During post-transcriptional gene regulation (PTGR), RNA binding proteins (RBPs) interact with all classes of RNA to control RNA maturation, stability, transport, and translation. Here, we describe Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), a transcriptome-scale method for identifying RBP binding sites on target RNAs with nucleotide-level resolution. This method is readily applicable to any protein directly contacting RNA, including RBPs that are predicted to bind in a sequence- or structure-dependent manner at discrete RNA recognition elements (RREs), and those that are thought to bind transiently, such as RNA polymerases or helicases.
Keywords: Binding site; Cross-linking and immunoprecipitation (CLIP); Noncoding RNA; Photoactivatable ribonucleoside enhanced cross-linking and immunoprecipitation (PAR-CLIP); Posttranscriptional gene regulation (PTGR); RNA; RNA recognition element (RRE); RNA-binding protein (RBP); mRNA.