Large-scale map of RNA-binding protein interactomes across the mRNA life cycle

mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While efforts have assigned RBPs to RNA substrates, less exploration has leveraged protein-protein interactions (PPIs) to study proteins in mRNA life-cycle stages. We generated an RNA-aware, RBP-centric PPI map across the mRNA life cycle in human cells by immunopurification-mass spectrometry (IP-MS) of ∼100 endogenous RBPs with and without RNase, augmented by size exclusion chromatography-mass spectrometry (SEC-MS). We identify 8,742 known and 20,802 unreported interactions between 1,125 proteins and determine that 73% of the IP-MS-identified interactions are RNA regulated. Our interactome links many proteins, some with unknown functions, to specific mRNA life-cycle stages, with nearly half associated with multiple stages. We demonstrate the value of this resource by characterizing the splicing and export functions of enhancer of rudimentary homolog (ERH), and by showing that small nuclear ribonucleoprotein U5 subunit 200 (SNRNP200) interacts with stress granule proteins and binds cytoplasmic RNA differently during stress. [Display omitted] •RBP-centric RNA-aware PPI network of the mRNA life cycle in human cells•Life-cycle stages assigned to network proteins, with ∼50% linked to multiple stages•Highly connected ERH affects nuclear speckle organization and mRNA export•SNRNP200 interacts with stress granules and has distinct cytoplasmic RNA occupancy Street, Rothamel, Brannan, et al. generate an RNA-aware RBP protein-protein interactome across the mRNA life cycle in human cells, leading to the discovery of previously unknown RBP interactions and functions. Investigation into the functions of the two most-connected proteins, ERH and SNRNP200, reveals the utility of the network for multifunctional RBP discovery.