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About the Authors:
Guillaume Riviere
* E-mail: [email protected]
Affiliations Normandy University, Caen, France, Université de Caen Normandie, UMR BOREA MNHN, UPMC, UCBN, CNRS-7208, IRD-207, Caen, France
ORCID http://orcid.org/0000-0001-8372-8715
Yan He
Contributed equally to this work with: Yan He, Samuele Tecchio
Affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
Samuele Tecchio
Contributed equally to this work with: Yan He, Samuele Tecchio
Affiliations Normandy University, Caen, France, Université de Caen Normandie, UMR BOREA MNHN, UPMC, UCBN, CNRS-7208, IRD-207, Caen, France
Elizabeth Crowell
Affiliations Normandy University, Caen, France, Université de Caen Normandie, UMR BOREA MNHN, UPMC, UCBN, CNRS-7208, IRD-207, Caen, France
ORCID http://orcid.org/0000-0003-1295-7400
Michaël Gras
Affiliations Normandy University, Caen, France, Université de Caen Normandie, UMR BOREA MNHN, UPMC, UCBN, CNRS-7208, IRD-207, Caen, France
ORCID http://orcid.org/0000-0001-9572-8456
Pascal Sourdaine
Affiliations Normandy University, Caen, France, Université de Caen Normandie, UMR BOREA MNHN, UPMC, UCBN, CNRS-7208, IRD-207, Caen, France
Ximing Guo
Affiliation: Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ, United States of America
Pascal Favrel
Affiliations Normandy University, Caen, France, Université de Caen Normandie, UMR BOREA MNHN, UPMC, UCBN, CNRS-7208, IRD-207, Caen, FranceAbstract
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 methylation maps reveal that the oyster genome displays a succession of methylated and non methylated 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...