The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development

Nucleic Acids Research, Jan 2015

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.

A PDF file should load here. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser.

Alternatively, you can download the file locally and open with any standalone PDF reader:

https://nar.oxfordjournals.org/content/43/1/115.full.pdf

The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development

Aur elie Lardenois 0 3 Igor Stuparevic 0 3 Yuchen Liu 3 Michael J. Law 2 Emmanuelle Becker 3 Fatima Smagulova 3 Karl Waern 1 Marie-H el e`ne Guilleux 3 Joe Horecka 6 Angela Chu 6 Christine Kervarrec 3 Randy Strich 2 Mike Snyder 1 Ronald W. Davis 5 6 Lars M. Steinmetz 4 Michael Primig 3 0 The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors. Present addresses: Aure lie Lardenois , INRA, UMR 703, ONIRIS, Nantes, F-44307 , France. Yuchen Liu, School of Medicine, Jianghan University , Wuhan 430056 , China 1 Department of Genetics, Stanford University , Stanford, CA 94395 , USA 2 School of Osteopathic Medicine, Rowan University , Stratford, NJ 08084 , USA 3 Inserm U1085-Irset, Universit e de Rennes 1 , Rennes, F-35042 , France 4 European Molecular Biology Laboratory , Heidelberg 69117 , Germany 5 Department of Biochemistry, Stanford University , Stanford, CA 94305 , USA 6 Stanford Genome Technology Center , Palo Alto, CA 94304 , USA 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. - Meiosis is a developmental pathway that leads to the formation of haploid gametes. The process deviates from the mitotic cell cycle in several ways including extensive recombination and the execution of two nuclear divisions without an intervening S-phase (1,2). Previous studies identified genes that are repressed during vegetative growth, and specifically induced during early, middle and late stages of meiotic development (35). Many members of the early class of meiotic genes are transcriptionally repressed during mitosis by a conserved histone deacetylase (HDAC) complex including the deacetylase Rpd3, the co-repressor Sin3 and the DNAbinding protein Ume6, which recognizes an upstream regulatory site 1 (URS1) (6,7). RNA profiling experiments and genome-wide DNA-binding assays analysing mitosis and meiosis revealed numerous differentially expressed genes, among them are many that are directly regulated by Rpd3 and Ume6 (810). The Rpd3 core complex represses its targets by stabilizing nucleosomes, and by an activity independent of histone deacetylation (11). Rpd3/Sin3/Ume6dependent repression is relieved through a two-step system targeting Ume6 for destruction. The first step occurs in cells switching from fermentation to respiration, which induces acetylation by the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex resulting in partial Ume6 destruction by the anaphase promoting complex/cyclosome (APC/C). Final Ume6 destruction occurs once the cells enter meiosis and requires the meiotic inducer Ime1. Ultimately, Ume6 re-accumulates during late stages of spore formation when it plays an important role in germination (1214). It is well established that DNA binding regulators cooperate with chromatin modification enzymes to repress meiosis-specific genes during vegetative growth (3). However, it has only recently emerged that a whole class of genes encodes several isoforms that change in lengthtypically due to variable 5 - and 3 -untranslated regions (UTRs)when yeast cells respond to stress (15,16), or when they exit mitosis and enter meiosis (1719). Little is known about the transcriptional mechanisms governing this process. UTRs control mRNA stability, transport and translation through interaction with numerous RNAbinding proteins. Their flexible architecture has therefore broad implications for the regulation of protein expression during mitosis (20), filamentous growth (21) and developmental pathways, such as meiosis and gametogenesis (2224). A well-studied mechanism of 5 -UTR-mediated translational control acts via upstrea (...truncated)


This is a preview of a remote PDF: https://nar.oxfordjournals.org/content/43/1/115.full.pdf

Aurélie Lardenois, Igor Stuparevic, Yuchen Liu, Michael J. Law, Emmanuelle Becker, Fatima Smagulova, Karl Waern, Marie-Hélène Guilleux, Joe Horecka, Angela Chu, Christine Kervarrec, Randy Strich, Mike Snyder, Ronald W. Davis, Lars M. Steinmetz, Michael Primig. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development, Nucleic Acids Research, 2015, pp. 115-128, 43/1, DOI: 10.1093/nar/gku1185