A. J. Levine, The Future of Systems Biology, Curr. Opin. Syst. Biol, vol.1, 2017.

C. Cosseau, Trends 3. Nicoglou, A. & Merlin, F. Epigenetics: A way to bridge the gap between biological fields, Stud. Hist

, Philos. Sci. Part C Stud. Hist. Philos. Biol. Biomed. Sci. 1, p.12, 2017.

R. D. Hotchkiss, The quantitative separation of purines, pyrimidines and nucleosides by paper 14 chromatography, J. Biol. Chem, vol.175, pp.315-332, 1948.

P. Ye, MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine 32 binding proteins in the amphioxus Branchiostoma floridae, Dev. Genes Evol, vol.218, pp.691-701, 2008.

M. Schaefer and F. Lyko, Solving the Dnmt2 enigma, Chromosoma, vol.119, pp.35-40, 2010.

G. Raddatz, Dnmt2-dependent methylomes lack defined DNA methylation patterns, Proc. Natl

. Acad and . Sci, , vol.110, pp.8627-8631, 2013.

M. Okano, S. Xie, and E. Li, Cloning and characterization of a family of novel mammalian DNA 37 (cytosine-5) methyltransferases, Nat. Am. Inc, vol.19, pp.219-220, 1998.

M. M. Suzuki and A. Bird, DNA methylation landscapes: provocative insights from epigenomics
DOI : 10.1038/nrg2341

. Rev and . Genet, , vol.9, pp.465-76, 2008.

A. G. Rivenbark, Epigenetic reprogramming of cancer cells via targeted DNA methylation

, Epigenetics, vol.7, pp.350-360, 2012.

C. M. Casimir, P. B. Gates, R. K. Patient, and J. P. Brockes, Evidence for dedifferentiation and 43 metaplasia in amphibian limb regeneration from inheritance of DNA methylation, Development, vol.104, pp.657-668, 1988.

C. Mugatroyd, Y. Wu, Y. Bockmühl, and D. Spengler, The janus face of DNA methylation in aging

, Aging, vol.2, pp.107-110, 2010.

S. Cortijo, Mapping the Epigenetic Basis of Complex Traits, vol.343, pp.1145-1148, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01193838

S. V. Yi and M. Goodisman, Computational approaches for understanding the evolution of DNA 3 methylation in animals, Epigenetics, vol.4, pp.551-556, 2009.

I. Bulla, Notos-a galaxy tool to analyze CpN observed expected ratios for inferring DNA 5 methylation types, BMC Bioinformatics, vol.19, p.105, 2018.

A. P. Bird, DNA methylation and the frequency of CpG in animal DNA, Nucleic Acids Res, vol.8, pp.1499-1506, 1980.

K. J. Fryxell and W. J. Moon, CpG mutation rates in the human genome are highly dependent on local 9 GC content, Mol. Biol. Evol, vol.22, pp.650-658, 2005.

D. N. Cooper and M. Krawczak, Cytosine methylation and the fate of CpG dinucleotides in vertebrate 11 genomes, Hum. Genet, vol.83, pp.181-188, 1989.

K. Jabbari and G. Bernardi, Cytosine methylation and CpG, TpG (CpA) and TpA frequencies, Gene, vol.13, pp.143-149, 2004.
DOI : 10.1016/j.gene.2004.02.043

A. Razin and H. Cedar, Distribution of 5-methylcytosine in chromatin, Proc. Natl. Acad. Sci. U. S. A, vol.15, issue.74, pp.2725-2728, 1977.

M. M. Suzuki, A. R. Kerr, D. De-sousa, and A. Bird, CpG methylation is targeted to transcription 17 units in an invertebrate genome, Genome Res, vol.17, pp.625-656, 2007.

M. R. Gavery and S. B. Roberts, DNA methylation patterns provide insight into epigenetic regulation 19 in the Pacific oyster (Crassostrea gigas), BMC Genomics, vol.11, p.483, 2010.

J. Park, Comparative analyses of DNA methylation and sequence evolution using Nasonia 21 genomes, Mol. Biol. Evol, vol.28, pp.3345-3354, 2011.

G. B. Dixon, L. K. Bay, and M. V. Matz, Bimodal signatures of germline methylation are linked with 23 gene expression plasticity in the coral Acropora millepora, BMC Genomics, vol.15, p.1109, 2014.

T. K. Walsh, A functional DNA methylation system in the pea aphid

, Insect Mol. Biol, vol.19, pp.215-228, 2010.

I. Bulla, Notos-a Galaxy tool to analyze CpN observed expected ratios for inferring DNA 27 methylation types, vol.28, p.37, 2017.
DOI : 10.1101/180463
URL : https://www.biorxiv.org/content/biorxiv/early/2017/08/25/180463.full.pdf

A. J. Bewick, K. J. Vogel, A. J. Moore, and R. J. Schmitz, Evolution of DNA Methylation across 29 Insects, Mol. Biol. Evol, vol.34, p.264, 2016.
DOI : 10.1093/molbev/msw264
URL : https://academic.oup.com/mbe/article-pdf/34/3/654/26290493/msw264.pdf

T. Driscoll, J. J. Gillespie, E. K. Nordberg, A. F. Azad, and B. W. Sobral, Bacterial DNA sifted from 31 the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial 32 endosymbiont, Genome Biol. Evol, vol.5, pp.621-645, 2013.

U. Storb and B. Arp, Methylation patterns of immunoglobulin genes in lymphoid cells: correlation of 34 expression and differentiation with undermethylation, Proc. Natl. Acad. Sci. U. S. A, vol.80, p.35, 1983.

A. J. Bewick and R. J. Schmitz, Gene body DNA methylation in plants, Curr. Opin. Plant Biol, vol.36, pp.103-110, 2017.
DOI : 10.1016/j.pbi.2016.12.007
URL : http://europepmc.org/articles/pmc5413422?pdf=render

X. He, T. Chen, and J. Zhu, Regulation and function of DNA methylation in plants and animals

, Cell Res, vol.21, pp.442-465, 2011.

D. Onofrio, G. Berná, L. Alvarez-valin, and F. , How fast is the sessile Ciona?, Comp. Funct. Genomics, vol.41, 2009.

J. Bowman, Genotype × environment interactions, Genet. Sel. Evol, vol.4, p.117, 1972.
URL : https://hal.archives-ouvertes.fr/hal-00892497

E. Danchin, Beyond DNA: integrating inclusive inheritance into an extended theory of 44 evolution, Nat. Rev. Genet, vol.12, pp.475-486, 2011.

E. Lamm, The Standford Encyclopedia of Philosophy, p.46

S. Lab and . University, PLoS Biol, vol.8, 2010.

S. Fneich, 5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria 2 glabrata, a snail intermediate host of Schistosoma mansoni, Parasit. Vectors, vol.6, p.167, 2013.

Y. Wurm, The genome of the fire ant Solenopsis invicta, Proc Natl Acad Sci U S A, vol.108, pp.5679-5683, 2011.

D. F. Simola, Social insect genomes exhibit dramatic evolution in gene composition and 6 regulation while preserving regulatory features linked to sociality, Genome Res, vol.23, pp.1235-1247, 2013.

X. Wang, Function and Evolution of DNA Methylation in Nasonia vitripennis, PLoS Genet, vol.9, p.9, 2013.

K. L. Robinson, D. Tohidi-esfahani, N. Lo, S. J. Simpson, and G. A. Sword, Evidence for 11 widespread genomic methylation in the migratory locust, Locusta migratoria (orthoptera: Acrididae)

, PLoS One, vol.6, 2011.

H. Xiang, Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

, Nat. Biotechnol, vol.28, pp.516-181, 2010.

C. B. Cunningham, The Genome and Methylome of a Beetle with Complex Social Behavior, p.16

, Nicrophorus vespilloides (Coleoptera: Silphidae), Genome Biol. Evol, vol.7, pp.3383-96, 2015.

M. W. Simmen, Nonmethylated transposable elements and methylated genes in a chordate 18 genome, Science, vol.283, pp.1164-1167, 1999.

F. Chen, T. Chuang, H. Lin, and M. Hsu, , p.20

, Arabidopsis species-the influences of DNA methylation, relative exon position, and exon length, 21 BMC Evol. Biol, vol.14, p.145, 2014.