HyPR-MS for Multiplexed Discovery of MALAT1, NEAT1, and NORAD lncRNA Protein Interactomes

RNA–protein
interactions are integral to the regulation
of gene expression. RNAs have diverse functions and the protein interactomes
of individual RNAs vary temporally, spatially, and with physiological
context. These factors make the global acquisition of individual RNA–protein
interactomes an essential endeavor. Although techniques have been
reported for discovery of the protein interactomes of specific RNAs
they are largely laborious, costly, and accomplished singly in individual
experiments. We developed HyPR-MS for the discovery and analysis of
the protein interactomes of multiple RNAs in a single experiment while
also reducing design time and improving efficiencies. Presented here
is the application of HyPR-MS to simultaneously and selectively isolate
the interactomes of lncRNAs MALAT1, NEAT1, and NORAD. Our analysis
features the proteins that potentially contribute to both known and
previously undiscovered roles of each lncRNA. This platform provides
a powerful new multiplexing tool for the efficient and cost-effective
elucidation of specific RNA–protein interactomes.