Abstract:
:Thyroid hormone receptors (TRs) are members of the nuclear hormone receptor superfamily, which act as transcription factors upon binding to specific DNA sequences called thyroid hormone (T3) response elements (TREs). Such elements are found in the upstream regulatory region of promoters as well as in intragenic sequences of T3-responsive genes. In this report, we demonstrate that SV40 late (SVL) promoter activity is strongly down-regulated by TR in the absence of ligand. Addition of T3 releases this repression, but does not further induce SVL promoter activity. Electrophoretic mobility shift analyses reveal a TR binding element that overlaps with the SV40 major late transcription initiation site. This element closely fits the consensus TRE, formed of two hexanucleotides organized in a tandem repeat separated by 4 nt, and is able to confer T3 responsiveness on a heterologous promoter. We further show that, although the presence of TR leads to quantitatively modified expression of an SVL-driven reporter gene, neither displacement of the site of transcription initiation nor modification of the splicing pattern of the primary transcripts occur.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Desvergne B,Favez Tdoi
10.1093/nar/25.9.1774subject
Has Abstractpub_date
1997-05-01 00:00:00pages
1774-81issue
9eissn
0305-1048issn
1362-4962pii
gka297journal_volume
25pub_type
杂志文章abstract::In Saccharomyces cerevisiae, DNA double-strand breaks (DSBs) initiate meiotic recombination at open sites in chromatin, which display a meiosis-specific increase in micrococcal nuclease (MNase) sensitivity. The arg4 promoter contains such a DSB site. When arg4 sequences are placed in a pBR322-derived insert at HIS4 (h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.10.2175
更新日期:1999-05-15 00:00:00
abstract::We show that using low denaturation temperatures (80-88 degrees C) during ligation mediated PCR (LM PCR) of bacterial DNA leads to the amplification of limited sets of the less stable DNA fragments. A set of electrophoretic patterns of such fragments obtained at different denaturation temperatures forms the PCR meltin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng116
更新日期:2003-09-15 00:00:00
abstract::Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw095
更新日期:2016-06-02 00:00:00
abstract::Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buff...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx553
更新日期:2017-09-06 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::Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets ...
journal_title:Nucleic acids research
pub_type: 杂志文章,meta分析
doi:10.1093/nar/gkp093
更新日期:2009-05-01 00:00:00
abstract::Pentatricopeptide repeat (PPR) proteins are helical-repeat proteins that offer a promising scaffold for the engineering of proteins to bind specified RNAs. PPR tracts bind RNA in a modular 1-repeat, 1-nucleotide fashion. An amino acid code specifying the bound nucleotide has been elucidated. However, this code does no...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1288
更新日期:2018-03-16 00:00:00
abstract::The TransTerm database of termination codon contexts has been extended to include sense codon usage, and initiation codon contexts. The database was constructed from 23,721 coding sequences from 93 organisms. The database contains: a) the sequence around the termination codon (-10, +10); b) the sequence around the ini...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.17.3620
更新日期:1994-09-01 00:00:00
abstract::RNA polymerase (RNAP) is a major target of gene regulation. Thermus thermophilus bacteriophage P23-45 encodes two RNAP binding proteins, gp39 and gp76, which shut off host gene transcription while allowing orderly transcription of phage genes. We previously reported the structure of the T. thermophilus RNAP•σA holoenz...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1162
更新日期:2018-01-09 00:00:00
abstract::Human cytomegalovirus (HCMV) terminase is composed of subunits pUL56 (130 kDa) and pUL89 ( approximately 75 kDa), encoded by the UL56 and UL89 genes. In a recent investigation, we demonstrated that the main ATPase activity is associated with the large terminase subunit pUL56. The protein has two putative ATP-binding s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg229
更新日期:2003-03-01 00:00:00
abstract::The alcohol dehydrogenase (Adh) gene of D. melanogaster is transcribed from two different promoters during fly development: the distal (adult) and the proximal (embryonic-larval). Certain aspects of Adh gene regulation are represented in Drosophila continuous cell lines. We have used Drosophila tissue culture cells in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.19.7903
更新日期:1987-10-12 00:00:00
abstract::The transcription factor Sox5 has previously been shown in chicken to be expressed in early neural crest cells and neural crest-derived peripheral glia. Here, we show in mouse that Sox5 expression also continues after neural crest specification in the melanocyte lineage. Despite its continued expression, Sox5 has litt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn527
更新日期:2008-10-01 00:00:00
abstract::The rpoA gene, encoding the alpha subunit of RNA polymerase, was cloned from Streptomyces coelicolor A3(2). It is preceded by rpsK and followed by rplQ, encoding ribosomal proteins S11 and L17, respectively, similar to the gene order in Bacillus subtilis. The rpoA gene specifies a protein of 339 amino acids with deduc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.22.4565
更新日期:1996-11-15 00:00:00
abstract::The alpha/beta-hydrolase fold is characterized by a beta-sheet core of five to eight strands connected by alpha-helices to form a alpha/beta/alpha sandwich. In most of the family members the beta-strands are parallels, but some show an inversion in the order of the first strands, resulting in antiparallel orientation....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh141
更新日期:2004-01-01 00:00:00
abstract::Nuclei from frozen calf thymus suspended in buffer were analyzed for metal content prior to and after repeated washing. After three such extractions about 0.1 micrograms Zn/mg DNA and 0.025 micrograms Cu/mg DNA remained tightly associated with chromatin. This level of metal was essentially unchanged with subsequent wa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.21.5811
更新日期:1981-11-11 00:00:00
abstract::Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt153
更新日期:2013-04-01 00:00:00
abstract::The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn846
更新日期:2008-12-01 00:00:00
abstract::Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history trai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1148
更新日期:2016-01-04 00:00:00
abstract::Two dimensional (2D) NMR and molecular dynamics simulations have been used to determine the three dimensional (3D) structure of a hairpin DNA, d-CTA-GAGGATCC-TUTT-GGATCCT (22mer; abbreviated as U2-hairpin), which has uracil at the second position from the 5' end of the tetraloop. The(1)H resonances of this hairpin hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.9.1906
更新日期:2000-05-01 00:00:00
abstract::Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv632
更新日期:2015-11-16 00:00:00
abstract::Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is an Out...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.102
更新日期:1998-01-01 00:00:00
abstract::The interaction of several synthetic analogues of d-ApA with Poly U and Poly dT was examined to explore the effects of substituents at phosphorus on binding properties of oligonucleotides. These analogues contained a bulky, lipophilic group (2,2,2-trichloroethoxy or 2,2,2-trichloro-1,1-dimethylethoxy) a small, uncharg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.8.3487
更新日期:1986-04-25 00:00:00
abstract::The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks709
更新日期:2012-11-01 00:00:00
abstract::In fragile X syndrome, hypermethylation of the expanded CGG repeat and of the upstream promoter leads to transcriptional silencing of the FMR1 gene. Absence of the FMR1 protein results in mental retardation. We previously proved that treatment with 5-azadeoxycytidine (5-azadC) of fragile X cell lines results in reacti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf434
更新日期:2002-07-15 00:00:00
abstract::X chromosome inactivation results in the cis-limited inactivation of most, but not all, genes on one of the two X chromosomes in mammalian females. The molecular basis for inactivation is unknown. In order to examine the transcriptional activity of human X-linked genes, a series of mouse-human somatic cell hybrids und...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.14.4191
更新日期:1990-07-25 00:00:00
abstract::The numerous genomic sequences and ESTs released by the Arabidopsis thaliana Genome Initiative (AGI) have allowed a systematic and functional study of the DEAD box RNA helicase family. Sequencing and in silico analysis led to the characterization of 28 novel A. thaliana DEAD box RNA helicases forming a family of 32 me...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.628
更新日期:1999-01-15 00:00:00
abstract::Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interacti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1011
更新日期:2018-01-04 00:00:00
abstract::Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt636
更新日期:2013-10-01 00:00:00
abstract::Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx037
更新日期:2017-05-05 00:00:00
abstract::A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku155
更新日期:2014-04-01 00:00:00