Exploring functional complexes and disease networks within human RNA-binding protein interactomes

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PROJECT SUMMARY RNA binding proteins (RBPs) bind to both coding and non-coding RNA to influence every step of the RNA life- cycle, including pre-mRNA processing, RNA localization, and control of translation and degradation. More and more evidence reveals that disruption of RNA metabolism is a hallmark of many human neurodegenerative diseases including Amyotrophic Lateral Sclerosis. Understanding how RBPs act in coordinated networks to regulate RNA fate is key to uncovering the molecular mechanisms underlying these disease pathologies. A complete catalogue of human RBPs is elusive due to the emergence of new classes of RBPs that interact with unpolyadenylated pre-mRNAs or non-canonical RBPs that lack characterized RNA-binding domains, and thus evade traditional RNA-interactome capture studies. We developed a computational RBP classifier based on the observation that protein-protein interaction networks that depend on co-binding of RNA molecules can be used to discover new classes of RBPs. This proposal seeks to utilize predictions from this classifier to accomplish 3 main goals. 1. Phase 1: Determine the biological function of RNA-binding by the disease-associated non-canonical nucleocytoplasmic transport related candidate RBP RANGAP1. 2. Phase 2: Determine the biological function of RNA-binding for an expanded group of disease- associated non-canonical nucleocytoplasmic transport related candidate RBPs. 3. Phase 2: Build an RBP centered protein-protein interaction network to expand the repertoire of human RBPs to characterize ALS relevant higher order RNP complexes. My extensive experience in the study of DNA and RNA binding proteins makes me an ideal candidate to perform the research proposed here. These aims will build towards the completion of a comprehensive list of human RBPs that will help provide detailed maps of RNA regulatory networks. The Yeo lab at UCSD is a leader in the field of RNA biology, and therefore is an excellent environment to perform the proposed training and build an independent research program. The Yeo lab is situated at the heart of a major biomedical research hub at UCSD, adjacent to the Salk Institute, and other research institutes and biotechnology companies in La Jolla. Conducting the proposed training program here will give me access to leaders in stem cell biology and proteomic methods that I hope to master as I transition to independence.