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Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification

Abstract : Chromatin modification enzymes are important regulators of gene expression and some are evolutionarily conserved from yeast to human. Saccharomyces cerevisiae is a major model organism for genome-wide studies that aim at the identification of target genes under the control of conserved epigenetic regulators. Ume6 interacts with the upstream repressor site 1 (URS1) and represses transcription by recruiting both the conserved histone deacetylase Rpd3 (through the co-repressor Sin3) and the chromatin-remodeling factor Isw2. Cells lacking Ume6 are defective in growth, stress response, and meiotic development. RNA profiling studies and in vivo protein-DNA binding assays identified mRNAs or transcript isoforms that are directly repressed by Ume6 in mitosis. However, a comprehensive understanding of the transcriptional alterations, which underlie the complex ume6Δ mutant phenotype during fermentation, respiration, or sporulation, is lacking. We report the protein-coding transcriptome of a diploid MAT a/α wild-type and ume6/ume6 mutant strains cultured in rich media with glucose or acetate as a carbon source, or sporulation-inducing medium. We distinguished direct from indirect effects on mRNA levels by combining GeneChip data with URS1 motif predictions and published high-throughput in vivo Ume6-DNA binding data. To gain insight into the molecular interactions between successive waves of Ume6-dependent meiotic genes, we integrated expression data with information on protein networks. Our work identifies novel Ume6 repressed genes during growth and development and reveals a strong effect of the carbon source on the derepression pattern of transcripts in growing and developmentally arrested ume6/ume6 mutant cells. Since yeast is a useful model organism for chromatin-mediated effects on gene expression, our results provide a rich source for further genetic and molecular biological work on the regulation of cell growth and cell differentiation in eukaryotes.
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https://hal-univ-rennes1.archives-ouvertes.fr/hal-01151619
Contributor : Laurent Jonchère Connect in order to contact the contributor
Submitted on : Wednesday, May 13, 2015 - 11:45:34 AM
Last modification on : Wednesday, October 20, 2021 - 3:19:23 AM

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Aurélie Lardenois, Emmanuelle Becker, Thomas Walther, Michael J. Law, Bingning Xie, et al.. Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification. Molecular Genetics and Genomics, Springer Verlag, 2015, 290 (5), pp.2031-2046. ⟨10.1007/s00438-015-1051-5⟩. ⟨hal-01151619⟩

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