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

• Published in: Journal of proteome research 2018-09, Vol.17 (9), p.3022-3038
• Main Authors: Spiniello, Michele, Knoener, Rachel A, Steinbrink, Maisie I, Yang, Bing, Cesnik, Anthony J, Buxton, Katherine E, Scalf, Mark, Jarrard, David F, Smith, Lloyd M
• Format: Article
• Language: English
• Subjects: Base Sequence; Cell Line, Tumor; Gene Expression Regulation; Gene Ontology; Humans; Mass Spectrometry - methods; Molecular Sequence Annotation; Protein Binding; Proteomics - methods; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA-Binding Proteins - classification; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/acs.jproteome.8b00189

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.