A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (mRNA-seq)

ABSTRACT: Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365 nm UV light. We found small differences in the accuracy of these methods in identifying binding sites of HuR, a protein that binds low-complexity sequences and Argonaute 2, which has a complex binding specificity. We show that crosslink-induced mutations lead to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect sufficiently their sites under the denaturing conditions used during t

ORGANISM(S): Homo sapiens

SUBMITTER: Jean Hausser 

PROVIDER: E-GEOD-28864 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress