A framework for the exploration of multifaceted subcellular RNA-binding proteins (IP-MS)

The ability of RNA binding proteins (RBPs) to form complexes with other biomolecules underpins a very broad range of functions and remarkable structural properties. Understanding the precise spatiotemporal dynamics of RBPs and their interacting partners in the steady state and upon perturbation is key to deciphering these aspects. Here, we present the coRIC (compartmentalized RNA Interactome Capture) map, an experimental resource and analytical framework to study the subcellular dynamics of RBPs through multimodal dataset integration and machine learning. Using this approach, we have generated an atlas comprising 1,768 RBPs distributed in a broad panel of subcellular compartments and delineated their intermolecular and intercompartmental relationships. We have also defined the hierarchy of RBP-containing complexes across the cell, uncovering previously unknown functions of multiple RBPs. Furthermore, we have investigated the changes in RBP complex composition and subcellular distribution in response to DNA damage stress and exposure to C9ORF72 amyotrophic lateral sclerosis/frontotemporal dementia dipeptide repeats. The coRIC map provides a valuable new approach for defining the roles of RBPs in homeostasis and disease.