T. Chan, S. Yuen, C. Kong, Y. Chan, and A. Chan, Heritable germline epimutation of MSH2 in a family with hereditary nonpolyposis colorectal cancer, Nature Genetics, vol.59, issue.10, pp.1178-1183, 2006.
DOI : 10.1038/sj.onc.1205968

C. Suter, D. Martin, and R. Ward, Germline epimutation of MLH1 in individuals with multiple cancers, Nature Genetics, vol.62, issue.5, pp.497-501, 2004.
DOI : 10.1136/gut.48.6.821

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

E. Richards, Population epigenetics, Current Opinion in Genetics & Development, vol.18, issue.2, pp.221-226, 2008.
DOI : 10.1016/j.gde.2008.01.014

R. Margueron, P. Trojer, and D. Reinberg, The key to development: interpreting the histone code?, Current Opinion in Genetics & Development, vol.15, issue.2, pp.163-176, 2005.
DOI : 10.1016/j.gde.2005.01.005

C. Liu, T. Kaplan, M. Kim, S. Buratowski, and S. Schreiber, Singlenucleosome mapping of histone modifications in S. cerevisiae, PLoS Biol, vol.3, 2005.

C. Koch, R. Andrews, P. Flicek, S. Dillon, and U. Karaoz, The landscape of histone modifications across 1% of the human genome in five human cell lines, Genome Research, vol.17, issue.6, pp.691-707, 2007.
DOI : 10.1101/gr.5704207

Z. Wang, C. Zang, J. Rosenfeld, D. Schones, and A. Barski, Combinatorial patterns of histone acetylations and methylations in the human genome, Nature Genetics, vol.18, issue.7, 2008.
DOI : 10.1073/pnas.0400782101

T. Mikkelsen, J. Hanna, X. Zhang, M. Ku, and M. Wernig, Dissecting direct reprogramming through integrative genomic analysis, Nature, vol.44, issue.7200, pp.49-55, 2008.
DOI : 10.1038/nature07056

B. Bernstein, M. Kamal, K. Lindblad-toh, S. Bekiranov, and D. Bailey, Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse, Cell, vol.120, issue.2, pp.169-181, 2005.
DOI : 10.1016/j.cell.2005.01.001

B. Turner, Defining an epigenetic code, Nature Cell Biology, vol.442, issue.1, pp.2-6, 2007.
DOI : 10.1038/ncb0107-2

R. Sims and D. Reinberg, Is there a code embedded in proteins that is based on post-translational modifications?, Nature Reviews Molecular Cell Biology, vol.4, issue.10, pp.815-820, 2008.
DOI : 10.1038/nrm2502

X. Zhang, S. Shiu, C. A. Borevitz, and J. , Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays, PLoS Genet, vol.4, 2008.

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

J. Hu, J. Pham, I. Dey, T. Li, and T. Vu, Allele-Specific Histone Acetylation Accompanies Genomic Imprinting of the Insulin-Like Growth Factor II Receptor Gene, Endocrinology, vol.141, issue.12, pp.4428-4435, 2000.
DOI : 10.1210/en.141.12.4428

C. Shindo, C. Lister, P. Crevillen, M. Nordborg, and C. Dean, Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response, Genes & Development, vol.20, issue.22, pp.3079-3083, 2006.
DOI : 10.1101/gad.405306

S. Nogami, Y. Ohya, and G. Yvert, Genetic Complexity and Quantitative Trait Loci Mapping of Yeast Morphological Traits, PLoS Genetics, vol.14, issue.2, 2007.
DOI : 10.1371/journal.pgen.0030031.st005

URL : https://hal.archives-ouvertes.fr/ensl-00135760

E. Perlstein, D. Ruderfer, D. Roberts, S. Schreiber, and L. Kruglyak, Genetic basis of individual differences in the response to small-molecule drugs in yeast, Nature Genetics, vol.100, issue.4, pp.496-502, 2007.
DOI : 10.1038/ng1991

R. Brem and L. Kruglyak, The landscape of genetic complexity across 5,700 gene expression traits in yeast, Proceedings of the National Academy of Sciences, vol.102, issue.5, pp.1572-1577, 2005.
DOI : 10.1073/pnas.0408709102

T. Gatbonton, M. Imbesi, M. Nelson, J. Akey, and D. Ruderfer, Telomere length as a quantitative trait: genome-wide survey and genetic mapping of telomere length-control genes in yeast, PLoS Genet, vol.2, 2006.

R. Brem, G. Yvert, R. Clinton, and L. Kruglyak, Genetic Dissection of Transcriptional Regulation in Budding Yeast, Science, vol.296, issue.5568, pp.752-755, 2002.
DOI : 10.1126/science.1069516

L. David, W. Huber, M. Granovskaia, J. Toedling, and C. Palm, 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

W. Lee, D. Tillo, N. Bray, R. Morse, and R. Davis, A high-resolution atlas of nucleosome occupancy in yeast, Nature Genetics, vol.32, issue.10, 2007.
DOI : 10.1038/ng2117

G. Yuan, Y. Liu, M. Dion, M. Slack, and L. Wu, Genome-Scale Identification of Nucleosome Positions in S. cerevisiae, Science, vol.309, issue.5734, pp.626-630, 2005.
DOI : 10.1126/science.1112178

S. Shivaswamy, A. Bhinge, Y. Zhao, S. Jones, and M. Hirst, Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation, PLoS Biol, vol.6, 2008.

D. Pokholok, C. Harbison, S. Levine, M. Cole, and N. Hannett, Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast, Cell, vol.122, issue.4, pp.517-527, 2005.
DOI : 10.1016/j.cell.2005.06.026

Y. Benjamini and Y. Hochberg, Controlling the False Discovery Rate -a Practical and Powerful Approach to Multiple Testing, Journal of the Royal Statistical Society Series B-Methodological, vol.57, pp.289-300, 1995.

J. Smith and J. Boeke, An unusual form of transcriptional silencing in yeast ribosomal DNA., Genes & Development, vol.11, issue.2, pp.241-254, 1997.
DOI : 10.1101/gad.11.2.241

F. Winston, D. Chaleff, B. Valent, and G. Fink, Mutations affecting Tymediated expression of the HIS4 gene of Saccharomyces cerevisiae, Genetics, vol.107, pp.179-197, 1984.

A. Morillon, L. Benard, M. Springer, and P. Lesage, Differential Effects of Chromatin and Gcn4 on the 50-Fold Range of Expression among Individual Yeast Ty1 Retrotransposons, Molecular and Cellular Biology, vol.22, issue.7, pp.2078-2088, 2002.
DOI : 10.1128/MCB.22.7.2078-2088.2002

M. Carrozza, B. Li, L. Florens, T. Suganuma, and S. Swanson, Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription, Cell, vol.123, issue.4, pp.581-592, 2005.
DOI : 10.1016/j.cell.2005.10.023

J. Ansel, H. Bottin, C. Rodriguez-beltran, C. Damon, and M. Nagarajan, Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait, PLoS Genetics, vol.35, issue.2, 2008.
DOI : 10.1371/journal.pgen.1000049.s006

URL : https://hal.archives-ouvertes.fr/ensl-00272739

A. Barski, S. Cuddapah, K. Cui, T. Roh, and D. Schones, High-Resolution Profiling of Histone Methylations in the Human Genome, Cell, vol.129, issue.4, pp.823-837, 2007.
DOI : 10.1016/j.cell.2007.05.009

K. Macisaac, T. Wang, D. Gordon, D. Gifford, and G. Stormo, 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

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. Landry, B. Lemos, S. Rifkin, W. Dickinson, and D. Hartl, Genetic Properties Influencing the Evolvability of Gene Expression, Science, vol.317, issue.5834, pp.118-121, 2007.
DOI : 10.1126/science.1140247

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

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

H. Reinke and W. Horz, Histones Are First Hyperacetylated and Then Lose Contact with the Activated PHO5 Promoter, Molecular Cell, vol.11, issue.6, pp.1599-1607, 2003.
DOI : 10.1016/S1097-2765(03)00186-2

B. Panaretou, G. Siligardi, P. Meyer, A. Maloney, and J. Sullivan, Activation of the ATPase Activity of Hsp90 by the Stress-Regulated Cochaperone Aha1, Molecular Cell, vol.10, issue.6, pp.1307-1318, 2002.
DOI : 10.1016/S1097-2765(02)00785-2

S. Rutherford and S. Henikoff, Quantitative epigenetics, Nature Genetics, vol.33, issue.1, pp.6-8, 2003.
DOI : 10.1016/S1097-2765(00)00078-2

V. Sollars, X. Lu, L. Xiao, X. Wang, and M. Garfinkel, Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolution, Nature Genetics, vol.7, issue.1, pp.70-74, 2003.
DOI : 10.1038/366223a0

E. Foss, D. Radulovic, S. Shaffer, D. Ruderfer, and A. Bedalov, Genetic basis of proteome variation in yeast, Nature Genetics, vol.74, issue.11, pp.1369-1375, 2007.
DOI : 10.1038/ng.2007.22

H. Bjornsson, M. Fallin, and A. Feinberg, An integrated epigenetic and genetic approach to common human disease, Trends in Genetics, vol.20, issue.8, pp.350-358, 2004.
DOI : 10.1016/j.tig.2004.06.009

F. Johannes, V. Colot, and R. Jansen, Epigenome dynamics: a quantitative genetics perspective, Nature Reviews Genetics, vol.128, issue.11, pp.883-890, 2008.
DOI : 10.1038/nrg2467

G. Elaut, V. Rogiers, and T. Vanhaecke, The Pharmaceutical Potential of Histone Deacetylase Inhibitors, Current Pharmaceutical Design, vol.13, issue.25, pp.2584-2620, 2007.
DOI : 10.2174/138161207781663064

C. Brachmann, A. Davies, G. Cost, E. Caputo, and J. Li, 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.115-132, 1998.
DOI : 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2

M. Braunstein, A. Rose, S. Holmes, C. Allis, and J. Broach, Transcriptional silencing in yeast is associated with reduced nucleosome acetylation., Genes & Development, vol.7, issue.4, pp.592-604, 1993.
DOI : 10.1101/gad.7.4.592

M. Pfaffl, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Research, vol.29, issue.9, p.45, 2001.
DOI : 10.1093/nar/29.9.e45

S. Kurtz, A. Phillippy, A. Delcher, M. Smoot, and M. Shumway, 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

A. Delcher, D. Harmon, S. Kasif, O. White, and S. Salzberg, Improved microbial gene identification with GLIMMER, Nucleic Acids Research, vol.27, issue.23, pp.4636-4641, 1999.
DOI : 10.1093/nar/27.23.4636

URL : http://doi.org/10.1093/nar/27.23.4636

A. Lomsadze, V. Ter-hovhannisyan, Y. Chernoff, and M. Borodovsky, Gene identification in novel eukaryotic genomes by self-training algorithm, Nucleic Acids Research, vol.33, issue.20, pp.6494-6506, 2005.
DOI : 10.1093/nar/gki937

F. Perocchi, Z. Xu, S. Clauder-munster, and L. Steinmetz, Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D, Nucleic Acids Research, vol.35, issue.19, p.128, 2007.
DOI : 10.1093/nar/gkm683

B. Bolstad, R. Irizarry, M. Astrand, and T. Speed, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, vol.19, issue.2, pp.185-193, 2003.
DOI : 10.1093/bioinformatics/19.2.185

R. Irizarry, B. Bolstad, C. F. Cope, L. Hobbs, and B. , Summaries of Affymetrix GeneChip probe level data, Nucleic Acids Research, vol.31, issue.4, p.15, 2003.
DOI : 10.1093/nar/gng015