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At least 865 records · Page 48Linked to original sources
PubMed2003

The cell biology of a novel chromosomal RNA: chromosome painting by XIST/Xist RNA initiates a remodeling cascade.

X chromosome inactivation begins when a novel chromosomal RNA (cRNA) from the imprinted mouse Xist or human XIST locus coats or "paints" one X chromosome in cis and initiates a cascade of chromosome remodeling events. Molecular cytological studies have proven invaluable for understanding the distinctive cellular behavior of this singular RNA involved in chromosome structure and regulation. While the detailed mechanism of XIST/Xist (X-inactivation Specific Transcript) RNA function remains largely unknown, recent advances provide new insights into the complex cellular factors which impact the RNA's localization to the chromosome, as well as the early events of chromosome remodeling that follow painting by Xist RNA. Because chromatin changes can be directly visualized on a silenced chromosome, X chromosome inactivation provides an advantageous model to investigate genome-wide heterochromatin formation and maintenance, with wide-ranging implications for normal cells and disease.

Animals↗
PubMed1988

Retroviral activation of a novel gene encoding a zinc finger protein in IL-3-dependent myeloid leukemia cell lines.

Normal hematopoietic stem cells proliferate and differentiate in the presence of growth factors such as interleukin-3 (IL-3). Transformation can alter their growth factor requirements, the ability of the cells to differentiate, or both. To identify genes that are capable of transforming hematopoietic cells, IL-3-dependent cell lines, isolated from retrovirus induced myeloid leukemias, were examined for viral insertions in proto-oncogenes and in common sites of viral integration. Five of 37 cell lines contained proviruses in a common viral integration site termed the ecotropic virus integration 1 site (Evi-1). The integrations were correlated with the activation of transcription from the locus. Sequencing of cDNA clones and genomic clones demonstrated that the integrations had occurred near or in 5' noncoding exons of a novel gene. The sequence of the cDNA clones predicts that the gene product is a 120 kd protein that contains two domains with seven and three repeats of a DNA binding consensus sequence (zinc finger) initially described in the Xenopus transcription factor III A (TFIIIA). This represents the first demonstration of the retroviral activation of a gene encoding a zinc finger protein and the first implication for a member of this gene family in the transformation of hematopoietic cells.

Amino Acid Sequence↗
PubMedDate not supplied

Novel intergenic repeats of Escherichia coli K-12.

An online catalog of intergenic DNA repeat sequence elements is added to the EcoGene Escherichia coli K-12 genome sequence annotation and analysis project (bmb.med.miami.edu/EcoGene). A library of noncoding (intergenic) DNA sequences depleted of known intergenic repeat classes was searched for DNA sequence similarities to identify novel DNA repeat sequence classes.

Base Sequence↗
PubMed1999

Regulatory elements and expression profiles.

There has been steady progress in the computational analysis of transcription control regions, but current methods of predicting the gene regulatory features of noncoding sequences are still not accurate enough to be useful in automatic genome annotation. Therefore, detailed information on the expression patterns of newly sequenced genes is more likely to come from microarray-based high-throughput mRNA quantitation technologies, which have made revolutionary progress over the past few years and are now ready for genome-wide application. Future solutions to the regulatory element prediction problem may be found by the combined analysis of genome sequence and expression data.

Animals↗
PubMed2006

Sealed with a X.

Explore the source record for details and available documents.

Animals↗
PubMed1999

GBV-C/HGV-RNA in serum and peripheral blood mononuclear cells in hemodialysis patients.

BACKGROUND: Hemodialysis patients are at high risk of hepatitis B, C, and G virus infection. The prevalence of GBV-C/HGV-RNA was analyzed in serum and peripheral blood mononuclear cells (PBMCs) from 52 hemodialysis patients. METHODS: GBV-C/HGV-RNA detection was performed by reverse transcription-polymerase chain reaction (RT-PCR) with primers of 5'-noncoding (5'-NC) and NS3 regions of the GBV-C/HGV genome. To increase sensitivity, serum samples were ultracentrifuged prior to the RT-PCR to concentrate the viral particles. The amplified products from 20 serum and 5 peripheral blood mononuclear cells (PBMC) samples were sequenced. RESULTS: GBV-C/HGV-RNA was detected in sera of 9 (17%) and in PBMCs of 30 (58%) patients. After serum ultracentrifugation, GBV-C/HGV-RNA was positive in 20 (95%) of the patients, with GBV-C/HGV-RNA only in PBMCs. Thus, GBV-C/HGV-RNA was detected in serum and PBMCs from 29 (56%) patients, four of whom had antibodies against GBV-C/HGV E2 protein (anti-HGE2); one patient (2%) had GBV-C/HGV-RNA only in PBMCs, but was anti-HGE2 positive. Seven (32%) patients who did not have GBV-C/HGV-RNA were anti-HGE2 positive. The nucleotide sequence homology between serum samples from the patients who were GBV-C/HGV-RNA positive after ultracentrifugation, and paired serum and PBMCs from five of them, ranged from 90 to 96% and from 92 to 98%, respectively. CONCLUSIONS: We found a high prevalence of GBV-C/HGV-RNA in serum and PBMC samples from hemodialysis patients. Whether or not this finding can be extended to other populations requires further study.

Aged↗
PubMed2024

Stroke genetics and how it Informs novel drug discovery.

INTRODUCTION: Stroke is one of the main causes of death and disability worldwide. Nevertheless, despite the global burden of this disease, our understanding is limited and there is still a lack of highly efficient etiopathology-based treatment. It is partly due to the complexity and heterogenicity of the disease. It is estimated that around one-third of ischemic stroke is heritable, emphasizing the importance of genetic factors identification and targeting for therapeutic purposes. AREAS COVERED: In this review, the authors provide an overview of the current knowledge of stroke genetics and its value in diagnostics, personalized treatment, and prognostication. EXPERT OPINION: As the scale of genetic testing increases and the cost decreases, integration of genetic data into clinical practice is inevitable, enabling assessing individual risk, providing personalized prognostic models and identifying new therapeutic targets and biomarkers. Although expanding stroke genetics data provides different diagnostics and treatment perspectives, there are some limitations and challenges to face. One of them is the threat of health disparities as non-European populations are underrepresented in genetic datasets. Finally, a deeper understanding of underlying mechanisms of potential targets is still lacking, delaying the application of novel therapies into routine clinical practice.

Humans↗
PubMed2002

A theoretical limit to coding space in chromosomes of bacteria.

A mathematical model of cluster patterns for mapped genes with known phenotypes in Escherichia coli predicted thatfunctional genes may account for a maximum of two-thirds of the total chromosomal space. The corollary prediction was that one-third of the chromosome comprised noncoding space. Open reading frame (ORF) analyses for 15 phylogenetically diverse bacterial genomes and for 30 fully sequenced prokaryotic genomes supported the gene cluster model prediction of a two-thirds tendency for coding space. Our results suggest that only 3-4% of unassigned ORFs in E. coli represent genes with potential phenotype and that ORFs marking novel genes in prokaryotes are far fewer than previously thought.

Chromosomes, Bacterial↗
PubMed2006

Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri.

The role of small RNAs as critical components of global regulatory networks has been highlighted by several recent studies. An important class of such small RNAs is represented by CsrB and CsrC of Escherichia coli, which control the activity of the global regulator CsrA. Given the critical role played by CsrA in several bacterial species, an important problem is the identification of CsrA-regulating small RNAs. In this paper, we develop a computer program (CSRNA_FIND) designed to locate potential CsrA-regulating small RNAs in bacteria. Using CSRNA_FIND to search the genomes of bacteria having homologs of CsrA, we identify all the experimentally known CsrA-regulating small RNAs and also make predictions for several novel small RNAs. We have verified experimentally our predictions for two CsrA-regulating small RNAs in Vibrio fischeri. As more genomes are sequenced, CSRNA_FIND can be used to locate the corresponding small RNAs that regulate CsrA homologs. This work thus opens up several avenues of research in understanding the mode of CsrA regulation through small RNAs in bacteria.

Aliivibrio fischeri↗
PubMed1994

Characterization of hamster CYP1A1 gene: inducible expression and negative regulation.

A genomic clone encoding the hamster CYP1A1 gene was isolated from a hamster EMBL-3 genomic library and characterized. The CYP1A1 gene contained seven exons including the noncoding first exon as determined for CYP1A1 of other species. DNA sequence analysis up to -2307 bp of the CYP1A1 gene revealed the occurrence of five consensus xenobiotic responsive elements (XREs) and one basal transcription element (BTE) in addition to the canonical TATA box. For functional analysis, transfection experiments were performed in human hepatoma HepG2 cells with reporter gene constructs consisting of fragments with various lengths of the 5'-flanking region of the CYP1A1 gene and bacterial chloramphenicol acetyltransferase (CAT) gene. External deletion of the upstream region from the reporter gene resulted in a stepwise decrease of the CAT activity, suggesting that XREs were responsible for inducible expression of CYP1A1 gene by 3-methylcholanthrene (MC). A negative regulatory element (NRE) was also identified in the 5'-flanking region at -833 to -642. Removal of the NRE from the CYP1A1-CAT fusion gene resulted in about 3-fold increase of MC-inducible CAT activity. Using gel retardation assays with HepG2 nuclear extract, we demonstrated the presence of a specific protein which bound to the NRE fragment. Further competition analysis and methylation interference assays revealed that the nuclear protein bound to a 22-base fragment (from -688 to -709) of the NRE region, whose sequences were conserved among hamster, human, and rat CYP1A1 genes.

Animals↗
PubMed1986

Molecular cloning of cDNA from hepatitis A virus strain HM-175 after multiple passages in vivo and in vitro.

Hepatitis A virus (HAV) strain HM-175 was passaged six times in marmosets, 59 times in cell culture and purified from infected cell culture supernatant fluid. The viral RNA was extracted, copied into cDNA and the cDNA:RNA hybrids were cloned into the PstI site of plasmid pBR322. The cDNA clones were authenticated by hybridization to RNA extracted from HAV-infected cells and clones representing the 3' end of the genome were identified using a previously authenticated cDNA clone. The clones represented all but 29 bases of the HAV genome. They were compared to HAV strain HM-175 cDNA cloned from viral RNA after three passages in marmosets on the basis of restriction endonuclease mapping and DNA sequencing. No differences were found in either the presence or absence of restriction endonuclease sites using 33 different restriction enzymes. Sequencing of cDNA representing bases 29 to 1002 of the HAV genome revealed eight base changes all of which were within the 5' noncoding region.

Animals↗
PubMed1990

Analysis of the role of brome mosaic virus 1a protein domains in RNA replication, using linker insertion mutagenesis.

Brome mosaic virus (BMV) belongs to a "superfamily" of plant and animal positive-strand RNA viruses that share, among other features, three large domains of conserved sequence in nonstructural proteins involved in RNA replication. Two of these domains reside in the 109-kDa BMV 1a protein. To examine the role of 1a, we used biologically active cDNA clones of BMV RNA1 to construct a series of linker insertion mutants bearing two-codon insertions dispersed throughout the 1a gene. The majority of these mutations blocked BMV RNA replication in protoplasts, indicating that both intervirally conserved domains function in RNA replication. Coinoculation tests with a large number of mutant combinations failed to reveal detectable complementation between mutations in the N- and C-terminal conserved domains, implying that these two domains either function in some directly interdependent fashion or must be present in the same protein. Four widely spaced mutations with temperature-sensitive (ts) defects in RNA replication were identified, including a strongly ts insertion near the nucleotide-binding consensus of the helicaselike C-terminal domain. Temperature shift experiments with this mutant show that 1a protein is required for continued accumulation of all classes of viral RNA (positive strand, negative strand, and subgenomic) and is required for at least the first 10 h of infection. ts mutations were also identified in the 3' noncoding region of RNA1, 5' to conserved sequences previously implicated in cis for replication. Under nonpermissive conditions, the cis-acting partial inhibition of RNA1 accumulation caused by these noncoding mutations was also associated with reduced levels of the other BMV genomic RNAs. Comparison with previous BMV mutant results suggests that RNA replication is more sensitive to reductions in expression of 1a than of 2a, the other BMV-encoded protein involved in replication.

Amino Acid Sequence↗
PubMed1994

The X inactivation centre and X chromosome imprinting.

Genetic imprinting is an important component of X chromosome inactivation, since in marsupials and extraembryonic cell lineages of mice and rats, the paternally derived X chromosome is preferentially inactivated. This imprinting is thought to be mediated via the X inactivation centre. The gene symbolized Xist is a strong candidate for a role in the function of the X inactivation centre and the paper reviews the evidence that Xist shows imprinted behaviour and that differential methylation is the possible basis of the imprint. This paper is the text of the speech given by Dr. Mary Lyon after the awarding of the Mauro Baschirotto prize at the meeting of the European Society of Human Genetics in Paris, June 1994 (see page 305).

Animals↗
PubMed2025

Genetic mapping in the red mason bee implicates ANTSR as an ancient sex-determining locus in bees and ants.

Haplodiploid inheritance, in which females are diploid and males are haploid, is found in all species of Hymenoptera. Sex in haplodiploids is commonly determined by the alleles present at a complementary sex determination (CSD) locus, with heterozygosity triggering the female developmental pathway. The identity of this locus differs among taxa and is only known in a few species. Here, we map a single CSD locus to a 2 kbp region in the genome of the red mason bee Osmia bicornis. It overlaps the long noncoding RNA ANTSR, which has been identified as the sex-determining gene in the invasive ant Linepithema humile. This locus is homozygous in diploid males and exhibits extremely high levels of haplotype diversity, consistent with the action of frequency-dependent selection. The elevated levels of heterozygosity in the CSD locus enable us to fine-map potentially functional genetic variation within it. We also identify elevated levels of genetic diversity in the ortholog of the CSD locus in five other bee and ant genera, suggesting that it may govern sex determination widely in Hymenoptera. Our data are consistent with the hypothesis that ANTSR evolved a role in sex determination over 150 million years ago and is the ancestral sex-determination locus of bees and ants.

Animals↗