Characterization of RBM15 protein binding with long noncoding RNAs

Abstract

The RNA binding motif 15 protein (RBM15) plays a critical role in post-transcriptional regulation. Its role in facilitating m6A modification, specifically through guiding the writer complex (WTAP METTL13 METTL14) to DRACH sequence motifs, has been demonstrated for several RNAs, including long noncoding RNAs (lncRNAs). The structural mechanism that underlies how RBM15 interacts with RNA has yet to be elucidated. In this study, we mined and bioinformatically assessed publicly available genome wide RNA 2D structural probing and RBP cross linking and immunoprecipitation data to investigate the propensity of lncRNAs to interact with RBM15. We then experimentally characterized how this interaction occurs with two lncRNAs, FIRRE and XIST. RBM15, which possesses three RNA recognition motifs (RRMs), primarily interacts with stem loop structures adopted by lncRNAs through its two terminal RRMs, RRMs 2 and 3. Using solution NMR, we find RRMs 2 and 3 are rigidly confined in solution, in the absence of RNA. Altogether, this work provides clarity on the molecular mechanism by which RBM15 interacts with RNAs to govern biological function.