Discovering new writers and patterns underlying the CTD code

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RNA polymerase II (Pol II) is the protein machine that transcribes the majority of genes in the eukaryotic cell into RNA. Pol II core component consists of 12 proteins, and the tail end of the largest protein, called the C-terminal domain (CTD), is the site of interaction with other proteins and cellular machines. In this project, we will earn how these interactions are affected by chemical changes of the CTD in the baker's yeast cells. Since CTD-related mechanisms are highly conserved in evolution, the research will enable our understanding of gene expression in other eukaryotes, including humans. The program will expand the horizons of students and colleagues by working in teams that bring expertise from multiple disciplines, train the next generation of globally engaged scientists/technologists, and provide widely enabling tools to the scientific community. To engage the next generation of students in STEM subjects, as well as the larger community, we will in particular develop a computer game that begins with the collection and assembly of basic biological processes that underlie The Central Dogma of Molecular Biology and leads the players to identify features required to form a "minimal living genome."The "CTD code" hypothesis posits that the engagement of relevant proteins with Pol II is coordinated by sequential post-translational modifications of the CTD. An important feature of this unusual domain is the occurrence of a repeating hepta-peptide that is modified on all five of the hydroxyl-bearing amino side chains. This project focuses on phosphorylation of threonine in position four of this hepta-peptide repeat; such phosphorylation has been implicated in directing the post-transcriptional modification of a specific set of Pol II-transcribed genes. The project will integrate chemical, biological and computational approaches to identify cellular kinases that phosphorylate threonine four of the Pol II CTD from Saccharomyces cerevisiae. The next level of experimentation and analysis will focus on obtaining mechanistic insights into how phosphorylation of this residue contributes to global versus gene class-specific transcriptional control.