Role of the yeast histone methyltransferase Set2 and its regulatory domains in RNA polymerase II transcription

Eukaryotic transcription requires the careful regulation of chromatin structure in order to allow access of RNA polymerase II (RNAPII) to DNA. Histone modifications are well established as regulators of chromatin structure and gene transcription. Although the influences of histone acetylation and phosphorylation have been investigated extensiviely, the role of histone methylation has recently become a topic of intense study in the field of chromatin biology. The newly discovered histone H3 methylase Set2 is the sole enzyme in yeast responsible for H3 lysine 36 (K36) methylation. Although earlier work suggested a role for Set2 and K36 methylation in transcriptional repression, the role of K36 methylation in yeast remained largely unexplored. Through the studies presented here, we have identified and characterized a link between Set2 and actively transcribing RNA polymerase II (RNAPII). Importantly, in Chapter 2 we present data identifying a novel domain in Set2 that is responsible for interaction with RNAPII. Further analysis of this domain revealed its presence in a number of Set2 homologues in other species, thereby stimulating further studies of the role of Set2 and K36 methylation in gene transcription across multiple organisms. In addition to studies of the downstream roles of Set2 and K36 methylation in transcription, in Chapter 3 we describe our investigation into a network of proteins that are involved in the upstream regulation of Set2. These studies suggest an important link between the regulation of nucleosome conformation and subsequent K36 methylation, further supported by concurrent studies from other laboratories. Through our studies of Set2 and histone methylation, we also developed and improved several experimental methods that are presented in Chapter 4. Finally, in Chapter 5 we describe the contributions of our work in the larger context of recent studies from other laboratories. We also discuss relevant questions for future work regarding Set2 as well as histone modifications in general