Journal
JOURNAL OF PROTEOME RESEARCH
Volume 17, Issue 9, Pages 3022-3038Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.8b00189
Keywords
IncRNA; RNA-binding proteins; mass spectrometry; proteomics; hybridization capture; interactomes; RNA
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Funding
- NIH-NCI grant [R01CA193481]
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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, NEAT 1, and NORAD. Our analysis features the proteins that potentially contribute to both known and previously undiscovered roles of each IncRNA. This platform provides a powerful new multiplexing tool for the efficient and cost-effective elucidation of specific RNA-protein interactomes.
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