Research Activities
Structure and CTD recognition of transcription termination factors:
This project focuses on how the RNA polymerase II C-terminal domain’s dynamic phosphorylation/dephosphorylation cycle results in altered recruitment of RNA processing complexes to the transcript. In an effort to better understand how the phosphorylation pattern of the CTD recruits transcription termination factors to the CTD, I created a library of CTD phosphopeptides containing two complete CTD repeats differing in the position of the phosphorylated residue. I used these peptides to measure the binding affinities of the CTD interacting domains (CIDs) of several transcription termination factors using both NMR and fluorescence anisotropy. I used NMR to determine the structure of a phosphorylated CTD peptide bound to the CID of Rtt103. From this structure, I was able to show how the CIDs of Rtt103 and Pcf11 differ in their binding affinities for the CTD and showed that it’s possible to swap the specificities between the two domains by making a single amino acid change. I am currently exploring CID recognition of longer CTD peptides and I am using Paramagnetic Relaxation Enhancement (PREs) to determine the molecular details for how the CIDs interact with these longer CTD peptides.