Developing RNP-MaP into a broad-spectrum toolset for discovery, definition, and drug targeting of RNA-protein complexes in live cells

ABSTRACT My laboratory is interested in how interactions between RNA and RNA-binding proteins drive diverse biology and disease, and how these RNA-protein complexes might be targeted to alter their functions. Existing knowledge includes only a small fraction of protein-RNA interactions in the cell, and we know particularly little of how RNA- binding proteins cooperate to form complexes on noncoding RNAs, which make up the vast majority of human transcripts. Further, while pipelines for identifying protein-binding molecules for therapeutic development are informed by significant understanding of protein structure, there is no existing equivalent for designing small molecules that target RNA and RNA-binding interfaces. Critically, there remains a lack of straightforward technologies for discovery, definition, and drug targeting of protein-RNA interactions inside cells. To illuminate features of RNA-protein complexes and discover new ways to control their functions, my laboratory is developing a suite of novel live-cell chemical probing technologies based around my unique RNP-MaP approach (RNA-protein networks analyzed by mutational profiling). By enhancing and modularly extending the base RNP-MaP framework, we will develop new facile methods for 1) mapping multi-protein networks on RNA across transcriptomes and identifying associated RNA-binding proteins, 2) mapping transcriptome-wide targets of RNA-binding proteins while simultaneously measuring RNA site-specific occupancy, and 3) mapping small molecule RNA-targeting potential inside cells. Our ultimate goal is to create a set of tools that could enable any medical research laboratory to identify, characterize, and target any RNA-protein interface relevant to their disease/pathway/model of interest. By providing the means to probe the uncharted landscapes of RNA-protein networks, this work will be foundational for expansive new RNA biology discoveries and RNA-targeted therapeutics.