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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

Item Type:Article
Title:Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
Creators Name:Hafner, M. and Landthaler, M. and Burger, L. and Khorshid, M. and Hausser, J. and Berninger, P. and Rothballer, A. and Ascano, M. and Jungkamp, A.C. and Munschauer, M. and Ulrich, A. and Wardle, G.S. and Dewell, S. and Zavolan, M. and Tuschl, T.
Abstract:RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
Keywords:Base Sequence, Cross-Linking Reagents, Genetic Techniques, MicroRNAs, Molecular Sequence Data, Nucleosides, Point Mutation, Untranslated RNA, RNA-Binding Proteins, Ribonucleic Acid Regulatory Sequences, Sequence Alignment
Source:Cell
ISSN:0092-8674
Publisher:Cell Press (U.S.A.)
Volume:141
Number:1
Page Range:129-141
Date:2 April 2010
Official Publication:https://doi.org/10.1016/j.cell.2010.03.009
PubMed:View item in PubMed

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