Investigating the regulation of the chromatin landscape by Set4 in Saccharomyces cerevisiae

Abstract

The regulation of chromatin is important for transcription, DNA replication and DNA damage repair. In the presence of environmental stress, the cell mounts stress response pathways that involve changes in chromatin structure to promote cell survival. Set4 belongs to the Set3 subfamily of SET domain-containing proteins in yeast. Other members of this subfamily are budding yeast Set3, Drosophila melanogaster UpSET and the mammalian proteins MLL5 and SETD5. The defining features of this subfamily are the presence of a divergent SET domain and the presence of a PHD finger, with the exception of SETD5. Set4'sparalog, Set3 has been shown to work in a complex and catalyze histone deacetylation leading to gene repression through binding H3K4 methylation via its PHD finger. Set4 shares sequence similarity to fly UpSET and human MLL5, however, little is known about the biochemical or biological roles of Set4. We have shown a role for Set4 in promoting cell survival during oxidative stress by contributing to stress response gene expression programs. We also determined that Set4 regulates genes enriched near telomeres under normal and stress conditions. We also found that deleting Set4 disrupts the histone deacetylase complex occupancy at telomeres, thereby leading to changes in the chromatin landscape. Similar to other members of the Set3 subfamily, Set4 does not possess methyltransferase activity due to the inactive SET domain, therefore we hypothesize that it functions through directing other chromatin regulators, including histone deacetylases, to chromatin. Set4 has a PHD finger as well and we found that although other PHD fingers generally bind to methylated lysines on histone tails, Set4'sPHD finger does not bind to histones. However, we did find that Set4'sPHD finger is important for its chromatin localization and binds to nucleic acids in vitro. This suggests that Set4 may regulate gene expression through a mechanism independent of histone methylation. This work has defined a role for Set4 as a regulator of the telomeric chromatin landscape by working in conjunction with histone deacetylases and as a calibrator of stress defense pathways. The study of Set4 has expanded our understanding of the Set3 subfamily of SET domain-containing proteins in gene expression control during environmental stress response.