Elucidating the RNA–Protein Interactomes of Target RNAs in Tissue

RNA–protein interactions are key to many aspects
of cellular
homeostasis and their identification is important to understanding
cellular function. Multiple strategies have been developed for the
RNA-centric characterization of RNA–protein complexes. However,
these studies have all been done in immortalized cell lines that do
not capture the complexity of heterogeneous tissue samples. Here,
we develop hybridization purification of RNA–protein complexes
followed by mass spectrometry (HyPR-MS) for use in tissue samples.
We isolated both polyadenylated RNA and the specific long noncoding
RNA MALAT1 and characterized their protein interactomes. These results
demonstrate the feasibility of HyPR-MS in tissue for the multiplexed
characterization of specific RNA–protein complexes.