Cross-Linking Immunoprecipitation (CLIP)-seq

Excerpts from "RNA Immunoprecipitation (RIP) & Cross-Linking Immunoprecipitation (CLIP)"

"Unlike DNA-protein crosslinking which is done with formaldehyde, CLIP uses ultraviolet (UV) light. Unlike formaldehyde, UV crosslinking is irreversible. UV crosslinks are also more specific and only link proteins to RNAs that are in very close proximity. Further, UV crosslinks do not form between two proteins (Brimacombe et al., 1988). For these reasons, UV has become the standard in RNA research. The RNA-RBP complexes are then immunoprecipitated. Due to the irreversibility of the crosslinks, the next step is digestion with a proteinase."