Abstract:
:RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in Escherichia coli , as well as knowledge on the organization of the genes and regulatory signals into operons in the chromosome. The operon is the basic structure used in RegulonDB to describe the elements and properties of transcriptional regulation. The current version contains information around some 500 regulation mechanisms, essentially for sigma 70 promoters.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Huerta AM,Salgado H,Thieffry D,Collado-Vides Jdoi
10.1093/nar/26.1.55subject
Has Abstractpub_date
1998-01-01 00:00:00pages
55-9issue
1eissn
0305-1048issn
1362-4962pii
gkb023journal_volume
26pub_type
杂志文章abstract::The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype-phenotype relationships. Here, we describe a computational method, dubbed C...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1263
更新日期:2017-03-17 00:00:00
abstract::Reversible methylation of the N6 or N1 position of adenine in RNA has recently been shown to play significant roles in regulating the functions of RNA. RNA can also be alkylated upon exposure to endogenous and exogenous alkylating agents. Here we examined how regio-specific methylation at the hydrogen bonding edge of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx515
更新日期:2017-09-06 00:00:00
abstract::Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (N...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.10.2457
更新日期:1998-05-15 00:00:00
abstract::Multiple myeloma, the second most frequent hematologic tumor after lymphomas, is an incurable cancer. Recent sequencing efforts have identified the ribonuclease DIS3 as one of the most frequently mutated genes in this disease. DIS3 represents the catalytic subunit of the exosome, a macromolecular complex central to th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv387
更新日期:2015-05-26 00:00:00
abstract::CCG repeats are highly over-represented in exons of the human genome. Usually they are located in the 5' UTR but are also abundant in translated sequences. The CCG repeats are associated with three tri-nucleotide repeat disorders: Huntington's disease, myotonic dystrophy type 1 and chromosome X-linked mental retardati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks557
更新日期:2012-09-01 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::The mRNAs for different variant surface antigens of Trypanosoma brucei start with the same 35 nucleotides. This sequence is encoded by a separate mini-exon, located in a 1.35-kb repetitive element. We have reported that trypanosomes contain many transcripts that hybridize to mini-exon probes, even if they do not make ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3777
更新日期:1984-05-11 00:00:00
abstract::The unwinding of supercoiled phi X174 RFI DNA induced by the tumorigenic (+) and non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) has been investigated by agarose slab-gel and ethidium titration tube gel electrophoresis. The differences in adduct conformat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.23.6167
更新日期:1992-12-11 00:00:00
abstract::We have adapted a method for making libraries of mutations in any specific gene for use in the fission yeast Schizosaccharomyces pombe . This elegant and simple method consists of PCR amplification of the gene of interest, followed by co-transformation of fission yeast with the PCR fragment and a linearized plasmid ve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.20.4783
更新日期:1998-10-15 00:00:00
abstract::Repair of DNA double-strand breaks (DSBs) with homologous chromosomes is a hallmark of meiosis that is mediated by recombination 'bridges' between homolog axes. This process requires cooperation of DMC1 and RAD51 to promote homology search and strand exchange. The mechanism(s) regulating DMC1/RAD51-ssDNA nucleoprotein...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa406
更新日期:2020-07-09 00:00:00
abstract::The spliceosomal protein Prp1 (Prp6/U5-102 K) is necessary for the integrity of pre-catalytic spliceosomal complexes. We have identified a novel regulatory function for Prp1. Expression of mutations in the N-terminus of Prp1 leads to the accumulation of pre-catalytic spliceosomal complexes containing the five snRNAs U...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1155
更新日期:2010-03-01 00:00:00
abstract::Unmethylated CpG rich islands are a feature of vertebrate DNA: they are associated with housekeeping and many tissue specific genes. CpG islands on the active X chromosome of mammals are also unmethylated. However, islands on the inactive X chromosome are heavily methylated. We have identified a CpG island in the 5' r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9527
更新日期:1988-10-25 00:00:00
abstract::It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq399
更新日期:2010-07-01 00:00:00
abstract::Primase synthesizes decaribonucleotides for priming of lagging and possibly leading strand synthesis at a replication fork. The sites of initiation by purified mouse primase were shown to be highly specific within the SV40 origin of replication. This study further examines the role of the 27-bp inverted repeat in the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.5.1953
更新日期:1989-03-11 00:00:00
abstract::Ribosomal RNA (rRNA) in intact ribosomes is cleaved into discrete products on incubation of reticulocyte lysates or L-cell extracts with ppp(A2'p)3A. Cleavage of rRNA may, therefore, provide a useful assay for 2-5A (ppp)A2'p)nA; n = 2 to 4) or for the presence of a 2-5A-dependent nuclease. The results with reticulocyt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.7.1571
更新日期:1981-04-10 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::This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.9.2951
更新日期:1982-05-11 00:00:00
abstract::A downstream G-rich sequence (GRS), GGGGGAGGUGUGGG, has been previously shown to influence the efficiency of 3' end processing of the SV40 late polyadenylation signal. We have now defined several important parameters for GRS-mediated polyadenylation. The ability of the GRS to influence 3' end processing efficiency was...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.9.1625
更新日期:1995-05-11 00:00:00
abstract::The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1072
更新日期:2017-01-04 00:00:00
abstract::The tumor suppressor p53 is a sequence-specific transcription factor, which regulates the expression of target genes involved in different stress responses. To understand p53's essential transcriptional functions, unbiased analysis of its DNA-binding repertoire is pivotal. In a genome-wide tiling ChIP-on-chip approach...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn232
更新日期:2008-06-01 00:00:00
abstract::Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt177
更新日期:2013-05-01 00:00:00
abstract::OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa392
更新日期:2020-07-09 00:00:00
abstract::Multiple regulatory modules contribute to the complex expression programs realized by many loci. Although long thought of as isolated components, recent studies demonstrate that such regulatory sequences can physically associate with promoters and with each other and may localize to specific sub-nuclear transcription ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1160
更新日期:2011-04-01 00:00:00
abstract::Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, the large computational cost associated to these analyses is a limiting factor that often preve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq953
更新日期:2011-03-01 00:00:00
abstract::The remarkable selectivity of N-methyl mesoporphyrin IX (NMM) for G-quadruplexes (GQs) is long known, however its ability to stabilize and bind GQs has not been investigated in detail. Through the use of circular dichroism, UV-visible spectroscopy and fluorescence resonance energy transfer (FRET) melting assay we have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks152
更新日期:2012-07-01 00:00:00
abstract::The final step in the maturation of paramyxoviruses, orthomyxoviruses and viruses of several other families, entails the budding of the viral nucleocapsid through the plasma membrane of the host cell. Many medically important viruses, such as influenza, parainfluenza, respiratory syncytial virus (RSV) and Ebola, can f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm246
更新日期:2007-01-01 00:00:00
abstract::The accurate structural modeling of B- and T-cell receptors is fundamental to gain a detailed insight in the mechanisms underlying immunity and in developing new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web server (http://www.cbs.dtu.dk/services/LYRA/) implements a complete and automated ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv535
更新日期:2015-07-01 00:00:00
abstract::The RecQ family of helicases is highly conserved both structurally and functionally from bacteria to humans. Defects in human RecQ helicases are associated with genetic diseases that are characterized by cancer predisposition and/or premature aging. RecQ proteins exhibit 3'-5' helicase activity and play critical roles...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz708
更新日期:2019-10-10 00:00:00
abstract::The nucleotide sequence of Neurospora crassa 5.8 S rDNA and adjacent regions has been determined. The deduced 5.8 S rRNA sequence of Neurospora differs from the 5.8 S rRNA sequence of Saccharomyces cerevisiae at 13 of 158 residues. Nine of these differences are clustered in a segment capable of forming a short hairpin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.7.2561
更新日期:1979-06-11 00:00:00
abstract::The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (-) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.24.9729
更新日期:1986-12-22 00:00:00