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

Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule

Research output: Contribution to journalArticle

129 Citations (Scopus)
133 Downloads (Pure)

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.
Original languageEnglish
Pages (from-to)R67
JournalGenome Biology
Volume13
Issue number8
Early online date3 Aug 2012
DOIs
Publication statusPublished - 2012

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