Abstract:
:The transcriptional potential of the hsp70 heat shock gene promoter is established prior to induction by stress. It has been shown previously that the TBP subunit of TFIID is associated with the TATA element and that RNA polymerase II is paused downstream from the transcription start site. In order to identify new interactions involved in establishing this potentiated state, a detailed analysis of the molecular architecture of a single copy of the hsp70 promoter was performed. A suitably marked promoter was stably integrated using P-element-mediated transformation so as to overcome any ambiguity that might be associated with analyzing the five copies of the endogenous gene. Genomic footprinting using DNase I revealed two previously unidentified interactions. First, the GAGA element located at -120 is protected by protein. Secondly, the pattern of DNase I cleavage in the vicinity of the transcription start is found to bear significant similarity to the pattern associated with binding of purified TFIID. Noting that purified GAGA factor and TFIID interact similarly with the hsp70 and H3 promoters, the architecture of the endogenous H3 promoter was analyzed to determine what interactions might be needed to establish a potentiated state containing a paused polymerase. Despite the detection of TFIID and GAGA on the H3 promoter, no paused polymerase is evident. In addition, no proteins appear to interact with the transcription start. These results suggest that the GAGA factor and TFIID are not sufficient to establish a potentiated state containing paused polymerase and that TFIID interactions downstream from the TATA element could be important for pausing.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Weber JA,Gilmour DSdoi
10.1093/nar/23.16.3327subject
Has Abstractpub_date
1995-08-25 00:00:00pages
3327-34issue
16eissn
0305-1048issn
1362-4962pii
5t0132journal_volume
23pub_type
杂志文章abstract::Highly toxic DNA double-strand breaks (DSBs) readily trigger the DNA damage response (DDR) in cells, which delays cell cycle progression to ensure proper DSB repair. In Saccharomyces cerevisiae, mitotic S phase (20-30 min) is lengthened upon DNA damage. During meiosis, Spo11-induced DSB onset and repair lasts up to 5 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa587
更新日期:2020-09-04 00:00:00
abstract::A physical map is presented for the 1200 kb genome of Mycoplasma mycoides subsp. mycoides Y, locating 32 cleavage sites for 8 restriction endonucleases. The large restriction fragments involved were separated and sized by pulsed-field agarose gel electrophoresis. Their locations on the map were determined by probing S...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.13.6027
更新日期:1988-07-11 00:00:00
abstract::The mammalian target of rapamycin (mTOR) is a critical regulator of cell growth, integrating multiple signalling cues and pathways. Key among the downstream activities of mTOR is the control of the protein synthesis machinery. This is achieved, in part, via the co-ordinated regulation of mRNAs that contain a terminal ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1189
更新日期:2021-01-11 00:00:00
abstract::The study of pathogenic mitochondrial DNA mutations has, in most cases, relied on the production of transmitochondrial cybrids. Although the procedure to produce such cybrids is well established, it is laborious and cumbersome. Moreover, the mechanical enucleation procedure is inefficient and different techniques have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng100
更新日期:2003-08-15 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::In silico screening based on the structures of the ligands or of the receptors has become an essential tool to facilitate the drug discovery process but compound collections are needed to carry out such in silico experiments. It has been recognized that absorption, distribution, metabolism, excretion and toxicity (ADM...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl065
更新日期:2006-07-01 00:00:00
abstract::The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv081
更新日期:2015-02-27 00:00:00
abstract::The process of strand exchange is considered to be the hallmark of DNA recombination. Proteins known to carry out such exchange are believed to operate via one or the other of two mechanisms. RecA-like proteins promote the formation of a three-stranded or triplex synaptic intermediate in which strand exchange occurs, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.20.4004
更新日期:1997-10-15 00:00:00
abstract::The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The objective of ENA is to support and promote the use of nucleotide sequencing as an experimen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq967
更新日期:2011-01-01 00:00:00
abstract::Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites. TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture. COMPEL compri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.1.265
更新日期:1997-01-01 00:00:00
abstract::Genome browsers are widely used for individually exploring various types of genomic data. A handful of genome browsers offer limited tools for collaboration among multiple users. Here, we describe PBrowse, an integrated real-time collaborative genome browser that enables multiple users to simultaneously view and acces...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1358
更新日期:2017-05-19 00:00:00
abstract::Restriction fragments containing established curved regions, such as the pBR322 tn3 region, the phage lambda attP region and the SV40 T-antigen and terminus of replication regions, exhibit systematically retarded elution upon anion exchange based HPLC. Using this method, we were able to detect readily other SV40 curve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.15.4181
更新日期:1991-08-11 00:00:00
abstract::A protein-DNA complex has less gel electrophoretic mobility than the free DNA fragment. One parameter for the degree of retardation of a linear DNA fragment in a protein-DNA complex is the molecular weight of the bound protein(s). The quotient of the migration distances of free DNA (m) and protein-DNA complex (m') is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5241
更新日期:1988-06-24 00:00:00
abstract::Plasmid encoded replication initiation (Rep) proteins recruit host helicases to plasmid replication origins. Previously, we showed that RepD recruits directionally the PcrA helicase to the pC221 oriD, remains associated with it, and increases its processivity during plasmid unwinding. Here we show that RepD forms a co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1153
更新日期:2010-04-01 00:00:00
abstract::Impaired DNA damage repair, especially deficient transcription-coupled nucleotide excision repair, leads to segmental progeroid syndromes in human patients as well as in rodent models. Furthermore, DNA double-strand break signalling has been pinpointed as a key inducer of cellular senescence. Several recent findings s...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkm1065
更新日期:2007-01-01 00:00:00
abstract::The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.2801
更新日期:1978-08-01 00:00:00
abstract::The MF alpha 1 gene of Saccharomyces cerevisiae is an alpha specific gene whose expression is regulated by two upstream activation sites (UASMF alpha 1S), which are the binding sites for activator proteins, MAT alpha 1 and MCM1. UASMF alpha 1 elements act in a synergistic fashion; lack of either element causes reduced...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.11.3099
更新日期:1991-06-11 00:00:00
abstract::High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq972
更新日期:2011-01-01 00:00:00
abstract::Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn610
更新日期:2008-11-01 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::A repeat sequence 682 base pairs (bp) long produced by cleavage of human DNA with Xba I restriction enzyme is composed of four tandemly arranged subunits with lengths of 171, 170, 171, and 170 bp each. The sequence organization of the 682 bp Xba I repeat bears a striking resemblance to other complex satellite DNAs of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.2.521
更新日期:1985-01-25 00:00:00
abstract::Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a wide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky084
更新日期:2018-04-06 00:00:00
abstract::In mammalian cells, DNA double-strand breaks (DSBs) are repaired by three pathways, nonhomologous end-joining (NHEJ), gene conversion (GC) and single-strand annealing (SSA). These pathways are distinct with regard to repair efficiency and mutagenic potential and must be tightly controlled to preserve viability and gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn347
更新日期:2008-07-01 00:00:00
abstract::Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active in such a process. To estimate the impact of uORFs on the regulation of translation in humans, we first circumscribed the universe ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky188
更新日期:2018-04-20 00:00:00
abstract::Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding no...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr052
更新日期:2011-07-01 00:00:00
abstract::Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx999
更新日期:2017-12-01 00:00:00
abstract::We have sequenced the entire human S mu and S gamma 4 immunoglobulin heavy chain class switch regions, and have also completed the sequence of human S epsilon. S mu is composed predominantly of GAGCT and GGGCT pentameric repeats, with these units also being found in S epsilon at a much lower density. S mu-S gamma 4 ma...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.24.7305
更新日期:1990-12-25 00:00:00
abstract::The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) land...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1208
更新日期:2017-03-17 00:00:00
abstract::A 14 kb maize DNA fragment carrying nuclear rRNA genes and spacer regions was isolated and characterised by restriction enzyme mapping. A complete 3020 bp long external spacer region was sequenced and revealed 9 tandemly arranged 200 bp long repeat units with high homology. The repeat units lie upstream from two promi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.12.4969
更新日期:1986-06-25 00:00:00
abstract::Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic suc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv164
更新日期:2015-05-26 00:00:00