Across eukaryotes, the synthesis of messenger RNA (mRNA) for protein expression is tightly regulated by post-translational modifications of the RNA Polymerase II C-terminal domain (Pol II CTD). Phosphorylation in particular is critical for the recruitment of transcription initiation, elongation and termination factors responsible for processing the nascent RNA and regulating transcription rate. The Pol II CTD is made up of repeating heptapeptides (Y1S2P3T4S5P6S7) highly conserved in eukaryotes. In most genes across the Saccharomyces cerevisiae genome, the S5 position is hyperphosphorylated (S5P) upon transcription initiation. As Pol II clears the promoter, S5 becomes dephosphorylated and S2 becomes hyperphosphorylated (S2P). This S5P/S2P balance determines which factors are recruited across at different stages of the transcription cycle.
CTD phosphorylation also determines the fate of transcription termination in a gene-class dependent manner. At mRNA genes, high levels of S2P CTD recruit factors that dismantle the elongation complex as it transcribes the cleavage and polyadenylation signal. At functional non-coding RNA genes (such small nucleolar RNAs) high levels of S5P CTD recruit the Nrd1-Sen1-Nab3 complex which is required for termination and processing at these genes. Dr. Rodriguez-Martinez' recent work has focused on elucidating the genome-wide distribution of Sen1 and how a specific mutation abolishes its ability to bind tightly to low levels of S2P. In collaboration with Dr. Michael Culbertson, Juan and colleagues have provided insight into the differential recognition of high and low levels of CTD phosphorylation as part of a CTD code hypothesis.