IRBIS: a systematic search for conserved complementarity.
Identifieur interne : 001875 ( PubMed/Corpus ); précédent : 001874; suivant : 001876IRBIS: a systematic search for conserved complementarity.
Auteurs : Dmitri D. PervouchineSource :
- RNA (New York, N.Y.) [ 1469-9001 ] ; 2014.
English descriptors
- KwdEn :
- Animals, Base Sequence, Caenorhabditis elegans (genetics), Conserved Sequence (genetics), Drosophila melanogaster (genetics), Exons (genetics), Genes (genetics), Humans, Introns (genetics), Molecular Sequence Data, RNA Splicing (genetics), RNA, Small Nucleolar (genetics), Sequence Homology, Nucleic Acid, Software.
- MESH :
- chemical , genetics : RNA, Small Nucleolar.
- genetics : Caenorhabditis elegans, Conserved Sequence, Drosophila melanogaster, Exons, Genes, Introns, RNA Splicing.
- Animals, Base Sequence, Humans, Molecular Sequence Data, Sequence Homology, Nucleic Acid, Software.
Abstract
IRBIS is a computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences. Unlike other methods, it follows the "first-fold-then-align" principle in which all possible combinations of complementary k-mers are searched for simultaneous conservation. The novel trimming procedure reduces the size of the search space and improves the performance to the point where large-scale analyses of intra- and intermolecular RNA-RNA interactions become possible. In this article, I provide a rigorous description of the method, benchmarking on simulated and real data, and a set of stringent predictions of intramolecular RNA structure in placental mammals, drosophilids, and nematodes. I discuss two particular cases of long-range RNA structures that are likely to have a causal effect on single- and multiple-exon skipping, one in the mammalian gene Dystonin and the other in the insect gene Ca-α1D. In Dystonin, one of the two complementary boxes contains a binding site of Rbfox protein similar to one recently described in Enah gene. I also report that snoRNAs and long noncoding RNAs (lncRNAs) have a high capacity of base-pairing to introns of protein-coding genes, suggesting possible involvement of these transcripts in splicing regulation. I also find that conserved sequences that occur equally likely on both strands of DNA (e.g., transcription factor binding sites) contribute strongly to the false-discovery rate and, therefore, would confound every such analysis. IRBIS is an open-source software that is available at http://genome.crg.es/~dmitri/irbis/.
DOI: 10.1261/rna.045088.114
PubMed: 25142064
Links to Exploration step
pubmed:25142064Le document en format XML
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Pervouchine</name><affiliation><nlm:affiliation>Centre for Genomic Regulation and UPF, Barcelona 08003, Spain Faculty of Bioengineering and Bioinformatics, Moscow State University, 119992 Moscow, Russia dp@crg.eu.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25142064</idno><idno type="pmid">25142064</idno><idno type="doi">10.1261/rna.045088.114</idno><idno type="wicri:Area/PubMed/Corpus">001875</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001875</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">IRBIS: a systematic search for conserved complementarity.</title><author><name sortKey="Pervouchine, Dmitri D" sort="Pervouchine, Dmitri D" uniqKey="Pervouchine D" first="Dmitri D" last="Pervouchine">Dmitri D. Pervouchine</name><affiliation><nlm:affiliation>Centre for Genomic Regulation and UPF, Barcelona 08003, Spain Faculty of Bioengineering and Bioinformatics, Moscow State University, 119992 Moscow, Russia dp@crg.eu.</nlm:affiliation></affiliation></author></analytic><series><title level="j">RNA (New York, N.Y.)</title><idno type="eISSN">1469-9001</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Caenorhabditis elegans (genetics)</term><term>Conserved Sequence (genetics)</term><term>Drosophila melanogaster (genetics)</term><term>Exons (genetics)</term><term>Genes (genetics)</term><term>Humans</term><term>Introns (genetics)</term><term>Molecular Sequence Data</term><term>RNA Splicing (genetics)</term><term>RNA, Small Nucleolar (genetics)</term><term>Sequence Homology, Nucleic Acid</term><term>Software</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Small Nucleolar</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Caenorhabditis elegans</term><term>Conserved Sequence</term><term>Drosophila melanogaster</term><term>Exons</term><term>Genes</term><term>Introns</term><term>RNA Splicing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Humans</term><term>Molecular Sequence Data</term><term>Sequence Homology, Nucleic Acid</term><term>Software</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">IRBIS is a computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences. Unlike other methods, it follows the "first-fold-then-align" principle in which all possible combinations of complementary k-mers are searched for simultaneous conservation. The novel trimming procedure reduces the size of the search space and improves the performance to the point where large-scale analyses of intra- and intermolecular RNA-RNA interactions become possible. In this article, I provide a rigorous description of the method, benchmarking on simulated and real data, and a set of stringent predictions of intramolecular RNA structure in placental mammals, drosophilids, and nematodes. I discuss two particular cases of long-range RNA structures that are likely to have a causal effect on single- and multiple-exon skipping, one in the mammalian gene Dystonin and the other in the insect gene Ca-α1D. In Dystonin, one of the two complementary boxes contains a binding site of Rbfox protein similar to one recently described in Enah gene. I also report that snoRNAs and long noncoding RNAs (lncRNAs) have a high capacity of base-pairing to introns of protein-coding genes, suggesting possible involvement of these transcripts in splicing regulation. I also find that conserved sequences that occur equally likely on both strands of DNA (e.g., transcription factor binding sites) contribute strongly to the false-discovery rate and, therefore, would confound every such analysis. IRBIS is an open-source software that is available at http://genome.crg.es/~dmitri/irbis/. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25142064</PMID><DateCompleted><Year>2015</Year><Month>01</Month><Day>29</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-9001</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>10</Issue><PubDate><Year>2014</Year><Month>Oct</Month></PubDate></JournalIssue><Title>RNA (New York, N.Y.)</Title><ISOAbbreviation>RNA</ISOAbbreviation></Journal><ArticleTitle>IRBIS: a systematic search for conserved complementarity.</ArticleTitle><Pagination><MedlinePgn>1519-31</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1261/rna.045088.114</ELocationID><Abstract><AbstractText>IRBIS is a computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences. Unlike other methods, it follows the "first-fold-then-align" principle in which all possible combinations of complementary k-mers are searched for simultaneous conservation. The novel trimming procedure reduces the size of the search space and improves the performance to the point where large-scale analyses of intra- and intermolecular RNA-RNA interactions become possible. In this article, I provide a rigorous description of the method, benchmarking on simulated and real data, and a set of stringent predictions of intramolecular RNA structure in placental mammals, drosophilids, and nematodes. I discuss two particular cases of long-range RNA structures that are likely to have a causal effect on single- and multiple-exon skipping, one in the mammalian gene Dystonin and the other in the insect gene Ca-α1D. In Dystonin, one of the two complementary boxes contains a binding site of Rbfox protein similar to one recently described in Enah gene. I also report that snoRNAs and long noncoding RNAs (lncRNAs) have a high capacity of base-pairing to introns of protein-coding genes, suggesting possible involvement of these transcripts in splicing regulation. I also find that conserved sequences that occur equally likely on both strands of DNA (e.g., transcription factor binding sites) contribute strongly to the false-discovery rate and, therefore, would confound every such analysis. IRBIS is an open-source software that is available at http://genome.crg.es/~dmitri/irbis/. </AbstractText><CopyrightInformation>© 2014 Pervouchine; Published by Cold Spring Harbor Laboratory Press for the RNA Society.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pervouchine</LastName><ForeName>Dmitri D</ForeName><Initials>DD</Initials><AffiliationInfo><Affiliation>Centre for Genomic Regulation and UPF, Barcelona 08003, Spain Faculty of Bioengineering and Bioinformatics, Moscow State University, 119992 Moscow, Russia dp@crg.eu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>1R01MH090941-01</GrantID><Acronym>MH</Acronym><Agency>NIMH NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U54 HG004557</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>1U54HG004555-01</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>1U54HG004557-01</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 MH090941</GrantID><Acronym>MH</Acronym><Agency>NIMH NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U54 HG004555</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate 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