Differential Repression of Alternative Transcripts: A Screen for miRNA Targets
Identifieur interne : 000195 ( France/Analysis ); précédent : 000194; suivant : 000196Differential Repression of Alternative Transcripts: A Screen for miRNA Targets
Auteurs : Matthieu Legendre [France] ; William Ritchie [France] ; Fabrice Lopez [France] ; Daniel Gautheret [France]Source :
- PLoS Computational Biology [ 1553-734X ] ; 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.
Url:
DOI: 10.1371/journal.pcbi.0020043
PubMed: 16699595
PubMed Central: 1458965
Affiliations:
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PMC:1458965Le document en format XML
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négative</term><term>Transcription génétique</term><term>microARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Expressed Sequence Tags</term><term>Humans</term><term>Mice</term><term>Organ 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"><p>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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name></author><author><name sortKey="Chen, Cz" uniqKey="Chen C">CZ Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brennecke, J" uniqKey="Brennecke J">J Brennecke</name></author><author><name sortKey="Stark, A" uniqKey="Stark A">A Stark</name></author><author><name sortKey="Russell, Rb" uniqKey="Russell R">RB Russell</name></author><author><name sortKey="Cohen, Sm" uniqKey="Cohen S">SM Cohen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lewis, Bp" uniqKey="Lewis B">BP Lewis</name></author><author><name sortKey="Burge, Cb" uniqKey="Burge C">CB Burge</name></author><author><name sortKey="Bartel, Dp" 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sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name></author><author><name sortKey="Morgenstern, B" uniqKey="Morgenstern B">B Morgenstern</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Morgenstern, B" uniqKey="Morgenstern B">B Morgenstern</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tiffin, N" uniqKey="Tiffin N">N Tiffin</name></author><author><name sortKey="Kelso, Jf" uniqKey="Kelso J">JF Kelso</name></author><author><name sortKey="Powell, Ar" uniqKey="Powell A">AR Powell</name></author><author><name sortKey="Pan, H" uniqKey="Pan H">H Pan</name></author><author><name sortKey="Bajic, Vb" uniqKey="Bajic V">VB Bajic</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hofacker, Il" uniqKey="Hofacker I">IL Hofacker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, Jd" uniqKey="Thompson J">JD Thompson</name></author><author><name sortKey="Higgins, Dg" uniqKey="Higgins D">DG Higgins</name></author><author><name sortKey="Gibson, Tj" uniqKey="Gibson T">TJ Gibson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gardner, Pp" uniqKey="Gardner P">PP Gardner</name></author><author><name sortKey="Giegerich, R" uniqKey="Giegerich R">R Giegerich</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li></country><region><li>Provence-Alpes-Côte d'Azur</li></region><settlement><li>Marseille</li></settlement><orgName><li>Université de la Méditerranée</li></orgName></list><tree><country name="France"><region name="Provence-Alpes-Côte d'Azur"><name sortKey="Legendre, Matthieu" sort="Legendre, Matthieu" uniqKey="Legendre M" first="Matthieu" last="Legendre">Matthieu Legendre</name></region><name sortKey="Gautheret, Daniel" sort="Gautheret, Daniel" uniqKey="Gautheret D" first="Daniel" last="Gautheret">Daniel Gautheret</name><name sortKey="Lopez, Fabrice" sort="Lopez, Fabrice" uniqKey="Lopez F" first="Fabrice" last="Lopez">Fabrice Lopez</name><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Differential Repression of Alternative Transcripts: A Screen for miRNA Targets
}}
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