ELM-the eukaryotic linear motif resource in 2020.


: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.


Nucleic Acids Res


Nucleic acids research


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 TJ




Has Abstract


2020-01-08 00:00:00














  • COBRA: a sensitive and quantitative DNA methylation assay.

    abstract::We report here on a quantitative technique called COBRA to determine DNA methylation levels at specific gene loci in small amounts of genomic DNA. Restriction enzyme digestion is used to reveal methylation-dependent sequence differences in PCR products of sodium bisulfite-treated DNA as described previously. We show t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Xiong Z,Laird PW

    更新日期:1997-06-15 00:00:00

  • Interplay between positive and negative activities that influence the role of Bicoid in transcription.

    abstract::The Drosophila mophogenetic protein Bicoid (Bcd) can activate transcription in a concentration-dependent manner in embryos. It contains a self-inhibitory domain that can interact with the co-repressor Sin3A. In this report, we study a Bcd mutant, Bcd(A57-61), which has a strengthened self-inhibitory function and is un...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fu D,Ma J

    更新日期:2005-07-19 00:00:00

  • Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells.

    abstract::Targeted modulation of gene expression represents a valuable approach to understand the mechanisms governing gene regulation. In a therapeutic context, it can be exploited to selectively modify the aberrant expression of a disease-causing gene or to provide the target cells with a new function. Here, we have establish...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mlambo T,Nitsch S,Hildenbeutel M,Romito M,Müller M,Bossen C,Diederichs S,Cornu TI,Cathomen T,Mussolino C

    更新日期:2018-05-18 00:00:00

  • Exposition of a family of RNA m(5)C methyltransferases from searching genomic and proteomic sequences.

    abstract::The Escherichia coli fmu gene product has recently been determined to be the 16S rRNA m(5)C 967 methyltransferase. As such, Fmu represents the first protein identified as an S -adenosyl-L-methionine (AdoMet)- dependent RNA m(5)C methyltransferase whose amino acid sequence is known. Using the amino acid sequence of Fmu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Reid R,Greene PJ,Santi DV

    更新日期:1999-08-01 00:00:00

  • Bipartite pattern discovery by entropy minimization-based multiple local alignment.

    abstract::Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel bipartite algorithm, bipartite pattern discovery (Bipad), which produces a mathematical model based on information maximizatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bi C,Rogan PK

    更新日期:2004-09-23 00:00:00

  • Rapid Cdc13 turnover and telomere length homeostasis are controlled by Cdk1-mediated phosphorylation of Cdc13.

    abstract::Budding yeast telomerase is mainly activated by Tel1/Mec1 (yeast ATM/ATR) on Cdc13 from late S to G2 phase of the cell cycle. Here, we demonstrated that the telomerase-recruitment domain of Cdc13 is also phosphorylated by Cdk1 at the same cell cycle stage as the Tel1/Mec1-dependent regulation. Phosphor-specific gel an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tseng SF,Shen ZJ,Tsai HJ,Lin YH,Teng SC

    更新日期:2009-06-01 00:00:00

  • Determination of base pairing in Escherichia coli and Bacillus stearothermophilus 5S RNAs by infrared spectroscopy.

    abstract::The extent of base pairing in Escherichia coli and Bacillus stearothermophilus 5S RNAs was determined by infrared spectroscopy. From the infrared spectra taken at 20 degrees and 52 degrees C it is concluded that E. coli and B. stearothermophlius 5S RNAs possess a large number of base pairs (Table I). Comparison of our...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Appel B,Erdmann VA,Stulz J,Ackerman T

    更新日期:1979-10-25 00:00:00

  • Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants.

    abstract::Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chen P,Lepikhova T,Hu Y,Monni O,Hautaniemi S

    更新日期:2011-10-01 00:00:00

  • PARP10 promotes cellular proliferation and tumorigenesis by alleviating replication stress.

    abstract::During carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and difficult to replicate genomic regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 inte...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schleicher EM,Galvan AM,Imamura-Kawasawa Y,Moldovan GL,Nicolae CM

    更新日期:2018-09-28 00:00:00

  • Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: effect of mRNA target sequence and chimera design.

    abstract::Use of antisense oligonucleotides is a versatile strategy for achieving control of gene expression. Unfortunately, the interpretation of antisense-induced phenotypes is sometimes difficult, and chemical modifications that improve the potency and specificity of antisense action would be useful. The introduction of lock...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Braasch DA,Liu Y,Corey DR

    更新日期:2002-12-01 00:00:00

  • Vespucci: a system for building annotated databases of nascent transcripts.

    abstract::Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the uniq...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Allison KA,Kaikkonen MU,Gaasterland T,Glass CK

    更新日期:2014-02-01 00:00:00

  • Conserved principles of mammalian transcriptional regulation revealed by RNA half-life.

    abstract::RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from m...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Friedel CC,Dölken L,Ruzsics Z,Koszinowski UH,Zimmer R

    更新日期:2009-09-01 00:00:00

  • Sequence analysis of T1 ribonuclease fragments of 18S ribosomal RNA by 5'-terminal labeling, partial digestion, and homochromatography fingerprinting.

    abstract::The method employed to determine the sequence of a T1 RNase fragment, A-A-A-A-A-U-A-A-C-A-A-U-A-C-A-Gp, from Novikoff rat hepatoma 18S ribosomal RNA is described. This method is applicable to any oligoribonucleotide produced by specific endonucleases that leave the newly cleaved 5'-end free for labeling with polynucle...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fuke M,Busch H

    更新日期:1977-02-01 00:00:00

  • SLIRP stabilizes LRPPRC via an RRM-PPR protein interface.

    abstract::LRPPRC is a protein that has attracted interest both for its role in post-transcriptional regulation of mitochondrial gene expression and more recently because numerous mutated variants have been characterized as causing severe infantile mitochondrial neurodegeneration. LRPPRC belongs to the pentatricopeptide repeat (...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Spåhr H,Rozanska A,Li X,Atanassov I,Lightowlers RN,Chrzanowska-Lightowlers ZM,Rackham O,Larsson NG

    更新日期:2016-08-19 00:00:00

  • Mammalian enzymes for preventing transcriptional errors caused by oxidative damage.

    abstract::8-Oxo-7,8-dihydroguanine (8-oxoGua) is produced in cells by reactive oxygen species normally formed during cellular metabolic processes. This oxidized base can pair with both adenine and cytosine, and thus the existence of this base in messenger RNA would cause translational errors. The MutT protein of Escherichia col...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ishibashi T,Hayakawa H,Ito R,Miyazawa M,Yamagata Y,Sekiguchi M

    更新日期:2005-07-07 00:00:00

  • The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.

    abstract::The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Koscielny G,Yaikhom G,Iyer V,Meehan TF,Morgan H,Atienza-Herrero J,Blake A,Chen CK,Easty R,Di Fenza A,Fiegel T,Grifiths M,Horne A,Karp NA,Kurbatova N,Mason JC,Matthews P,Oakley DJ,Qazi A,Regnart J,Retha A,Santos

    更新日期:2014-01-01 00:00:00

  • A high throughput screening for rarely transcribed differentially expressed genes.

    abstract::A novel method combining elements of suppression subtractive hybridization with high throughput differential screening permits the efficient and rapid cloning of rarely transcribed differentially expressed genes. The experimental strategy virtually excludes the possibility of isolating false positive clones. The poten...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: von Stein OD,Thies WG,Hofmann M

    更新日期:1997-07-01 00:00:00

  • Critical lysine residues within the overlooked N-terminal domain of human APE1 regulate its biological functions.

    abstract::Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is involved in base excision DNA repair (BER) and in regulation of gene expression, acting as a redox co-activator of several transcription factors. Recent findings highlight a novel role for APE1 in RNA metabolism, which is modulated by nuc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fantini D,Vascotto C,Marasco D,D'Ambrosio C,Romanello M,Vitagliano L,Pedone C,Poletto M,Cesaratto L,Quadrifoglio F,Scaloni A,Radicella JP,Tell G

    更新日期:2010-12-01 00:00:00

  • Nucleotide sequence analysis of the linked left and right hand terminal regions of adenovirus type 5 DNA present in the transformed rat cell line 5RK20.

    abstract::A peculiar phenomenon is observed in several adenovirus type 2 or 5 (Ad2 or Ad5) transformed cell lines: the right hand and left hand terminal regions of the viral genome present in the viral DNA insertions of these cell lines are found to be linked together. A large part of the viral DNA insertion present in the Ad5 ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Visser L,Reemst AC,van Mansfeld AD,Rozijn TH

    更新日期:1982-04-10 00:00:00

  • Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions.

    abstract::Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily fo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Stojanovic N,Florea L,Riemer C,Gumucio D,Slightom J,Goodman M,Miller W,Hardison R

    更新日期:1999-10-01 00:00:00

  • Early effects of phytohemagglutinin on induction of DNA polymerase, thymidine kinase, deoxyribonucleoside triphosphate pools and DNA synthesis in human lymphocytes.

    abstract::In phytohemagglutinin stimulated human lymphocytes the time relationship was determined between induction of the parameters mentioned. The results indicate that the induction occurred in a specific sequence. Thus, a simultaneous increase in the activity of DNA polymerase and thymidinekinase occurred after 15 h of incu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tyrsted G,Munch-Petersen B

    更新日期:1977-08-01 00:00:00

  • YM500: a small RNA sequencing (smRNA-seq) database for microRNA research.

    abstract::MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Cheng WC,Chung IF,Huang TS,Chang ST,Sun HJ,Tsai CF,Liang ML,Wong TT,Wang HW

    更新日期:2013-01-01 00:00:00

  • Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition.

    abstract::LINE1s occupy 17% of the human genome and are its only active autonomous mobile DNA. L1s are also responsible for genomic insertion of processed pseudogenes and >1 million non-autonomous retrotransposons (Alus and SVAs). These elements have significant effects on gene organization and expression. Despite the importanc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Goodier JL,Cheung LE,Kazazian HH Jr

    更新日期:2013-08-01 00:00:00

  • Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons.

    abstract::Minigenes encoding the peptide Met-Arg-Arg have been used to study the mechanism of toxicity of AGA codons proximal to the start codon or prior to the termination codon in bacteria. The codon sequences of the 'mini-ORFs' employed were initiator, combinations of AGA and CGA, and terminator. Both, AGA and CGA are low-us...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Cruz-Vera LR,Magos-Castro MA,Zamora-Romo E,Guarneros G

    更新日期:2004-08-18 00:00:00

  • Nucleotide sequence of pS194, a streptomycin-resistance plasmid from Staphylococcus aureus.

    abstract::pS194 is a naturally occurring Staphylococcus aureus plasmid encoding streptomycin resistance. The plasmid has a copy number of about 25 per cell, and belongs to the inc5 incompatibility group. The nucleotide sequence of pS194 has been determined and consists of 4397 base pairs including four open reading frames poten...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Projan SJ,Moghazeh S,Novick RP

    更新日期:1988-03-25 00:00:00

  • Nucleotide sequence of the melA gene, coding for alpha-galactosidase in Escherichia coli K-12.

    abstract::Melibiose uptake and hydrolysis in E.coli is performed by the MelB and MelA proteins, respectively. We report the cloning and sequencing of the melA gene. The nucleotide sequence data showed that melA codes for a 450 amino acid long protein with a molecular weight of 50.6 kd. The sequence data also supported the assum...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liljeström PL,Liljeström P

    更新日期:1987-03-11 00:00:00

  • COUP-TF gene: a structure unique for the steroid/thyroid receptor superfamily.

    abstract::Two different genomic genes for the COUP-transcription factor, COUP-TF I and COUP-TF II, have been isolated from a human cosmid genomic library using a [32P]-labeled cDNA probe. Data obtained from Southern blot analysis of these cosmid clones indicated that two closely related genes exist in the human genome and have ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ritchie HH,Wang LH,Tsai S,O'Malley BW,Tsai MJ

    更新日期:1990-12-11 00:00:00

  • The initiator element of the Drosophila beta2 tubulin gene core promoter contributes to gene expression in vivo but is not required for male germ-cell specific expression.

    abstract::The tissue-specific expression of the Drosophila beta 2 tubulin gene ( B2t ) is accomplished by the action of a 14-bp activator element (beta2UE1) in combination with certain regulatory elements of the TATA-less, Inr-containing B2t core promoter. We performed an in vivo analysis of the Inr element function in the B2t ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Santel A,Kaufmann J,Hyland R,Renkawitz-Pohl R

    更新日期:2000-03-15 00:00:00

  • Sequence-specific functions of the early palindrome domain within the SV40 core origin of replication.

    abstract::The early palindrome domain within the SV40 core origin of replication is essential for the initiation of replication. Studies with single point mutants in this region suggested that the early palindrome domain does not function as a cruciform structure, but may be involved in the initiation of SV40 DNA replication in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kim YS,Kang HS

    更新日期:1989-11-25 00:00:00

  • CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes.

    abstract::Combinatorial interactions of sequence-specific trans-acting factors with localized genomic cis-element clusters are the principal mechanism for regulating tissue-specific and developmental gene expression. With the emergence of expanding numbers of genome-wide expression analyses, the identification of the cis-elemen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jegga AG,Gupta A,Gowrisankar S,Deshmukh MA,Connolly S,Finley K,Aronow BJ

    更新日期:2005-07-01 00:00:00