M. Vaughn, T. Ic, M. Lippman, Z. Jiang, H. Carrasquillo et al., Epigenetic Natural Variation in Arabidopsis thaliana, PLoS Biology, vol.11, issue.7, p.174, 2007.
DOI : 10.1371/journal.pbio.0050174.st009

E. Schilling, C. Chartouni, and M. Rehli, Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences, Genome Research, vol.19, issue.11, pp.2028-2063, 2009.
DOI : 10.1101/gr.095562.109

S. Liu, K. Sun, T. Jiang, J. Ho, B. Liu et al., Natural epigenetic variation in the female great roundleaf bat (Hipposideros armiger) populations, Molecular Genetics and Genomics, vol.86, issue.8, pp.643-50, 2012.
DOI : 10.1007/s00438-012-0704-x

D. Zhang, L. Cheng, J. Badner, C. Chen, Q. Chen et al., Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain, The American Journal of Human Genetics, vol.86, issue.3, pp.411-420, 2010.
DOI : 10.1016/j.ajhg.2010.02.005

J. Gibbs, M. Van-der-brug, D. Hernandez, B. Traynor, M. Nalls et al., Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain, PLoS Genetics, vol.34, issue.5, p.1000952, 2010.
DOI : 10.1371/journal.pgen.1000952.s014

M. Nagarajan, J. Veyrieras, M. De-dieuleveult, H. Bottin, S. Fehrmann et al., Natural Single-Nucleosome Epi-Polymorphisms in Yeast, PLoS Genetics, vol.31, issue.4, p.1000913, 2010.
DOI : 10.1371/journal.pgen.1000913.s014
URL : https://hal.archives-ouvertes.fr/ensl-00811500

H. Kilpinen, S. Waszak, A. Gschwind, S. Raghav, R. Witwicki et al., Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription, Science, vol.342, issue.6159, pp.744-751, 2013.
DOI : 10.1126/science.1242463

M. Kasowski, S. Kyriazopoulou?panagiotopoulou, F. Grubert, J. Zaugg, A. Kundaje et al., Extensive Variation in Chromatin States Across Humans, Science, vol.342, issue.6159, pp.750-752, 2013.
DOI : 10.1126/science.1242510

G. Mcvicker, B. Van-de-geijn, J. Degner, C. Cain, N. Banovich et al., Identification of Genetic Variants That Affect Histone Modifications in Human Cells, Science, vol.342, issue.6159, pp.747-756, 2013.
DOI : 10.1126/science.1242429

R. Mcdaniell, B. Lee, L. Song, Z. Liu, A. Boyle et al., Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans, Science, vol.328, issue.5975, pp.235-244, 2010.
DOI : 10.1126/science.1184655

X. Chai, S. Nagarajan, K. Kim, K. Lee, and J. Choi, Regulation of the Boundaries of Accessible Chromatin, PLoS Genetics, vol.10, issue.9, p.1003778, 2013.
DOI : 10.1371/journal.pgen.1003778.s008

A. Moghaddam, F. Roudier, M. Seifert, C. Bérard, M. Magniette et al., Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids, The Plant Journal, vol.42, issue.4, pp.691-700, 2011.
DOI : 10.1111/j.1365-313X.2011.04628.x

C. Rintisch, M. Heinig, A. Bauerfeind, S. Schafer, C. Mieth et al., Natural variation of histone modification and its impact on gene expression in the rat genome, Genome Research, vol.24, issue.6, pp.942-53, 2014.
DOI : 10.1101/gr.169029.113

M. Kadota, H. Yang, N. Hu, C. Wang, Y. Hu et al., Allele-Specific Chromatin Immunoprecipitation Studies Show Genetic Influence on Chromatin State in Human Genome, PLoS Genetics, vol.4, issue.5, p.81, 2007.
DOI : 10.1371/journal.pgen.0030081.st008

A. Abraham, M. Nagarajan, J. Veyrieras, H. Bottin, L. Steinmetz et al., Genetic Modifiers of Chromatin Acetylation Antagonize the Reprogramming of Epi-Polymorphisms, PLoS Genetics, vol.8, issue.9, p.1002958, 2012.
DOI : 10.1371/journal.pgen.1002958.s011
URL : https://hal.archives-ouvertes.fr/ensl-00811503

C. Liu, T. Kaplan, M. Kim, S. Buratowski, S. Schreiber et al., Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae, PLoS Biology, vol.57, issue.10, p.328, 2005.
DOI : 10.1371/journal.pbio.0030328.sg007

D. Pokholok, C. Harbison, S. Levine, M. Cole, N. Hannett et al., Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast, Cell, vol.122, issue.4, pp.517-544, 2005.
DOI : 10.1016/j.cell.2005.06.026

C. Chabbert, S. Adjalley, K. B. Fritsch, E. Gupta, I. Pelechano et al., A high-throughput ChIP-Seq for large-scale chromatin studies, Molecular Systems Biology, vol.11, issue.1, p.777, 2015.
DOI : 10.15252/msb.20145776

W. Wei, J. Mccusker, R. Hyman, T. Jones, Y. Ning et al., Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789, Proceedings of the National Academy of Sciences, vol.104, issue.31, pp.12825-12855, 2007.
DOI : 10.1073/pnas.0701291104

G. Liti, D. Carter, A. Moses, J. Warringer, L. Parts et al., Population genomics of domestic and wild yeasts, Nature, vol.26, issue.7236, pp.337-378, 2009.
DOI : 10.1038/nature07743

R. Brem, G. Yvert, R. Clinton, and L. Kruglyak, Genetic Dissection of Transcriptional Regulation in Budding Yeast, Science, vol.296, issue.5568, pp.752-757, 2002.
DOI : 10.1126/science.1069516

D. Ruderfer, S. Pratt, H. Seidel, and L. Kruglyak, Population genomic analysis of outcrossing and recombination in yeast, Nature Genetics, vol.132, issue.9, pp.1077-81, 2006.
DOI : 10.1093/bioinformatics/18.2.337

J. Gagneur, H. Sinha, F. Perocchi, R. Bourgon, W. Huber et al., Genome-wide allele- and strand-specific expression profiling, Molecular Systems Biology, vol.338, p.274, 2009.
DOI : 10.1126/science.1072545
URL : http://doi.org/10.1038/msb.2009.31

J. Dai, E. Hyland, D. Yuan, H. Huang, J. Bader et al., Probing Nucleosome Function: A Highly Versatile Library of Synthetic Histone H3 and H4 Mutants, Cell, vol.134, issue.6, pp.1066-78, 2008.
DOI : 10.1016/j.cell.2008.07.019

J. Breunig, S. Hackett, J. Rabinowitz, and L. Kruglyak, Genetic Basis of Metabolome Variation in Yeast, PLoS Genetics, vol.248, issue.3, p.1004142, 2014.
DOI : 10.1371/journal.pgen.1004142.s008

P. Mews, B. Zee, S. Liu, G. Donahue, B. Garcia et al., Histone Methylation Has Dynamics Distinct from Those of Histone Acetylation in Cell Cycle Reentry from Quiescence, Molecular and Cellular Biology, vol.34, issue.21, pp.3968-80, 2014.
DOI : 10.1128/MCB.00763-14

M. Kuo, J. Brownell, R. Sobel, T. Ranalli, R. Cook et al., Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines, Nature, vol.383, issue.6597, pp.269-72, 1996.
DOI : 10.1038/383269a0

L. Rosaleny, A. Ruiz?garcía, J. García?martínez, J. Pérez?ortín, and V. Tordera, The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes, Genome Biology, vol.8, issue.6, p.119, 2007.
DOI : 10.1186/gb-2007-8-6-r119

S. Vicente?muñoz, P. Romero, L. Magraner?pardo, C. Martinez?jimenez, V. Tordera et al., Comprehensive analysis of interacting proteins and genome-wide location studies of the Sas3-dependent NuA3 histone acetyltransferase complex, FEBS Open Bio, vol.275, issue.1, pp.996-1006, 2014.
DOI : 10.1016/j.fob.2014.11.001

D. Robyr, Y. Suka, I. Xenarios, S. Kurdistani, A. Wang et al., Microarray Deacetylation Maps Determine Genome-Wide Functions for Yeast Histone Deacetylases, Cell, vol.109, issue.4, pp.437-483, 2002.
DOI : 10.1016/S0092-8674(02)00746-8

S. Li and M. Shogren?knaak, The Gcn5 Bromodomain of the SAGA Complex Facilitates Cooperative and Cross-tail Acetylation of Nucleosomes, Journal of Biological Chemistry, vol.284, issue.14, pp.9411-9418, 2009.
DOI : 10.1074/jbc.M809617200

A. Cieniewicz, L. Moreland, A. Ringel, S. Mackintosh, A. Raman et al., The Bromodomain of Gcn5 Regulates Site Specificity of Lysine Acetylation on Histone H3, Molecular & Cellular Proteomics, vol.13, issue.11, pp.114-038174, 2014.
DOI : 10.1074/mcp.M114.038174

E. Smith and L. Kruglyak, Gene???Environment Interaction in Yeast Gene Expression, PLoS Biology, vol.21, issue.4, p.83, 2008.
DOI : 10.1371/journal.pbio.0060083.sd003

Y. Mosesson, Y. Voichek, and N. Barkai, Divergence and Selectivity of Expression-Coupled Histone Modifications in Budding Yeasts, PLoS ONE, vol.49, issue.7, p.101538, 2014.
DOI : 10.1371/journal.pone.0101538.s001

L. Churchman and J. Weissman, Nascent transcript sequencing visualizes transcription at nucleotide resolution, Nature, vol.14, issue.7330, pp.368-73, 2011.
DOI : 10.1038/nature09652

B. Schwalb, D. Schulz, M. Sun, B. Zacher, S. Dümcke et al., Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA), Bioinformatics, vol.28, issue.6, pp.884-889, 2012.
DOI : 10.1093/bioinformatics/bts052

Z. Jónsson, S. Jha, J. Wohlschlegel, and A. Dutta, Rvb1p/Rvb2p Recruit Arp5p and Assemble a Functional Ino80 Chromatin Remodeling Complex, Molecular Cell, vol.16, issue.3, pp.465-77, 2004.
DOI : 10.1016/j.molcel.2004.09.033

R. Vargas, S. Tenreiro, M. Teixeira, A. Fernandes, and I. Sa?correia, Saccharomyces cerevisiae Multidrug Transporter Qdr2p (Yil121wp): Localization and Function as a Quinidine Resistance Determinant, Antimicrobial Agents and Chemotherapy, vol.48, issue.7, pp.2531-2538, 2004.
DOI : 10.1128/AAC.48.7.2531-2537.2004

H. Pace, S. Hodawadekar, A. Draganescu, J. Huang, P. Bieganowski et al., Crystal structure of the worm NitFhit Rosetta Stone protein reveals a Nit tetramer binding two Fhit dimers, Current Biology, vol.10, issue.15, pp.907-924, 2000.
DOI : 10.1016/S0960-9822(00)00621-7

D. Wall, A. Hirsh, H. Fraser, J. Kumm, G. Giaever et al., Functional genomic analysis of the rates of protein evolution, Proceedings of the National Academy of Sciences, vol.102, issue.15, pp.5483-5491, 2005.
DOI : 10.1073/pnas.0501761102

C. Landry, B. Lemos, S. Rifkin, W. Dickinson, and D. Hartl, Genetic Properties Influencing the Evolvability of Gene Expression, Science, vol.317, issue.5834, pp.118-139, 2007.
DOI : 10.1126/science.1140247

I. Tirosh, A. Weinberger, M. Carmi, and N. Barkai, A genetic signature of interspecies variations in gene expression, Nature Genetics, vol.431, issue.7, pp.830-834, 2006.
DOI : 10.1038/ng1819

C. Miller, B. Schwalb, K. Maier, D. Schulz, S. Dumcke et al., Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast, Molecular Systems Biology, vol.472, issue.1, p.458, 2011.
DOI : 10.1186/1471-2105-11-194

F. Chuffart, F. Filleton, and G. Yvert, NucleoMiner 2.0: detecting intra?species quantitative epigenomic variation at single?nucleosome resolution

A. Jansen and K. Verstrepen, Nucleosome Positioning in Saccharomyces cerevisiae, Microbiology and Molecular Biology Reviews, vol.75, issue.2, pp.301-321, 2011.
DOI : 10.1128/MMBR.00046-10

K. Macisaac, T. Wang, D. Gordon, D. Gifford, G. Stormo et al., An improved map of conserved regulatory sites for Saccharomyces cerevisiae, BMC Bioinformatics, vol.7, issue.1, p.113, 2006.
DOI : 10.1186/1471-2105-7-113

A. Hughes, Y. Jin, O. Rando, and K. Struhl, A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern, Molecular Cell, vol.48, issue.1, pp.5-15, 2012.
DOI : 10.1016/j.molcel.2012.07.003

K. Yen, V. Vinayachandran, K. Batta, R. Koerber, and B. Pugh, Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers, Cell, vol.149, issue.7, pp.1461-73, 2012.
DOI : 10.1016/j.cell.2012.04.036

J. Ronald, R. Brem, J. Whittle, and L. Kruglyak, Local Regulatory Variation in Saccharomyces cerevisiae, PLoS Genetics, vol.22, issue.2, p.25, 2005.
DOI : 10.1371/journal.pgen.0010025.st003

. Filleton, The complex pattern of epigenomic variation between natural yeast strains at single-nucleosome resolution, Epigenetics & Chromatin, vol.18, issue.1, p.26, 2015.
DOI : 10.1186/s13072-015-0019-3
URL : https://hal.archives-ouvertes.fr/ensl-01224448

D. Ginsburg, T. Anlembom, J. Wang, S. Patel, B. Li et al., NuA4 Links Methylation of Histone H3 Lysines 4 and 36 to Acetylation of Histones H4 and H3, Journal of Biological Chemistry, vol.289, issue.47, pp.32656-70, 2014.
DOI : 10.1074/jbc.M114.585588

V. Maltby, B. Martin, J. Brind-'amour, A. Chruscicki, K. Mcburney et al., Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae, Proceedings of the National Academy of Sciences, vol.109, issue.45, pp.18505-18515, 2012.
DOI : 10.1073/pnas.1202070109

C. Brachmann, A. Davies, G. Cost, E. Caputo, J. Li et al., Designer deletion strains derived fromSaccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications, Yeast, vol.11, issue.2, pp.115-147, 1998.
DOI : 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-366, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352

A. Quinlan and I. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-843, 2010.
DOI : 10.1093/bioinformatics/btq033

S. Kurtz, A. Phillippy, A. Delcher, M. Smoot, M. Shumway et al., Versatile and open software for comparing large genomes, Genome Biology, vol.5, issue.2, p.12, 2004.
DOI : 10.1186/gb-2004-5-2-r12

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biology, vol.11, issue.10, p.106, 2010.
DOI : 10.1186/gb-2010-11-10-r106

S. Nogami, Y. Ohya, and G. Yvert, Genetic Complexity and Quantitative Trait Loci Mapping of Yeast Morphological Traits, PLoS Genetics, vol.14, issue.2, p.31, 2007.
DOI : 10.1371/journal.pgen.0030031.st005
URL : https://hal.archives-ouvertes.fr/ensl-00135760

A. Weiner, A. Hughes, M. Yassour, O. Rando, and N. Friedman, High-resolution nucleosome mapping reveals transcription-dependent promoter packaging, Genome Research, vol.20, issue.1, pp.90-100, 2010.
DOI : 10.1101/gr.098509.109
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798834

I. Tirosh and N. Barkai, Two strategies for gene regulation by promoter nucleosomes, Genome Research, vol.18, issue.7, pp.1084-91, 2008.
DOI : 10.1101/gr.076059.108