IRFinder: assessing the impact of intron retention on mammalian gene expression
Identifieur interne : 000A51 ( Main/Exploration ); précédent : 000A50; suivant : 000A52IRFinder: assessing the impact of intron retention on mammalian gene expression
Auteurs : Robert Middleton [Australie] ; Dadi Gao [Australie, États-Unis] ; Aubin Thomas [France] ; Babita Singh [Espagne] ; Amy Au [Australie] ; Justin J-L Wong [Australie] ; Alexandra Bomane [France] ; Bertrand Cosson [France] ; Eduardo Eyras [Espagne] ; John E. J. Rasko [Australie] ; William Ritchie [Australie, France]Source :
- Genome Biology [ 1474-7596 ] ; 2017.
Descripteurs français
- KwdFr :
- Animaux, Biologie informatique (), Cycle cellulaire (génétique), Différenciation cellulaire (génétique), Exons, Humains, Introns, Logiciel, Motifs nucléotidiques, Protéines de liaison à l'ARN (métabolisme), Régulation de l'expression des gènes, Sites de fixation, Épissage alternatif, Épissage des ARN.
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : RNA-Binding Proteins.
- genetics : Cell Cycle, Cell Differentiation.
- methods : Computational Biology.
- Alternative Splicing, Animals, Binding Sites, Exons, Gene Expression Regulation, Humans, Introns, Nucleotide Motifs, RNA Splicing, Software.
Abstract
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.
The online version of this article (doi:10.1186/s13059-017-1184-4) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13059-017-1184-4
PubMed: 28298237
PubMed Central: 5353968
Affiliations:
- Australie, Espagne, France, États-Unis
- Languedoc-Roussillon, Massachusetts, Occitanie (région administrative)
- Montpellier
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Le document en format XML
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989X</institution-id><institution-id institution-id-type="GRID">grid.425902.8</institution-id><institution></institution><institution>Catalan Institution for Research and Advanced Studies, ICREA,</institution></institution-wrap>Passeig Lluís Companys 23, E08010 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Passeig Lluís Companys 23, E08010 Barcelona</wicri:regionArea><wicri:noRegion>E08010 Barcelona</wicri:noRegion></affiliation></author><author><name sortKey="Rasko, John E J" sort="Rasko, John E J" uniqKey="Rasko J" first="John E. J." last="Rasko">John E. J. Rasko</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050 Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown</wicri:regionArea><wicri:noRegion>Camperdown</wicri:noRegion></affiliation><affiliation><nlm:aff id="Aff7"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 834X</institution-id><institution-id institution-id-type="GRID">grid.1013.3</institution-id><institution>Sydney Medical School,</institution><institution>University of Sydney,</institution></institution-wrap>Sydney, NSW 2006 Australia</nlm:aff><wicri:noCountry code="subfield">NSW 2006 Australia</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff11"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 0385 0051</institution-id><institution-id institution-id-type="GRID">grid.413249.9</institution-id><institution></institution><institution>Cell and Molecular Therapies, Royal Prince Alfred Hospital,</institution></institution-wrap>Camperdown, 2050 Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Camperdown</wicri:regionArea></affiliation></author><author><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 0444 7512</institution-id><institution-id institution-id-type="GRID">grid.248902.5</institution-id><institution>Bioinformatics Laboratory,</institution><institution>Centenary Institute,</institution></institution-wrap>Camperdown, 2050 Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Camperdown</wicri:regionArea></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff5">CNRS, UPR 1142, Montpellier, 34094 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CNRS, UPR 1142, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff12">CNRS, UMR 5203, Montpellier, 34094 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CNRS, UMR 5203, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1474-7596</idno><idno type="eISSN">1474-760X</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alternative Splicing</term><term>Animals</term><term>Binding Sites</term><term>Cell Cycle (genetics)</term><term>Cell Differentiation (genetics)</term><term>Computational Biology (methods)</term><term>Exons</term><term>Gene Expression Regulation</term><term>Humans</term><term>Introns</term><term>Nucleotide Motifs</term><term>RNA Splicing</term><term>RNA-Binding Proteins (metabolism)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Biologie informatique ()</term><term>Cycle cellulaire (génétique)</term><term>Différenciation cellulaire (génétique)</term><term>Exons</term><term>Humains</term><term>Introns</term><term>Logiciel</term><term>Motifs nucléotidiques</term><term>Protéines de liaison à l'ARN (métabolisme)</term><term>Régulation de l'expression des gènes</term><term>Sites de fixation</term><term>Épissage alternatif</term><term>Épissage des ARN</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Cycle</term><term>Cell Differentiation</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cycle cellulaire</term><term>Différenciation cellulaire</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines de liaison à l'ARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alternative Splicing</term><term>Animals</term><term>Binding Sites</term><term>Exons</term><term>Gene Expression Regulation</term><term>Humans</term><term>Introns</term><term>Nucleotide Motifs</term><term>RNA Splicing</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Biologie informatique</term><term>Exons</term><term>Humains</term><term>Introns</term><term>Logiciel</term><term>Motifs nucléotidiques</term><term>Régulation de l'expression des gènes</term><term>Sites de fixation</term><term>Épissage alternatif</term><term>Épissage des ARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-017-1184-4) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pan, Q" uniqKey="Pan Q">Q Pan</name></author><author><name sortKey="Shai, O" uniqKey="Shai O">O Shai</name></author><author><name sortKey="Lee, Lj" uniqKey="Lee L">LJ Lee</name></author><author><name sortKey="Frey, Bj" uniqKey="Frey B">BJ Frey</name></author><author><name sortKey="Blencowe, Bj" uniqKey="Blencowe B">BJ Blencowe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Buckley, Pt" uniqKey="Buckley P">PT Buckley</name></author><author><name sortKey="Lee, Mt" uniqKey="Lee M">MT 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sortKey="Anders, S" uniqKey="Anders S">S Anders</name></author><author><name sortKey="Reyes, A" uniqKey="Reyes A">A Reyes</name></author><author><name sortKey="Huber, W" uniqKey="Huber W">W Huber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weischenfeldt, J" uniqKey="Weischenfeldt J">J Weischenfeldt</name></author><author><name sortKey="Waage, J" uniqKey="Waage J">J Waage</name></author><author><name sortKey="Tian, G" uniqKey="Tian G">G Tian</name></author><author><name sortKey="Zhao, J" uniqKey="Zhao J">J Zhao</name></author><author><name sortKey="Damgaard, I" uniqKey="Damgaard I">I Damgaard</name></author><author><name sortKey="Jakobsen, Js" uniqKey="Jakobsen J">JS Jakobsen</name></author><author><name sortKey="Kristiansen, K" uniqKey="Kristiansen K">K Kristiansen</name></author><author><name sortKey="Krogh, A" uniqKey="Krogh A">A Krogh</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Porse, Bt" uniqKey="Porse B">BT Porse</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>Espagne</li><li>France</li><li>États-Unis</li></country><region><li>Languedoc-Roussillon</li><li>Massachusetts</li><li>Occitanie (région administrative)</li></region><settlement><li>Montpellier</li></settlement></list><tree><country name="Australie"><noRegion><name sortKey="Middleton, Robert" sort="Middleton, Robert" uniqKey="Middleton R" first="Robert" last="Middleton">Robert Middleton</name></noRegion><name sortKey="Au, Amy" sort="Au, Amy" uniqKey="Au A" first="Amy" last="Au">Amy Au</name><name sortKey="Gao, Dadi" sort="Gao, Dadi" uniqKey="Gao D" first="Dadi" last="Gao">Dadi Gao</name><name sortKey="Gao, Dadi" sort="Gao, Dadi" uniqKey="Gao D" first="Dadi" last="Gao">Dadi Gao</name><name sortKey="Rasko, John E J" sort="Rasko, John E J" uniqKey="Rasko J" first="John E. J." last="Rasko">John E. J. Rasko</name><name sortKey="Rasko, John E J" sort="Rasko, John E J" uniqKey="Rasko J" first="John E. J." last="Rasko">John E. J. Rasko</name><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name><name sortKey="Wong, Justin J L" sort="Wong, Justin J L" uniqKey="Wong J" first="Justin J-L" last="Wong">Justin J-L Wong</name><name sortKey="Wong, Justin J L" sort="Wong, Justin J L" uniqKey="Wong J" first="Justin J-L" last="Wong">Justin J-L Wong</name></country><country name="États-Unis"><region name="Massachusetts"><name sortKey="Gao, Dadi" sort="Gao, Dadi" uniqKey="Gao D" first="Dadi" last="Gao">Dadi Gao</name></region><name sortKey="Gao, Dadi" sort="Gao, Dadi" uniqKey="Gao D" first="Dadi" last="Gao">Dadi Gao</name></country><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Thomas, Aubin" sort="Thomas, Aubin" uniqKey="Thomas A" first="Aubin" last="Thomas">Aubin Thomas</name></region><name sortKey="Bomane, Alexandra" sort="Bomane, Alexandra" uniqKey="Bomane A" first="Alexandra" last="Bomane">Alexandra Bomane</name><name sortKey="Cosson, Bertrand" sort="Cosson, Bertrand" uniqKey="Cosson B" first="Bertrand" last="Cosson">Bertrand Cosson</name><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name></country><country name="Espagne"><noRegion><name sortKey="Singh, Babita" sort="Singh, Babita" uniqKey="Singh B" first="Babita" last="Singh">Babita Singh</name></noRegion><name sortKey="Eyras, Eduardo" sort="Eyras, Eduardo" uniqKey="Eyras E" first="Eduardo" last="Eyras">Eduardo Eyras</name><name sortKey="Eyras, Eduardo" sort="Eyras, Eduardo" uniqKey="Eyras E" first="Eduardo" last="Eyras">Eduardo Eyras</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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