Dynamics of DNA methylomes underlie oyster development

Guillaume Rivière (1) , Yan He (2) , Samuele Tecchio (1) , Elizabeth Crowell (1) , Michael Gras (1) , Pascal Sourdaine (1) , Ximing Guo (3) , Pascal Favrel (1)

1 BOREA - Biologie des Organismes et Ecosystèmes Aquatiques
2 OUC - Ocean University of China
3 Rutgers University [Newark]

DNA methylation is a critical epigenetic regulator of development in mammals and social insects, but its significance in development outside these groups is not understood. Here we investigated the genome-wide dynamics of DNA methylation in a mollusc model, the oyster Crassostrea gigas, from the egg to the completion of organogenesis. Large-scale methyla-tion maps reveal that the oyster genome displays a succession of methylated and non meth-ylated regions, which persist throughout development. Differentially methylated regions (DMRs) are strongly regulated during cleavage and metamorphosis. The distribution and levels of methylated DNA within genomic features (exons, introns, promoters, repeats and transposons) show different developmental lansdscapes marked by a strong increase in the methylation of exons against introns after metamorphosis. Kinetics of methylation in gene-bodies correlate to their transcription regulation and to distinct functional gene clusters, and DMRs at cleavage and metamorphosis bear the genes functionally related to these steps, respectively. This study shows that DNA methylome dynamics underlie development through transcription regulation in the oyster, a lophotrochozoan species. To our knowledge, this is the first demonstration of such epigenetic regulation outside vertebrates and ecdy-sozoan models, bringing new insights into the evolution and the epigenetic regulation of developmental processes.

Domaines: Sciences du Vivant [q-bio]

Guillaume Rivière, Yan He, Samuele Tecchio, Elizabeth Crowell, Michael Gras, et al.. Dynamics of DNA methylomes underlie oyster development. PLoS Genetics, 2017, 13 (6), pp.e1006807. ⟨10.1371/journal.pgen.1006807⟩. ⟨hal-02153935⟩