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PubMedDate not supplied

Polymerase chain reaction typing of nonviable Mycobacterium tuberculosis isolates.

Repetitive element polymerase chain reaction (PCR) typing was applied to two Mycobacterium tuberculosis isolates for which both viable and nonviable cultures were available. DNA extracted from the nonviable cultures and from fresh subcultures of the viable cultures was amplified with primers directed against the insertion sequence IS6110 and the polymorphic GC-rich repetitive sequence. For both isolates, the nonviable cultures generated PCR-banding patterns identical to those generated by the fresh subcultures.

Bacterial Typing Techniques↗
PubMed2002

Spoligotyping and IS6110-RFLP typing of Mycobacterium tuberculosis from French Guiana: a comparison of results with international databases underlines interregional transmission from neighboring countries.

In this investigation, 94 clinical isolates of Mycobacterium tuberculosis obtained over a 3-year period (1996-1998) from French Guiana were characterized by spoligotyping and IS6110-RFLP and the patterns obtained were compared with genotypes representing the worldwide diversity in an international spoligotyping database (n = 4269) and a IS6110-RFLP database (n = 4189). All the clustered isolates giving < or = 6 copies of IS6110 were further typed using the double-repetitive element (DRE)-PCR. The results obtained underlined the highly diverse nature of the M. tuberculosis population in French Guiana with potential links to neighboring countries within the Americas. It may be hypothesized that the genetic heterogeneity of tubercle bacilli in French Guiana is linked to the high number of imported cases of tuberculosis, that may account for as high as 68% of all tuberculosis cases. Although an epidemiological investigation based on direct interrogation of patients was not performed, available medical records suggested that the clustering of isolates was mostly linked to the following risk factors: pulmonary tuberculosis, smear-positive samples, foreign-born nationals and/or immigrants, and a high rate of HIV-TB coinfection. Thus the persisting foci of endemic disease and increased active transmission due to high population flux and HIV coinfection may be largely responsible for the relatively high incidence of tuberculosis in French Guiana.

Adult↗
PubMed1994

Transcriptional control of the human biliary glycoprotein gene, a CEA gene family member down-regulated in colorectal carcinomas.

Biliary glycoprotein (BGP) isoantigens are derived by alternative splicing from a single gene and are the human homologs of rat C-CAM and the mouse Bgp species. These glycoproteins represent a family of cell-adhesion molecules. The mouse Bgp isoforms also act as receptors for the hepatitis viral capsid-protein. BGP is a member of the carcinoembryonic antigen (CEA) gene family, which belongs to the immunoglobulin supergene family, yet it displays restricted expression patterns and unique functions. Since the loss or reduced expression of BGP is associated with human colorectal carcinomas, the elements in its upstream regulatory region were analyzed. A cluster of transcriptional initiation sites and the minimal promoter, located within 150 bp upstream of the major transcriptional start site, were active in human colon carcinoma and hepatoma cells. Unlike the CEA gene, BGP gene transcription was not modulated by a silencer region; repetitive elements in the BGP upstream region were not involved in activation or repression. Footprinting experiments identified two cis-acting elements and mobility-shift assays demonstrated that these elements bound several transcription factors, among them, USF, HNF-4 and an AP-2-like factor. In cotransfection experiments, both the USF and HNF-4 transcription factors transactivate the BGP gene promoter and compete for the same regulatory element. The Sp1 transcription factor, shown to be involved in CEA gene transcriptional regulation, does not bind to the BGP gene promoter. We, therefore, propose that the relative distributions and interactions of these transcription factors mediate distinct transcriptional regulation of the BGP gene in colon and liver; this regulation could be distorted during the oncogenic process.

Animals↗
PubMed2001

RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse.

In mouse brain cDNA libraries generated from small RNA molecules we have identified a total of 201 different expressed RNA sequences potentially encoding novel small non-messenger RNA species (snmRNAs). Based on sequence and structural motifs, 113 of these RNAs can be assigned to the C/D box or H/ACA box subclass of small nucleolar RNAs (snoRNAs), known as guide RNAs for rRNA. While 30 RNAs represent mouse homologues of previously identified human C/D or H/ACA snoRNAs, 83 correspond to entirely novel snoRNAS: Among these, for the first time, we identified four C/D box snoRNAs and four H/ACA box snoRNAs predicted to direct modifications within U2, U4 or U6 small nuclear RNAs (snRNAs). Furthermore, 25 snoRNAs from either class lacked antisense elements for rRNAs or snRNAS: Therefore, additional snoRNA targets have to be considered. Surprisingly, six C/D box snoRNAs and one H/ACA box snoRNA were expressed exclusively in brain. Of the 88 RNAs not belonging to either snoRNA subclass, at least 26 are probably derived from truncated heterogeneous nuclear RNAs (hnRNAs) or mRNAS: Short interspersed repetitive elements (SINEs) are located on five RNA sequences and may represent rare examples of transcribed SINES: The remaining RNA species could not as yet be assigned either to any snmRNA class or to a part of a larger hnRNA/mRNA. It is likely that at least some of the latter will represent novel, unclassified snmRNAS:

Animals↗
PubMed2001

The R3 region, one of three major repetitive regions of human herpesvirus 6, is a strong enhancer of immediate-early gene U95.

An immediate-early (IE) gene of human herpesvirus 6 (HHV-6), U95, has similarity at the amino acid level to the murine cytomegalovirus (MCMV) IE2 gene and is related to the human cytomegalovirus (HCMV) US22 gene family. Sequence analyses of U95 cDNA clones revealed that the transcription start site was located about 1.6 kbp upstream of the putative initiating ATG and that the transcript consisted of two exons. A single intron extended from nucleotides 142589 to 144229, which contained ORF U94. A protein with a molecular mass of about 120 kDa was translated from this cDNA clone in an in vitro transcription-translation assay. The transcription start site was found to be 220 bp downstream of the R3 region by primer extension analysis. HHV-6 has three repetitive elements, R1, R2, and R3, in or near the IE-A locus. R3 is composed of 24 copies of a 104- to 107-bp sequence element, which contains multiple putative binding sites for cellular transcription factors such as AP2 and NF-kappaB, and its biological significance has yet to be elucidated. The region between -710 and +46 relative to the transcription start site of U95 was analyzed in this study. Deletion from -710 to -396, corresponding to three copies of an R3 unit, decreased the promoter activity by 15-fold, and coexpression of IkappaBalpha(S32A/S36A) repressed it to almost the same level. Electrophoretic mobility shift assays showed that NF-kappaB family members p50 and c-Rel bound to NF-kappaB sites derived from the R3 region. These results demonstrate that R3 strongly enhances the U95 promoter activity and that NF-kappaB and binding sites for NF-kappaB in the R3 region play an important role in its activation. Because U95 promoter activity correlated with the number of R3 units, which each contained an NF-kappaB site, the repetitive organization of R3 is important for regulating U95 transcription.

Base Sequence↗
PubMed1993

The structure of two murine class-mu glutathione transferase genes coordinately induced by butylated hydroxyanisole.

We report the sequences of two coordinately induced murine glutathione transferase genes, mGSTM1 (GT8.7, Yb1) and mGSTM3 (GT9.3). Genomic clones covering the entire mGSTM1 gene were isolated; comparison of the mGSTM1 gene with genomic sequences from rat class-mu glutathione transferase genes suggests that the mGSTM1 gene is orthologous to the rGSTM1 (rat3, Yb1) gene. The start of mGSTM1 mRNA transcription was mapped by primer extension and RNase protection to 37 nucleotides upstream from the initiation codon. The 160 nucleotides 5'-proximal to the start of transcription match exactly the 5'-end of the class-mu glutathione transferase cDNA clone pmGT10. An mRNA transcript was found approximately 2.0 kb upstream from the start of mGSTM1 transcription; its sequence does not show significant similarity to other sequences in the DNA or protein sequence databases. The mGSTM1 gene contains a TATAAA sequence at -31 nucleotides upstream from the start of transcription, but no exact match to the antioxidant response element (RGTGACNNNGC), the xenobiotic response element (TNGCGTG), or the AP-1 consensus (TGASTMA) is found in the 5'-flanking region, although near matches are found in the 5'-flanking region, in intron 1, and in other parts of the gene. A genomic clone containing the first five exons of the mGSTM3 gene was also isolated. The mGSTM3 gene contains several repetitive elements--two upstream from the start of transcription and one within intron 2--that disrupt its similarity with the mGSTM1 gene. The 5'-flanking sequence of the mGSTM3 gene does not contain a TATAAA sequence or any exact matches to ARE or XRE consensus sequences, although an Sp1 binding site is found at -66. mGSTM3 and mGSTM1 diverge substantially outside their exons and share less than 60% sequence identity in the 5'-flanking region. Thus, it is likely that the mGSTM1-mGSTM3 gene duplication predates the rat-mouse divergence. The strongest region of conservation between the mGSTM1 gene and the mGSTM3 gene occurs in exon 3, intron 3, and exon 4; this region also shares strong similarity with the rGSTM1 (rat3, Yb1) and rGSTM2 (rat4, Yb2) genes.

Amino Acid Sequence↗
PubMed2005

Comparison of five repetitive-sequence-based PCR typing methods for molecular discrimination of Salmonella enterica isolates.

Five repetitive-element PCR (rep-PCR) techniques [primer sets ERIC1R-ERIC2 and REP1R-REP2I and primers ERIC2, BOXA1R, and (GTG)5] were evaluated for the discrimination of Salmonella enterica isolates at the serotype level. On the basis of number, even distribution over the whole fingerprint, and clarity of bands in the fingerprints, the enterobacterial repetitive intergenic consensus (ERIC) primer set and the (GTG)5 primer were chosen for use in the following experiments. For these two primer sets, reproducibility was tested on different lysates of five selected serotypes of Salmonella in the same PCR by using three different PCR runs. Reproducibility was poor between different PCR runs but high within the same PCR run. Furthermore, 80 different serotypes and five isolates which were not typeable by serotyping were fingerprinted. All strains were typeable by the ERIC primer set and the (GTG)5 primer and generated unique fingerprints, except for some strains with incomplete antigenic codes. Finally, 55 genetically different strains belonging to 10 serotypes were fingerprinted to examine the genetic diversity of the rep-PCR within serotypes. This experiment showed that one serotype did not always correlate to only one ERIC or (GTG)5 fingerprint but that the fingerprint heterogeneity within a serotype was limited. In epidemiological studies, ERIC- and/or (GTG)5-PCR can be used to limit the number of strains that have to be serotyped. The reproducibility of isolates in one PCR run, the discriminatory power, and the genetic diversity (stability) of the fingerprint were similar for the Eric primer set and the (GTG)5 primer, so both are equally able to discriminate Salmonella serotypes.

Bacterial Typing Techniques↗
PubMed2000

Genomic and transcriptional characterization of the human ACHE locus: complex involvement with acquired and inherited diseases.

BACKGROUND: Abnormal levels of the acetylcholinesterase enzyme or aberrations involving the long arm of chromosome 7, harboring the ACHE gene at 7q22, occur in various diseases such as Alzheimer's, Parkinson's, and leukemias. However, the cause(s) of these abnormalities are still unknown. OBJECTIVE: To search for the genomic elements and transcriptional processes controlling ACHE gene expression and the plausible stability of its locus, by isolating, sequencing and characterizing the human (h)ACHE locus and its mRNA products. METHODS: Three clones containing the ACHE gene were isolated from a human chromosome 7 cosmid library. Two of these clones were thereafter sequenced and searched for repetitive elements, open reading frames and corresponding expressed sequence tags. Reverse transcription-polymerase chain reaction was employed to further explore these findings. RESULTS: The locus harboring the G,C-rich ACHE gene was found to be exceptionally rich in Alu repeats. It includes an additional, inversely oriented gene (ARS), tentatively associated with arsenite resistance. EST clones corresponding to both genes were found in cDNA libraries from 11 different human tissue sources, with ARS expressed in 10 additional tissues. Co-regulation of brain ACHE and ARS was suggested from their mutually increased expression following acute psychological stress. CONCLUSIONS: The abundance of Alu retrotransposones may predispose the ACHE locus to chromosomal rearrangements. Additionally, coordinated transcriptional regulation is implied from the joint ARS-AChE expression in stress insult responses. Disease-related changes in AChE may therefore reflect locus-specific regulation mechanisms affecting multiple tissues.

Acetylcholinesterase↗
PubMed1991

Sequence and localization of the gene encoding yeast phosphoglycerate mutase.

In this study we report on the complete nucleotide sequence of the yeast phosphoglycerate mutase gene (GPM1) and its essential 5' and 3' non-coding regions. The transcriptional start points were determined by S1-mapping and sequencing of a cDNA clone. Several sequences identified as important for transcriptional regulation in yeast promoters are present upstream of the transcription start point. 3' to the coding region we sequenced a composite repetitive element which, apparently, originated from a recombination between a delta- and a tau-element. Finally, we mapped the GPM1 gene 13 cM distal to fas1 on chromosome XI.

Amino Acid Sequence↗
PubMed1994

Structure of the gene encoding pig phosphoglucose isomerase.

Genomic clones encoding pig phosphoglucose isomerase (PGI) have been isolated and partially sequenced. The gene (Pgi) contains 18 exons, 17 introns and spans about 32 kb. This structure is partially conserved between plant and animal. A major transcription start point (tsp) has been identified 74 nucleotides (nt) upstream from the AUG. The nt sequence around the tsp is very G+C rich; a 5'-ATAAA sequence, as well as four putative Sp1-binding sites, are present. In the 3'-flanking region, an AATAAA signal has been identified. Extending from the 5'-flanking region to the first intron, a 0.6-kb CpG island has been identified. The Pgi structural gene contains several DNA repetitive elements in its non-coding regions.

Alternative Splicing↗
PubMedDate not supplied

[Tandem and interspersed repeats contribute to the mosaic structure of segmented duplications in the human genome].

Intrachromosomal and interchromosomal segmental duplications account for more than 5% of the human genome. To analyze the processes resulting in the complex mosaic structure of duplicons, a draft human genome sequence was searched for duplicated segments of a genomic fragment of the pericentric region of the chromosome 21 short arm. The duplicons found consist of modules having paralogs in various genome regions. Module ends are flanked with various tandem or interspersed repeats, which are more unstable as compared with unique sequences. In most cases, the boundaries of duplicated segments exactly coincide with or are in close proximity to hot spots of various rearrangements within repeats or boundaries between repeats and unique sequences or between two different repeats. Homologous recombination between repetitive elements was assumed to be the major mechanism contributing to the mosaic structure of duplicons.

Chromosomes, Human, Pair 21↗
PubMed1996

Human uracil-DNA glycosylase gene: sequence organization, methylation pattern, and mapping to chromosome 12q23-q24.1.

The human uracil-DNA glycosylase gene (UNG) spans approximately 13.5 kb including the promoter. UNG comprises 6 exons and 5 introns and was assigned to chromosome 12q23-q24.1 by radiation hybrid mapping. UNG exhibits typical features of housekeeping genes, including a 5' CpG island of 1.2 kb and a very GC-rich TATA-less promoter containing a number of elements involved in constitutive expression and cell cycle regulation. A smaller CpG island is located just downstream of the gene. Within the 15-kb sequence we identified 16 Alu retroposons, 2 of which contain putative competent RNA polymerase III promoters, 3 copies of medium reiteration frequency repeats, and 1 copy of a mammalian-wide interspersed repetitive element, as well as a 300-bp TA-dinucleotide repeat. In vitro methylation of the UNG promoter strongly reduced promoter activity, but methylation may not be involved in regulation of UNG in vivo since a narrow region of the 5' CpG island comprising the putative transcription factor binding region appears to be invariably methylation-free.

Amino Acid Sequence↗
PubMed2003

In-depth view of structure, activity, and evolution of rice chromosome 10.

Rice is the world's most important food crop and a model for cereal research. At 430 megabases in size, its genome is the most compact of the cereals. We report the sequence of chromosome 10, the smallest of the 12 rice chromosomes (22.4 megabases), which contains 3471 genes. Chromosome 10 contains considerable heterochromatin with an enrichment of repetitive elements on 10S and an enrichment of expressed genes on 10L. Multiple insertions from organellar genomes were detected. Collinearity was apparent between rice chromosome 10 and sorghum and maize. Comparison between the draft and finished sequence demonstrates the importance of finished sequence.

Chromosomes, Plant↗
PubMed2000

Trichoplusia ni lebocin, an inducible immune gene with a downstream insertion element.

A cDNA clone encoding a lebocin-like protein was obtained from the cabbage looper Trichoplusia ni by using differential display PCR. Northern blot analysis showed that lebocin gene expression was inducible upon bacterial challenge. Transcripts were mainly found in fat body but were also observed in hemocytes. Expression reached its highest level at 20 h and continued at least until 60 h after bacterial injection. The deduced protein is proline-rich and contains 143 amino acid residues. At position 128, a possible O-glycosylation site is observed. The whole protein shows 35% identity to Bombyx mori lebocin. The mature peptide displays an N-terminus similar to that of lebocin and a C-terminus to that of Drosophila metchnikowin. A 39-bp repetitive element is located downstream of the coding region.

Amino Acid Sequence↗
PubMed1993

Vb6 T-cell receptor elements in artiodactyls: conservation and germline polymorphisms.

By use of primers specific for human T-cell receptor (Tcr) Vb6 gene elements, a typing system for Tcr Vb variability in several artiodactyl species has been established. The amplified polymorphic locus is homologous to the human Vb6 gene element. Like the human counterpart, the artiodactyl Vb6 element contains a polymorphic intronic simple (gt)n repeat stretch. Extensive length polymorphism of this simple repeat sequence in some artiodactyls should allow efficient association studies in a multiplex approach, especially including MHC class II genes. On the protein level the Vb regions display little variability in the inter-species comparison among artiodactyls. The amino acid substitutions are not concentrated in the putative complementarity determining regions, suggesting evolutionary conservation. In addition, the simple repetitive element has been preserved in the same genomic location for more than 7 x 10(7) years. Similar evolutionary persistence has already been demonstrated for a (gt)n(ga)m repeat stretch in the second intron of the MHC-DRB locus. The reasons for these parallel developments in evolution are so far not clear, but they may point to a biological meaning if not function of the intronic simple repeat element.

Amino Acid Sequence↗
PubMedDate not supplied

Cell lineage-specific undermethylation of mouse repetitive DNA.

Several distinct cell lineages are established during mouse embryogenesis. The trophectoderm and primitive endoderm give rise to extraembryonic structures alone, while the primitive ectoderm becomes the fetus proper. Recent studies suggest that the levels of DNA modification are lower in inactive X chromosomes from extraembryonic tissues than in embryonic and adult somatic tissues. Using HpaII/MspI isoschizomers, Southern blots and cloned probes, we show here that repetitive DNA sequences from all derivatives of the two extraembryonic lineages, trophectoderm and primitive endoderm, are substantially undermethylated compared with primitive ectoderm derivatives. This contrasts with the highly methylated state of these repetitive elements observed in adult somatic tissues. Specific demethylation or inhibition of de novo methylation, or a combination of both mechanisms, may be involved. These findings suggest that elements of gene regulation dependent on DNA modification may be different in extraembryonic cell lineages.

Animals↗
PubMed1994

Identification of a mariner-like repetitive sequence in C. elegans.

A repetitive element in C.elegans has been found that bears high homology to the element mariner of Drosophila mauritiana (EMBL accession number X77804). This element is present in about 20 copies in the N2 strain of C.elegans, and appears in roughly equal copy numbers in the related strain BO and in the hybrid strains RW7097 and TR679. There is only one copy of this MLE in three related species of Caenorhabditis. A cDNA of this mariner-like element (MLE) codes for a protein with 58% homology to the Drosophila transposase. The mariner-like element is not mobile in N2. This class of elements has now been described in insects, planaria and nematodes (GenBank accession number M98552 and this report).

Animals↗