Differential repression of alternative transcripts: a screen for miRNA targets.
Identifieur interne : 002139 ( PubMed/Checkpoint ); précédent : 002138; suivant : 002140Differential repression of alternative transcripts: a screen for miRNA targets.
Auteurs : Matthieu Legendre [France] ; William Ritchie ; Fabrice Lopez ; Daniel GautheretSource :
- PLoS computational biology [ 1553-7358 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : MicroRNAs, Protein Isoforms, RNA, Messenger.
- genetics : Down-Regulation, Transcription, Genetic.
- Animals, Base Sequence, Expressed Sequence Tags, Humans, Mice, Organ Specificity.
Abstract
Alternative polyadenylation sites produce transcript isoforms with 3' untranslated regions (UTRs) of different lengths. If a microRNA (miRNA) target is present in the UTR, then only those target-containing isoforms should be sensitive to control by a cognate miRNA. We carried out a systematic examination of 3' UTRs containing multiple poly(A) sites and putative miRNA targets. Based on expressed sequence tag (EST) counts and EST library information, we observed that levels of isoforms containing targets for miR-1 or miR-124, two miRNAs causing downregulation of transcript levels, were reduced in tissues expressing the corresponding miRNA. This analysis was repeated for all conserved 7-mers in 3' UTRs, resulting in a selection of 312 motifs. We show that this set is significantly enriched in known miRNA targets and mRNA-destabilizing elements, which validates our initial hypothesis. We scanned the human genome for possible cognate miRNAs and identified phylogenetically conserved precursors matching our motifs. This analysis can help identify target-miRNA couples that went undetected in previous screens, but it may also reveal targets for other types of regulatory factors.
DOI: 10.1371/journal.pcbi.0020043
PubMed: 16699595
Affiliations:
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Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Humains</term><term>Souris</term><term>Spécificité d'organe</term><term>Séquence nucléotidique</term><term>Étiquettes de séquences exprimées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Alternative polyadenylation sites produce transcript isoforms with 3' untranslated regions (UTRs) of different lengths. If a microRNA (miRNA) target is present in the UTR, then only those target-containing isoforms should be sensitive to control by a cognate miRNA. We carried out a systematic examination of 3' UTRs containing multiple poly(A) sites and putative miRNA targets. Based on expressed sequence tag (EST) counts and EST library information, we observed that levels of isoforms containing targets for miR-1 or miR-124, two miRNAs causing downregulation of transcript levels, were reduced in tissues expressing the corresponding miRNA. This analysis was repeated for all conserved 7-mers in 3' UTRs, resulting in a selection of 312 motifs. We show that this set is significantly enriched in known miRNA targets and mRNA-destabilizing elements, which validates our initial hypothesis. We scanned the human genome for possible cognate miRNAs and identified phylogenetically conserved precursors matching our motifs. This analysis can help identify target-miRNA couples that went undetected in previous screens, but it may also reveal targets for other types of regulatory factors.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16699595</PMID><DateCompleted><Year>2007</Year><Month>05</Month><Day>21</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1553-7358</ISSN><JournalIssue CitedMedium="Internet"><Volume>2</Volume><Issue>5</Issue><PubDate><Year>2006</Year><Month>May</Month></PubDate></JournalIssue><Title>PLoS computational biology</Title><ISOAbbreviation>PLoS Comput. Biol.</ISOAbbreviation></Journal><ArticleTitle>Differential repression of alternative transcripts: a screen for miRNA targets.</ArticleTitle><Pagination><MedlinePgn>e43</MedlinePgn></Pagination><Abstract><AbstractText>Alternative polyadenylation sites produce transcript isoforms with 3' untranslated regions (UTRs) of different lengths. If a microRNA (miRNA) target is present in the UTR, then only those target-containing isoforms should be sensitive to control by a cognate miRNA. We carried out a systematic examination of 3' UTRs containing multiple poly(A) sites and putative miRNA targets. Based on expressed sequence tag (EST) counts and EST library information, we observed that levels of isoforms containing targets for miR-1 or miR-124, two miRNAs causing downregulation of transcript levels, were reduced in tissues expressing the corresponding miRNA. This analysis was repeated for all conserved 7-mers in 3' UTRs, resulting in a selection of 312 motifs. We show that this set is significantly enriched in known miRNA targets and mRNA-destabilizing elements, which validates our initial hypothesis. We scanned the human genome for possible cognate miRNAs and identified phylogenetically conserved precursors matching our motifs. This analysis can help identify target-miRNA couples that went undetected in previous screens, but it may also reveal targets for other types of regulatory factors.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Legendre</LastName><ForeName>Matthieu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>INSERM ERM 206, Université de la Méditerranée, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ritchie</LastName><ForeName>William</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Lopez</LastName><ForeName>Fabrice</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Gautheret</LastName><ForeName>Daniel</ForeName><Initials>D</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. 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IdType="pubmed">12624257</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2003 Jun;13(6B):1273-89</Citation><ArticleIdList><ArticleId IdType="pubmed">12819125</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2003 Jul 1;31(13):3429-31</Citation><ArticleIdList><ArticleId IdType="pubmed">12824340</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2003;4(7):R42</Citation><ArticleIdList><ArticleId IdType="pubmed">12844358</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2003 Jul 18;301(5631):336-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12869753</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11</Citation><ArticleIdList><ArticleId IdType="pubmed">14681370</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2004;5(3):R13</Citation><ArticleIdList><ArticleId IdType="pubmed">15003116</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2004 May;14(5):925-8</Citation><ArticleIdList><ArticleId IdType="pubmed">15078858</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2003 Dec 23;4:66</Citation><ArticleIdList><ArticleId IdType="pubmed">14693042</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2004 May;5(5):396-400</Citation><ArticleIdList><ArticleId IdType="pubmed">15143321</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Biol. 2004 Jun;2(6):e162</Citation><ArticleIdList><ArticleId IdType="pubmed">15103394</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W20-5</Citation><ArticleIdList><ArticleId IdType="pubmed">15215342</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W33-6</Citation><ArticleIdList><ArticleId IdType="pubmed">15215344</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1993 May 25;21(10):2315-22</Citation><ArticleIdList><ArticleId IdType="pubmed">8506129</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1994 Nov 11;22(22):4673-80</Citation><ArticleIdList><ArticleId IdType="pubmed">7984417</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 1998 May;8(5):524-30</Citation><ArticleIdList><ArticleId IdType="pubmed">9582195</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2004 Sep 30;5:140</Citation><ArticleIdList><ArticleId IdType="pubmed">15458580</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Biol. 2004 Nov;2(11):e363</Citation><ArticleIdList><ArticleId IdType="pubmed">15502875</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2005;33(1):201-12</Citation><ArticleIdList><ArticleId IdType="pubmed">15647503</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2005 Jan 14;120(1):15-20</Citation><ArticleIdList><ArticleId IdType="pubmed">15652477</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2005 Jan 14;120(1):21-4</Citation><ArticleIdList><ArticleId IdType="pubmed">15652478</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9</Citation><ArticleIdList><ArticleId IdType="pubmed">15665081</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2005 Feb 17;433(7027):769-73</Citation><ArticleIdList><ArticleId IdType="pubmed">15685193</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2005 Mar 11;120(5):623-34</Citation><ArticleIdList><ArticleId IdType="pubmed">15766526</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2005;33(5):1544-52</Citation><ArticleIdList><ArticleId IdType="pubmed">15767279</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2005 Mar 17;434(7031):338-45</Citation><ArticleIdList><ArticleId IdType="pubmed">15735639</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Biol. 2005 Mar;3(3):e85</Citation><ArticleIdList><ArticleId IdType="pubmed">15723116</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2005 Jul;37(7):766-70</Citation><ArticleIdList><ArticleId IdType="pubmed">15965474</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2005 Aug 26;122(4):553-63</Citation><ArticleIdList><ArticleId IdType="pubmed">16122423</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2005;6(12):R100</Citation><ArticleIdList><ArticleId IdType="pubmed">16356263</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Genet. 2002 Mar;18(3):150-7</Citation><ArticleIdList><ArticleId 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