Abstract：
:Linear motifs are short, evolutionarily plastic components of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling protein turnover and directing protein localization. Given their importance, our understanding of motifs is surprisingly limited, largely as a result of the difficulty of discovery, both experimentally and computationally. The Eukaryotic Linear Motif (ELM) resource at http://elm.eu.org provides the biological community with a comprehensive database of known experimentally validated motifs, and an exploratory tool to discover putative linear motifs in user-submitted protein sequences. The current update of the ELM database comprises 1800 annotated motif instances representing 170 distinct functional classes, including approximately 500 novel instances and 24 novel classes. Several older motif class entries have been also revisited, improving annotation and adding novel instances. Furthermore, addition of full-text search capabilities, an enhanced interface and simplified batch download has improved the overall accessibility of the ELM data. The motif discovery portion of the ELM resource has added conservation, and structural attributes have been incorporated to aid users to discriminate biologically relevant motifs from stochastically occurring non-functional instances.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dinkel H,Michael S,Weatheritt RJ,Davey NE,Van Roey K,Altenberg B,Toedt G,Uyar B,Seiler M,Budd A,Jödicke L,Dammert MA,Schroeter C,Hammer M,Schmidt T,Jehl P,McGuigan C,Dymecka M,Chica C,Luck K,Via A,Chatr-Aryamontdoi
10.1093/nar/gkr1064subject
Has Abstractpub_date
2012-01-01 00:00:00pages
D242-51issue
Database issueeissn
0305-1048issn
1362-4962pii
gkr1064journal_volume
40pub_type
杂志文章abstract：:The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Here we identi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks755
更新日期：2012-10-01 00:00:00
abstract：:The HIRA histone chaperone complex deposits histone H3.3 into nucleosomes in a DNA replication- and sequence-independent manner. As herpesvirus genomes enter the nucleus as naked DNA, we asked whether the HIRA chaperone complex affects herpesvirus infection. After infection of primary cells with HSV or CMV, or transie...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx771
更新日期：2017-11-16 00:00:00
abstract：:EpoDB is a database of genes expressed in vertebrate red blood cells. It is also a prototype for the creation of cell and tissue-specific databases from multiple external sources. The information in EpoDB obtained from GenBank, SWISS-PROT, Transfac, TRRD and GERD is curated to provide high quality data for sequence an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.1.200
更新日期：1999-01-01 00:00:00
abstract：:Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku527
更新日期：2014-07-01 00:00:00
abstract：:HORMA domain-containing proteins (HORMADs) play an essential role in meiosis in many organisms. The meiotic HORMADs, including yeast Hop1, mouse HORMAD1 and HORMAD2, and Arabidopsis ASY1, assemble along chromosomes at early prophase and the closure motif at their C-termini has been hypothesized to be instrumental for ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa527
更新日期：2020-11-18 00:00:00
abstract：:To generate long arrays of nucleosomes within a topologically defined chromatin domain we have assembled minichromosomes on negatively supercoiled plasmid DNA with extracts from Drosophila preblastoderm embryos. These minichromosomes are dynamic substrates for energy-dependent nucleosome remodeling machines that facil...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.16.3657
更新日期：1998-08-15 00:00:00
abstract：:In kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g)RNAs. Currently popular mechanisms for the editing process envisage a series of consecutive 'cut-and-paste' reactions, carried out by a compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.14.2950
更新日期：2001-07-15 00:00:00
abstract：:Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buff...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx553
更新日期：2017-09-06 00:00:00
abstract：:The direct sequencing of DNA generated by the polynucleotide chain reaction, via the incorporation of phosphorothioate nucleotides and followed by treatment with an alkylating reagent that cleaves specifically at the phosphorothioate positions, is described. The Taq polymerase used in the amplification reaction incorp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.21.9947
更新日期：1988-11-11 00:00:00
abstract：:SMILE (small heterodimer partner interacting leucine zipper protein) has been identified as a coregulator in ER signaling. In this study, we have examined the effects of SMILE on other NRs (nuclear receptors). SMILE inhibits GR, CAR and HNF4 alpha-mediated transactivation. Knockdown of SMILE gene expression increases ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp333
更新日期：2009-07-01 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：: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：: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：:To investigate the mechanism of N4-aminocytidine-induced mutagenesis, N'-alkyl-N4-aminocytidines and N4-alkyl-N4-aminocytidines were prepared and their mutagenicity on bacteria were assayed. N'-Methyl-N4-aminocytidine, N'-(2-hydroxyethyl)-N4-aminocytidine and N',N'-dimethyl-N4-aminocytidine showed direct-acting mutage...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.24.8893
更新日期：1985-12-20 00:00:00
abstract：:A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries. We present a fast and effective method that aims to eliminate the problems repeats cause in the process of clustering. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki511
更新日期：2005-04-14 00:00:00
abstract：:We have sequenced the Escherichia coli grpE gene and shown that it encodes a 197-amino acid residue protein of 21,668-Mr. The predicted N-terminal amino acid sequence, as well as the overall amino acid composition agree well with that of the purified protein. From Northern analysis, we have shown that transcription of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.15.7545
更新日期：1988-08-11 00:00:00
abstract：:Mismatch uracil DNA glycosylase (Mug) from Escherichia coli is an initiating enzyme in the base-excision repair pathway. As with other DNA glycosylases, the abasic product is potentially more harmful than the initial lesion. Since Mug is known to bind its product tightly, inhibiting enzyme turnover, understanding how ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq913
更新日期：2011-04-01 00:00:00
abstract：:The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.19.4467
更新日期：1993-09-25 00:00:00
abstract：:31P NMR chemical shifts of the selected mono- and oligonucleotide derivatives, including the compounds with P-N, P-C, P-S bonds and phosphite nucleotide analogues have been presented. The influence of substituents upon 31P chemical shifts has been discussed. The concrete examples of 31P chemical shifts data applicatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.14.5547
更新日期：1984-07-25 00:00:00
abstract：:The catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) is a member of a sub-family of phosphatidylinositol (PI) 3-kinases termed PIK-related kinases. A distinguishing feature of this sub-family is the presence of a conserved C-terminal region downstream of a PI 3-kinase domain. Mutants defective in DNA-P...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.8.1965
更新日期：1998-04-15 00:00:00
abstract：:Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called 'CentroidHomfold'), which includes information about homologous sequences into the prediction of the secondary structu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr290
更新日期：2011-07-01 00:00:00
abstract：:Micrococcal nuclease has been shown to preferentially cleave chromatin in the region of genes actively engaged in transcription. We have used this preferential cleavage to show that the metallothionein (MT) gene in adult mouse liver, when induced to produce mRNA by injection of cadmium, becomes more susceptible to nuc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.10.3255
更新日期：1983-05-25 00:00:00
abstract：:Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of nearly 6000 oligopeptides have been identified from >1000 organisms representing all the biological kingdoms. We have compiled the known physical, chemical and biological properties of these oligopeptides--whether synthe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj008
更新日期：2006-01-01 00:00:00
abstract：:The 3374 nucleotide sequence of RNA2 from the British PEBV strain SP5 has been determined. The RNA includes three open reading frames flanked by 5' and 3' noncoding regions of 509 and 480 nucleotides. The open reading frames specify coat protein, a 29.6K product homologous to the 29.1K product of TRV(TCM) RNA2 and a 2...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.15.4507
更新日期：1990-08-11 00:00:00
abstract：:An adequate supply of nucleotides is essential for DNA replication and DNA repair. Moreover, inhibition of TTP synthesis can cause cell death by a poorly characterized mechanism called thymine-less death. In the yeast Saccharomyces cerevisiae, the genes encoding thymidylate synthetase (CDC21) and thymidylate kinase (C...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki219
更新日期：2005-01-28 00:00:00
abstract：:Despite the increasing wealth of available data, the structure of cancer transcriptional space remains largely unknown. Analysis of this space would provide novel insights into the complexity of cancer, assess relative implications in complex biological processes and responses, evaluate the effectiveness of cancer mod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr533
更新日期：2011-10-01 00:00:00
abstract：:We have determined the nucleotide sequence at the 3' end of the vesicular stomatitis virus (VSV) polymerase or L gene and compared it to that obtained from a defective interfering particle (DI) RNA generated by this virus. The latter (DI 0.50) contains a large internal deletion within this gene. The deletion begins ex...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.21.6919
更新日期：1982-11-11 00:00:00
abstract：:The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and format...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1096
更新日期：2008-02-01 00:00:00
abstract：:DNA polymerase delta (Pol δ) is responsible for the elongation and maturation of Okazaki fragments in eukaryotic cells. Proliferating cell nuclear antigen (PCNA) recruits Pol δ to the DNA and serves as a processivity factor. Here, we show that PCNA also stimulates the catalytic rate of Saccharomyces cerevisiae Pol δ b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1321
更新日期：2019-02-28 00:00:00
abstract：:The class II genes of the major histocompatibility complex (MHC) encode a family of cell surface glycoproteins that present processed antigen to the T cell receptor. Class II genes are regulated coordinately, responding to both immunologic and developmental signals. Conserved sequence elements 5' to class II genes hav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.6.1243
更新日期：1991-03-25 00:00:00
