Abstract：
:Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 cassette exons that exhibited higher transcript-normalized expression in muscle than in other normal adult tissues. Intron sequences flanking these exons were then analyzed to identify candidate regulatory motifs for muscle-specific alternative splicing. Correlation of motif parameters with gene-normalized exon expression levels was examined using linear regression and linear splines on RNA words and degenerate weight matrices, respectively. Our unbiased analysis uncovered multiple candidate regulatory motifs for muscle-specific splicing, many of which are phylogenetically conserved among vertebrate genomes. The most prominent downstream motifs were binding sites for Fox1- and CELF-related splicing factors, and a branchpoint-like element acuaac; pyrimidine-rich elements resembling PTB-binding sites were most significant in upstream introns. Intriguingly, our systematic study indicates a paucity of novel muscle-specific elements that are dominant in short proximal intronic regions. We propose that Fox and CELF proteins play major roles in enforcing the muscle-specific alternative splicing program, facilitating expression of unique isoforms of cytoskeletal proteins critical to muscle cell function.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Das D,Clark TA,Schweitzer A,Yamamoto M,Marr H,Arribere J,Minovitsky S,Poliakov A,Dubchak I,Blume JE,Conboy JGdoi
10.1093/nar/gkm485subject
Has Abstractpub_date
2007-01-01 00:00:00pages
4845-57issue
14eissn
0305-1048issn
1362-4962pii
gkm485journal_volume
35pub_type
杂志文章abstract：:Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structur...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1057
更新日期：2011-01-01 00:00:00
abstract：:Addition of thiol compounds containing an anionic group to the 3'-terminal unsaturated sugar of the 5' fragment obtained from an oligonucleotide containing an AP site cleaved by beta-elimination, can be followed by gel electrophoresis. The technique enables to distinguish between two mechanisms of cleavage of the C3'-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.20.9489
更新日期：1988-10-25 00:00:00
abstract：:Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1003
更新日期：2018-01-04 00:00:00
abstract：:The MF alpha 1 gene of Saccharomyces cerevisiae is an alpha specific gene whose expression is regulated by two upstream activation sites (UASMF alpha 1S), which are the binding sites for activator proteins, MAT alpha 1 and MCM1. UASMF alpha 1 elements act in a synergistic fashion; lack of either element causes reduced...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.11.3099
更新日期：1991-06-11 00:00:00
abstract：:DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1142
更新日期：2011-04-01 00:00:00
abstract：:The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The B...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg032
更新日期：2003-01-01 00:00:00
abstract：:An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been ide...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.16.3424
更新日期：2001-08-15 00:00:00
abstract：:The interaction of several synthetic analogues of d-ApA with Poly U and Poly dT was examined to explore the effects of substituents at phosphorus on binding properties of oligonucleotides. These analogues contained a bulky, lipophilic group (2,2,2-trichloroethoxy or 2,2,2-trichloro-1,1-dimethylethoxy) a small, uncharg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.8.3487
更新日期：1986-04-25 00:00:00
abstract：:The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf523
更新日期：2002-09-15 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：:To understand how potential for G-quadruplex formation might influence regulation of gene expression, we examined the 2 kb spanning the transcription start sites (TSS) of the 18 217 human RefSeq genes, distinguishing contributions of template and nontemplate strands. Regions both upstream and downstream of the TSS are...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1138
更新日期：2008-03-01 00:00:00
abstract：:RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp388
更新日期：2009-07-01 00:00:00
abstract：:SINE-VNTR-Alu (SVA) elements are non-autonomous, hominid-specific non-LTR retrotransposons and distinguished by their organization as composite mobile elements. They represent the evolutionarily youngest, currently active family of human non-LTR retrotransposons, and sporadically generate disease-causing insertions. S...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr863
更新日期：2012-02-01 00:00:00
abstract：:Release of phosphorothioate antisense oligonucleotides (PS-ASOs) from late endosomes (LEs) is a rate-limiting step and a poorly defined process for productive intracellular ASO drug delivery. Here, we examined the role of Golgi-endosome transport, specifically M6PR shuttling mediated by GCC2, in PS-ASO trafficking and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1171
更新日期：2020-02-20 00:00:00
abstract：:JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister's Millennium Project. The aim of this undertaking is to identify and collate up to 150 000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.158
更新日期：2002-01-01 00:00:00
abstract：:In many organisms (e.g., gram-positive eubacteria) Gin-tRNA is not formed by direct glutaminylation of tRNAGln but by a specific transamidation of Glu-tRNAGln. We wondered whether a similar transamidation pathway also operates in the formation of Asn-tRNA in these organisms. Therefore we tested in S-100 preparations o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.14.2648
更新日期：1996-07-15 00:00:00
abstract：:We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt605
更新日期：2013-09-01 00:00:00
abstract：:This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transiti...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/15.23.9985
更新日期：1987-12-10 00:00:00
abstract：:The alcohol dehydrogenase (Adh) gene of D. melanogaster is transcribed from two different promoters during fly development: the distal (adult) and the proximal (embryonic-larval). Certain aspects of Adh gene regulation are represented in Drosophila continuous cell lines. We have used Drosophila tissue culture cells in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.19.7903
更新日期：1987-10-12 00:00:00
abstract：:DNA from healthy Malaysian newborns was studied on gene maps after digestion with different restriction endonucleases. Of 65 newborns, two were found to be carriers of two different variants of triplicated alpha-globin loci. In variant no. 1, found in an Malay, the three alpha-globin genes are in an elongated DNA frag...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3707
更新日期：1981-08-11 00:00:00
abstract：:ATRX and MeCP2 belong to an expanding group of chromatin-associated proteins implicated in human neurodevelopmental disorders, although their gene-regulatory activities are not fully resolved. Loss of ATRX prevents full repression of an imprinted gene network in the postnatal brain and in this study we address the mec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku564
更新日期：2014-07-01 00:00:00
abstract：:DNA-PKcs and Ku are essential components of the complex that catalyzes non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Ku, a heterodimeric protein, binds to DNA ends and facilitates recruitment of the catalytic subunit, DNA-PKcs. We have investigated the effect of DNA strand orientation and seque...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki157
更新日期：2005-01-07 00:00:00
abstract：:Cultured mammalian cells transduced with the Escherichia coli gene, Ecogpt, synthesize the bacterial enzyme xanthine-guanine phosphoribosyl transferase (XGPT) (1). This paper describes a method for measuring XGPT activity in crude cell extracts by following the conversion of 14C-xanthine (X) to 14C-xanthine monophosph...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.8.2921
更新日期：1985-04-25 00:00:00
abstract：:We have analyzed the ATPase activity exhibited by the UvrABC DNA repair complex. The UvrA protein is an ATPase whose lack of DNA dependence may be related to the ATP induced monomer-dimer transitions. ATP induced dimerization may be responsible for the enhanced DNA binding activity observed in the presence of ATP. Alt...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.11.4145
更新日期：1989-06-12 00:00:00
abstract：:Chromatin footprinting in Drosophila tissue culture cells has detected the binding of a non-histone protein at +8 of the distal Adh RNA start site, on a 10-bp direct repeat motif abutting a nucleosome positioned over the inactive Adh distal promoter. Alternatively the active promoter is bound by a transcription initia...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.17.4481
更新日期：1992-09-11 00:00:00
abstract：:Here we describe a method of labelling short oligonucleotide probes with enzyme without purification or chemical modifications. Biotinylated oligonucleotides as short as 10 nt are coupled with streptavidin-conjugated enzyme, hybridised and detected with enzyme-triggered chemiluminescence. The detection of hybridisatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.2.703
更新日期：1999-01-15 00:00:00
abstract：:G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz463
更新日期：2019-07-09 00:00:00
abstract：:The inducibility of the vir genes (virA, -B, -C, -D, -E, and -G) on pRiA4 was examined at the transcriptional level, and the RNA-starting sites were determined by S1-nuclease mapping and primer-extension experiments. All of these genes were inducible, while virA, -E, and -G were transcribed even under noninducing cond...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.21.8711
更新日期：1989-11-11 00:00:00
abstract：:We present the sequences of five additional human U2 pseudogenes which are very similar to the U2.13 pseudogene reported previously [Van Arsdell et al. (1981) Cell 26, 11-17]. All six U2 pseudogenes preserve the 5' end of the mature U2 snRNA sequence, and all six are flanked by nearly perfect direct repeats that diffe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.3.1463
更新日期：1984-02-10 00:00:00
abstract：:In flowering plants, RNA editing is a posttranscriptional process that converts specific C to U in organelle mRNAs. Nicotiana tabacum is an allotetraploid species derived from the progenitors of Nicotiana sylvestris and Nicotiana tomentosiformis. These Nicotiana species have been used as a model for understanding the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn629
更新日期：2008-11-01 00:00:00
