Differential repression of alternative transcripts: a screen for miRNA targets.

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 e...

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Autores principales:	Matthieu Legendre, William Ritchie, Fabrice Lopez, Daniel Gautheret
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2006
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/ace1bf72b577430f96dc2fb321c2f332
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spelling	oai:doaj.org-article:ace1bf72b577430f96dc2fb321c2f3322021-11-25T05:41:06ZDifferential repression of alternative transcripts: a screen for miRNA targets.1553-734X1553-735810.1371/journal.pcbi.0020043https://doaj.org/article/ace1bf72b577430f96dc2fb321c2f3322006-05-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.0020043https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Alternative 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.Matthieu LegendreWilliam RitchieFabrice LopezDaniel GautheretPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 2, Iss 5, p e43 (2006)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Matthieu Legendre William Ritchie Fabrice Lopez Daniel Gautheret Differential repression of alternative transcripts: a screen for miRNA targets.
description	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.
format	article
author	Matthieu Legendre William Ritchie Fabrice Lopez Daniel Gautheret
author_facet	Matthieu Legendre William Ritchie Fabrice Lopez Daniel Gautheret
author_sort	Matthieu Legendre
title	Differential repression of alternative transcripts: a screen for miRNA targets.
title_short	Differential repression of alternative transcripts: a screen for miRNA targets.
title_full	Differential repression of alternative transcripts: a screen for miRNA targets.
title_fullStr	Differential repression of alternative transcripts: a screen for miRNA targets.
title_full_unstemmed	Differential repression of alternative transcripts: a screen for miRNA targets.
title_sort	differential repression of alternative transcripts: a screen for mirna targets.
publisher	Public Library of Science (PLoS)
publishDate	2006
url	https://doaj.org/article/ace1bf72b577430f96dc2fb321c2f332
work_keys_str_mv	AT matthieulegendre differentialrepressionofalternativetranscriptsascreenformirnatargets AT williamritchie differentialrepressionofalternativetranscriptsascreenformirnatargets AT fabricelopez differentialrepressionofalternativetranscriptsascreenformirnatargets AT danielgautheret differentialrepressionofalternativetranscriptsascreenformirnatargets
_version_	1718414536052047872

Differential repression of alternative transcripts: a screen for miRNA targets.

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