Large-scale characterization of the function of RNA regulatory elements

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PROJECT SUMMARY Once an RNA is transcribed in the nucleus, it is bound by RNA binding proteins and other regulatory RNAs which control its sequence (by altering splicing), half-life (by modulating RNA stability and decay) and translation (through mediation of ribosome initiation and elongation) among other RNA processing steps. Individual RBP binding sites can have significant physiological importance, as emphasized by the recent example of the drug Spinraza, which is an antisense oligonucleotide that blocks a single RBP:RNA interaction in order to cure Spinal Muscular Atrophy. Recent advances in genomics techniques have dramatically increased our ability to identify the interaction sites for these regulatory RBPs and RNAs, and we now have catalogs of over a million such interaction sites that are candidate RNA regulatory elements. However, it is clear that only a small fraction of these elements truly function as regulatory modules, as few show differences in RNA processing when the RBP is knocked down or otherwise altered. As such, large-scale assays to sift through these elements to identify the subset that are function are an essential missing piece in converting these element databases into a useful tool for researchers interested in understanding whether human genetic variation will alter RNA biology. In this proposal, I describe my research group’s proposed efforts to address this major knowledge gap in two areas: 1. Using orthogonal approaches (rapid degradation of RBPs followed by genomics profiling to identify direct regulatory targets of RBPs and massively parallel reporter assays) to characterize which RBP binding sites confer regulation. 2. Large-scale identification of regulatory targets for snoRNAs, snRNAs, and other regulatory RNAs through improved genomics techniques. My extensive expertise in developing experimental and computational genomics methods to map and understand RNA processing regulatory networks makes my newly founded lab an ideal location to undertake these efforts, and build an improved global picture of the RNA processing regulatory landscape. Further, it will support my efforts to develop an independent research group that will lay the foundation to the broader effort to understand how human genetic variation affects disease through mis-regulation of RNA processing.