RNA-protein (RNP) complexes are central to many fundamental processes of gene regulation and genome maintenance in all kingdoms of life.  The RNA components of these molecular machines often carry out diverse functions, acting as guide, template, scaffold, or catalyst.  Despite this versatility, RNAs require protein partners to function, and the interactions that form between these components often dictate the overall activity of the RNP complex.  Our lab is interested in understanding the molecular mechanisms underlying the function of RNPs from diverse cellular pathways.  To that end, we combine a broad range of biochemical, structural and cellular tools to study RNA and protein structure, interactions and function.

Understanding endogenous CRISPR-Cas function

All forms of life require immune systems to stave off infection from viruses and other pathogens. In bacteria and archaea, clustered regularly interspaced short palindromic repeats (CRISPR) loci and CRISPR-associated (Cas) proteins provide adaptive immunity against invading DNA from bacteriophages and plasmids. CRISPR-Cas systems adapt to infection by incorporating a short segment of foreign DNA into the host CRISPR locus as a “spacer” between repeating sequence elements. CRISPRs subsequently serve as templates for short CRISPR RNAs (crRNAs), which act as guide strands in an RNA-directed interference mechanism that destroys the invading DNA, thereby neutralizing the infection. Although the Cas proteins required for these adaptation and interference mechanisms are distinct, the two stages of CRISPR immunity are thought to be linked, as the interference machinery has been shown to accelerate acquisition of new spacers through a mechanism known as “priming”.

Our goal is to understand how Cas proteins and the sequences of the crRNA and target DNA influence each stage of CRISPR immunity. We combine high-throughput in vivo and in vitro tools with biochemical and biophysical approaches to dissect the function of each component of the CRISPR-Cas system.