Investigation of the role of the PHD domain of Set4 in stress-mediated chromatin regulation in Saccharomyces cerevisiae

Abstract

Chromatin regulation is a dynamic process and an essential aspect of cell growth and survival. It further allows cells to adapt to changing environmental conditions, by regulating the expression of genes essential for survival during stress. One essential class of chromatin regulators are methyltransferases, a class of enzymes that methylate histones to promote differential gene expression. The yeast chromatin regulator Set4 is a member of the Set3 subfamily of SET-domain containing methyltransferases that appear to have inactive catalytic domains. This family consists of Set3 and Set4 in S. cerevisiae and homologues UpSET in Drosophila, SET-9 and SET-26 in C. elegans, and MLL5 and SETD5 in mammals. In addition to the conserved SET domains, the majority of these factors include PHD fingers that bind to H3K4 methylation and facilitate their recruitment to chromatin. In yeast, Set3 recruits histone deacetylases Hos2 and Hst1 and functions primarily as a repressor of gene expression. Despite a high sequence similarity, Set4 seems to have distinct functions in the cell. Set4 promotes cell survival in stress conditions such as oxidative stress and hypoxia. It wasshown to localize to the promoter regions of stress response genes and work with histone deacetylases in regulating their expression. Interestingly, the Set4 PHD finger is not known to bind histones in standard assays and the mechanism by which it is recruited to chromatin is unknown. The goal of this dissertation was to characterize the PHD domain of Set4 and its contribution to the regulation of stress response genes by Set4. We have shown here that the PHD domain of Set4 is important for its localization at chromatin and for its function in gene regulation. We also show that Set4 PHD binds to DNA in vitro and identify residues that mediate this interaction. Lastly, we provide evidence that Set4 chromatin binding is heavily dependent on the presence of histone acetylation in the genome. Altogether, this work provides new insights into a poorly understood chromatin regulator which plays critical roles during stress responses.