta (rpoB) and beta' (rpoC) subunits of RNA polymerase are fused in the gastric pathogen Helicobacter pylori but separate in other taxonomic groups. To better understand how the unique fused structure evolved, we determined DNA sequences at and around the rpoB-rpoC junction in 10 gastric and nongastric species of Helicobacter and in members of the related genera Wolinella, Arcobacter, Sulfurospirillum, and Campylobacter. We found the fusion to be specific to Helicobacter and Wolinella genera; rpoB and rpoC overlap in the other genera. The fusion may have arisen by a frameshift mutation at the site of rpoB and rpoC overlap. Loss of good Shine-Dalgarno sequences might then have fixed the fusion in the Helicobacteraceae, even if fusion itself did not confer a selective advantage.

Amino Acid Sequence↗
PubMed1990

Functional expression of the genomic DNA sequences encoding mouse Na,K-ATPase alpha 1 gene by cotransfection of overlapping genomic DNA segments.

The entire 33-kb coding region of the mouse Na,K-ATPase alpha 1 subunit gene was cloned in two overlapping cosmids which contain inserts of 40 kb. To assess the functional expression of the mouse alpha 1 gene, the two cosmids were cotransfected into ouabain-sensitive CV-1 monkey cells yielding an average of 64 resistant colonies per 10(6) cells per microgram of DNA. Analysis of the DNA transferred to the ouabain-resistant transformants by the two cosmids suggests that the generation of a functional gene can occur by homologous recombination between the two introduced segments, as demonstrated by generation of a novel diagnostic restriction fragment. The ability to reconstruct the intact mouse alpha 1 gene in a heterologous host cell and to monitor its functional expression with a selection protocol permits direct identification and isolation of regulatory sequences for the gene.

Animals↗
PubMed2005

The hepatitis C virus alternate reading frame (ARF) and its family of novel products: the alternate reading frame protein/F-protein, the double-frameshift protein, and others.

The hepatitis C virus (HCV) has an alternate reading frame (ARF) that overlaps the core protein gene. The overlapping reading frame distinguishes HCV from all of its known viral relatives, with the possible exception of GB virus B (GBV-B). The ARF is expressed during natural HCV infections and stimulates specific immune responses. Like several essential genes in other viruses (e.g., the human immunodeficiency virus polymerase) the ARF lacks an in-frame AUG start codon, suggesting that its expression involves unusual translation-level events. In vitro studies indicate that ribosomal frameshifting may be one of several processes that can lead to translation of the ARF. Frameshifting yields chimeric proteins that have segments encoded in the core gene covalently attached to amino acids encoded in the ARF. A consistent nomenclature for the ARF's protein products has yet to be established. We propose that all proteins that contain amino acids encoded in the + 1 ARF be called alternate reading frame proteins (ARFPs) and that specific ARFPs, such as the ARFP/F-protein, the double-frameshift protein, and the short form of core + 1, be designated as follows: ARFP/F (ARFP/F-protein), ARFP/DF (double-frameshift), and ARFP/S (short form of core + 1). The roles of ARFPs in the HCV life cycle are not yet known. There is a significant possibility that ARFPs may be responsible for some of the effects attributed to the core protein, given that most studies seeking to define the function of the core protein have employed materials likely to contain a combination of the core protein and ARFPs. The observed effects of the core protein include the induction of liver cancer, transformation of cells, and alterations of immune responses. This article reviews the discovery of ARF, describes the RNA structural elements involved in core/ARF gene expression, discusses possible functions of ARFPs, and considers the potential usefulness of ARFPs in vaccines. The HCV ARF is the focus of a new and rapidly expanding area of research, and the results of many ongoing studies are currently available in abstract form only. The preliminary nature of investigations that have not yet been reviewed by peers is noted in the text.

Animals↗
PubMed1996

The human alpha 2(XI) collagen gene (COL11A2): completion of coding information, identification of the promoter sequence, and precise localization within the major histocompatibility complex reveal overlap with the KE5 gene.

Type XI collagen, a fibril-forming collagen, is important for the integrity and development of the skeleton because mutations in the genes encoding its consituent alpha chains have been found in some osteochondrodysplasias. We provide data that complete information for the coding sequence of human alpha 2(XI) procollagen, with details of the promoter region and intron-exon organization at the 5' and 3' ends of the gene (COL11A2), including the transcription start and polyadenylation sites. COL11A2 is 30.5 kb with a minimum of 62 exons, differing from other reported fibrillar collagen genes because the amino propeptide is encoded by 14 not 5 to 8 exons. But exon numbers for the carboxy propeptide and 3'-untranslated region are conserved. The promoter region of COL11A2 lacks a TATA box but is GC-rich with two potential SP1 binding sites. Mouse alpha 2(XI) collagen mRNAs undergo complex alternative splicing involving three amino-terminal propeptide exons but only one of these has been reported for COL11A2. We have located these missing human exons and have identified splice signals that point to additional splice variants. We have precisely mapped COL11A2 within the major histocompatibility complex on chromosome 6. The retinoid X receptor beta (RXR beta) gene is located 1.1 kb upstream of COL11A2. KE5, previously thought to be a distinct transcribed gene sequence, was mapped within COL11A2 in the alternatively spliced region, raising the question whether KE5 and COL11A2 are separate genes.

Alternative Splicing↗
PubMed1983

Sequence analysis of fowl plague virus mutant ts47 reveals a nonsense mutation in the NS1 gene.

A mutant of fowl plague virus, ts47, induces the synthesis in infected cells of a truncated NS1 polypeptide at both permissive and restrictive temperatures. Nucleotide sequence analysis of the segment coding for the NS1 polypeptide, segment 8, indicates that this aberration is due to a nonsense mutation. This mutation occurs in the region of the NS1 gene which overlaps with the NS2 gene and there is a corresponding amino acid substitution in the NS2 polypeptide. While it is not clear which polypeptide is responsible for the thermal instability of ts47, the loss of the COOH-terminal 28 amino acid residues from the NS1 polypeptide does not affect replication of the virus at permissive temperatures.

Base Sequence↗
PubMed1997

Conservation of a putative AP1 binding site and complete homology to a fetal brain EST in a region upstream of the core muscle promoter in the human dystrophin gene.

A region of 744 basepairs (bp) upstream of the muscular dystrophin promoter (UMDP) was amplified by inverse-polymerase chain reaction (PCR), cloned and sequenced. Analysis of this sequence for the presence of putative transcriptional control elements identified several similarities with known cis-acting sequence motifs including two MyoD and two Ap1 motifs. One of these Ap1 motifs was found to be completely conserved within an otherwise highly variable region among five primate species. Complete homology to a human fetal brain expressed sequence tag (EST) was also observed over 201 bp at the 5' end of the UMDP region. Northern blot analysis using a radiolabelled EST probe identified a 1 kb mRNA expressed in human placenta and at lower levels in the heart. These results raise the possibility that additional transcriptional regulatory elements are located upstream of the core muscle promoter, and provide the first evidence for the existence of a gene that overlaps the human dystrophin gene.

Base Sequence↗
PubMed2003

IL-10 induces gene expression in macrophages: partial overlap with IL-5 but not with IL-4 induced genes.

The hypothesis that IL-10, in addition to down-regulating pro-inflammatory activities of macrophages, induces an alternative state of macrophage reactivity was tested. We therefore conducted a systematic search for genes induced by IL-10 using the method of suppression subtractive hybridisation. Of an initial 1,300 candidate clones obtained, several screening rounds led to the identification of 51 clones which were reproducibly at least twofold up-regulated in mouse J774 macrophages in response to treatment with IL-10. Of these, 41 genes were homologous to known genes involved in cell metabolism or immunoregulation, five contained novel sequences and another five were homologous to ESTs without known function. One major finding was that about 25% of the IL-10 genes were also found expressed in response to IFNgamma, and several of these also reappeared in IL-4 or IL-5 induced mRNA species. Hence, Th1 and Th2 type cytokines may elicit a common basal activation response in macrophages. The second major finding was that 57% of IL-10 induced genes reappeared in IL-5 induced mRNA but no more than 18% were also found in IL-4 induced mRNA of J774 cells. We conclude that the gene expression response to IL-10 in macrophages is partially different from the response to IL-5 and is substantially different from the response to IL-4, which suggests an unexpected diversity of biological phenotypes induced by different Th2 type cytokines.

Animals↗
PubMed2004

Archaeal integrases and mechanisms of gene capture.

Archaeal integrases facilitate the formation of two distinctive types of integrated element within archaeal chromosomes: the SSV type and pNOB8 type. The former carries a smaller N-terminal and a larger C-terminal integrase gene fragment, and the latter an intact integrase gene. All integrated elements overlap tRNA genes that were target sites for integration. It has been demonstrated that SSV (Sulfolobus spindle virus) viruses, carrying an SSV-type integrase gene, and conjugative plasmids, carrying a pNOB8-type integrase, are integrative elements. Two mechanisms have been proposed for stably maintaining an integrated element within archaeal chromosomes. There is also evidence for changes having occurred in the captured integrated elements present in archaeal genomes. Thus we infer that site-specific integration constitutes an important mechanism for horizontal gene transfer and genome evolution.

Archaea↗
PubMed1989

Cloning of the cDNA and gene for a human D2 dopamine receptor.

A clone encoding a human D2 dopamine receptor was isolated from a pituitary cDNA library and sequenced. The deduced protein sequence is 96% identical with that of the cloned rat receptor with one major difference: the human receptor contains an additional 29 amino acids in its putative third cytoplasmic loop. Southern blotting demonstrated the presence of only one human D2 receptor gene. Two overlapping phage containing the gene were isolated and characterized. DNA sequence analysis of these clones showed that the coding sequence is interrupted by six introns and that the additional amino acids present in the human pituitary receptor are encoded by a single exon of 87 base pairs. The involvement of this sequence in alternative splicing and its biological significance are discussed.

Amino Acid Sequence↗
PubMed2006

Statistically designing microarrays and microarray experiments to enhance sensitivity and specificity.

Gene expression signatures from microarray experiments promise to provide important prognostic tools for predicting disease outcome or response to treatment. A number of microarray studies in various cancers have reported such gene signatures. However, the overlap of gene signatures in the same disease has been limited so far, and some reported signatures have not been reproduced in other populations. Clearly, the methods used for verifying novel gene signatures need improvement. In this article, we describe an experiment in which microarrays and sample hybridization are designed according to the statistical principles of randomization, replication and blocking. Our results show that such designs provide unbiased estimation of differential expression levels as well as powerful tests for them.

Breast Neoplasms↗
PubMed2006

A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations.

MOTIVATION: The identification of signatures of positive selection can provide important insights into recent evolutionary history in human populations. Current methods mostly rely on allele frequency determination or focus on one or a small number of candidate chromosomal regions per study. With the availability of large-scale genotype data, efficient approaches for an unbiased whole genome scan are becoming necessary. METHODS: We have developed a new method, the whole genome long-range haplotype test (WGLRH), which uses genome-wide distributions to test for recent positive selection. Adapted from the long-range haplotype (LRH) test, the WGLRH test uses patterns of linkage disequilibrium (LD) to identify regions with extremely low historic recombination. Common haplotypes with significantly longer than expected ranges of LD given their frequencies are identified as putative signatures of recent positive selection. In addition, we have also determined the ancestral alleles of SNPs by genotyping chimpanzee and gorilla DNA, and have identified SNPs where the non-ancestral alleles have risen to extremely high frequencies in human populations, termed 'flipped SNPs'. Combining the haplotype test and the flipped SNPs determination, the WGLRH test serves as an unbiased genome-wide screen for regions under putative selection, and is potentially applicable to the study of other human populations. RESULTS: Using WGLRH and high-density oligonucleotide arrays interrogating 116 204 SNPs, we rapidly identified putative regions of positive selection in three populations (Asian, Caucasian, African-American), and extended these observations to a fourth population, Yoruba, with data obtained from the International HapMap consortium. We mapped significant regions to annotated genes. While some regions overlap with genes previously suggested to be under positive selection, many of the genes have not been previously implicated in natural selection and offer intriguing possibilities for further study. AVAILABILITY: the programs for the WGLRH algorithm are freely available and can be downloaded at http://www.affymetrix.com/support/supplement/WGLRH_program.zip.

Algorithms↗
PubMed1995

Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris.

We have determined the complete nucleotide (nt) sequence of the mitochondrial genome of an oligochaete annelid, the earthworm Lumbricus terrestris. This genome contains the 37 genes typical of metazoan mitochondrial DNA (mtDNA), including ATPase8, which is missing from some invertebrate mtDNAs. ATPase8 is not immediately upstream of ATPase6, a condition found previously only in the mtDNA of snails. All genes are transcribed from the same DNA strand. The largest noncoding region is 384 nt and is characterized by several homopolymer runs, a tract of alternating TA pairs, and potential secondary structures. All protein-encoding genes either overlap the adjacent downstream gene or end at an abbreviated stop codon. In Lumbricus mitochondria, the variation of the genetic code that is typical of most invertebrate mitochondrial genomes is used. Only the codon ATG is used for translation initiation. Lumbricus mtDNA is A + T rich, which appears to affect the codon usage pattern. The DHU arm appears to be unpaired not only in tRNAser(AGN), as is typical for metazoans, but perhaps also in tRNAser(UCN), a condition found previously only in a chiton and among nematodes. Relating the Lumbricus gene organization to those of other major protostome groups requires numerous rearrangements.

Amino Acid Sequence↗
PubMed2005

Identifying simple discriminatory gene vectors with an information theory approach.

In the feature selection of cancer classification problems, many existing methods consider genes individually by choosing the top genes which have the most significant signal-to-noise statistic or correlation coefficient. However the information of the class distinction provided by such genes may overlap intensively, since their gene expression patterns are similar. The redundancy of including many genes with similar gene expression patterns results in highly complex classifiers. According to the principle of Occam's razor, simple models are preferable to complex ones, if they can produce comparable prediction performances to the complex ones. In this paper, we introduce a new method to learn accurate and low-complexity classifiers from gene expression profiles. In our method, we use mutual information to measure the relation between a set of genes, called gene vectors, and the class attribute of the samples. The gene vectors are in higher-dimensional spaces than individual genes, therefore, they are more diverse, or contain more information than individual genes. Hence, gene vectors are more preferable to individual genes in describing the class distinctions between samples since they contain more information about the class attribute. We validate our method on 3 gene expression profiles. By comparing our results with those from literature and other well-known classification methods, our method demonstrated better or comparable prediction performances to the existing methods, however, with lower-complexity models than existing methods.

Algorithms↗
PubMed2006

Mutations affecting the replication capacity of the hepatitis B virus.

The genetic variability of the hepatitis B virus (HBV) encounters two compounding forces: a high viral copy number produced during active replication and the lack of proofreading activity in the HBV polymerase, resulting in a high mutational rate. A large pool of quasispecies is generated in which the fittest virus, i.e. the virus that replicates best, becomes the dominant species. Immune and antiviral selection pressures result in vaccine/immunoglobulin escape mutants and antiviral resistant variants. Viruses encoding changes associated with antiviral resistance often have reduced replication in vitro, but the accumulation of additional mutations helps restore viral fitness. These compensatory mutations may occur not only in the polymerase gene but also in other genes such as the overlapping envelope gene, the precore gene, or in regulatory regions such as the basal core promoter. In this report we aim to review the new findings that have appeared in recent months.

Hepatitis B↗
PubMed1997

Composition and primary structure of the F1F0 ATP synthase from the obligately anaerobic bacterium Clostridium thermoaceticum.

The subunit composition and primary structure of the proton-translocating F1F0 ATP synthase have been determined in Clostridium thermoaceticum. The isolated enzyme has a subunit composition identical to that of the F1F0 ATP synthase purified from Clostridium thermoautotrophicum (A. Das, D. M. Ivey, and L. G. Ljungdahl, J. Bacteriol. 179:1714-1720, 1997), both having six different polypeptides. The molecular masses of the six subunits were 60, 50, 32, 17, 19, and 8 kDa, and they were identified as alpha, beta, gamma, delta, epsilon, and c, respectively, based on their reactivity with antibodies against the F1 ATPase purified from C. thermoautotrophicum and by comparing their N-terminal amino acid sequences with that deduced from the cloned genes of the C. thermoaceticum atp operon. The subunits a and b found in many bacterial ATP synthases could not be detected either in the purified ATP synthase or crude membranes of C. thermoaceticum. The C. thermoaceticum atp operon contained nine genes arranged in the order atpI (i), atpB (a), atpE (c), atpF (b), atpH (delta), atpA (alpha), atpG (gamma), atpD (beta), and atpC (epsilon). The deduced protein sequences of the C. thermoaceticum ATP synthase subunits were comparable with those of the corresponding subunits from Escherichia coli, thermophilic Bacillus strain PS3, Rhodospirillum rubrum, spinach chloroplasts, and the cyanobacterium Synechococcus strain PCC 6716. The analysis of total RNA by Northern hybridization experiments reveals the presence of transcripts (mRNA) of the genes i, a, and b subunits not found in the isolated enzyme. Analysis of the nucleotide sequence of the atp genes reveals overlap of the structural genes for the i and a subunits and the presence of secondary structures (in the b gene) which could influence the posttranscriptional regulation of the corresponding genes.

Amino Acid Sequence↗
PubMed2002

AerR, a second aerobic repressor of photosynthesis gene expression in Rhodobacter capsulatus.

Open reading frame orf192, which is located immediately upstream of the aerobic repressor gene crtJ, was genetically and biochemically demonstrated to code for a second aerobic repressor (AerR) of photosynthesis gene expression in Rhodobacter capsulatus. Promoter-mapping studies indicate that crtJ has its own promoter but that a significant proportion of crtJ expression is promoted by read-through transcription of orf192 (aerR) transcripts through crtJ. Disruption of aerR resulted in increased photopigment biosynthesis during aerobic growth to a level similar to that of disruption of crtJ. Like that reported for CrtJ, beta-galactosidase assays of reporter gene expression indicated that disruption of aerR resulted in a two- to threefold increase in aerobic expression of the crtI and pucB operons. However, unlike CrtJ, AerR aerobically represses puf operon expression and does not aerobically repress bchC expression. Gel mobility shift analysis with purified AerR indicates that AerR does not bind to a bchC promoter probe but does bind to the crtI, puc, and puf promoter probes. These results indicate that AerR is a DNA-binding protein that targets genes partially overlapping a subset of genes that are also controlled by CrtJ. We also provide evidence for cooperative binding of AerR and CrtJ to the puc promoter region.

Aerobiosis↗