In:
RNA, Cold Spring Harbor Laboratory, Vol. 21, No. 1 ( 2015-01), p. 135-143
Abstract:
RNA–protein interactions are central to biological regulation. Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA–protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and nonhuman RNAs. Here we present FAST-iCLIP, an integrated pipeline with improved CLIP biochemistry and an automated informatic pipeline for comprehensive analysis across protein coding, noncoding, repetitive, retroviral, and nonhuman transcriptomes. FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2-bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA–protein recognition across the diversity of human and pathogen RNAs.
Type of Medium:
Online Resource
ISSN:
1355-8382
,
1469-9001
DOI:
10.1261/rna.047803.114
Language:
English
Publisher:
Cold Spring Harbor Laboratory
Publication Date:
2015
detail.hit.zdb_id:
1475737-0
SSG:
12