caa a22 4500 528783513 20190327083855.0 cr unu---uuuuu 180924e20080908xx s 000 0 eng 10.3929/ethz-b-000011224 doi 10.1371/journal.pone.0003164 doi (ETHRESEARCH)oai:www.research-collection.ethz.ch:20.500.11850/11224 Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system [Elektronische Daten] [Alessia Galgano, Michael Forrer, Lukasz Jaskiewicz, Alexander Kanitz, Mihaela Zavolan, André P. Gerber] PLoS ONE Open access ethresearch Genome-wide identification of mRNAs regulated by RNA-binding proteins is crucial to uncover post-transcriptional gene regulatory systems. The conserved PUF family RNA-binding proteins repress gene expression post-transcriptionally by binding to sequence elements in 3′-UTRs of mRNAs. Despite their well-studied implications for development and neurogenesis in metazoa, the mammalian PUF family members are only poorly characterized and mRNA targets are largely unknown. We have systematically identified the mRNAs associated with the two human PUF proteins, PUM1 and PUM2, by the recovery of endogenously formed ribonucleoprotein complexes and the analysis of associated RNAs with DNA microarrays. A largely overlapping set comprised of hundreds of mRNAs were reproducibly associated with the paralogous PUM proteins, many of them encoding functionally related proteins. A characteristic PUF-binding motif was highly enriched among PUM bound messages and validated with RNA pull-down experiments. Moreover, PUF motifs as well as surrounding sequences exhibit higher conservation in PUM bound messages as opposed to transcripts that were not found to be associated, suggesting that PUM function may be modulated by other factors that bind conserved elements. Strikingly, we found that PUF motifs are enriched around predicted miRNA binding sites and that high-confidence miRNA binding sites are significantly enriched in the 3′-UTRs of experimentally determined PUM1 and PUM2 targets, strongly suggesting an interaction of human PUM proteins with the miRNA regulatory system. Our work suggests extensive connections between the RBP and miRNA post-transcriptional regulatory systems and provides a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs. Creative Commons Attribution 3.0 Unported http://creativecommons.org/licenses/by/3.0 ethresearch Galgano Alessia joint author Forrer Michael joint author Jaskiewicz Lukasz joint author Kanitz Alexander joint author Zavolan Mihaela joint author Gerber André P. joint author PLoS ONE Lawrence : Public Library of Science (PLoS) 3 (9), p. e3164 1932-6203 http://hdl.handle.net/20.500.11850/11224 text/html WWW-Backlink auf das Repository (Open access) 1 Journal Article ethresearch ETHRESEARCH 856 40 http://hdl.handle.net/20.500.11850/11224 text/html WWW-Backlink auf das Repository (Open access) ETHRESEARCH 700 1- Galgano Alessia joint author ETHRESEARCH 700 1- Forrer Michael joint author ETHRESEARCH 700 1- Jaskiewicz Lukasz joint author ETHRESEARCH 700 1- Kanitz Alexander joint author ETHRESEARCH 700 1- Zavolan Mihaela joint author ETHRESEARCH 700 1- Gerber André P. joint author ETHRESEARCH 773 0- PLoS ONE Lawrence : Public Library of Science (PLoS) 3 (9), p. e3164 1932-6203 BK010053 XK010053 XK010000 ETHRESEARCH ETHRESEARCH ETHRESEARCH Journal Article Open access