Isolation of the RNA Cross-Linking Immunoprecipitation (CLIP) Tags, 5'-Linker Ligation, Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Amplification, and Sequencing

Immunoprecipitation and SDS-PAGE for Cross-Linking Immunoprecipitation (CLIP)

This first part of this protocol is designed to optimize purification of the RNABP by immunoprecipitation for cross-linking immunoprecipitation (CLIP) experiments. The key variables to assess are the quality and quantity of antibody needed to immunoprecipitate most but not quite all of the RNABP (the titration will decrease nonspecific binding), and the tolerance of the antibody:antigen interaction to stringent wash conditions. The results of these experiments can be checked first by western blot, and subsequently using the pilot CLIP protocol described in the second half of this protocol. RNase-treated cross-linked RNABP:RNA complexes from mixed lysates or cell pellets are immunoprecipitated using conditions optimized in the first half of the protocol. 3' Linkers are added, the RNA is radiolabeled, and the complexes are purified on SDS-PAGE. The pilot experiment will identify the optimal RNase concentration for the particular sample and will assess the quality and purity of the RNABP-RNA complexes following labeling of the RNA tags with ³²P. This can be done without ligation of the 3' linker as described in the main protocol below. The pilot experiment assesses whether sufficient RNA-protein complexes can be detected by autoradiography and whether contaminating RNA ligands are present in immunoprecipitations compared with control samples. Once it is confirmed that the signal-to-noise ratio for detection of RNA-protein complexes after immunoprecipitation is sufficient, the optimal immunoprecipitation conditions should be incorporated into the general CLIP protocol including the steps of cross-linking, RNase digestion, linker ligation, and labeling of RNA "tags," and the results analyzed by autoradiography.

Mapping of In Vivo RNA-Binding Sites by Ultraviolet (UV)-Cross-Linking Immunoprecipitation (CLIP)

RNA "CLIP" (cross-linking immunoprecipitation), the method by which RNA-protein complexes are covalently cross-linked and purified and the RNA sequenced, has attracted attention as a powerful means of developing genome-wide maps of direct, functional RNA-protein interaction sites. These maps have been used to identify points of regulation, and they hold promise for understanding the dynamics of RNA regulation in normal cell function and its dysregulation in disease.

3'-Linker Ligation and Size Selection by SDS-PAGE for Cross-Linking Immunoprecipitation (CLIP)

This protocol describes the purification by denaturing polyacrylamide gel electrophoresis of RNA linkers for cross-linking immunoprecipitation (CLIP). Purification is necessary because if the 3' linker loses the puromycin blocking group, concatemerization of the 3' linker will occur during the 3' linker ligation reaction. In addition, truncated linkers make bioinformatic processing of the sequencing results more difficult than it need be. Additionally, this protocol describes the treatment of coimmunoprecipitated RNA tags for CLIP with alkaline phosphatase to remove the 3' phosphate remaining after RNase digestion. Dephosphorylation prevents intramolecular circularization of RNA during subsequent ligation to the linker. The purified RNA linker, blocked with puromycin at its 3' end to prevent linker-linker multimerization, is then ligated to the 3' end of the RNA tag. Removal of free linker is accomplished by performing the ligation while the RNABP:RNA complex is associated, via antibody, to protein A Dynabeads, allowing thorough washing and linker removal. Additional purification is achieved by SDS-PAGE and transfer of the size-selected RNABP:RNA complexes to nitrocellulose.