期刊
GENOME BIOLOGY
卷 13, 期 8, 页码 -出版社
BMC
DOI: 10.1186/gb-2012-13-8-r67
关键词
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资金
- European Research Council [206726-CLIP]
- Slovenian Research Agency [P2-0209, Z7-3665]
- Medical Research Council [U105185858]
- Human Frontiers Science Program Postdoctoral Fellowship
- Nakajima Foundation
- MRC [G0800784, MC_U105185858, G0801904] Funding Source: UKRI
- Medical Research Council [G0801904, G0800784B, MC_U105185858, G0800784] Funding Source: researchfish
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.
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