Harnessing RNA Regulation to Direct Protein Evolution and Control Mammalian Gene Expression
I will present two recent technologies our group has developed that harness RNA regulation – one for basic science purposes and one for therapeutic development. First, I will describe new methods that use our RNA polymerase-based biosensors to harness evolution in order to probe the emergence of “selectivity” between biomolecular interfaces, in particular, protein-protein interactions (PPIs). Using a combination of high-throughput biochemical methods, ancestral reconstruction, and a new rapid evolution technology, we developed a model system involving the BCL-2 family of apoptotic regulatory proteins to probe fundamental evolutionary questions about PPIs and how selectivity (or not) emerges between them. In the second half of the talk, I will discuss therapeutic opportunities involving RNA regulation and “epitranscriptomics”. While RNA regulation offers exciting opportunities to create genetic therapies that are reversible and tunable, most current approaches rely on large, microbially-derived systems that pose clinical challenges. We developed the CRISPR/Cas-inspired RNA targeting system (CIRTS), a new protein engineering strategy for constructing programmable RNA regulatory systems entirely from human protein parts. The small size and human-derived nature of CIRTS provides a less-perturbative method for fundamental studies as well as a potential strategy to avoid immune issues when applied to epitranscriptomic therapies.