title: 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.
authors.affiliation: Inserm U1085-IRSET, University of Rennes 1, 35042, Rennes, France.|INRA, UMR 703, ONIRIS, 44307, Nantes, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Lardenois
authors.affiliation: Inserm U1085-IRSET, University of Rennes 1, 35042, Rennes, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Becker
authors.affiliation: Biozentrum, University of Basel, 4056, Basel, Switzerland.|INSA, UMR CNRS 5504 and INRA 792, 31077, Toulouse, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Walther
authors.affiliation: School of Osteopathic Medicine, Rowan University, Stratford, NJ, 08084, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Law
authors.affiliation: Inserm U1085-IRSET, University of Rennes 1, 35042, Rennes, France.
authors.forename: Bingning
authors.initials: B
authors.lastname: Xie
authors.affiliation: Biozentrum, University of Basel, 4056, Basel, Switzerland.
authors.forename: Philippe
authors.initials: P
authors.lastname: Demougin
authors.affiliation: School of Osteopathic Medicine, Rowan University, Stratford, NJ, 08084, USA.
authors.forename: Randy
authors.initials: R
authors.lastname: Strich
authors.affiliation: Inserm U1085-IRSET, University of Rennes 1, 35042, Rennes, France. michael.primig@inserm.fr.
authors.forename: Michael
authors.initials: M
authors.lastname: Primig
mesh_terms: D002843:Chromatin / Q000378:metabolism*; D004171:Diploidy; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D008540:Meiosis; D059748:Proteolysis; D012331:RNA, Fungal / Q000235:genetics; D011995:Recombination, Genetic; D012097:Repressor Proteins / Q000502:physiology*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000254:growth & development*; D029701:Saccharomyces cerevisiae Proteins / Q000502:physiology*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D012331:RNA, Fungal; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; C089979:UME6 protein, S cerevisiae
keywords: Interactome; Isw2; Rpd3; Sin3; Transcriptome; Ume6