Chapter 15. Co-immunoprecipitation techniques for assessing RNA-protein interactions in vivo

From the moment a nascent transcript emerges from an RNA polymerase until its ultimate destruction, an RNA is bound by proteins that govern its fate. Thus, in order to understand posttranscriptional regulation of gene expression, it is essential to ascertain which proteins bind a given RNA in vivo. This chapter describes three immunoprecipitation-based assays designed to query the in vivo makeup of RNA-protein complexes. Two of these, UV cross-linking and RNA immunoprecipitation (RIP), include cross-linking steps that trap complexes formed in vivo. A third, a cell mixing experiment, verifies that an interaction occurs in vivo by controlling for RNA-protein association subsequent to cell lysis. Using these protocols, this chapter presents evidence that the abundant nuclear RNA-binding protein hnRNP C interacts with the Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA in vivo.