This proposal will use the molecular genetics of Saccharomyces cerevisiae and Candida albicans to determine the role of polyploidy and gene duplications in gene expression. Genomes have evolved by duplication of existing genetic material, either whole genomes or individual genes; however, such duplications can lead to abnormal growth. Many tumors contain a large proportion of cells that are hyperploid, and, for some, increased ploidy carries a good prognosis, predicting an increased sensitivity to anti-mitotic drugs. Experiments are designed to identify all the Saccharomyces genes required for polyploid formation and for the survival of polyploid cells in stationary phase using whole genome knockout libraries. The role of gene silencing in the control of gone expression in polyploids will be determined by whole genome chromatin immunoprecipitation. The mechanism of gene silencing and variegation will be elucidated for the FLO genes, a highly duplicated gone family with one expressed locus (FL011), and many silent subtelomeric members. These experiments will determine the role of chromatin factors, nutrition, mutation, and recombination in silencing and desilencing the ensemble of FLO genes. Experiments are also designed to reveal the mechanism by which the non-telomeric gene FL011 switches epigenetically between the """"""""on"""""""" and """"""""off"""""""" states. A genome wide screen will identify the prevalence of variegation in gene expression. As FLO genes are the cell surface adhesins of fungi, their ability to switch could be critical virulence factors in pathogens. The importance of silencing and desilencing for human health will be determined in the human fungal pathogen, Candida albicans, an obligate diploid. Candida's resistance to the antifungal agent, fluconazole, is unstable in strains heterozygous for the recessive erg3 mutation. We will determine the role of diploidy and the histone deactylases in generating high-level drug resistance and will screen the Candida genome for other genes that lead to fluconazole resistance by this silencing mechanism. These Candida studies could identify the factors that will improve the effectiveness of current antifungal therapies. Experiments using DNA microarrays are designed to identify compounds used by Saccharomyces to sense its density. The experiments proposed will lead to a deeper understanding of the ability to proliferate at low cell densities, a more realistic scenario for fungal pathogens.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genetics Study Section (GEN)
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Anderson, James J
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Whitehead Institute for Biomedical Research
United States
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Vyas, Valmik K; Bushkin, G Guy; Bernstein, Douglas A et al. (2018) New CRISPR Mutagenesis Strategies Reveal Variation in Repair Mechanisms among Fungi. mSphere 3:
Vyas, Valmik K; Barrasa, M Inmaculada; Fink, Gerald R (2015) A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families. Sci Adv 1:e1500248
Wang, Benjamin L; Ghaderi, Adel; Zhou, Hang et al. (2014) Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol 32:473-8
Lam, Felix H; Ghaderi, Adel; Fink, Gerald R et al. (2014) Biofuels. Engineering alcohol tolerance in yeast. Science 346:71-5
Schwartz, Schraga; Bernstein, Douglas A; Mumbach, Maxwell R et al. (2014) Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159:148-162
Edwards, Matthew D; Symbor-Nagrabska, Anna; Dollard, Lindsey et al. (2014) Interactions between chromosomal and nonchromosomal elements reveal missing heritability. Proc Natl Acad Sci U S A 111:7719-22
Avalos, José L; Fink, Gerald R; Stephanopoulos, Gregory (2013) Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nat Biotechnol 31:335-41
Schwartz, Schraga; Agarwala, Sudeep D; Mumbach, Maxwell R et al. (2013) High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155:1409-21
Jansen, An; van der Zande, Elisa; Meert, Wim et al. (2012) Distal chromatin structure influences local nucleosome positions and gene expression. Nucleic Acids Res 40:3870-85
Chin, Brian L; Ryan, Owen; Lewitter, Fran et al. (2012) Genetic variation in Saccharomyces cerevisiae: circuit diversification in a signal transduction network. Genetics 192:1523-32

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