The School of Natural Sciences
RNA-binding protein (RBP) interactomes: Large-scale approaches for mapping networks and targets
Kristopher Brannan, Ph.D.
Department of Cellular and Molecular Medicine
University of California San Diego
Monday, June 7th, 2021
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RNA binding proteins (RBPs) orchestrate gene expression by operating in context dependent networks that shape the transcriptome and dictate cell state. Two layers of information are key to defining RBP function: 1) protein-protein interaction (PPI) maps of higher order RBP complexes and networks and 2) transcriptome-wide maps of RBP-RNA interactions. Current PPI networks lack information about RNA-dependent interactions, and current approaches for assessing RBP-RNA interactions, such as crosslinking and immunoprecipitation (CLIP), cannot define RBP targets with isoform or single-cell resolution. To increase the resolution for probing RBP protein interactomes, we have utilized a collection of IP-validated commercial antibodies to purify, in the presence or absence of RNase treatment, a panel of 80 endogenous RBPs representing complexes involved in all steps of the mRNA life-cycle. To increase the resolution for probing RBP-RNA interactomes, we have developed an antibody-free approach termed STAMP (Surveying Targets by APOBEC Mediated Profiling), which elucidates isoform-specific binding profiles from long-reads and detects RBP-targets and ribosome occupancy in single cells. Integrating single-cell, isoform-aware RBP target maps with RNA-aware PPI maps will be powerful for delineating RBP network functionality.
Dr. Brannan’s work has focused on the mRNA life-cycle since he began his scientific training as an undergraduate at the University of Colorado Boulder. He received his Ph.D. in molecular biology and biochemistry at the University of Colorado School of Medicine where he studied co-transcriptional RNA processing and RNA polymerase termination mechanisms. His research at the University of California San Diego has sought to define co- and post-transcriptional protein-protein and RNA-protein interactions that mechanistically control gene-expression programs. His focus is on the systems biology of RNA-binding protein (RBP) interactions and regulatory networks in human cell culture models, with a concentration on technology development for RNA-targeting strategies and RNA-protein interaction detection approaches. Dr. Brannan’s future work will explore how RNA-protein contacts important for nucleocytoplasmic-transport function to control gene expression in the context of neurodegeneration.
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