Large-scale map of RNA binding protein interactomes across the mRNA life-cycle (Street, Rothamel, and Brannan et al., 2024)

mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While substantial effort has 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 by immunopurification-mass spectrometry of ~100 endogenous RBPs in the presence or absence of RNase, augmented by size exclusion chromatography-mass spectrometry. We identify 8,742 known and 20,802 novel interactions between 1125 proteins and determine that 73% of IP interactions are RNA-regulated. Our interactome links proteins, many of unknown function, with distinct life-cycle stages, linking nearly half the proteins to multiple stages. We demonstrate the value of this resource by assigning novel functions to the two most connected proteins. We show that ERH functions in multiple stages, including splicing and export, and that splicing protein SNRNP200 interacts with stress granule proteins and binds cytoplasmic RNA differently during stress