Abstract:
:To unravel the network of transcription factors established during development it is important to understand how genes specifically expressed during embryogenesis are regulated. Oct-4 is a transcription factor whose expression is associated with an undifferentiated cell phenotype in the early mouse embryo and is downregulated when such cells differentiate. An enhancer in the upstream region of Oct-4 has previously been reported as being sufficient to mediate the cell-type specific expression and RA-dependent down-regulation in EC cells, although the enhancer contains no retinoic acid receptor (RAR) binding sites. Here we report the identification of promoter elements important for the regulation of the Oct-4 gene in EC cells. A region of the proximal Oct-4 promoter contains an overlapping set of regulatory elements including a high affinity binding site for Sp1 and three direct repeats of an AGGTCA-like sequence with either +1 or 0 spacing. Binding and transient transfection assays reveal that Oct-4 is subject to negative regulation by different members of the steroid-thyroid hormone receptor superfamily. Specifically, important roles for ARP-1 and RAR in Oct-4 expression are indicated.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sylvester I,Schöler HRdoi
10.1093/nar/22.6.901subject
Has Abstractpub_date
1994-03-25 00:00:00pages
901-11issue
6eissn
0305-1048issn
1362-4962journal_volume
22pub_type
杂志文章abstract::The basal transcription factor TFE enhances transcription initiation by catalysing DNA strand-separation, a process that varies with temperature and ionic strength. Canonical TFE forms a heterodimeric complex whose integrity and function critically relies on a cubane iron-sulphur cluster residing in the TFEβ subunit. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1302
更新日期:2018-03-16 00:00:00
abstract::Mitochondrial-DNA diseases have no effective treatments. Allotopic expression-synthesis of a wild-type version of the mutated protein in the nuclear-cytosolic compartment and its importation into mitochondria-has been proposed as a gene-therapy approach. Allotopic expression has been successfully demonstrated in yeast...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq769
更新日期:2011-01-01 00:00:00
abstract::We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA+ ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1322
更新日期:2017-03-17 00:00:00
abstract::Based on parameters governing promoter activity and using regulatory elements of the lac, ara and tet operon transcription control sequences were composed which permit the regulation in Escherichia coli of several gene activities independently and quantitatively. The novel promoter PLtetO-1 allows the regulation of ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.6.1203
更新日期:1997-03-15 00:00:00
abstract::RNA editing in protozoan parasites is a mitochondrial RNA processing reaction in which exclusively uridylate residues are inserted into, and less frequently deleted from, pre-mRNAs. Molecules central to the process are so-called guide RNAs (gRNAs) which function as templates in the reaction. For a detailed molecular u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.12.2311
更新日期:1997-06-15 00:00:00
abstract::The nucleotide sequence of Drosophila melanogaster tRNA 5 Lys is pGCCCGGAUAm2GCUCAGDCGGDAGAGCA psi psi GGACUsU*UUt6A*A psi CCAAGGm7GDm5CCAGGGTm psi CAm1AGUCCCUGUUCGGGCGCCA. The sU* is probably 5-methylcarboxymethyl-2-thiouridine and t6A* is a mixture of modified derivatives of t6A including t6A itself and a component ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.20.6393
更新日期:1982-10-25 00:00:00
abstract::A cDNA (2855 nt) encoding a putative cytotoxic ribonuclease (rapLR1) related to the antitumor protein onconase was cloned from a library derived from the liver of gravid female amphibian Rana pipiens. The cDNA was mainly comprised (83%) of 3' untranslated region (UTR). Secondary structure analysis predicted two unusua...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.12.2375
更新日期:2000-06-15 00:00:00
abstract::Friedreich ataxia (FRDA) is caused by hyperexpansion of GAA*TTC repeats located in the first intron of the FXN gene, which inhibits transcription leading to the deficiency of frataxin. The FXN gene is an excellent target for therapeutic intervention since (i) 98% of patients carry the same type of mutation, (ii) the m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn604
更新日期:2008-11-01 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::Many small RNAs contribute essential activities to eukaryotic cells. In mammalian genomes dispersed repetitive sequences which exhibit homology to small RNAs often exist as pseudogenes which can complicate identification, localization, and analysis of the authentic gene. We mapped a productive human 7SK small nuclear ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.5.722
更新日期:1994-03-11 00:00:00
abstract::We investigate the role of water molecules in 89 protein-RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein-RNA interfaces are hydrated less than protein-DNA interfaces, but more than protein-protein interfaces. Majo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku679
更新日期:2014-09-01 00:00:00
abstract::LTR-IS elements are middle repetitive sequences in the mouse genome with structural features of solitary retroviral LTRs. In order to get some insight in the possible functional role of these sequences the promotor activity of two LTR-IS representatives differing by 105 bp in their U3 region was investigated. Gene fus...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.7.2631
更新日期:1985-04-11 00:00:00
abstract::The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multip...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg608
更新日期:2003-07-01 00:00:00
abstract::The cnjC gene from the protozoan Tetrahymena thermophila was completely sequenced. The deduced gene product was found to have significant sequence similarity to the yeast and prokaryotic RNA polymerase subunits involved with subunit assembly. Since cnjC is active only during the sexual stage (conjugation) of Tetrahyme...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.10.2953
更新日期:1990-05-25 00:00:00
abstract::TropGeneDB (http://tropgenedb.cirad.fr) was created to store genetic, molecular and phenotypic data on tropical crop species. The most common data stored in TropGeneDB are molecular markers, quantitative trait loci, genetic and physical maps, genetic diversity, phenotypic diversity studies and information on genetic r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1105
更新日期:2013-01-01 00:00:00
abstract::We have used 2-aminopurine (2AP) as a fluorescent probe in the template strand of a 13/20mer primer/template (D) to detect deoxynucleoside triphosphates (N)-dependent conformational changes exhibited by RB69 DNA polymerase (ED) complexes. The rates and amplitudes of fluorescence quenching depend hyperbolically on the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm587
更新日期:2007-01-01 00:00:00
abstract::In vitro repair of single strand breaks in T4 and phage DNA caused by 32p decay was studied. Zone centrifugation procedure showed that polynucleotide kinase, ligase enzyme system failed to repair 32P-damages. It was found that damaged DNA contained gaps and could be repaired by DNA-polymerase I, polynucleotide ligase ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.5.635
更新日期:1975-05-01 00:00:00
abstract::The H19 lncRNA has been implicated in development and growth control and is associated with human genetic disorders and cancer. Acting as a molecular sponge, H19 inhibits microRNA (miRNA) let-7. Here we report that H19 is significantly decreased in muscle of human subjects with type-2 diabetes and insulin resistant ro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1160
更新日期:2014-12-16 00:00:00
abstract::The rabbit homolog to the locus control region (LCR) of the human beta-like globin gene cluster was isolated, and long segments containing the DNase I hypersensitive sites (HS) were sequenced. The order and spacing of HS4, HS3, HS2 and HS1 are conserved between rabbit and human. Alignment of these sequences with their...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.5.1265
更新日期:1993-03-11 00:00:00
abstract::MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. Here, we developed a new method and an R package, to easily infer candidate miRNA-mRNA target interactions that could be functional during a given biological process. Using this method, we described, for the first time, a comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx327
更新日期:2017-06-02 00:00:00
abstract::ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky420
更新日期:2018-07-02 00:00:00
abstract::Advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox-II that incorporates molecular ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky318
更新日期:2018-07-02 00:00:00
abstract::The aspartate protease of Mucor pusillus (Mucor pusillus rennin; MPR) is a milk-clotting enzyme used in the cheese industry. The partial amino acid sequence of MPR was determined and oligonucleotide probes were synthesized for cloning of the MPR gene. A clone giving positive hybridization with the probes was selected ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.19.7557
更新日期:1986-10-10 00:00:00
abstract::The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with an apparent molecular weight of 104-1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.22.6043
更新日期:1992-11-25 00:00:00
abstract::The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz944
更新日期:2020-01-08 00:00:00
abstract::An updated list of DNA sequences cloned from the human genome over the past year (1991) is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic probes comprising both gene and pseudogene sequences. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.suppl.2181
更新日期:1992-05-11 00:00:00
abstract::Transcription of RNA from the beta-globin (major) gene in nuclei from induced mouse erythroleukemia cells terminates within the region between 700 to 2000 bases downstream from the poly(A) addition site, but not at particularly favored sites. In addition we present the first analysis of in vivo labeled RNA from a cell...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.22.8723
更新日期:1984-11-26 00:00:00
abstract::Three new proteins which selectively bind to UV-damaged DNA were identified and purified to near homogeneity from UV-irradiated Drosophila melanogaster embryos through several column chromatographies. These proteins, tentatively designated as D-DDB P1, P2 and P3, can be identified as different complex bands in a gel s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.14.2600
更新日期:1995-07-25 00:00:00
abstract::A highly polymorphic locus associated with the variable tandem repetition of a 35 bp consensus sequence was mapped to chromosome 10, band q26. Examination of leukocyte DNA from a cancer patient revealed the twenty-fold amplification of one allelic fragment of this locus, while the other allelic fragment demonstrated a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.20.7929
更新日期:1986-10-24 00:00:00
abstract::Analysis of intergenic sequences for purposes such as the investigation of transcriptional signals or the identification of small RNA genes is frequently complicated by traditional biological database structures. Genome data is commonly treated as chromosome-length sequence records, detailed by gene calls demarcating ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg013
更新日期:2003-01-01 00:00:00