Abstract:
:The hypoxia-inducible factor-1 (HIF-1) was first described as a DNA binding activity that specifically recognizes an 8 bp motif known to be essential for hypoxia-inducible erythropoietin gene transcription. Subsequently HIF-1 activity has also been found in cell lines which do not express erythropoietin, suggesting that HIF-1 is part of a widespread oxygen sensing mechanism. In electrophoretic mobility shift assays HIF-1 DNA binding activity is only detectable in nuclear extracts of cells cultivated in a low oxygen atmosphere. In addition to HIF-1, a constitutive DNA binding activity also specifically binds the HIF1 probe. Here we report that CRE and AP1 oligonucleotides efficiently competed for binding of the HIF1 probe to this constitutive factor, whereas HIF-1 activity itself remained unaffected. Monoclonal antibodies raised against the CRE binding factors ATF-1 and CREB-1 supershifted the constitutive factors ATF-1 and CREB-1 supershifted the constitutive factor, while Jun and Fos family members, which constitute the AP-1 factor, were immunologically undetectable. Recombinant ATF-1 and CREB-1 proteins bound HIF1 probes either as homodimers or as heterodimers, indicating a new binding specificity for ATF-1/CREB-1. Finally, reporter gene assays in HeLa cells treated with either a cAMP analogue or a phorbol ester suggest that the PKA, but not the PKC signalling pathway is involved in oxygen sensing.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kvietikova I,Wenger RH,Marti HH,Gassmann Mdoi
10.1093/nar/23.22.4542subject
Has Abstractpub_date
1995-11-25 00:00:00pages
4542-50issue
22eissn
0305-1048issn
1362-4962pii
5w0172journal_volume
23pub_type
杂志文章abstract::The rpoH genes encoding homologs of Escherichia coli sigma 32 (heat shock sigma factor) were isolated and sequenced from five gram negative proteobacteria (gamma or alpha subgroup): Enterobacter cloacae (gamma), Serratia marcescens (gamma), Proteus mirabilis (gamma), Agrobacterium tumefaciens (alpha) and Zymomonas mob...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:
更新日期:1995-11-11 00:00:00
abstract::Poly 2'0-ethylcytidylic acid (poly (Ce)) was prepared by polymerization of 2'-0-ethylcytidine-5'-pyrophosphate with Escherichia coli polynucleotide phosphorylase in the presence of Mn++, and its properties compared with those of poly (rC), poly (Cm) and poly (dC). The neutral form of pOLY (Ce) exhibits properties simi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.3.817
更新日期:1976-03-01 00:00:00
abstract::The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.2.555
更新日期:1988-01-25 00:00:00
abstract::This study unveils Mycobacterium smegmatis DinB2 as the founder of a clade of Y-family DNA polymerase that is naturally adept at incorporating ribonucleotides by virtue of a leucine in lieu of a canonical aromatic steric gate. DinB2 efficiently scavenges limiting dNTP and rNTP substrates in the presence of manganese. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku752
更新日期:2014-01-01 00:00:00
abstract::The DNA sequence of the spacer (plus flanking) regions separating the 16S rRNA and 23S rRNA genes of two presumptive rDNA operons of the archaebacterium Methanococcus vannielii was determined. The spacers are 156 and 242 base pairs in size and they share a sequence homology of 49 base pairs following the 3' terminus o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.21.7537
更新日期:1983-11-11 00:00:00
abstract::RNA-Seq is gradually becoming the standard tool for transcriptomic expression studies in biological research. Although considerable progress has been recorded in the development of statistical algorithms for the detection of differentially expressed genes using RNA-Seq data, the list of detected genes can differ signi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1273
更新日期:2015-02-27 00:00:00
abstract::The alternatively spliced RNA species of tumor suppressor gene p53, containing an additional 96 bases derived from intron 10, is present at approximately 25 to 30% the level of regularly spliced p53 RNA in both normal epidermal and carcinoma cells. The presence of this alternatively spliced RNA in 10T1/2 fibroblast ce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.8.1979
更新日期:1992-04-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.3.461
更新日期:1991-02-11 00:00:00
abstract::A cDNA that encodes a transcription factor able to recognize the thyroglobulin gene promoter in vitro was isolated from a dog thyroid cDNA expression library in lambda gt11. The library was screened with a multimerized 20 bp-oligonucleotide probe corresponding to the -126 to -107 bp region of the bovine thyroglobulin ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.5.1121
更新日期:1991-03-11 00:00:00
abstract::In Saccharomyces cerevisiae, the DNA damage response (DDR) is activated by the spatio-temporal colocalization of Mec1-Ddc2 kinase and the 9-1-1 clamp. In the absence of direct means to monitor Mec1 kinase activation in vivo, activation of the checkpoint kinase Rad53 has been taken as a proxy for DDR activation. Here, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1222
更新日期:2010-04-01 00:00:00
abstract::Interactions between subunits in the Saccharomyces cerevisiae ribosome are mediated by universal and eukaryote-specific intersubunit bridges. Universal bridges are positioned close to the ribosomal functional centers, while eukaryote-specific bridges are mainly located on the periphery of the ribosome. Two bridges, eB...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1083
更新日期:2019-01-10 00:00:00
abstract::Array based DNA pooling techniques facilitate genome-wide scale genotyping of large samples. We describe a structured analysis method for pooled data using internal replication information in large scale genotyping sets. The method takes advantage of information from single nucleotide polymorphisms (SNPs) typed in par...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl136
更新日期:2006-04-20 00:00:00
abstract::A key complication in comparative genomics for reliable gene function prediction is the existence of duplicated genes. To study the effect of gene duplication on function prediction, we analyze orthologs between pairs of genomes where in one genome the orthologous gene has duplicated after the speciation of the two ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki913
更新日期:2005-10-27 00:00:00
abstract::WebProAnalyst is a web-accessible analysis tool (http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/) designed for scanning quantitative structure-activity relationships in protein families. The tool allows users to search correlations between protein activity and physicochemical characteristics (i.e. hydrophobicity or...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki421
更新日期:2005-07-01 00:00:00
abstract::Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1019
更新日期:2014-02-01 00:00:00
abstract::DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq173
更新日期:2010-07-01 00:00:00
abstract::Members of the pentatricopeptide repeat domain (PPR) protein family bind RNA and are important for post-transcriptional control of organelle gene expression in unicellular eukaryotes, metazoans and plants. They also have a role in human pathology, as mutations in the leucine-rich PPR-containing (LRPPRC) gene cause sev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1132
更新日期:2014-12-16 00:00:00
abstract::The open state of human topoisomerase I has been probed by molecular dynamics simulation, starting from the coordinates of the closed structure of the protein complexed with DNA, after elimination of the 22-bp DNA duplex oligonucleotide. A repulsion force between the two lips of the protein has been introduced for a s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm199
更新日期:2007-01-01 00:00:00
abstract::Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to techn...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz474
更新日期:2019-09-05 00:00:00
abstract::A number of novel phosphate triester derivatives of the anti-cancer nucleoside analogue araC have been prepared by a rapid 2-step procedure, not necessitating prior sugar protection. Spectroscopic and lipophilicity data have been collected on these compounds. An in vitro assay indicated inhibition of thymidine incorpo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.18.7195
更新日期:1989-09-25 00:00:00
abstract::Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intron. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.1.143
更新日期:1990-01-11 00:00:00
abstract::The relationship between the similarity of expression patterns for a pair of genes and interaction of the proteins they encode is demonstrated both for the simple genome of the bacteriophage T7 and the considerably more complex genome of the yeast Saccharomyces cerevisiae. Statistical analysis of large-scale gene expr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.17.3513
更新日期:2001-09-01 00:00:00
abstract::Ribosome biogenesis is a dynamic multistep process, many features of which are still incompletely documented. Here, we show that changes in this pathway can be captured and annotated by means of a graphic set of pre-rRNA ratios, a technique we call Ratio Analysis of Multiple Precursors (RAMP). We find that knocking do...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku787
更新日期:2014-01-01 00:00:00
abstract::The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1068
更新日期:2015-01-01 00:00:00
abstract::The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1124
更新日期:2008-03-01 00:00:00
abstract::AvrBs3, the founding member of the Xanthomonas transcription-activator-like effectors (TALEs), is translocated into the plant cell where it localizes to the nucleus and acts as transcription factor. The DNA-binding domain of AvrBs3 consists of 17.5 nearly-identical 34 amino acid-repeats. Each repeat specifies binding ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku341
更新日期:2014-06-01 00:00:00
abstract::To investigate molecular controls of cardiomyocyte proliferation, we utilized cardiomyocytes induced to proliferate indefinitely by SV40 large T antigen (T-ag). In the T-ag-immortalized AT-1, AT-2 and HL-1 cardiomyocytes, normal cellular proteins associating with T-ag and p53 were identified, isolated and micro-sequen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.15.2882
更新日期:2000-08-01 00:00:00
abstract::Cre recombinase catalyzes the cleavage and religation of DNA at loxP sites. The enzyme is a homotetramer in its functional state, and the symmetry of the protein complex enforces a pseudo-palindromic symmetry upon the loxP sequence. The Cre-lox system is a powerful tool for many researchers. However, broader applicati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv901
更新日期:2015-10-15 00:00:00
abstract::The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw401
更新日期:2016-08-19 00:00:00
abstract::Mouse DNA contains two equally abundant, homologous subfamilies of MspI 3.6 and 5 kb repeated fragments. The first subfamily corresponds to the previously described (1) Bam 4 kb repeats, the second one to Bam repeated fragments of higher molecular weight. These subfamilies account for the vast majority of long Bam rep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.3.1593
更新日期:1984-02-10 00:00:00