High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) is a variant of CLIP[1] for genome-wide mapping protein–RNA binding sites or RNA modification sites in vivo.
[2][3][4] HITS-CLIP was originally used to generate genome-wide protein-RNA interaction maps for the neuron-specific RNA-binding protein and splicing factor NOVA1 and NOVA2;[3] since then a number of other splicing factor maps have been generated, including those for PTB,[5] RbFox2,[6] SFRS1,[7] hnRNP C,[8] and even N6-Methyladenosine (m6A) mRNA modifications.
[4][9] HITS-CLIP of the RNA-binding protein Argonaute has been performed for the identification of microRNA targets[10] by decoding microRNA-mRNA and protein-RNA interaction maps in mouse brain,[11][12] and subsequently in Caenorhabditis elegans,[13] embryonic stem cells[14] and tissue culture cells.
[15] As a novel modification of HITS-CLIP, m6A-CLIP was developed to precisely map N6-Methyladenosine(m6A) locations in mRNA by UV-crosslinking m6A antibody to the target RNA.
[4][9] Recently, improved bioinformatics applied to Argonaute HITS-CLIP enables identification of binding sites with single nucleotide resolution.