Dissecting noncoding and pathogen RNA-protein interactomes

RNA. 2015 Jan;21(1):135-43. doi: 10.1261/rna.047803.114. Epub 2014 Nov 19.


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.

Keywords: RNA–protein interactions; genomics; noncoding RNA; virology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Cell Line, Tumor
  • Consensus Sequence
  • Gene Expression Profiling*
  • Hepacivirus / physiology
  • Host-Pathogen Interactions
  • Humans
  • Immunoprecipitation
  • Protein Binding
  • RNA, Messenger / metabolism
  • RNA, Untranslated / metabolism*
  • RNA, Viral / metabolism
  • RNA-Binding Proteins / metabolism*
  • Transcriptome


  • RNA, Messenger
  • RNA, Untranslated
  • RNA, Viral
  • RNA-Binding Proteins