RNA-chromatin immunoprecipitations (RNA-ChIP) in mammalian cells (PROT28)

RNA-protein interactions play important roles within the cell. Using a variation of the widely-used chromatin immunoprecipitation (ChIP) assay, the potential association of cellular RNAs and candidate proteins can be evaluated in a process named “RNA-ChIP”. This technique has been successfully used in mammalian cells, for example to examine the relationship of noncoding RNAs with histone proteins (References 1, 2) or to examine interactions between viral RNAs and proteins in the host mammalian cell (Reference 3). In RNA-ChIP, RNA-protein interactions are fixed by reversible chemical cross-linking with formaldehyde followed by immunoprecipitation with antibodies against the candidate protein(s). RNAs that are associated with the protein are detected by reverse transcriptase-PCR (RT-PCR). The following procedure was used to examine protein-RNA interactions in mouse embryonic stem cells, but can be modified for other cell types.