HIGH RESOLUTION EPIGENOMIC MAPS OF YEAST IN RESPONSE TO ENVIRONMENTAL STRESS

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Gene regulation is central to all life, normal and diseased. The long-term goal of this research project is to un- derstand at single bp resolution the molecular organization (architecture) of proteins assembled on the Sac- charomyces (budding yeast) genome. Budding yeast represent an ideal model cellular system due to its simple genome, ease of genetic manipulation, and conservation of transcription and chromatin regulators with human cells. By understanding the precise molecular architecture of epigenomes, we gain a holistic view of genome regulation mechanisms. This project will build on our published set of genome-wide ChIP-exo data that com- prehensively measures the yeast epigenome consisting of over 400 distinct proteins. This expansion will in- volve understanding how epigenomes are reprogrammed by environmental signals. Two broad classes of re- programming will be examined: acute stress responses (e.g., heat shock and oxidative stress) and long-term unfolding of developmental pathways (e.g., starvation responses) brought on by chronic stress. Responses to acute stress reveal molecular architectures that pre-exist in the cell and then re-organize within a few minutes of sensing extracellular signaling. These events are typically transient and so must be captured upon reaching their temporal maxima. In contrast, developmental pathways unfold over hours in yeast and typically rely on de novo synthesis of gene-specific transcription factors. This project will map the precise positional organiza- tion of hundreds of epigenomic components in response to heat shock and oxidative stress, and smaller set of components in response to a much broader array of acute stresses and developmental pathways. This project will also define the functional interdependencies of epigenomic factors, with particular focus on the gene in- duction cofactors Mediator and SAGA. Relevant components of induced transcription will be rapidly depleted, then their impact on Mediator and SAGA binding to promoters examined. Other interdependencies, informed by the organization of epigenomes that will be defined during reprogramming/induction will also be examined. Together these aims will help provide a more thorough understanding of the protein architecture of gene regu- lation that should allow computational prediction of novel gene-environment interactions in diseased tissue.