Histone modifications and histone modifying enzymes in the budding yeast Saccharomyces cerevisiae

Eukaryotic DNA exists in a complex with histone proteins and this structure is known as chromatin. Post-translational modifications of histones can influence chromatin structure and thereby regulate important processes such as transcription. The budding yeast Saccharomyces cerevisiae has been used as a model organism to study these histone modifications as they have been largely conserved from yeast to mammalian cells. This thesis is divided into three main chapters representing three separate research studies. The first one represents a study on Ubp8, a component of the SAGA co-activator complex. Here, we have provided evidence that an interaction between Ubp8 and Sgf11, a newly identified component of SAGA, is required for association of Ubp8 with the SAGA complex as well as its function as an H2B deubiquitylating enzyme. Furthermore, our results indicate that Ubp8 and Sgf11 constitute a functional module which is separate from other modules within SAGA. The second chapter consists of our study of histone sumoylation in yeast. Previous to this study, there had not been any histone modifications associated with transcriptional repression in S. cerevisiae. Here, we have shown that all four core histones are sumoylated in budding yeast. We have identified specific sumoylation sites on histone H2B and shown that sumoylated H2B is directly involved in transcriptional repression. Additionally, our results suggest that histone sumoylation may oppose activating mechanisms such as histone acetylation. The subject of the third and final research study is a histone demethylating enzyme. Two classes of histone demethylases have recently been found in mammalian cells, the LSD1 class and the JmjC class. Here we have provided a detailed analysis of the demethylation activity of Kdm5, a JmjC domain containing protein in S. cerevisiae. This protein has specific in vitro activity towards all methylated states of lysine 4 on histone H3. Our in vivo studies provide evidence for a role of Kdm5 both in modulating the level of lysine 4 methylation during the peak of GAL1 transcription, as well as removing the modification during repression.