, This work was supported by the French ANR programs "miRNAdapt" and "GWAPHID

, UMR 1349 IGEPP, vol.35327

, Université Montpellier 2, UMR1333 DGIMI, F-34095

J. J. Landry, P. T. Pyl, T. Rausch, T. Zichner, M. M. Tekkedil et al., The genomic and transcriptomic landscape of a HeLa cell line, vol.3, pp.1213-1237, 2013.

M. Macville, E. Schröck, H. Padilla-nash, C. Keck, B. Ghadimi et al., Comprehensive and definitive molecular cytogenetic characterization of HeLa cells by spectral karyotyping, Cancer Res, vol.59, pp.141-150, 1999.

. Consortium, The i5K initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment, J Heredity, vol.104, pp.595-600, 2013.

, Genome10K Community of Scientists: Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species, J Heredity, vol.100, pp.659-674, 2009.

U. Sauer, M. Heinemann, and N. Zamboni, Getting closer to the whole picture, Science, vol.316, pp.550-551, 2007.

. Encode-project-consortium, E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigó et al., Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, vol.447, pp.799-816, 2007.

. Encode-project-consortium, I. Dunham, A. Kundaje, S. F. Aldred, P. J. Collins et al., An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, pp.57-74, 2012.

, The International HapMap Consortium: A second generation human haplotype map of over 3.1 million SNPs, Nature, vol.449, pp.851-861, 2007.

. Genomes-project-consortium, G. R. Abecasis, D. Altshuler, A. Auton, L. D. Brooks et al., A map of human genome variation from population-scale sequencing, Nature, vol.467, pp.1061-1073, 2010.

. Nih-hmp-working, . Group, J. Peterson, S. Garges, M. Giovanni et al., The NIH human microbiome project, Genome Res, vol.19, pp.2317-2323, 2009.

M. B. Gerstein, Z. J. Lu, E. L. Van-nostrand, C. Cheng, B. I. Arshinoff et al., Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project, Science, vol.330, pp.1775-1787, 2010.

. Modencode-consortium, S. Roy, J. Ernst, P. V. Kharchenko, P. Kheradpour et al., Identification of functional elements and regulatory circuits by Drosophila modENCODE, Science, vol.330, pp.1787-1797, 2010.

M. D. Adams, S. E. Celniker, R. A. Holt, C. A. Evans, J. D. Gocayne et al., The genome sequence of Drosophila melanogaster, Science, vol.287, pp.2185-2195, 2000.

, International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome, Nature, vol.409, pp.860-921, 2001.

J. C. Venter, M. D. Adams, E. W. Myers, P. W. Li, R. J. Mural et al., The sequence of the human genome, Science, vol.291, pp.1304-1351, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00465088

D. Graur, Y. Zheng, N. Price, R. Azevedo, R. Zufall et al., On the immortality of television sets: "Function" in the human genome according to the evolution-free gospel of ENCODE, Genome Biol Evol, vol.5, pp.578-590, 2013.

S. R. Eddy, The ENCODE project: mistakes overshadowing a success, Curr Biol, vol.23, pp.259-261, 2013.

S. Zhan, C. Merlin, J. L. Boore, and S. M. Reppert, The Monarch butterfly genome yields insights into long-distance migration, Cell, vol.147, pp.1171-1185, 2011.

W. Doolittle, Is junk DNA bunk? A critique of ENCODE, Proc Natl Acad Sci U S A, vol.110, pp.5294-5300, 2013.

M. Gerstein, C. Bruce, J. Rozowsky, D. Zheng, J. Du et al., What is a gene, post-ENCODE? History and updated definition, Genome Res, vol.17, pp.669-681, 2007.

C. Moorman, L. V. Sun, J. Wang, E. De-wit, W. Talhout et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster, Proc Natl Acad Sci, vol.103, pp.12027-12032, 2006.

N. Nègre, C. D. Brown, L. Ma, C. A. Bristow, S. W. Miller et al., A cis-regulatory map of the Drosophila genome, Nature, vol.471, pp.527-531, 2011.

E. Kvon, G. Stampfel, J. Yáñez-cuna, B. Dickson, and A. Stark, HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature, Genes Dev, vol.26, pp.908-913, 2012.

. Encode-project-consortium, R. M. Myers, J. Stamatoyannopoulos, M. Snyder, I. Dunham et al., A user's guide to the encyclopedia of DNA elements (ENCODE), PLoS Biol, vol.9, issue.4, p.1001046, 2011.

B. E. Miner, D. Meester, L. Pfrender, M. E. Lampert, W. Hairston et al., Linking genes to communities and ecosystems: Daphnia as an ecogenomic model, Proc R Soc B, vol.279, pp.1873-1882, 2012.

B. Peterson, J. Weber, E. Kay, H. Fisher, and H. Hoekstra, Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species, PLoS ONE, vol.2012, issue.5, p.37135

Y. Ni, A. Hall, A. Battenhouse, and V. Iyer, Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data, BMC Genet, vol.13, p.79, 2012.

J. Goecks, A. Nekrutenko, J. Taylor, E. Afgan, G. Ananda et al., Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol, vol.11, p.86, 2010.

B. R. Graveley, A. N. Brooks, J. W. Carlson, M. O. Duff, J. M. Landolin et al., The developmental transcriptome of Drosophila melanogaster, Nature, vol.471, pp.473-479, 2011.

P. G. Giresi, J. Kim, R. M. Mcdaniell, V. R. Iyer, and J. D. Lieb, FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin, Genome Res, vol.17, pp.877-885, 2007.

N. Ponts, E. Y. Harris, J. Prudhomme, I. Wick, C. Eckhardt-ludka et al., Nucleosome landscape and control of transcription in the human malaria parasite, Genome Res, vol.20, pp.228-238, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02668939

M. Tan, H. Luo, S. Lee, J. F. Yang, J. S. Montellier et al., Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification, Cell, vol.146, pp.1016-1028, 2011.

G. Filion, J. Van-bemmel, U. Braunschweig, W. Talhout, J. Kind et al., Systematic protein location mapping reveals five principal chromatin types in Drosophila cells, Cell, vol.143, p.12, 2010.

P. V. Kharchenko, A. A. Alekseyenko, Y. B. Schwartz, A. Minoda, N. C. Riddle et al., Comprehensive analysis of the chromatin landscape in Drosophila melanogaster, Nature, vol.471, pp.480-485, 2011.

D. Schmidt, P. C. Schwalie, M. D. Wilson, B. Ballester, A. Gonçalves et al., Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages, Cell, vol.148, p.832, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01615154

X. Ni, Y. E. Zhang, N. Nègre, S. Chen, M. Long et al., Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome, PLoS Biol, vol.10, p.1001420, 2012.

P. Heger, B. Marin, and E. Schierenberg, Loss of the insulator protein CTCF during nematode evolution, BMC Mol Biol, vol.10, p.84, 2009.

A. Castello, B. Fischer, M. W. Hentze, and T. Preiss, RNA-binding proteins in Mendelian disease, Trends Genet, vol.29, pp.318-327, 2013.

J. D. Keene, RNA regulons: coordination of post-transcriptional events, Nat Rev Genet, vol.8, pp.533-543, 2007.

N. T. Ingolia, G. A. Brar, S. Rouskin, A. M. Mcgeachy, and J. S. Weissman, The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments, Nat Protoc, vol.7, pp.1534-1550, 2012.

. Tagu, Submit your next manuscript to BioMed Central and take full advantage of: ? Convenient online submission ? Thorough peer review ? No space constraints or color figure charges ? Immediate publication on acceptance ? Inclusion in PubMed, CAS, Scopus and Google Scholar ? Research which is freely available for redistribution, BMC Genomics, vol.15, p.490, 2014.