Abstract:
:Electrophoretic mobility shift assays (EMSA) were used to define the regions of the INO1 promoter that interact with factors present in extracts prepared from the yeast, Saccharomyces cerevisae. These experiments identified three different types of protein:DNA complexes that assemble with the INO1 promoter. Formation of one type of complex depended on functional alleles of previously described regulatory genes, INO2 and INO4, that encode positive regulatory factors. Formation of the INO2/INO4-dependent complexes was increased when extracts prepared from cells grown under derepressing conditions (i.e. absence of inositol and choline). A second type of complex was dependent on the OPI1 gene, that encodes a negative regulator. Computer-aided sequence analysis of the promoters of several genes encoding phospholipid biosynthetic enzymes revealed a highly conserved nine basepair element (5'-ATGTGAAAT-3'), designated 'nonamer' motif, that is similar to the octamer motif identified in the promoters of mammalian immunoglobulin genes. The nonamer motif was shown to form a specific complex with a factor, designated nonamer binding factor (NBF). Extracts prepared from Schizosaccharomyces pombe formed a nonamer-specific complex.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lopes JM,Henry SAdoi
10.1093/nar/19.14.3987keywords:
subject
Has Abstractpub_date
1991-07-25 00:00:00pages
3987-94issue
14eissn
0305-1048issn
1362-4962journal_volume
19pub_type
杂志文章abstract::Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a large number of economically-significant crops. Traditional 'dot-blot hybridization' or PCR-based assays for identifyin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.7.e23
更新日期:2000-04-01 00:00:00
abstract::We have previously shown that hedamycin, a GC-rich DNA-binding antitumor agent, downregulates survivin transcription (Wu et al. (2005) Molecular mechanism of inhibition of survivin transcription by the GC-rich sequence selective DNA-binding antitumor agent, hedamycin: evidence of survivin downregulation associated wit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm149
更新日期:2007-01-01 00:00:00
abstract::Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including CMAR, STAC, GISTIC and KC-SMART...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt155
更新日期:2013-05-01 00:00:00
abstract::TcruziDB (http://TcruziDB.org) is an integrated genome database for the parasitic organism Trypanosoma cruzi, the causative agent of Chagas' disease. The database currently incorporates all available sequence data (Genomic, BAC, EST) in a single user-friendly location. The database contains a variety of tools specific...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh049
更新日期:2004-01-01 00:00:00
abstract::A 5',7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa743
更新日期:2020-10-09 00:00:00
abstract::DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 880 115 entries or 1 134 086 245 bases in the period from July 2006 to June 2007. The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others. Our computer system has been upgraded since March 2007. Anoth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm889
更新日期:2008-01-01 00:00:00
abstract::Recent studies indicate that controlling the nuclear decondensation and intra-nuclear localization of plasmid DNA (pDNA) would result in an increased transfection efficiency. In the present study, we established a technology for imaging the nuclear condensation/decondensation status of pDNA in nuclear subdomains using...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1327
更新日期:2011-04-01 00:00:00
abstract::The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm231
更新日期:2007-07-01 00:00:00
abstract::An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucle...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.8.1941
更新日期:1993-04-25 00:00:00
abstract::YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous sequences, combined with a flexible hit criterion used to identify groups of seeds that are likely to exhibit significant ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki478
更新日期:2005-07-01 00:00:00
abstract::We present NetCore, a novel network propagation approach based on node coreness, for phenotype-genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves improved re-ranking of genes after propag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa639
更新日期:2020-09-25 00:00:00
abstract::Giant chromatin-modifying complexes regulate gene transcription in eukaryotes by acting on chromatin substrates and 'setting' the histone code. The histone deacetylase (HDAC)-associated mammalian Sin3 corepressor complex regulates a wide variety of genes involved in all aspects of cellular physiology. The recruitment ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp051
更新日期:2009-04-01 00:00:00
abstract::Human transcription factor IIIC contains a 55 kDa polypeptide which specifically interacts with the Adenovirus 2 VAI gene promoter and which mimics most of the DNA binding properties of the entire factor. The specificity and affinity of this protein:DNA interaction was demonstrated by: (i) Separation of purified fract...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.16.4743
更新日期:1990-08-25 00:00:00
abstract::The transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas9) utlilize distinct molecular mechanisms in targeting site recognition. The two proteins can be modified to carry additional functional domains to regulate exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku836
更新日期:2014-11-10 00:00:00
abstract::In order to direct antisense oligonucleotides to specific tissues or cell types in vivo, we are exploring the possibility to utilize lipoproteins as transport vehicles. A 16-mer oligonucleotide (ODN) was derivatized at the 5' prime through a 32P phosphate spacer with cholesterol, yielding a 32P-labeled amphiphatic cho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.17.4695
更新日期:1991-09-11 00:00:00
abstract::Simian cells have been transformed with SV40 origin-defective recombinant plasmids containing the tsA209 T-antigen gene. These plasmids contain deletions of either 5 or 52 nucleotides that include the BglI site at the SV40 ori, are defective for replication in COS-1 cells but retain a functional SV40 early promoter. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.22.7913
更新日期:1985-11-25 00:00:00
abstract::MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target inte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1258
更新日期:2016-01-04 00:00:00
abstract::Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks681
更新日期:2012-10-01 00:00:00
abstract::During telomere replication in yeast, chromosome ends acquire a long single-stranded extension of the strand making the 3' end. Previous work showed that these 3' tails are generated late in S-phase, when conventional replication is virtually complete. In addition, the extensions were also observed in cells that lacke...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.23.5365
更新日期:1998-12-01 00:00:00
abstract::Human cells are, in general, poor recipients of foreign DNA, which has severely hampered the cloning of genes by direct phenotypic correction of deficient human cell lines after DNA mediated gene transfer. In this communication a methodology is presented which largely circumvents this problems. The method relies on th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.18.4861
更新日期:1991-09-25 00:00:00
abstract::Tissue-specific gene expression is critical in understanding biological processes, physiological conditions, and disease. The identification and appropriate use of tissue-specific genes (TissGenes) will provide important insights into disease mechanisms and organ-specific therapeutic targets. To better understand the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx850
更新日期:2018-01-04 00:00:00
abstract::We have studied the structure of recombinant rat UBF (rrUBF), an RNA polymerase I transcription factor, by electron microscopy and image analysis of single particles contrasted with methylamine tungstate. Recombinant rat UBF appeared to be a flat, U-shaped protein with a central region of low density. In the dominant ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.8.1472
更新日期:1996-04-15 00:00:00
abstract::The DNA damage checkpoint halts cell cycle progression in G2 in response to genotoxic insults. Central to the execution of cell cycle arrest is the checkpoint-induced stabilization of securin-separase complex (yeast Pds1-Esp1). The checkpoint kinases Chk1 and Chk2 (yeast Chk1 and Rad53) are thought to critically contr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa355
更新日期:2020-06-19 00:00:00
abstract::Two analog uridine triphosphates tethering additional functionality, one a primary amino group and the second a mercapto group, were prepared and tested for their compatibility with in vitro RNA selection procedures. 5-(3-Aminopropyl)uridine triphosphate (UNH(2)) as a uridine substitute was a more effective substrate ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.17.3316
更新日期:2000-09-01 00:00:00
abstract::MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1238
更新日期:2013-01-01 00:00:00
abstract::Biophysical properties of DNA such as its longitudinal and torsional persistence length govern many processes and phenomena in biology, DNA nanotechnology and biotechnology. It has, for example, long been known that the circularization efficiency of short DNA fragments shows a periodic pattern where fragments with int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1238
更新日期:2018-01-25 00:00:00
abstract::MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1293
更新日期:2012-04-01 00:00:00
abstract::We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.14.2774
更新日期:1996-07-15 00:00:00
abstract::The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5' and 3' untran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp902
更新日期:2010-01-01 00:00:00
abstract::Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn808
更新日期:2009-01-01 00:00:00