The goal of the proposed research is to determine how changes in cis-regulatory sequences alter transcriptional dynamics. Whereas transcription factors are well known to determine when a gene is turned on and off, cis-regulatory sequences have the ability to fine-tune how a gene responds to these signals. The precise timing and rate of gene activation/repression are key to a cell's ability to appropriately respond to it's biotic and abiotic environment. In microbes, which must survive and compete in ever changing environments, fitness may depend more on gene expression dynamics than expression levels under steady state conditions. To ascertain how changes in cis-regulatory sequences modulate gene expression dynamics we will use a high-throughput reporter system capable of testing hundreds of cis-regulatory variants in yeast. We will map causal variants upstream of genes that exhibit allele-specific differences in their gene expression dynamics. Our preliminary studies demonstrate that there is extensive variation in gene expression dynamics in yeast and this allelic variation can be recapitulated in our reporter system. In the first aim we will map SNPs and InDels between strains of Saccharomyces cerevisiae that alter expression dynamics following depletion of glucose. By characterizing causal cis-regulatory variants we will specifically test whether insertions and deletions that change the position of known regulatory motifs is a major mode by which gene expression dynamics are altered, and more generally whether changes within or outside of transcription factor binding sites are more often responsible for altered expression levels or dynamics. In the second aim we will map substitutions between Saccharomyces species that alter the heat shock response. Because compensatory changes are a common feature of cis-regulatory divergence between species, expression levels and dynamics may not evolve independently of one another. We will test whether coincident divergence in expression levels and dynamics is a consequence of mutation or co-evolution. By including random promoter mutants as part of our investigation we will generate expected patterns of divergence in the absence of constraint, enabling us to measure the extent to which divergence in gene expression levels and dynamics are constrained during evolution. The completion of these aims will fill an important gap in our understanding of which noncoding variants alter gene expression and how cis-regulatory sequences evolve.

Public Health Relevance

Gene regulation is a critical aspect of how cells respond to their environment. This project will identify regulatory mutations in yeast that alter when and how fast a gene responds to altered environmental conditions. Because mechanisms of gene regulation are conserved across species, the completion of this project will improve our ability to identify mutations in the human genome with adverse health consequences.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Janes, Daniel E
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University of Rochester
Schools of Arts and Sciences
United States
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Mezzetti, Francesco; Fay, Justin C; Giudici, Paolo et al. (2017) Genetic variation and expression changes associated with molybdate resistance from a glutathione producing wine strain of Saccharomyces cerevisiae. PLoS One 12:e0180814
Li, Xueying C; Fay, Justin C (2017) Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species. Genome Biol Evol 9:1120-1129
Peris, David; Moriarty, Ryan V; Alexander, William G et al. (2017) Hybridization and adaptive evolution of diverseSaccharomycesspecies for cellulosic biofuel production. Biotechnol Biofuels 10:78
Bergen, Andrew C; Olsen, Gerilyn M; Fay, Justin C (2016) Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression. Mol Biol Evol 33:1270-9
Dashko, Sofia; Liu, Ping; Volk, Helena et al. (2016) Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations. Front Microbiol 7:215
Ludlow, Catherine L; Cromie, Gareth A; Garmendia-Torres, Cecilia et al. (2016) Independent Origins of Yeast Associated with Coffee and Cacao Fermentation. Curr Biol 26:965-71
Scienski, Kathy; Fay, Justin C; Conant, Gavin C (2015) Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex. Genome Biol Evol 7:3249-58
Williams, Kathryn M; Liu, Ping; Fay, Justin C (2015) Evolution of ecological dominance of yeast species in high-sugar environments. Evolution 69:2079-93
Swain Lenz, Devjanee; Riles, Linda; Fay, Justin C (2014) Heterochronic meiotic misexpression in an interspecific yeast hybrid. Mol Biol Evol 31:1333-42
Engle, Elizabeth K; Fay, Justin C (2013) ZRT1 Harbors an Excess of Nonsynonymous Polymorphism and Shows Evidence of Balancing Selection in Saccharomyces cerevisiae. G3 (Bethesda) 3:665-673

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