Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Genome Biol. 2012 Aug 3;13(8):R67. doi: 10.1186/gb-2012-13-8-r67.


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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens, Neoplasm / chemistry*
  • COS Cells
  • Chlorocebus aethiops
  • Gene Library
  • HeLa Cells
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Immunoprecipitation / methods*
  • Methyltransferases / chemistry
  • Mice
  • Molecular Sequence Annotation
  • Nerve Tissue Proteins / chemistry*
  • RNA / chemistry*
  • RNA-Binding Proteins / chemistry*
  • Sequence Analysis, DNA
  • Sequence Deletion


  • Antigens, Neoplasm
  • Nerve Tissue Proteins
  • Nova antigen
  • RNA-Binding Proteins
  • RNA
  • Methyltransferases
  • NSUN2 protein, human