Bioinformatic and experimental characterization of the RBM15 RNA binding protein

The RNA binding motif 15 protein (RBM15) binds both RNA and proteins to regulate a wide repertoire of processes in the cell, including the positing of N6 methyladenosine marks on RNA, the silencing of genes on the inactive X-chromosome, and even hematopoiesis. Although its C-terminal SPOC domain has been found to facilitate protein-protein interactions, the structural mechanism that underlies how its three N-terminal RNA recognition motifs (RRMs) interact with RNA remains to be elucidated. In this crowdsourced study, we bioinformatically assessed publicly available, genome-wide RNA 2D structural probing and RNA binding protein (RBP) cross-linking and immunoprecipitation (CLIP) data to identify RNAs that bind with RBM15. Binding assays reveal that the RRMs work in concert to bind stem-loop structured RNA motifs with nanomolar binding affinity. Structural modeling and nuclear magnetic resonance (NMR) spectroscopy analysis suggest that RRMs 2 and 3 are coaxially stacked to form a heterodimer; they create a sandwich-like motif around structured RNA. Altogether, this work provides insight into the structural mechanism by which RBM15 interacts with RNAs to govern biological function.