Using Native RIP, UV-CLIP or fCLIP to Address Protein-RNA Interactions In Vivo

Stable and transient interactions between molecules are determinant for cell function. Among those, numerous proteins contact coding and noncoding RNAs to modulate their fate and promote their activity. The identification of such interactions as well as the cellular and molecular conditions of these interactions represent key information for the characterization of the role of each partner. RNA immunoprecipitation (RIP) is the leading technique to detect in vivo the association of individual proteins with RNA species. Two main approaches exist: native RIP is largely used to identify and quantify RNA interactions, while crosslinked RIP (CLIP) may inform about direct interactions as well as their extent in the unaltered cellular condition, i.e., before cell lysis. In this chapter, both techniques applied to mammalian cells are described with a series of precautions regarding their design.