Research
We study the molecular mechanisms of transcription and pre-mRNA splicing, using yeast as a model eukaryote. Our transcription studies focus on termination by RNA polymerase (Pol) II. We discovered a pathway that uses the helicase Sen1 and a collection of RNA-binding proteins to terminate short Pol II transcripts (Left fig.). We were the first to measure Pol II occupancy across the entire yeast genome at high resolution by ChIP, and thereby identified the first examples of regulation by attenuation in eukaryotes. We are continuing our genetic and genomic studies of Pol II, and we're developing a purified in vitro system to dissect the detailed mechanism of Sen1-dependent termination.
In our splicing studies, we examine the mechanism and function of dynamic RNA-RNA and RNA-protein interactions in assembling the active site of the spliceosome on an intron. We are defining a complex network of interactions (Right fig.) that involves 3 RNAs (U2, U4 and U6), two helicases, an RNA-binding protein (Prp24), and the largest and most conserved spliceosomal protein (Prp8). We use detailed mutational studies, in vitro splicing, and RNA-binding assays to dissect the mechanism by which these factors enable spliceosome activation. In collaboration with the Butcher and Phillips labs, we are also determining the NMR and crystal structures of these splicing factors, starting with U6 RNA and Prp24.
