Abstract:
:The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 of the genes encoding mitochondrial-localized ARSs were weakly induced. Most of the activated genes have a functional CARE near the transcription start site (TSS), but for others the CARE is downstream. Regardless of the location of CARE enhancer, for all ARS genes there was constitutive association of RNA polymerase II (Pol II) and the general transcription machinery near the TSS. However, for those genes with a downstream CARE, Atf4, C/ebp-homology protein (Chop), Pol II and TATA-binding protein exhibited enhanced recruitment to the CARE during AA limitation. Increased Atf4 binding regulated the association of elongation factors at both the promoter and the enhancer regions, and inhibition of cyclin-dependent kinase 9 (CDK9), that regulates these elongation factors, blocked induction of the AA-responsive ARS genes. Protein pull-down assays indicated that Atf4 directly interacts with CDK9 and its associated protein cyclin T1. The results demonstrate that AA availability modulates the ARS gene family through modulation of transcription elongation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Shan J,Zhang F,Sharkey J,Tang TA,Örd T,Kilberg MSdoi
10.1093/nar/gkw667subject
Has Abstractpub_date
2016-11-16 00:00:00pages
9719-9732issue
20eissn
0305-1048issn
1362-4962pii
gkw667journal_volume
44pub_type
杂志文章abstract::Cis-elements (-933 to -641) upstream of the human M creatine kinase gene cap site contain an enhancer that confers developmental and tissue-specific expression to the chloramphenicol acetyltransferase gene in C2C12 myogenic cells transfected in culture. Division of the enhancer at -770 into a 5' fragment that includes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.9.2313
更新日期:1992-05-11 00:00:00
abstract::Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku923
更新日期:2014-11-10 00:00:00
abstract::Telomeric regions of the genome are inherently difficult-to-replicate due to their propensity to generate DNA secondary structures and form nucleoprotein complexes that can impede DNA replication fork progression. Precisely how cells respond to DNA replication stalling within a telomere remains poorly characterized, l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz158
更新日期:2019-05-21 00:00:00
abstract::The laminin (LM)-database, hosted at http://www.lm.lncc.br, was published in the NAR database 2011 edition. It was the first database that provided comprehensive information concerning a non-collagenous family of extracellular matrix proteins, the LMs. In its first version, this database contained a large amount of in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt901
更新日期:2014-01-01 00:00:00
abstract::Equilibrium and kinetics of thermal melting of yeast 5S ribosomal RNA in aqueous NaCl with or without Mg2+ were investigated by differential thermal melting and temperature jump methods. Two peaks (1 and 2) and a shoulder were observed in each of melting curves at ionic strength I=0.002-0.5 and linearity between each ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.10.3363
更新日期:1983-05-25 00:00:00
abstract::Transposable elements (TEs) and their relics play major roles in genome evolution. However, mobilization of TEs is usually deleterious and strongly repressed. In plants and mammals, this repression is typically associated with DNA methylation, but the relationship between this epigenetic mark and TE sequences has not ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr324
更新日期:2011-09-01 00:00:00
abstract::We have measured the amount of 5S-ribosomal DNA in the genomes of Xenopus laevis, Triturus cristatus carnifex and Ambystoma mexicanum, three species of Amphibians which have widely different C-values. Our best estimate is that these organisms have about 24,000, 32,000 and 61,000 5S-genes per haploid genome respectivel...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.8.2381
更新日期:1983-04-25 00:00:00
abstract::A simple and effective modified ethanol precipitation-based protocol is described for the preparation of DNA from ancient human bones. This method is fast and requires neither hazardous chemicals nor special devices. After the powdering and incubating of the bone samples Dextran Blue was added as a carrier for removin...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章
doi:10.1093/nar/28.12.e67
更新日期:2000-06-15 00:00:00
abstract::Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional charact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq119
更新日期:2010-05-01 00:00:00
abstract::The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1098
更新日期:2018-01-04 00:00:00
abstract::Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric recognition sites oriented head-to-head to elicit double-strand break 25-27 bp downstream of one of the two sites. The proposed DNA cleavage mechanism involves ATP-dependent DNA translocation. The sequence context of the recogni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh899
更新日期:2004-10-22 00:00:00
abstract::GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm929
更新日期:2008-01-01 00:00:00
abstract::The multi-protein complex WRAD, formed by WDR5, RbBP5, Ash2L and Dpy30, binds to the MLL SET domain to stabilize the catalytically active conformation required for histone H3K4 methylation. In addition, the WRAD complex contributes to the targeting of the activated complex to specific sites on chromatin. RbBP5 is cent...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky199
更新日期:2018-04-20 00:00:00
abstract::TGGCA-binding proteins are nuclear proteins with high affinity for double-stranded DNA homologous to the prototype recognition sequence 5'YTGGCANNNTGCCAR 3'. Their ubiquitous tissue distribution in higher vertebrates characterizes them as a class of highly conserved proteins which may exert a basic function. To obtain...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.6.2045
更新日期:1985-03-25 00:00:00
abstract::A detailed scheme of the Peptidyl Transferase Centre of bacterial ribosomes is proposed by summarizing the literature data on the substrate specificity of the acceptor and donor sites. According to the proposed scheme only the elements of the donor and acceptor having a stable structure bind with the ribosome. The pre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.12.2223
更新日期:1975-12-01 00:00:00
abstract::MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally. Previous studies, which characterized miRNA function, revealed their involvement in fundamental biological processes. Importantly, miRNA expression is deregulated in many human diseases. Specific inhibition of miRNAs usin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt823
更新日期:2013-12-01 00:00:00
abstract::Members of the HMG-I(Y) family of mammalian nonhistone proteins are of importance because they have been demonstrated to bind specifically to the minor groove of A.T-rich sequences both in vitro and in vivo and to function as gene transcriptional regulatory proteins in vivo. Here we report the cloning, sequencing, cha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.18.4259
更新日期:1993-09-11 00:00:00
abstract::Smad proteins transduce signals from transforming growth factor-beta (TGF-beta) receptors and regulate transcription of target genes. TGF-beta is implicated in the regulation of the smooth muscle cell specific gene SM22alpha, but little is known about how Smads are involved in SM22alpha gene transcription. In this rep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg224
更新日期:2003-02-15 00:00:00
abstract::GenBank is a comprehensive database that contains publicly available DNA sequences for more than 140 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin program an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh045
更新日期:2004-01-01 00:00:00
abstract::Primers4clades is an easy-to-use web server that implements a fully automatic PCR primer design pipeline for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized organisms, belonging to user-specified phylogenetic clades or taxa. The server takes a set of non-aligned protein cod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp377
更新日期:2009-07-01 00:00:00
abstract::Most E2F-binding sites repress transcription through the recruitment of Retinoblastoma (RB) family members until the end of the G1 cell-cycle phase. Although the MYB promoter contains an E2F-binding site, its transcription is activated shortly after the exit from quiescence, before RB family members inactivation, by u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx641
更新日期:2017-09-29 00:00:00
abstract::Microsatellites are widely used as genetic markers because they are co-dominant, multiallelic, easily scored and highly polymorphic. A major drawback of microsatellite markers is the time and cost required to characterise them. We have developed a novel technique to reduce this cost by producing a microsatellite-rich ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.21.4369
更新日期:1996-11-01 00:00:00
abstract::Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx246
更新日期:2017-07-03 00:00:00
abstract::The Fos and Jun family of transcription factors contain an invariant sequence motif lysine-cysteine-arginine (KCR) in the highly conserved DNA-binding region. Reduction of the cysteine residue is necessary to facilitate DNA-binding. Here, we examined the potential dual roles of the flanking lysine and arginine residue...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.25.5831
更新日期:1993-12-25 00:00:00
abstract::Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks671
更新日期:2012-10-01 00:00:00
abstract::The dhp1+ gene of Schizosaccharomyces pombe is a homolog of Saccharomyces cerevisiae HKE1/RAT1/TAP1 gene that is involved in RNA metabolism such as RNA trafficking and RNA synthesis. dhp1+ is also related to S. cerevisiae DST2 (SEP1) that encodes a DNA strand exchange protein required for sporulation and homologous re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.357
更新日期:1995-02-11 00:00:00
abstract::Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1074
更新日期:2012-01-01 00:00:00
abstract::The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw401
更新日期:2016-08-19 00:00:00
abstract::FIMM database (http://sdmc.krdl.org.sg:8080/fimm) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease associations. FIMM has a se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.226
更新日期:2002-01-01 00:00:00
abstract::Kinetically monitored, reverse transcriptase-initiated PCR (kinetic RT-PCR, kRT-PCR) is a novel application of kinetic PCR for high throughput transcript quantitation in total cellular RNA. The assay offers the simplicity and flexibility of an enzyme assay with distinct advantages over DNA microarray hybridization and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.2.e2
更新日期:2000-01-15 00:00:00