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<title lang=en>Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification</title>
<creator>Lardenois, Aurélie</creator>
<creator>Becker, Emmanuelle</creator>
<creator>Walther, Thomas</creator>
<creator>Law, Michael J.</creator>
<creator>Xie, Bingning</creator>
<creator>Demougin, Philippe</creator>
<creator>Strich, Randy</creator>
<creator>Primig, Michael</creator>
<contributor>Institut de recherche, santé, environnement et travail [Rennes] (Irset) ; Université d'Angers (UA) - Université des Antilles et de la Guyane (UAG) - Université de Rennes 1 (UR1) - École des Hautes Études en Santé Publique [EHESP] (EHESP) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )</contributor>
<contributor>Biozentrum ; University of Basel (Unibas)</contributor>
<contributor>Rowan University</contributor>
<description>International audience</description>
<source>ISSN: 1617-4615</source>
<source>EISSN: 1617-4623</source>
<source>Molecular Genetics and Genomics</source>
<publisher>Springer Verlag</publisher>
<identifier>hal-01151619</identifier>
<identifier>https://hal-univ-rennes1.archives-ouvertes.fr/hal-01151619</identifier>
<source>https://hal-univ-rennes1.archives-ouvertes.fr/hal-01151619</source>
<source>Molecular Genetics and Genomics, Springer Verlag, 2015, 290 (5), pp.2031-2046. 〈10.1007/s00438-015-1051-5〉</source>
<identifier>DOI : 10.1007/s00438-015-1051-5</identifier>
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<identifier>PUBMED : 25957495</identifier>
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<language>en</language>
<subject>[SDV] Life Sciences [q-bio]</subject>
<type>info:eu-repo/semantics/article</type>
<type>Journal articles</type>
<description lang=en>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.</description>
<date>2015</date>
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