Meiosis: how to create a specialized cell cycle, Current Opinion in Cell Biology, vol.13, issue.6, pp.770-777, 2001. ,
DOI : 10.1016/S0955-0674(00)00282-9
Meiosis: cell-cycle controls shuffle and deal, Nature Reviews Molecular Cell Biology, vol.19, issue.12, pp.983-997, 2004. ,
DOI : 10.1128/MCB.21.20.6984-6998.2001
Transcriptional regulation of meiosis in budding yeast, Int. Rev. Cytol, vol.224, pp.111-171, 2003. ,
DOI : 10.1016/S0074-7696(05)24004-4
The core meiotic transcriptome in budding yeasts, Nat. Genet, vol.26, pp.415-423, 2000. ,
The Transcriptional Program of Sporulation in Budding Yeast, Science, vol.282, issue.5389, pp.699-705, 1998. ,
DOI : 10.1126/science.282.5389.699
Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3, Nature, vol.392, pp.831-835, 1998. ,
Targeted Recruitment of the Sin3-Rpd3 Histone Deacetylase Complex Generates a Highly Localized Domain of Repressed Chromatin In Vivo, Molecular and Cellular Biology, vol.18, issue.9, pp.5121-5127, 1998. ,
DOI : 10.1128/MCB.18.9.5121
The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast, Proceedings of the National Academy of Sciences, vol.99, issue.21, pp.13431-13436, 2002. ,
DOI : 10.1073/pnas.202495299
Transcriptional regulatory code of a eukaryotic genome, Nature, vol.18, issue.7004, pp.99-104, 2004. ,
DOI : 10.1093/bioinformatics/15.7.607
Genome-wide binding map of the histone deacetylase Rpd3 in yeast, Nature Genetics, vol.31, issue.3, pp.248-254, 2002. ,
DOI : 10.1038/ng907
The Rpd3 Core Complex Is a Chromatin Stabilization Module, Current Biology, vol.22, issue.1, pp.56-63, 2012. ,
DOI : 10.1016/j.cub.2011.11.042
URL : http://doi.org/10.1016/j.cub.2011.11.042
Gcn5p-dependent acetylation induces degradation of the meiotic transcriptional repressor Ume6p, Molecular Biology of the Cell, vol.23, issue.9, pp.1609-1617, 2012. ,
DOI : 10.1091/mbc.E11-06-0536
Ume6p is required for germination and early colony development of yeast ascospores, FEMS Yeast Research, vol.11, issue.1, pp.104-113, 2011. ,
DOI : 10.1111/j.1567-1364.2010.00696.x
Meiosis-Specific Destruction of the Ume6p Repressor by the Cdc20-Directed APC/C, Molecular Cell, vol.27, issue.6, pp.951-961, 2007. ,
DOI : 10.1016/j.molcel.2007.08.019
Extensive Transcript Diversity and Novel Upstream Open Reading Frame Regulation in Yeast, G3: Genes|Genomes|Genetics, vol.3, issue.2, pp.343-352, 2013. ,
DOI : 10.1534/g3.112.003640
The undertranslated transcriptome reveals widespread translational silencing by alternative 5 transcript leaders, Genome Biology, vol.6, issue.13, p.111, 2005. ,
DOI : 10.1186/gb-2005-6-13-r111
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome, Proceedings of the National Academy of Sciences, vol.103, issue.47, pp.17846-17851, 2006. ,
DOI : 10.1073/pnas.0605645103
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution, Nature, vol.376, issue.7199, pp.1239-1243, 2008. ,
DOI : 10.1038/nature07002
Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae, RNA, vol.18, issue.6, pp.1142-1153, 2012. ,
DOI : 10.1261/rna.030510.111
Extensive transcriptional heterogeneity revealed by isoform profiling, Nature, vol.458, issue.7447, pp.127-131, 2013. ,
DOI : 10.1038/nature12121
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705217
morphological transition, Molecular Microbiology, vol.9, issue.3, pp.570-585, 2014. ,
DOI : 10.1111/mmi.12576
Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements, Cellular and Molecular Life Sciences, vol.17, issue.21, pp.3613-3634, 2012. ,
DOI : 10.1007/s00018-012-0990-9
Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets, Cell, vol.136, issue.4, pp.731-745, 2009. ,
DOI : 10.1016/j.cell.2009.01.042
Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae, Genome Biology, vol.14, issue.2, p.13, 2013. ,
DOI : 10.1093/bioinformatics/btl140
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast, BMC Genomics, vol.10, issue.1, p.7, 2009. ,
DOI : 10.1186/1471-2164-10-7
High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling, Science, vol.335, issue.6068, pp.552-557, 2012. ,
DOI : 10.1126/science.1215110
High-resolution transcription atlas of the mitotic cell cycle in budding yeast, Genome Biology, vol.11, issue.3, p.24, 2010. ,
DOI : 10.1186/gb-2010-11-3-r24
Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6, Proceedings of the National Academy of Sciences, vol.108, issue.3, pp.1058-1063, 2011. ,
DOI : 10.1073/pnas.1016459108
URL : https://hal.archives-ouvertes.fr/hal-00682830
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing, Science, vol.320, issue.5881, pp.1344-1349, 2008. ,
DOI : 10.1126/science.1158441
High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing, Proceedings of the National Academy of Sciences, vol.104, issue.5, pp.1522-1527, 2007. ,
DOI : 10.1073/pnas.0610354104
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1780280
Assessment of Algorithms for Inferring Positional Weight Matrix Motifs of Transcription Factor Binding Sites Using Protein Binding Microarray Data, PLoS ONE, vol.7, issue.9, p.46145, 2012. ,
DOI : 10.1371/journal.pone.0046145.s007
Sequencing and comparison of yeast species to identify genes and regulatory elements, Nature, vol.113, issue.6937, pp.241-254, 2003. ,
DOI : 10.1128/MCB.20.15.5766-5776.2000
Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting, Science, vol.301, issue.5629, pp.71-76, 2003. ,
DOI : 10.1126/science.1084337
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation, Briefings in Bioinformatics, vol.9, issue.4, pp.326-332, 2008. ,
DOI : 10.1093/bib/bbn016
Determining the specificity of protein???DNA interactions, Nature Reviews Genetics, vol.28, pp.751-760, 2010. ,
DOI : 10.1038/nrg2845
Computational methods for the detection of cis-regulatory modules, Briefings in Bioinformatics, vol.10, issue.5, pp.509-524, 2009. ,
DOI : 10.1093/bib/bbp025
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species, Nucleic Acids Research, vol.40, issue.D1, pp.162-168, 2012. ,
DOI : 10.1093/nar/gkr1180
A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes, Yeast, vol.21, issue.11, pp.947-962, 2004. ,
DOI : 10.1002/yea.1142
New heterologous modules for classical or PCR-based gene disruptions inSaccharomyces cerevisiae, Yeast, vol.109, issue.13, pp.1793-1808, 1994. ,
DOI : 10.1002/yea.320101310
The 50:50 method for PCR-based seamless genome editing in yeast, Yeast, vol.10, issue.3, pp.31-103, 2014. ,
DOI : 10.1002/yea.2992
Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Statist. Soc. B, vol.57, pp.289-300, 1995. ,
TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes, Nucleic Acids Research, vol.34, issue.90001, pp.108-110, 2006. ,
DOI : 10.1093/nar/gkj143
URL : http://doi.org/10.1093/nar/gkj143
Proteome analysis and genome-wide regulatory motif prediction identify novel potentially sex-hormone regulated proteins in rat efferent ducts, International Journal of Andrology, vol.23, issue.5, pp.661-674, 2010. ,
DOI : 10.1111/j.1365-2605.2009.01006.x
URL : https://hal.archives-ouvertes.fr/inserm-00517333
MEME SUITE: tools for motif discovery and searching, Nucleic Acids Research, vol.37, issue.Web Server, pp.202-208, 2009. ,
DOI : 10.1093/nar/gkp335
URL : http://doi.org/10.1093/nar/gkp335
DREME: motif discovery in transcription factor ChIP-seq data, Bioinformatics, vol.27, issue.12, pp.1653-1659, 2011. ,
DOI : 10.1093/bioinformatics/btr261
Quantifying similarity between motifs, Genome Biology, vol.8, issue.2, p.24, 2007. ,
DOI : 10.1186/gb-2007-8-2-r24
Detection of functional DNA motifs via statistical over-representation, Nucleic Acids Research, vol.32, issue.4, pp.1372-1381, 2004. ,
DOI : 10.1093/nar/gkh299
Primer3--new capabilities and interfaces, Primer3?new capabilities and interfaces, p.115, 2012. ,
DOI : 10.1093/nar/gks596
Population genomics of domestic and wild yeasts, Nature, vol.26, issue.7236, pp.337-341, 2009. ,
DOI : 10.1038/nature07743
Budding yeast centromere composition and assembly as revealed by in vivo??cross-linking, Genes & Development, vol.11, issue.24, pp.3401-3412, 1997. ,
DOI : 10.1101/gad.11.24.3401
Acetylation of the Transcriptional Repressor Ume6p Allows Efficient Promoter Release and Timely Induction of the Meiotic Transient Transcription Program in Yeast, Molecular and Cellular Biology, vol.34, issue.4, pp.631-642, 2014. ,
DOI : 10.1128/MCB.00256-13
Genome-wide analysis reveals novel molecular features of mouse recombination hotspots, Nature, vol.458, issue.7343, pp.375-378, 2011. ,
DOI : 10.1038/nature09869
URL : https://hal.archives-ouvertes.fr/hal-00877681
A high-resolution map of transcription in the yeast genome, Proceedings of the National Academy of Sciences, vol.103, issue.14, pp.5320-5325, 2006. ,
DOI : 10.1073/pnas.0601091103
Gene Ontology Annotations and Resources, Nucleic Acids Research, vol.41, issue.D1, pp.530-535, 2013. ,
DOI : 10.1093/nar/gks1050
The Sum1/Ndt80 Transcriptional Switch and Commitment to Meiosis in Saccharomyces cerevisiae, Microbiology and Molecular Biology Reviews, vol.76, issue.1, pp.1-15, 2012. ,
DOI : 10.1128/MMBR.05010-11
binuclear cluster that binds the URS1 DNA sequence in a zinc-dependent manner, Protein Science, vol.30, issue.9, pp.1832-1843, 1995. ,
DOI : 10.1002/pro.5560040918
Widespread Collaboration of Isw2 and Sin3-Rpd3 Chromatin Remodeling Complexes in Transcriptional Repression, Molecular and Cellular Biology, vol.21, issue.19, pp.6450-6460, 2001. ,
DOI : 10.1128/MCB.21.19.6450-6460.2001
UME6 is a key regulator of nitrogen repression and meiotic development., Genes & Development, vol.8, issue.7, pp.796-810, 1994. ,
DOI : 10.1101/gad.8.7.796
Microarray Deacetylation Maps Determine Genome-Wide Functions for Yeast Histone Deacetylases, Cell, vol.109, issue.4, pp.437-446, 2002. ,
DOI : 10.1016/S0092-8674(02)00746-8
URL : http://doi.org/10.1016/s0092-8674(02)00746-8
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription, Nature Genetics, vol.11, issue.3, pp.303-309, 2007. ,
DOI : 10.1073/pnas.250477697
Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex, Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, vol.1731, issue.2, pp.1731-77, 2005. ,
DOI : 10.1016/j.bbaexp.2005.09.005
The Regulation of Filamentous Growth in Yeast, Genetics, vol.190, issue.1, pp.23-49, 2012. ,
DOI : 10.1534/genetics.111.127456
Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network, Genome Research, vol.14, issue.3, pp.380-390, 2004. ,
DOI : 10.1101/gr.2020604
Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins, Cell, vol.154, issue.1, pp.240-251, 2013. ,
DOI : 10.1016/j.cell.2013.06.009
URL : http://doi.org/10.1016/j.cell.2013.06.009
Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis, Molecular & Cellular Proteomics, vol.11, issue.2, pp.111-012682, 2012. ,
DOI : 10.1074/mcp.M111.012682
URL : https://hal.archives-ouvertes.fr/hal-00682837
An atlas of active enhancers across human cell types and tissues, Nature, vol.45, issue.7493, pp.455-461, 2014. ,
DOI : 10.1093/bioinformatics/btq033
Diversity and dynamics of the Drosophila transcriptome, Nature, vol.34, issue.7515, pp.393-399, 2014. ,
DOI : 10.1038/nature12962
Two independent transcription initiation codes overlap on vertebrate core promoters, Nature, vol.9, issue.7492, pp.381-385, 2014. ,
DOI : 10.1038/nature12974
Translational Control in Spermatogenesis, Developmental Biology, vol.172, issue.2, pp.344-352, 1995. ,
DOI : 10.1006/dbio.1995.8049
Comparative genomics reveals gene-specific and shared regulatory sequences in the spermatid-expressed mammalian Odf1, Prm1, Prm2, Tnp1, and Tnp2 genes, Genomics, vol.92, issue.2, pp.101-106, 2008. ,
DOI : 10.1016/j.ygeno.2008.05.001
Transcriptome Profiling of the Murine Testis during the First Wave of Spermatogenesis, PLoS ONE, vol.40, issue.4, p.61558, 2013. ,
DOI : 10.1371/journal.pone.0061558.s009
Chromatin associated Sin3A is essential for male germ cell lineage in the mouse, Developmental Biology, vol.369, issue.2, pp.349-355, 2012. ,
DOI : 10.1016/j.ydbio.2012.07.006
Distinct requirements for Sin3a in perinatal male gonocytes and differentiating spermatogonia, Developmental Biology, vol.373, issue.1, pp.83-94, 2013. ,
DOI : 10.1016/j.ydbio.2012.10.009
Sin3a Is Required by Sertoli Cells to Establish a Niche for Undifferentiated Spermatogonia, Germ Cell Tumors, and Spermatid Elongation, STEM CELLS, vol.317, issue.8, pp.1424-1434, 2010. ,
DOI : 10.1002/stem.464
Sin3: Master scaffold and transcriptional corepressor, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1789, issue.6-8, pp.1789-443, 2009. ,
DOI : 10.1016/j.bbagrm.2009.05.007
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686104
Histone deacetylases and cancer, Molecular Oncology, vol.97, issue.6, pp.579-589, 2012. ,
DOI : 10.1016/j.molonc.2012.07.003
The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men, Nature Reviews Molecular Cell Biology, vol.110, issue.3, pp.206-218, 2008. ,
DOI : 10.1038/nrm2346
Sin3: a flexible regulator of global gene expression and genome stability, Current Genetics, vol.21, issue.1, pp.1-17, 2005. ,
DOI : 10.1007/s00294-004-0541-5
Sin3a acts through a multi-gene module to regulate invasion in Drosophila and human tumors, Oncogene, vol.14, issue.26, pp.3184-3197, 2012. ,
DOI : 10.1038/onc.2012.326