Deciphering the function of chromatin modifiers in genome regulation and maintenance in Saccharomyces cerevisiae

• Main Author: Lévesque, Nancy
• Language: English
• Published: University of British Columbia 2012
• Online Access: http://hdl.handle.net/2429/43352

Chromatin is a dynamic structure that facilitates DNA compaction inside the cell nucleus and contributes nuclear process regulation such as transcription, DNA repair and DNA replication. Chromatin structure can be modified by several mechanisms, including the incorporation of histone variants, histone sliding or removal by ATP-dependent remodelling enzymes, addition of post-translational modifications, and addition of methylation marks on DNA. This dissertation aims to comprehend better the role of chromatin modifiers like histone acetyltransferases (HATs) in cellular processes such as genome regulation and maintenance in yeast Saccharomyces cerevisiae. HATs play crucial roles in cells, as they are involved in transcription regulation and DNA damage response. This dissertation investigates the precise nature of the relationship between the histone acetyltransferase complexes NuA4 and picNuA4. I discovered that the smaller NuA4 counterpart picNuA4 is partially able to replace the function of the larger NuA4 when the latter is defective. Additionally, dissection of the NuA4 complex scaffolding subunit Eaf1 revealed that its C-terminus is largely required for NuA4-dependent function. While NuA4 shares subunits with SWR1-C, an ATP-dependent chromatin-remodelling complex that replaces histone H2A for the histone variant H2A.Z, the role of shared modules in chromatin remodelling complexes remains unclear. Here I explored the role of shared modules through investigation of Swc4 and Yaf9, two members of the NuA4 and SWR1-C. Biochemical, genetic, and gene expression assays demonstrated that both Yaf9 and Swc4 similarly contributed to the shared module functions and generally behaved more like SWR1-C, but also had distinct roles. For instance, large-scale genetic interaction profiles exposed noticeable differences between Yaf9 and Swc4, where Yaf9 behaved more similarly to SWR1-C NuA4, Swc4 to NuA4, in some cases. Upon DNA damage, several chromatin modifications occur, such as acetylation of histone H4 tails by NuA4 or methylation of H3K79 by Dot1. Herein I propose a model explaining the role of H3K79 trimethylation in the DNA damage response in the context where cells are deficient for components of the DNA damage response. I suggest that, directly or indirectly, H3K79 trimethylation inhibits the translesion synthesis pathway, an alternative repair pathway.