rec-Y2H matrix screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins

Abstract

RNA-binding proteins (RBPs) are crucial factors of post-transcriptional gene regulation and their modes of action are intensely investigated. At the center of attention are RNA motifs that guide where RBPs bind. However, sequence motifs are often poor predictors of RBP-RNA interactions in vivo. It is hence believed that many RBPs recognize RNAs as complexes, to increase specificity and regulatory potential. To probe the potential for complex formation among RBPs, we assembled a library of 978 mammalian RBPs and used rec-Y2H screening to detect direct interactions between RBPs, sampling >1M possible interactions. We discovered 1994 new interactions and demonstrate that our screening detects interactions between RBPs that bind RNA in proximity. We further find that the mRNA binding region preferences of an RBP can deviate, depending on its adjacently binding interaction partner. Finally, we reveal novel RBP interaction networks among major RNA processing steps and show that RBP mutations observed in cancer rewire spliceosomal interaction networks.

Mammalian Neuronal mRNA Transport Complexes: The Few Knowns and the Many Unknowns

“…Discovering essential building blocks of the neuronal mRNA transport machinery: while pulldown studies have provided a valuable pool of proteins that are involved in mRNA transport, they might fail to capture important transient interactions and do not report direct interactions. As a complementary technique, high-throughput (HT) screening for direct interactions with proper orthogonal validations could add valuable information to understand how mRNAs, mRNA-motor adaptors, and motor proteins directly interact (Yang et al, 2018 ; Garriga-Canut et al, 2019 ; Lang et al, 2020 ). HT screening can also help to narrow down essential linkers by interaction network analysis and function as a hypothesis-generator for subsequent mechanistic studies.…”

“…We further focus on low-throughput biochemical evidence and regard only those mRNA targets for which the binding site for the motor-coupling RBP is known. Finally, we argue that novel screening approaches detecting direct interactions between RBPs and motor proteins (Yang et al, 2018;Lang et al, 2020), advanced in vitro livebiochemistry assays (Heym et al, 2013;Sladewski et al, 2013;McClintock et al, 2018;Baumann et al, 2020), and fast perturbations in cells (Nishimura et al, 2009;van Bergeijk et al, 2015;Yesbolatova et al, 2020) offer a great potential to not only reveal the essential building blocks of the mammalian mRNA transport machinery, but also to discover their functionality.…”