Abstract:
:The eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SLiMs). Since the initial release almost 20 years ago, ELM has become an indispensable resource for the molecular biology community for investigating functional regions in many proteins. In this update, we have added 21 novel motif classes, made major revisions to 12 motif classes and added >400 new instances mostly focused on DNA damage, the cytoskeleton, SH2-binding phosphotyrosine motifs and motif mimicry by pathogenic bacterial effector proteins. The current release of the ELM database contains 289 motif classes and 3523 individual protein motif instances manually curated from 3467 scientific publications. ELM is available at: http://elm.eu.org.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kumar M,Gouw M,Michael S,Sámano-Sánchez H,Pancsa R,Glavina J,Diakogianni A,Valverde JA,Bukirova D,Čalyševa J,Palopoli N,Davey NE,Chemes LB,Gibson TJdoi
10.1093/nar/gkz1030subject
Has Abstractpub_date
2020-01-08 00:00:00pages
D296-D306issue
D1eissn
0305-1048issn
1362-4962pii
5611669journal_volume
48pub_type
杂志文章abstract::During mitosis the chromatin undergoes dramatic architectural changes with the halting of the transcriptional processes and evacuation of nearly all transcription associated machinery from genes and promoters. Molecular bookmarking of genes during mitosis is a mechanism of faithfully transmitting cell-specific transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1223
更新日期:2016-03-18 00:00:00
abstract::Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the repl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz090
更新日期:2019-05-07 00:00:00
abstract::WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz920
更新日期:2020-01-08 00:00:00
abstract::SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv351
更新日期:2015-07-01 00:00:00
abstract::Large expansions of the trinucleotide repeat GAA*TTC within the first intron of the X25 (frataxin) gene cause Friedreich's ataxia, the most common inherited ataxia. Expansion leads to reduced levels of frataxin mRNA in affected individuals. Here we show that GAA*TTC tracts, in the absence of any other frataxin gene se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.14.2815
更新日期:2000-07-15 00:00:00
abstract::Plant viruses ubiquitously mediate the induction of miR168 trough the activities of viral suppressors of RNA silencing (VSRs) controlling the accumulation of ARGONAUTE1 (AGO1), one of the main components of RNA silencing based host defence system. Here we used a mutant Tombusvirus p19 VSR (p19-3M) disabled in its main...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt846
更新日期:2014-01-01 00:00:00
abstract::A precursor of modified nucleoside Q isolated from E. coli methyl-deficient tRNA was determined to be 7-(aminomethyl)-7-deazaguanosine. The structure was deduced by means of its chromatographic and electrophoretic mobilities, and UV and mass spectra, in addition to comparison with the synthesized authentic compound. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.7.2289
更新日期:1978-07-01 00:00:00
abstract::The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration wi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1001
更新日期:2017-01-04 00:00:00
abstract::We have studied the role of the C-terminal domain of the alpha subunit (alphaCTD) of Escherichia coli RNA polymerase during transcription initiation at promoters lacking an UP-element. The temperature requirement for open complex formation was used as an indication of the kinetics of this process. We have previously s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.9.2051
更新日期:1999-05-01 00:00:00
abstract::Non-coding genetic variants/mutations can play functional roles in the cell by disrupting regulatory interactions between transcription factors (TFs) and their genomic target sites. For most human TFs, a myriad of DNA-binding models are available and could be used to predict the effects of DNA mutations on TF binding....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz363
更新日期:2019-07-02 00:00:00
abstract::Toxic metals are part of our environment, and undue exposure to them leads to a variety of pathologies. In response, most organisms adapt their metabolism and have evolved systems to limit this toxicity and to acquire tolerance. Ribosome biosynthesis being central for protein synthesis, we analyzed in yeast the effect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt335
更新日期:2013-07-01 00:00:00
abstract::Upon growth transition of Escherichia coli cells from exponential to stationary phase, RNA polymerase is converted into at least three different forms (S1, S2 and S3), which could be separately isolated by phosphocellulose column chromatography (Ozaki et al., 1991 (2)). Here, the promoter selectivity of these three st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.2.257
更新日期:1992-01-25 00:00:00
abstract::The chromatographic profiles of isoaccepting tRNAs were analyzed at five time points during the 96 hr, dimethylsulfoxide induced, erythroid-like differentiation of Friend leukemia cells. Sixty-four isoaccepting species of tRNA for 16 amino acids were resolved by RPC-5 chromatography. The relative amounts of tRNAphe, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.15.3467
更新日期:1980-08-11 00:00:00
abstract::Nuclear DNA binding protein p92 is a sequence specific octamer binding protein with identical molecular weight as the ubiquitous octamer binding protein Oct-1. It binds to octamer related sequences from the enhancer of human papillomavirus type 18. The activity and intracellular distribution of p92 is regulated by ext...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.20.5725
更新日期:1991-10-25 00:00:00
abstract::A series of plasmids were constructed in which a promoter was introduced into a lac-based operon fusion vector. A perfectly symmetrical oligonucleotide of 22-bp corresponding to an idealized binding site for cAMP receptor protein (CRP) of E. coli was chemically synthesized. The synthetic CRP site was placed between th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.15.7315
更新日期:1988-08-11 00:00:00
abstract::DNA strand exchange, the central step of homologous recombination, is considered to occur approximately independently of DNA sequence content. However, certain prokaryotic and eukaryotic genomic loci display either an enhanced or reduced frequency of genetic exchange. Here we show that the Homo sapiens DNA strand exch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl355
更新日期:2006-05-24 00:00:00
abstract::2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in y...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr896
更新日期:2012-03-01 00:00:00
abstract::Four pseudorevertants of a -10 region lacP mutation were isolated. Three of these mutations were found to activate nascent promoters. These mutations were: a -2 G/C----A/T change (-2A) promoting transcription at position +11, a +1 A/T----T/A change (+1T) promoting transcription initiation at position +13, and a +10 C/...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.10.3927
更新日期:1989-05-25 00:00:00
abstract::The current version of PLMItRNA has been realized to constitute a database for tRNA molecules and genes identified in the mitochondria of all green plants ( Viridiplantae ). It is the enlargement of a previous database originally restricted to seed plants [Ceci,L.R., Volpicella,M., Liuni,S., Volpetti,V., Licciulli,F. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.159
更新日期:2000-01-01 00:00:00
abstract::An 11 S ribonucleoprotein particle was isolated from maize endosperm and shown to be functionally and structurally equivalent to the mammalian signal recognition particle. However, unlike animal cells which apparently contain a single 7 SL RNA species, maize endosperm contains a heterogeneous population of 7 SL RNA. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.4.1573
更新日期:1989-02-25 00:00:00
abstract::DNA polymerase lambda (pol lambda) is a member of the X family DNA polymerases and is endowed with multiple enzymatic activities. In this work we investigated the in vitro miscoding properties of full-length, human pol lambda either in the absence or in the presence of the human auxiliary proteins proliferating cell n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl032
更新日期:2006-03-06 00:00:00
abstract::MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome som...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1239
更新日期:2010-04-01 00:00:00
abstract::Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.22.4607
更新日期:2001-11-15 00:00:00
abstract::Polyaromatic molecules with amino chain substituents, upon binding with DNA, selectively catalyze exchange of the A.T base pair protons with bulk water protons. The amine-catalyzed exchange is mediated by compounds which are A.T and G.C base sequence specific, intercalators, and outside binders. A mechanism for the se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.20.8511
更新日期:1987-10-26 00:00:00
abstract::Differential display of mRNA is a simple, sensitive and powerful method to identify differentially expressed gene fragments. The main drawback of differential display is the lack of reproducibility and the inability to read and compare complex gels. This issue results from employing unoptimized primer combinations and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.3.854
更新日期:1998-02-01 00:00:00
abstract::One of the most intensively studied chromatin binding factors is HP1α. HP1α is associated with silenced, heterochromatic regions of the genome and binds to H3K9me3. While H3K9me3 is necessary for HP1α recruitment to heterochromatin, it is becoming apparent that it is not sufficient suggesting that additional factors a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky632
更新日期:2018-10-12 00:00:00
abstract::RNase D was recently reported as a new enzymatic activity associated with HIV-1 reverse transcriptase (RT), cleaving RNA at two positions within the double-stranded region of the tRNA primer-viral RNA template complex (Ben-Artzi et al., Proc. Natl. Acad. Sci. USA 89 (1992) 927-931). This would make RNase D a fourth di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.21.5819
更新日期:1992-11-11 00:00:00
abstract::We have isolated the gene coding for the U2 analogue in trypanosomes. The 148 nucleotide long U2 RNA is capped and transcribed from a single copy gene. The 5' half of the molecule is highly homologous to mammalian U2 RNA, while the 3' half does not show any significant sequence homology with the mammalian counterpart....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.22.8893
更新日期:1986-11-25 00:00:00
abstract::Human ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz815
更新日期:2019-11-18 00:00:00
abstract::Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep)...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw689
更新日期:2016-10-14 00:00:00