Quick-irCLIP: Interrogating protein-RNA interactions using a rapid and simple cross-linking and immunoprecipitation technique

RNA-binding proteins (RBPs) are instrumental in the biochemical processing and physiological functioning of non-coding RNAs. Therefore, as interest in non-coding RNAs continues to expand, refining the techniques capable of probing protein-RNA interactions will prove ever more valuable in the characterization of these molecules. To identify the RNAs bound by a given RBP, cross-linking and immunoprecipitation (CLIP) and its iterations have been widely utilized, but these approaches can be complex, labor-intensive, and time consuming. Here, we describe a rapid and technically simple method based upon individual nucleotide resolution CLIP (iCLIP) and infrared CLIP (irCLIP). Termed quick-irCLIP, our protocol circumvents confounding steps, can be completed in less than three days, and is capable of interrogating protein-RNA interactions at single nucleotide resolution. Protocol name: Quick-irCLIP – rapid infrared adaptor based individual nucleotide resolution UV cross-linking and immunoprecipitation, Keywords: quick-irCLIP, iCLIP, irCLIP, CLIP, RNA-binding protein, RNA, Protein-RNA interaction