PROTEIN CLIP: Sites on RNA that interact with an RNA binding protein (RBP) can be identified in complexes fished out of cells using immunoprecipitation, an approach called CLIP. In one variation on this technique, known as PAR-CLIP, cells are incubated with a light-reactive nucleoside analog, 4-thiouridine?(U), that becomes incorporated into RNA. Irradiation with UV light crosslinks RNA-protein complexes, which are then isolated from cell lysates using antibodies. RNA located outside the protein binding pocket is degraded, and the remaining sequence is transcribed to DNA, a process that leads to a characteristic T to C mutation wherever the nucleoside analog incorporates. BRIEFINGS IN FUNCTIONAL GENOMICS, DOI: 10.1093/bfgp/elu020, 2014
RNAs are molecules with a wide-ranging repertory, acting in roles that frequently defy dogma and resist being neatly classified into well-defined categories. Once thought of as simply passive intermediates involved in the translation of genes into proteins, RNAs are now known to exist in myriad forms that perform a variety of important biological functions. They can regulate gene expression or catalyze biochemical reactions, jobs once thought to be carried out only by proteins. The job description of some RNAs can also include defending genomes against foreign nucleic acids and controlling genome organization and stability.
However, one thing that all RNAs are believed to do is function through interactions with proteins. Figuring out the details of these interactions, such as when and where they take place, ...
