hits-clip hits-clip high-throughput sequencing of rna isolated by crosslinking immunoprecipitation (hits-clip) is a variant of clip for genome-wide mapping protein–rna binding sites or rna modification sites in vivo. 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; since then a number of other splicing factor maps have been generated, including those for ptb, rbfox2, sfrs1, hnrnp c, and even n6-methyladenosine (m6a) mrna modifications. hits-clip of the rna-binding protein argonaute has been performed for the identification of microrna targets by decoding microrna-mrna and protein-rna interaction maps in mouse brain, and subsequently in caenorhabditis elegans, embryonic stem cells and tissue culture cells. 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. recently, improved bioinformatics applied to argonaute hits-clip enables identification of binding sites with single nucleotide resolution. similar methods par-clip, for identifying the binding sites of cellular rna-binding proteins (rbps) and microrna-containing ribonucleoprotein complexes (mirnps) in tissue culture cells. iclip, for a thorough amplification of the cdna library, including truncated cdnas, thus also enabling an additional means to identify crosslink sites.