An encyclopedic regulatory and functional atlas of RNA interactomes.

RNA molecules interact extensively with each other and with RNA-binding proteins (RBPs) to regulate gene expression. To improve detection of RBP-RNA and RNA-RNA interactions, we developed the rbsSeeker and rriScan tools and integrated the interactions into the Encyclopedia of RNA Interactomes (ENCORI), providing web-based modules to explore RNA interactions. Using this resource, we identified and validated novel N6-methyladenosine (m6A)-associated proteins, an orphan small nucleolar RNA guiding rRNA pseudouridines and target-directed microRNA degradation events, establishing ENCORI as a framework for studying RNA interactomes.