Abstract:
:The sequence requirements for transcriptional stimulation of the adenovirus major late promoter (MLP) by the products of the early transcription unit Ela and by the replication of viral DNA were analyzed by in vitro transcription. Sequences upstream of +33 are involved in the moderate Ela-responsiveness of the MLP, while sequences between +33 and +131 are required for its major replication-induced transcriptional activation. Dnase I footprinting experiments delineate a sequence component, extending from +76 to +120, which binds protein(s) only in extracts of cells where viral DNA replication occurred. Taken together, these results suggest that the replication-dependent stimulation of the MLP is mediated by the increased binding of this protein(s).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Jansen-Durr P,Boeuf H,Kédinger Cdoi
10.1093/nar/16.9.3771subject
Has Abstractpub_date
1988-05-11 00:00:00pages
3771-86issue
9eissn
0305-1048issn
1362-4962journal_volume
16pub_type
杂志文章abstract::Reagents for proteome research must of necessity be generated by high throughput methods. Aptamers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection procedures. We have developed automated selection methods, but must stil...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnf107
更新日期:2002-10-15 00:00:00
abstract::One-Block CYRCA is an automated procedure for identifying multiple-block alignments from single block queries (http://bioinfo.weizmann.ac.il/blocks/OneCYRCA). It is based on the LAMA and CYRCA block-to-block alignment methods. The procedure identifies whether the query blocks can form new multiple-block alignments (bl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki488
更新日期:2005-07-01 00:00:00
abstract::The cyanobacteirum Synechocystis sp. strain PCC 6803 possesses nine species of the sigma (sigma)-factor gene for RNA polymerase (RNAP). Here, we identify and characterize the novel-type promoter recognized by a group 3 sigma-factor, SigF. SigF autoregulates its own transcription and recognizes the promoter of pilA1 th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn453
更新日期:2008-09-01 00:00:00
abstract::POGO-DB (http://pogo.ece.drexel.edu/) provides an easy platform for comparative microbial genomics. POGO-DB allows users to compare genomes using pre-computed metrics that were derived from extensive computationally intensive BLAST comparisons of >2000 microbes. These metrics include (i) average protein sequence ident...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1094
更新日期:2014-01-01 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::Mutations in mammalian and Drosophila Hel308 and PolQ paralogues cause genome instability but their helicase functions are mysterious. By in vivo and in vitro analysis, we show that Hel308 from archaea (Hel308a) may act at stalled replication forks. Introducing hel308a into Escherichia coli dnaE strains that condition...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki685
更新日期:2005-06-30 00:00:00
abstract::Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and transla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg161
更新日期:2003-01-15 00:00:00
abstract::Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG(5)T, in ammonium acetate. The intermediates and products were separated according to their mass (number of strands and inner cations) and quantified. The study of the temporal ev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq208
更新日期:2010-08-01 00:00:00
abstract::We have previously shown that integration of a polyoma vector containing rodent repetitive elements into rat cellular DNA is non-random (Wallenburg et al. J. Virol. 50: 678-683). Junctions between the polyoma vector and the host DNA occur in the repetitive sequences of the vector about ten times more frequently than w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.19.7849
更新日期:1987-10-12 00:00:00
abstract::The role of the mRNA-binding protein human antigen R (HuR) in stabilization and translation of AU-rich elements (ARE) containing mRNAs is well established. However, the trafficking of HuR and bound mRNA cargo, which comprises a fundamental requirement for the aforementioned HuR functions is only poorly understood. By ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt663
更新日期:2013-10-01 00:00:00
abstract::PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct arch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz583
更新日期:2019-09-19 00:00:00
abstract::We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg571
更新日期:2003-07-01 00:00:00
abstract::An intronic hexanucleotide UGCAUG has been shown to play a critical role in the regulation of tissue-specific alternative splicing of pre-mRNAs in a wide range of tissues. Vertebrate Fox-1 has been shown to bind to this element, in a highly sequence-specific manner, through its RNA recognition motif (RRM). In mammals,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki338
更新日期:2005-04-11 00:00:00
abstract::Transcription and mRNA export are linked processes. However, the molecular mechanisms of this coordination are not clear. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator; TREX-2, which functions in mRNA biogenesis and export. Here, we investigate th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt272
更新日期:2013-06-01 00:00:00
abstract::Translesional DNA synthesis past abasic sites proceeds with the preferential incorporation of dAMP opposite the lesion and, depending on the sequence context, one or two base deletions. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of a DNA h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.10.2385
更新日期:1998-05-15 00:00:00
abstract::4'-Acylated thymidines represent a new class of DNA chain terminators, since they have been shown to act as post-incorporation chain-terminating nucleotides despite the presence of a free 3'-hydroxyl group. Here, we describe the action of the 4'-acetyl- (MeTTP) and 4'-propanoylthymidine 5'-triphosphate (EtTTP) on HIV-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.17.4063
更新日期:1998-09-01 00:00:00
abstract::The oncogene BMI1 encodes a polycomb group transcription factor that is required for embryonic development and self-renewal of stem cells. Despite these important functions little is known about the regulation of BMI1 expression. A cDNA microarray based search for target genes of E2F-1 in neuroblastoma cells expressin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl119
更新日期:2006-03-31 00:00:00
abstract::In a bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP)/transcription factor binding screen, we identified Mycobacterium smegmatis Ms6479 as the first c-di-GMP-responsive transcriptional factor in mycobacteria. Ms6479 could specifically bind with c-di-GMP and recognize the promoters of 37 lipid transport an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks923
更新日期:2012-12-01 00:00:00
abstract::Cloned coding sequences for rat and human ornithine transcarbamylase (OTC) were obtained by screening a rat and a human cDNA library respectively with a synthetic oligonucleotide corresponding to 27 bases of the rat sequence. These clones, 1100 bp long for the rat clone and 1300 bp for the human, contain approximately...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.1.155
更新日期:1985-01-11 00:00:00
abstract::By means of a combination of ion-exchange and sequence-specific affinity chromatography techniques, we have purified to homogeneity two protein complexes binding in a human DNA region (B48) previously recognized to contain a DNA replication origin. The DNA sequence used for the protein purification (B48 binding site) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.14.3257
更新日期:1993-07-11 00:00:00
abstract::The yeast retrotransposon Ty encodes proteins that assemble into virus-like particles (Ty-VLPs) which can be readily purified. We have recently shown that expression of the pl protein encoded by the TYA gene of Ty is sufficient for particle formation. In this paper we show that when a heterologous coding sequence, hum...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.18.7571
更新日期:1987-09-25 00:00:00
abstract::We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.18.4280
更新日期:1998-09-15 00:00:00
abstract::In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. All of the site-specificity factors of RNA editing identified so far are pentatricopeptide repeat (PPR) proteins. A defect in a specific PPR protein often impairs RNA editing at multiple sites, at which the cis-acting element...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks164
更新日期:2012-06-01 00:00:00
abstract::The mRNA export complex TREX (TREX) is known to contain Aly, UAP56, Tex1 and the THO complex, among which UAP56 is required for TREX assembly. Here, we systematically investigated the role of each human TREX component in TREX assembly and its association with the mRNA. We found that Tex1 is essentially a subunit of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1188
更新日期:2013-01-01 00:00:00
abstract::The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz898
更新日期:2020-01-08 00:00:00
abstract::LINKER was developed as an online server to assist biomedical researchers to design linker sequences for constructing functional fusion proteins. The program automatically generates a set of peptide sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. In addition to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh422
更新日期:2004-07-01 00:00:00
abstract::We have explored the functional relationships between spliceosome and Microprocessor complex activities in a novel class of microRNAs (miRNAs), named Splice site Overlapping (SO) miRNAs, whose pri-miRNA hairpins overlap splice sites. We focused on the evolutionarily conserved SO miR-34b, and we identified two indispen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt614
更新日期:2013-10-01 00:00:00
abstract::The genetic etiology of premature ovarian insufficiency (POI) has been well established to date, however, the role of long noncoding RNAs (lncRNAs) in POI is largely unknown. In this study, we identified a down-expressed lncRNA HCP5 in granulosa cells (GCs) from biochemical POI (bPOI) patients, which impaired DNA dama...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa127
更新日期:2020-05-07 00:00:00
abstract::FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger stand...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章,评审
doi:10.1093/nar/gkp1137
更新日期:2010-04-01 00:00:00
abstract::The proteins in a cell often assemble into complexes to carry out their functions and play an essential role of biological processes. The PCFamily server identifies template-based homologous protein complexes [called protein complex family (PCF)] and infers functional modules of the query proteins. This server first f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq464
更新日期:2010-07-01 00:00:00