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At least 1,081 records · Page 60Linked to original sources
PubMed1997

Organization and sequence of the human gene for the mitochondrial citrate transport protein.

The citrate (tricarboxylate) carrier transports citrate (or other tricarboxylates) across the inner membranes of mitochondria in an electroneutral exchange for malate (or other dicarboxylic acids). We have determined the sequence of the human citrate transporter gene from overlapping genomic clones generated by polymerase chain reactions by use of primers and probes based on the rat cDNA sequence and on emerging sequences. The gene is spread over 2.8 kb of human DNA and is divided into eight exons. All the introns are located at the level of the sequences coding for the extramembranous loops (and not for the transmembrane segments) of the mature protein. The open reading frame of the human gene encodes the mature protein consisting of 298 amino acids, preceded by a presequence of 13 amino acids to help to target it into mitochondria. 84 identities and 106 highly conservative substitutions are present in CTPs from man to yeast. In addition, we have determined the sequences of two human pseudogenes related to the citrate carrier gene encompassing the coding sequence of the gene between nucleotides 260 and 720.

Amino Acid Sequence↗
PubMed2002

Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites.

We present a tool for the prediction of mRNA 3'-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3'-processing sites indicates good agreement. All predicted or known yeast genes were analyzed to find probable 3'-processing sites. Known alternative 3'-processing sites, both within the 3'-untranslated region and within the protein coding sequence were successfully identified, leading to the possibility of prediction of previously unknown alternative sites. The lack of an apparent 3'-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences.

3' Untranslated Regions↗
PubMed1996

Defined large-scale alterations of the human cytomegalovirus genome constructed by cotransfection of overlapping cosmids.

We have constructed defined human cytomegalovirus (CMV) mutants by cotransfecting overlapping cosmid clones spanning the 230-kbp genome. Using this strategy, we have introduced a 13-kbp region of DNA from a virulent strain of CMV into a defined position within the avirulent CMV(Towne) genome. Although more than 80% of the genome of these recombinant viruses was derived from Towne DNA, their plaque morphology more closely resembled that of Toledo. To date, CMV is the largest virus and requires the greatest number of cosmids to be regenerated via overlapping cosmid cotransfection.

Cell Line↗
PubMed2006

The dynamic pattern of glucocorticoid receptor-mediated transcriptional responses in neuronal PC12 cells.

The aim of the current study was (i) to examine the overlap in the pattern of glucocorticoid receptor (GR)-mediated transcriptional responses between different neuronal substrates and (ii) to assess the nature of these responses by differentiating between primary and downstream GR-responsive genes. For this purpose, nerve growth factor-differentiated catecholaminergic PC12 cells were used in which endogenous GRs were activated briefly with a high dose of corticosterone followed by gene expression profiling 1 and 3 h afterwards using Affymetrix GeneChips. The results revealed a strikingly similar temporal pattern to that which was reported previously in hippocampus, with only down-regulated genes 1 h after GR activation and the majority of genes up-regulated 3 h after GR activation. Real-time quantatitive PCR of transcripts in cycloheximide-treated cells showed that all five GR-responsive genes selected from the 1-h time point were primary responsive, whereas all four GR-responsive genes selected from the 3-h time point were downstream responsive. At the level of individual genes, the overlap with the previously generated hippocampal data sets was small, illustrating the cell-type specifity of GR-mediated genomic responses. Finally, we identified a number of interesting genes, such as SWI/SNF, synaptosomal-associated protein 25 and certain Rab proteins which may play a role in the effects of glucocorticoids on catecholaminergic neuronal functioning.

Animals↗
PubMed1995

Coding sequence and alternative splicing of the mouse alpha 1(XI) collagen gene (Col11a1).

Several overlapping cDNA clones corresponding to the entire coding sequence of the mouse alpha 1(XI) collagen gene (Col11 a1) were isolated. The conceptual amino acid translation indicated a high degree of sequence identity (93%) with the human alpha 1(XI) chain. The cloning experiments also revealed alternative splicing of the sequence coding for 85 residues located within the acidic region of the amino-globular domain of alpha 1(XI). Analysis of RNA samples from different embryonic tissues suggested that alternative splicing might be confined to tissue destined to become bone.

Amino Acid Sequence↗
PubMed2000

Comparison of sequencing of the por gene and typing of the opa gene for discrimination of Neisseria gonorrhoeae strains from sexual contacts.

Typing of gonococcal strains is a valuable tool for the biological confirmation of sexual contacts. We have developed a typing method based on DNA sequencing of two overlapping por gene fragments generated by a heminested PCR. We compared sequencing of the por gene (POR sequencing) and typing of the opa gene (OPA typing) for the characterization of strains from 17 sexual partnerships. Both methods were highly discriminatory. A different genotype was detected in 15 of the 17 epidemiologically unconnected couples by POR sequencing and in 16 of the 17 couples by OPA typing with restriction enzyme HpaII. Within partnerships, identical genotypes were obtained from 16 of the 17 known sex contacts by POR sequencing and from 15 of the 17 by OPA typing. Compared to OPA typing, which relies on interpretation of bands in a gel, DNA sequence data offer the advantage of being objective and portable. As costs for sequencing decline, the method should become affordable for most laboratory personnel who wish to type gonococcal strains.

Antigens, Bacterial↗
PubMed2004

Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures.

The gene expression profiles of human postmortem parietal and prefrontal cortex samples of normal controls and patients with bipolar disease, or human neuroblastoma flat (NBFL) cells treated with the mood-stabilizing drug, valproate, were used to compare the performance of Affymetrix oligonucleotide U133A GeneChips and Agilent Human 1 cDNA microarrays. Among those genes represented on both platforms, the oligo array identified 26-53% more differentially expressed genes compared to the cDNA array in the three experiments, when identical fold change and t-test criteria were applied. The increased sensitivity was primarily the result of more robust fold changes measured by the oligonucleotide system. Essentially all gene changes overlapping between the two platforms were co-directional, and ranged from 4 to 19% depending upon the amount of biological variability within and between the comparison groups. Q-PCR validation rates were virtually identical for the two platforms, with 23-24% validation in the prefrontal cortex experiment, and 56% for both platforms in the cell culture experiment. Validated genes included dopa decarboxylase, dopamine beta-hydroxylase, and dihydropyrimidinase-related protein 3, which were decreased in NBFL cells exposed to valproate, and spinocerebellar ataxia 7, which was increased in bipolar disease. The modest overlap but similar validation rates show that each microarray system identifies a unique set of differentially expressed genes, and thus the greatest information is obtained from the use of both platforms.

Adult↗
PubMed1991

Reconstruction and analysis of human Alu genes.

The existing classification of human Alu sequences is revised and expanded using a novel methodology and a larger set of sequence data. Our study confirms that there are two major Alu subfamilies, Alu-J and Alu-S. The Alu-S subfamily consists of at least five distinct subfamilies referred to as Alu-Sx, Alu-Sq, Alu-Sp, Alu-Sc, and Alu-Sb. The Alu-Sp and Alu-Sq subfamilies have been revealed by this study. Alu subfamilies differ from one another in a number of positions called diagnostic. In this paper the diagnostic positions are defined in quantitative terms and are used to evaluate statistical significance of the observed subfamilies. Each Alu subfamily most likely represents pseudogenes retroposed from evolving functional source Alu genes. Evidence presented in this paper indicates that Alu-Sp and Alu-Sc pseudogenes were retroposed from different source genes, during overlapping periods of time, and at different rates. Our analysis also indicates that the previously identified Alu-type transcript BC200 comes from an active Alu gene that might have existed even before the origin of dimeric Alu sequences. The source genes for Alu pseudogene families are reconstructed. It is assumed that diagnostic differences between reconstructed source genes reflect mutations that have occurred in true source Alu genes under natural selection. Some of these mutations are compensatory and are used to reconstruct a common secondary structure of Alu RNAs transcribed from the source genes. The biological function of Alu RNA is discussed in the context of its homology to the elongation-arresting domain of 7SL RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1987

The genetic origin of murine lupus-associated autoantibodies.

Systemic lupus erythematosus and rheumatoid arthritis in human and murine systems are characterized by circulating autoantibodies and immune complex deposition in various organs causing tissue damage and disease. To define the molecular and clonotypic origin of these anti-self responses, and to determine whether abnormalities in Ig genes or somatic mechanisms generating autoantibody diversity may contribute to lupus etiology, we performed molecular analyses of the Ig germline gene organization and the Ig gene segments expressed in monoclonal autoantibodies from autoimmune mice. Comparative restriction fragment length polymorphism analysis of a large number of Ig gene loci from autoimmune and normal mice indicated that (a) lupus can develop in different Ig heavy and kappa light chain variable region gene haplotypes, and (b) the Ig germline genes in lupus mice might be normal. To determine whether autoantibodies are encoded by unique Ig gene segments present in the normal germline repertoire, but not expressed in exogenous responses, we compared nucleic acid sequences encoding lupus autoantibodies and antibodies against foreign antigens. Similar, and in some instances even identical, gene segments were expressed in both types of antibodies, indicating that anti-self and anti-foreign responses use the same, or at least an overlapping, germline gene repertoire. A large variety of Ig variable, diversity, and joining gene segments encoded these autoantibodies with different specificities. Hence, the overall murine lupus-associated anti-self response may be essentially unrestricted. Furthermore, limited evidence has been obtained that both germline genes and somatically mutated genes encode autospecificity, making gross abnormalities in mechanisms for somatic mutation of Ig variable genes unlikely.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1993

Differential effects of DNA-binding proteins on bidirectional transcription from the common promoter region of human collagen type IV genes COL4A1 and COL4A2.

Expression of the heterotrimeric collagen IV (alpha 1(IV))2 alpha 2(IV) is essential for the structural integrity and functional properties of basement membranes. The genes COL4A1 and COL4A2 coding for both subunits are located close to each other on the same chromosome and are transcribed from a common bidirectional promoter element. Binding of at least three different nuclear proteins could be detected within this promoter, a CCAAT-binding protein, Sp1 and a newly identified factor, designated 'CTCBF'. Mutagenesis of binding sites proved that these factors are essential for the efficient transcription of both genes, but revealed differential gene-specific effects. Therefore, the common promoter region of collagen IV does not represent an equally functional bidirectional element, but may be better understood as two overlapping gene-specific promoters with shared elements.

Base Sequence↗
PubMed2005

The tuberous sclerosis genes, TSC1 and TSC2, trigger different gene expression responses.

Tuberous sclerosis (TSC) is an autosomal dominant tumor suppressor gene syndrome affecting about 1 in 6000 individuals. It is characterized by mental retardation and epilepsy. A variety of tumors characteristically occur in different organs of TSC patients. The genes, TSC1 on chromosome 9q34, encoding hamartin, and TSC2 on chromosome 16p13.3, encoding tuberin are responsible for TSC. Hamartin and tuberin form a complex providing a tentative explanation for the similar disease phenotype in TSC patients with mutations in either of these genes. Besides overlap in many features of patients with TSC1 and TSC2 mutations, data accumulated provide evidence for specific clinical differences. Here, we performed microarray analyses of the gene expression response to overexpressed TSC1 or TSC2 in HeLa cells. Out of 2400 analysed genes we found 115 genes to be up-regulated > or =2-fold upon ectopic TSC1 overexpression and 284 genes to be up-regulated > or =2-fold via TSC2. Only 34 of these genes were up-regulated by both, TSC1 and TSC2. Whereas only 7 genes were down-regulated > or =2-fold via TSC1, ectopic TSC2 triggered a > or =2-fold down-regulation of 113 genes. Only 3 of these genes were down-regulated by TSC1 and TSC2. This study provides new insights into the cellular roles of TSC proteins and promotes discussion on whether separable functions of these proteins might be associated with the clinical differences of TSC1- and TSC2-associated disease.

Down-Regulation↗
PubMed1998

Overlapping coding regions and trancriptional units of two essential chromosomal genes (CCT8, TRP1)in the fungal pathogen Candida albicans.

Sequencing of the 3'-untranslated region of the CCT8 gene of the fungal pathogen Candida albicans revealed that the CCT8 coding region overlaps 13 bp with the coding region of the convergently orientated TRP1 gene. The same overlap was found in three strains with different genetic backgrounds. 3'-RACE was used to determine that the CCT8 and TRP1 transcripts extended significantly into the coding region of the adjacent gene, which also contained sequences encoding the poly(A) addition site. A strain retaining one wild-type CCT8/TRP1 locus on one chromosome and a deletion on the other homologous chromosome contained both CCT8 and TRP1 transcripts; this result indicates that both transcripts are synthesized from the same gene locus. The CCT8/TRP1 gene pair of C . albicans constitutes an extreme natural case of transcriptional overlap in a eukaryote. The results confirm that convergent overlapping transcription units are compatible with expression of the overlapping genes.

3' Untranslated Regions↗
PubMed2001

Genes targeted by protein kinase CK2: a genome-wide expression array analysis in yeast.

Protein kinase CK2, a tetramer composed of two catalytically active (CK2alpha isoforms) and two regulatory (CK2beta isoforms) subunits, is suspected to have, among others, a role in gene transcription. To identify the genes targeted by CK2, the transcriptional effect of silencing the CK2 subunit genes in Saccharomyces cerevisiae (CK2alpha isoform genes: CKA1 and CKA2; CK2beta isoform genes: CKB1 and CKB2) was examined using genome-wide expression array analysis (oligonucleotide array chips). Silencing did not influence the overwhelming majority (5801) of the over six thousand open reading frames composing the yeast genome. Cells knocked-out for both CKA1 and CKA2 and plasmid-rescued by Cka1 affected specifically at 2-fold discrimination level the transcription of 57 genes, and when rescued by Cka2, the transcription of 118 genes. In CKB1/CKB2 double knock-outs, transcription of 54 genes was specifically altered. Interestingly, aside overlaps between the gene spectra affected by CKA1 and CKA2 silencing, there were overlaps also between those influenced by CK2alpha and CK2beta isoform silencing. The data indicate a distinct role of CK2 in gene transcription control, identify specific functional differences between the two catalytic subunits in gene targeting, and reveal independent effects by the regulatory subunits.

Casein Kinase II↗
PubMed1999

Conditionally lethal genes in the N pilus region of plasmid pCU1.

Plasmid genes or regions that are conditionally lethal to Escherichia coli have been called kil and those lethal to Klebsiella but not to E. coli have been called kik. Both classes of genes are found in or close to the N pilus region of the plasmid pCU1 and the closely related plasmid pKM101. Here we describe two new and overlapping lethal genes that are located between kikA and traA of the plasmid pCU1 and display host specificity. KilC is lethal in E. coli and Klebsiella while kikC is lethal only in Klebsiella. The previously identified korA gene is sufficient to override the lethality of kilC in trans or in cis but is insufficient to override kikC. kilC expression in E. coli leads to cell death accompanied by an increase in average cell length without affecting septum formation.

Chromosome Mapping↗
PubMed2003

Comparison of expression patterns between CREB family transcription factor OASIS and proteoglycan core protein genes during murine tooth development.

The transcription factor OASIS gene, which encodes for a CREB/ATF family member, is specifically expressed in the salivary gland, the cartilage and the tooth germs of the mouse embryo. In the present study, the expression patterns were compared between OASIS mRNA and major vertebrate proteoglycans, which might be the downstream genes of OASIS in the tooth germs of mouse first mandibular molars, through in situ hybridization histochemistry. OASIS mRNA expression was observed in the inner enamel epithelium during the cap and bell stages (E14.5-E18.5) in the preodontoblasts during differentiation stage (E18.5-P0) and in the differentiating odontoblasts during the early secretory stage (P2.5-P4.5). Proteoglycans (versican, decorin, biglycan, glypican, syndecan-1, and syndecan-3) were expressed in the tooth germs in various patterns. Decorin, biglycan, syndecan-1 and syndecan-3 showed gene expressions overlapping with OASIS. Especially the expression pattern of decorin and syndecan-3 coincided temporally and spatially exactly with that of OASIS. These results suggest that the OASIS gene might be related to proteoglycan expression and may play an important role in the differentiation of the odontoblast and cells in inner enamel epithelium.

Aggrecans↗
PubMed1991

Nucleotide sequence and organization of genes flanking the transfer origin of promiscuous plasmid RP4.

The nucleotide sequence of the relaxase operon and the leader operon which are part of the Tra1 region of the promiscuous plasmid RP4 was determined. These two polycistronic operons are transcribed divergently from an intergenic region of about 360 bp containing the transfer origin and six close-packed genes. A seventh gene completely overlaps another one in a different reading frame. Conjugative DNA transfer proceeds unidirectionally from oriT with the leader operon heading the DNA to be transferred. The traI gene of the relaxase operon includes within its 3' terminal region a promoter controlling the 7.2-kb polycistronic primase operon. Comparative sequence analysis of the closely related IncP plasmid R751 revealed a similarity of 74% at the nucleotide sequence level, indicating that RP4 and R751 have evolved from a common ancestor. The gene organization of relaxase- and leader operons is conserved among the two IncP plasmids. The transfer origins and the genes traJ and traK exhibit greater sequence divergence than the other genes of the corresponding operons. This is conceivable, because traJ and traK are specificity determinants, the products of which can only recognize homologous oriT sequences. Surprisingly, the organization of the IncP relaxase operons resembles that of the virD operon of Agrobacterium tumefaciens plasmid pTiA6 that mediates DNA transfer to plant cells by a process analogous to bacterial conjugation. Furthermore, the IncP TraG proteins and the product of the virD4 gene share extended amino acid sequence similarity, suggesting a functional relationship.

Amino Acid Sequence↗
PubMed1999

Expression of Cx genes in liver and stomach of different embryonic stages.

AIM:To explore the relationship between the rules of Cx gene expression and cellular differentiation in organs of different embryonic stages.METHODS:A series of Cx gene serving as molecular probes and the Northern blot hybrydization were employed to study the Cx gene expression.RESULTS:Cx31,Cx31.1,Cx46 did not express while other Cx genes expressed in the embryonic liver and stomach. The Cx gene expression in the liver and stomach showed different state at different embryonic stages. The Cx gene expression had organic diversity. The expression of Cx26 gene was overlapping in the above organs. Cx43 did not express in the human liver after birth, but it expressed in the embryonic stage.CONCLUSION:The expression state of Cx genes is concordant with cellular differentiation. It might be a key candidate gene to regulate some differentiational events associated with cellular differentiation, proliferation,and morphogenesis in the early embryo.

Journal Article↗
PubMed1987

The nucleotide sequence and gene organization of the gerA spore germination operon of Bacillus subtilis 168.

The nucleotide sequence of the second and third genes in the Bacillus subtilis spore germination locus, gerA, has been determined and the amino acid (aa) sequence was derived. Two open reading frames (ORFs), corresponding to genes II and III, encode 364-aa residue and 373-aa residue polypeptides, respectively. The gene II product, Mr 41,257, would contain long stretches of hydrophobic aa residues and may be a membrane protein; the gene III product, Mr 42,363, is relatively hydrophilic but possesses an apparent signal peptide for transfer across, and perhaps localisation on, a membrane. The ORFs for genes I and II overlap by eleven codons and the termination codon of gene II overlaps the initiation codon of gene III. Insertional inactivation experiments using integrational plasmids have indicated that the gerA locus is a single transcriptional unit. The expression of the gerA genes has been studied using a lacZ transcriptional fusion; they constitute a developmentally regulated operon.

Amino Acid Sequence↗