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| Item Type: | Article |
|---|---|
| Title: | Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions |
| Creators Name: | Sugimoto, Y. and König, J. and Hussain, S. and Zupan, B. and Curk, T. and Frye, M. and Ule, J. |
| 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. |
| Keywords: | Sequence Bias, False Discovery Rate Threshold, Deletion Site, cDNA Truncation, Nova Protein, Animals, Mice |
| Source: | Genome Biology |
| ISSN: | 1474-760X |
| Publisher: | BioMed Central |
| Volume: | 13 |
| Number: | 8 |
| Page Range: | R67 |
| Date: | 3 August 2012 |
| Official Publication: | https://doi.org/10.1186/gb-2012-13-8-r67 |
| PubMed: | View item in PubMed |
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