Special Chemical Biology Seminar

The genomic era spurred a new phase of discovery, including the expanded regulatory roles of RNA that act via RNA structure, RNA modifications, and coordinated binding of RNA-binding proteins that together specify gene expression. These genomic approaches have been foundational to discovery but do not provide the quantitative information that will needed to predict gene expression. In contrast, biochemical approaches have predictive ability but have lacked the scale needed to address cellular complexity. To understand how these interactions regulate the gene expression program and modulate them for therapeutic intervention, we need predictive models for RNA structure and protein-binding—for an arbitrary RNA sequence—and we need to be able to predict their functional outcomes. I have developed high-throughput cellular biochemistry (HTCB) to bring biochemistry to genomic scale in cells. Using a designed library that varies individual RNA features that contribute to folding combined with DMS-MaPseq chemical probing, we measured the thermodynamic stability of thousands of RNA structures in vitro and in cells. This method allows for the quantification of differences in RNA structural ensembles in and out of cells, of the extent cellular unfolding, and of deficiencies in standard computational models used to predict RNA structures.