Epigenetic and Metabolic Regulation of Gene Silencing in Saccharomyces

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This application for a MIRA award seeks to consolidate the research in the PI's lab, funded by GM31105 Genetic Analysis of Genes Controlling a Position Effect, currently in its 37th year, and by GM120374 Metabolism and Epigenetics, currently in its fourth year, into one program. The work supported by these grants has produced a continuous series of fundamental discoveries about mechanisms of heterochromatic gene silencing, its epigenetic inheritance, and its sensitivity to metabolism. Most recently, these efforts have also included the development of transformative new genetic technologies, and the successful launch of a comprehensive investigation of the impact of metabolism on epigenetic processes, with an initial focus on those metabolism-altering mutations that are drivers of human cancers. The long legacy of GM31105 enabled the discovery of how the Sir genes control heterochromatin formation, the role of silencers in controlling gene expression, and the epigenetic inheritance of transcriptional states. Many ancillary discoveries made in the course of these investigations include (1) the first mutations defining the Origin Recognition Complex, and its separable roles in DNA replication and regulating transcription; (2) defining the molecular topography of heterochromatin; (3) single-cell assays revealing heterochromatin dynamics; and (4) discovery of unusual sterile mutations that led to the discovery of protein prenylation of a-factor and Ras. Recently, the work supported by GM120374 led to the discovery that mutations in components of the Krebs cycle that function as cancer driver mutations have unexpected impacts on histone demethylases and gene silencing, and identified new metabolic links to heterochromatin stability. Together, these grants have produced a transformative technique for the locus-specific labeling of individual nucleosomes that allowed resolution of one of the longest unsolved questions regarding chromatin, showing that individual nucleosome retain their genomic addresses through multiple DNA replication cycles. The newest data from these grants force a fundamental reconsideration of whether nucleosomes are the carriers of the memory of epigenetic states. The proposed research program will answer multiple long-standing questions in epigenetics such as determining where the memory component resides that allows epigenetic inheritance of transcriptional states and resolving the mechanism of that memory. In addition, the proposed research will resolve the mechanism by which gene silencing spreads laterally from its sites of nucleation. The cell-cycle requirements for the creation of new cell-type-specific states of gene expression will be identified. Finally, the mechanism by which the newly identified metabolic impacts on epigenetic silencing will be determined.