R. Feil and S. Khosla, Genomic imprinting in mammals: An interplay between chromatin and DNA methylation?, Trends Genet, vol.15, issue.11, pp.431-436, 1999.

B. J. Lesch, S. J. Silber, J. R. Mccarrey, and D. C. Page, Parallel evolution of male germline epigenetic poising and somatic development in animals, Nat Genet, vol.48, issue.8, pp.888-94, 2016.

A. Waclawska and M. Kurpisz, Key functional genes of spermatogenesis identified by microarray analysis, Syst Biol Reprod Med, vol.58, issue.5, pp.229-264, 2012.

M. G. Guenther, S. S. Levine, L. A. Boyer, R. Jaenisch, and R. A. Young, A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells, Cell, vol.130, issue.1, pp.77-88, 2007.

B. Zhang, H. Zheng, B. Huang, W. Li, Y. Xiang et al., Allelic reprogramming of the histone modification H3K4me3 in early mammalian development, Nature, vol.537, issue.7621, pp.553-560, 2016.

V. Azuara, P. Perry, S. Sauer, M. Spivakov, H. F. Jørgensen et al., Chromatin signatures of pluripotent cell lines, Nat Cell Biol, vol.8, issue.5, pp.532-540, 2006.

T. S. Mikkelsen, M. Ku, D. B. Jaffe, B. Issac, E. Lieberman et al., Genome-wide maps of chromatin state in pluripotent and lineage-committed cells, Nature, vol.448, issue.7153, pp.553-60, 2007.

D. Villar, C. Berthelot, S. Aldridge, T. F. Rayner, M. Lukk et al., Enhancer evolution across 20 mammalian species, Cell, vol.160, issue.3, pp.554-66, 2015.

J. C. Eissenberg and A. Shilatifard, Histone H3 lysine 4 (H3K4) methylation in development and differentiation, Dev Biol, vol.339, issue.2, pp.240-249, 2010.

S. Landt and G. Marinov, ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

, Genome ?, pp.1813-1844, 2009.

A. Li, S. Figueroa, T. Jiang, P. Wu, R. Widelitz et al., Diverse feather shape evolution enabled by coupling anisotropic signalling modules with self-organizing branching programme, Nat Commun, vol.8, p.14139, 2017.

S. Jahan, W. Xu, S. He, C. Gonzalez, G. P. Delcuve et al., The chicken erythrocyte epigenome, Epigenetics Chromatin, vol.9, issue.1, p.19, 2016.

J. Luo, A. Mitra, F. Tian, S. Chang, H. Zhang et al., Histone methylation analysis and pathway predictions in chickens after MDV infection, PLoS One, vol.7, issue.7, 2012.

K. Chokeshaiusaha, R. Thanawongnuwech, D. Puthier, and C. Nguyen, Inspection of C-type lectin superfamily expression profile in chicken and mouse dendritic cells, Thai J Vet Med, vol.46, issue.3, pp.443-53, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01460130

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, issue.4, pp.357-366, 2012.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: Ultrafast universal RNAseq aligner, Bioinformatics, vol.29, issue.1, pp.15-21, 2013.

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.

F. Ramírez, F. Dündar, S. Diehl, B. A. Grüning, and T. Manke, DeepTools: A flexible platform for exploring deep-sequencing data, Nucleic Acids Res, vol.42, issue.W1, 2014.

J. Feng, T. Liu, B. Qin, Y. Zhang, and X. S. Liu, Identifying ChIP-seq enrichment using MACS, Nat Protoc, vol.7, issue.9, pp.1728-1768, 2012.

N. L. Vastenhouw and A. F. Schier, Bivalent histone modifications in early embryogenesis, Curr Opin Cell Biol, vol.24, issue.3, pp.374-86, 2012.

C. S. Ross-innes, R. Stark, A. E. Teschendorff, K. A. Holmes, H. R. Ali et al., Differential oestrogen receptor binding is associated with clinical outcome in breast cancer, Nature, 2012.