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Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Yoichiro Sugimoto1, Julian König1, Shobbir Hussain2, Blaž Zupan3, Tomaž Curk3, Michaela Frye2 and Jernej Ule1*

Author Affiliations

1 MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK

2 The Wellcome Trust Centre for Stem Cell Research, Tennis Court Road, Cambridge CB2 1QR, UK

3 Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia

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Genome Biology 2012, 13:R67  doi:10.1186/gb-2012-13-8-r67

Published: 3 August 2012

Abstract

UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.