title: The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development.
abstract: It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression of distinct transcript isoforms during mitotic growth and meiotic development is unknown. In this study, we order developmentally regulated transcript isoforms according to their expression at specific stages during meiosis and gametogenesis, as compared to vegetative growth and starvation. We employ regulatory motif prediction, in vivo protein-DNA binding assays, genetic analyses and monitoring of epigenetic amino acid modification patterns to identify a novel role for Rpd3 and Ume6, two components of a histone deacetylase complex already known to repress early meiosis-specific genes in dividing cells, in mitotic repression of meiosis-specific transcript isoforms. Our findings classify developmental stage-specific early, middle and late meiotic transcript isoforms, and they point to a novel HDAC-dependent control mechanism for flexible transcript architecture during cell growth and differentiation. Since Rpd3 is highly conserved and ubiquitously expressed in many tissues, our results are likely relevant for development and disease in higher eukaryotes.
authors.affiliation: Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Lardenois
authors.affiliation: Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France.
authors.forename: Igor
authors.initials: I
authors.lastname: Stuparevic
authors.affiliation: Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France.
authors.forename: Yuchen
authors.initials: Y
authors.lastname: Liu
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, Université de Rennes 1, Rennes, F-35042, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Becker
authors.affiliation: Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France.
authors.forename: Fatima
authors.initials: F
authors.lastname: Smagulova
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94395, USA.
authors.forename: Karl
authors.initials: K
authors.lastname: Waern
authors.affiliation: Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France.
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Guilleux
authors.affiliation: Stanford Genome Technology Center, Palo Alto, CA 94304, USA.
authors.forename: Joe
authors.initials: J
authors.lastname: Horecka
authors.affiliation: Stanford Genome Technology Center, Palo Alto, CA 94304, USA.
authors.forename: Angela
authors.initials: A
authors.lastname: Chu
authors.affiliation: Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Kervarrec
authors.affiliation: School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
authors.forename: Randy
authors.initials: R
authors.lastname: Strich
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94395, USA.
authors.forename: Mike
authors.initials: M
authors.lastname: Snyder
authors.affiliation: Stanford Genome Technology Center, Palo Alto, CA 94304, USA Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
authors.forename: Ronald W
authors.initials: RW
authors.lastname: Davis
authors.affiliation: European Molecular Biology Laboratory, Heidelberg 69117, Germany.
authors.forename: Lars M
authors.initials: LM
authors.lastname: Steinmetz
authors.affiliation: Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France michael.primig@inserm.fr.
authors.forename: Michael
authors.initials: M
authors.lastname: Primig
mesh_terms: D018507:Gene Expression Regulation, Developmental; D006655:Histone Deacetylases / Q000378:metabolism*; D008540:Meiosis / Q000235:genetics*; D008938:Mitosis / Q000235:genetics*; D009154:Mutation; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D021122:Protein Subunits / Q000378:metabolism; D059368:RNA Isoforms / Q000235:genetics / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism; D012097:Repressor Proteins / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D024363:Transcription Initiation Site; D020506:Untranslated Regions; D033921:Vesicular Transport Proteins / Q000235:genetics; D039221:mRNA Cleavage and Polyadenylation Factors / Q000235:genetics; D012359:tRNA Methyltransferases
chemical_list: C450560:CFT2 protein, S cerevisiae; D021122:Protein Subunits; D059368:RNA Isoforms; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; C089979:UME6 protein, S cerevisiae; D020506:Untranslated Regions; D033921:Vesicular Transport Proteins; D039221:mRNA Cleavage and Polyadenylation Factors; C570232:RTT10 protein, S cerevisiae; D012359:tRNA Methyltransferases; D012319:RNA Polymerase II; C071665:RPD3 protein, S cerevisiae; D006655:Histone Deacetylases