Intergenerational transfer and sex differences of DNA methylation patterns in the Pacific oyster (Crassostrea gigas)

Apart from DNA-sequence-based inheritance, inheritance of epigenetic marks such as DNA methylation is controversial across the tree of life. In mammals, post-fertilization and primordial germ cell reprogramming processes erased most parental DNA methylation information. In nonmammalian vertebrates and insects, it has been proposed that DNA methylation is an essential hereditary carrier. However, how and to what extent general DNA methylation reprogramming affects intergenerational inheritance in molluscs remains unclear. Here, we investigated genome-wide DNA methylation in a mollusc model, the Pacific oyster (Crassostrea gigas), to test how epigenetic information transfers from parents to offspring. Analysis of global methylome revealed that the DNA methylation patterns are highly conserved within families. Almost half of the differentially methylated CpG dinucleotides (DMCs) between families in parents could transfer to offspring. These results provided the direct evidence for the hypothesis that the Pacific oyster DNA methylation patterns are inherited in generations. Moreover, distinct DNA methylation differences between male and female somatic tissues in C. gigas are revealed in this study. These sex-differential methylated genes significantly enriched in the regulation of Rho protein signal transduction process, which indicated that DNA methylation might have an essential role in the sexual differentiation of somatic tissues in C. gigas. Author SummaryTransgenerational inheritance of DNA methylation marks varies across the tree of life. In mammals, post-fertilization and primordial germ cell reprogramming processes obstructed the DNA methylation transmission from parents to child, and only some CpG dinucleotides retain gamete-inherited methylation. However, the DNA methylation inheritance seems apparent in nonmammalian vertebrates and insects. As one of the essential mollusc models, the Pacific oyster Crassostrea gigas have received the most substantial epigenetic studies, mainly focusing on the DNA methylation profiles. While a previous study suggested the existence of paternal inheritance of DNA methylation patterns in C. gigas, more data are needed to confirm this hypothesis. In this study, genome-wide DNA methylation analysis was performed to investigate the epigenetic inheritance in C. gigas. Almost half of the DNA methylation differences between families in parents were found to be transferred to children, indicating the absence of global DNA methylation reprogramming in C. gigas. Besides, extensive hypomethylation in C. gigas females compared with males were also unveiled. These hypomethylated genes were significantly enriched in the regulation of Rho protein signal transduction process. For example, guanine nucleotide exchange factors, including KALRN, FGD1, and FGD6, were hypomethylated in C. gigas females, and the corresponding transcriptions were significantly upregulated. Our findings provided insights into the evolution of DNA methylation patterns, transgenerational epigenetic inheritance, and sexual differentiation in molluscs.