Figure 1.

CLIP variants for studying RBP–RNA interactions (i). (A) High-throughput sequencing of RNA isolated by UV crosslinking and immunoprecipitation (HITS-CLIP) uses ultraviolet light (at the wavelength of 254 nm) to induce the formation of covalent crosslinks. The protein–RNA complexes are then immunoprecipitated using a RBP specific antibody and bound RNA measured using RNA-sequencing. (B) Individual nucleotide resolution CLIP (iCLIP) utilizes cDNA termination caused at the site of crosslinking to identify the position of RBP–RNA interaction. (C) Enhanced CLIP (eCLIP) protocol, a single adaptor is ligated at the 3′ end of the crosslinked RNA fragments, and then a second adaptor is ligated to the 3′ end of the cDNA after RT. PCR amplifies both truncated and read-through reads.