Schematic summary of CLIP and iCLIP methods. After UV cross-linking between protein and RNA, both methods purify the protein of interest, ligate the 3' adaptor, purify the protein-RNA complex, and digest the protein by proteinase K. In CLIP, a 5' adapter is ligated to the RNA before reverse transcription. Therefore, CLIP can only amplify cDNAs that read through the cross-link site. However, since the cross-linked nucleotides are covalently bound to the amino acid residue, a proportion of cDNAs truncate at the cross-link site. In iCLIP, truncated cDNAs are captured by circularization and subsequent linearization.