Abstract:
:We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Unique features are noted and discussed. Overall the introns have a mean A + T content of 85% (21% higher than neighbouring exons) with smaller introns tending towards a higher A + T content. Approximately half of the introns are less than 100 bp. Introns from other organisms (approximately 30 of each) were also examined. The introns of Dictyostelium discoideum, Caenorhabditis elegans and Drosophila melanogaster, like those of T. thermophila, have a much higher mean A + T content than their neighbouring exons (greater than 20%). Introns from plants, Neurospora crassa and Schizosaccharomyces pombe also have a significantly higher A + T content (10%-20%). Since a high A + T content is required for intron splicing in plants (58), the elevated A + T content in the introns of these other organisms may also be functionally significant. The introns of yeast (Saccharomyces cerevisiae) and mammals (humans) appear to lack this trait and thus in some aspects may be atypical. The polypyrimidine tract, so distinctive of vertebrate introns, is not a trait of the introns in the non-vertebrate organisms examined in this study.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Csank C,Taylor FM,Martindale DWdoi
10.1093/nar/18.17.5133subject
Has Abstractpub_date
1990-09-11 00:00:00pages
5133-41issue
17eissn
0305-1048issn
1362-4962journal_volume
18pub_type
杂志文章abstract::UV-induced reversion of the arg4-17 ochre allele in Saccharomyces cerevisiae is largely dependent on translesion polymerase eta (Rad30p), known to bypass cyclobutane-type TT dimers in an error-free fashion. arg4-17 locus reversion was predominantly due to T-->C transition of T127, the 3' T of a TT photoproduct site. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.5.1262
更新日期:2002-03-01 00:00:00
abstract::The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx315
更新日期:2017-07-27 00:00:00
abstract::A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way along which β-loop structures of ribosomal proteins uL4 and uL22 protrude into the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1190
更新日期:2020-02-28 00:00:00
abstract::Short DNA sequence motifs have been identified in viral and cellular enhancers which represent the binding sites for a variety of trans- acting factors. One such HeLa cell factor, EBP1, has been purified and shown to bind to sequences in the SV40 enhancer. The PRDII element in the human beta-interferon gene regulatory...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.2.499
更新日期:1989-01-25 00:00:00
abstract::We report here on a quantitative technique called COBRA to determine DNA methylation levels at specific gene loci in small amounts of genomic DNA. Restriction enzyme digestion is used to reveal methylation-dependent sequence differences in PCR products of sodium bisulfite-treated DNA as described previously. We show t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.12.2532
更新日期:1997-06-15 00:00:00
abstract::We have constructed a stable cell line, human embryonal kidney 293M+, containing a lacZ reporter gene controlled by an in vitro methylated hormone-responsive enhancer. Methylation of the enhancer-promoter abolishes lacZ expression controlled by ponasterone A (an analogue of ecdysone). Ponasterone A-induced expression ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.17.3603
更新日期:2001-09-01 00:00:00
abstract::Orthology is a widely used concept in comparative and evolutionary genomics. In addition to prokaryotic orthology, delineating eukaryotic orthology has provided insight into the evolution of higher organisms. Indeed, many eukaryotic ortholog databases have been established for this purpose. However, unlike prokaryotes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn227
更新日期:2008-06-01 00:00:00
abstract::The development of genetic switches and their integrated forms (genetic circuits) with desired specifications/functions is key for success in synthetic biology. Due to the difficulty in rational design, genetic switches and circuits with desirable specifications are mostly obtained by directed evolution. Based on a vi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1070
更新日期:2011-02-01 00:00:00
abstract::A dot hybridization method is presented for rapidly determining the relative concentrations of nucleic acids in a mixture, as well as the extent of sequence homology between related RNA or DNA species. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.6.1541
更新日期:1979-11-24 00:00:00
abstract::Differential display relies on a series of anchored primers to divide the total mRNA population into subsets of roughly equal size. However, this will only occur if the dinucleotide targeted by the anchor region of the anchored primers has a random frequency distribution [i.e. each of the 12 possible dinucleotides pre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.5.1386
更新日期:1999-03-01 00:00:00
abstract::The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1072
更新日期:2017-01-04 00:00:00
abstract::From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently atta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky887
更新日期:2018-11-30 00:00:00
abstract::Glucocorticoid (GC) signaling synchronizes the circadian rhythm of individual peripheral cells and induces the expression of circadian genes, including Period1 (Per1) and Period2 (Per2). However, no GC response element (GRE) has been reported in the Per2 promoter region. Here we report the molecular mechanisms of Per2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt307
更新日期:2013-07-01 00:00:00
abstract::Retroviral particles contain a dimeric RNA genome, which serves as template for the generation of double-stranded DNA by reverse transcription. Transfer between RNA strands during DNA synthesis is governed by both sequence similarity between templates and structural features of the dimeric RNA. A kissing hairpin, beli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh159
更新日期:2004-01-09 00:00:00
abstract::The bacteriophage ø29 DNA packaging motor that assembles on the precursor capsid (prohead) contains an essential 174-nt structural RNA (pRNA) that forms multimers. To determine the structural features of the CE- and D-loops believed to be involved in multimerization of pRNA, 35- and 19-nt RNA molecules containing the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm874
更新日期:2008-02-01 00:00:00
abstract::2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-cont...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv109
更新日期:2015-03-11 00:00:00
abstract::Exposure of Schizosaccharomyces pombe cells to UV light results in increased uvi15(+) gene expression at both the mRNA and protein levels, leading to elevated cell survival. This UV-induced expression of the uvi15(+) gene was reduced in Deltasty1 and Deltawis1 cells lacking the stress-activated protein kinase pathway,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.17.3392
更新日期:2000-09-01 00:00:00
abstract::As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality fac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.9.e43
更新日期:2000-05-01 00:00:00
abstract::We have isolated and sequenced a cDNA clone coding for human Retinol Binding Protein. The sequence indicates that Retinol Binding Protein is synthesized as a single polypeptide chain precursor which is then matured to the secreted protein by removal of a leader peptide. Southern and Northern blot analysis suggest that...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.22.7769
更新日期:1983-11-25 00:00:00
abstract::According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer-promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw371
更新日期:2016-09-06 00:00:00
abstract::The self-assembly of bis-biotinylated double-stranded DNA and the tetravalent biotin-binding protein streptavidin (STV) have been studied by non-denaturing gel electrophoresis and atomic force microscopy (AFM). The rapid self-assembly reproducibly generated populations of individual oligomeric complexes. Most striking...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.23.4553
更新日期:1999-12-01 00:00:00
abstract::The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn819
更新日期:2009-01-01 00:00:00
abstract::Prion proteins (PrPs) cause prion diseases, such as bovine spongiform encephalopathy. The conversion of a normal cellular form (PrP(C)) of PrP into an abnormal form (PrP(Sc)) is thought to be associated with the pathogenesis. An RNA aptamer that tightly binds to and stabilizes PrP(C) is expected to block this conversi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1132
更新日期:2013-01-01 00:00:00
abstract::The T box transcription antitermination regulatory system, found in Gram-positive bacteria, is dependent on a complex set of interactions between uncharged tRNA and the 5'-untranslated mRNA leader region of the regulated gene. One of these interactions involves the base pairing of the acceptor end of cognate tRNA with...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki546
更新日期:2005-05-06 00:00:00
abstract::The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw432
更新日期:2016-07-27 00:00:00
abstract::We characterize a component of the E. coli bacterial nucleoid H1a, which accumulates in stationary phase. This protein, identical with the major component of a plasmid-protein complex previously isolated in our laboratory, has a pI close to 7.5. Acrylamide gel electrophoresis and sedimentation in sucrose gradient have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.13.5321
更新日期:1984-07-11 00:00:00
abstract::Sexual differentiation in Drosophila is regulated through alternative splicing of doublesex. Female-specific splicing is activated through the activity of splicing enhancer complexes assembled on multiple repeat elements. Each of these repeats serves as a binding platform for the cooperative assembly of a heterotrimer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl984
更新日期:2006-01-01 00:00:00
abstract::Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been built to host and make available such data to the community, but these databases are frequently limited in scope and/or content. BioMuta, a database of cancer-associated si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx907
更新日期:2018-01-04 00:00:00
abstract::Immunoglobulin genes contain a conserved eight base sequence element 5' to the site of transcription initiation. This octamer can serve as a site for the binding of nuclear proteins which are presumably involved in the cell type specific expression of this family of genes. In studying the binding of nuclear proteins t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5503
更新日期:1988-06-24 00:00:00
abstract::Using the quenched flow technique the mechanism of seryl tRNA synthetase action has been investigated with respect to the presteady state kinetics of individual steps. Under conditions where the strong binding sites of the enzyme are nearly saturated and the steady state turnover number is about 1 s-1, rate constants ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.4021
更新日期:1980-09-11 00:00:00