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.
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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)