Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification

Abstract

Background: There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change are experienced by coastal ecosystems. Environmentally-induced changes to the methylome can regulate gene expression, but methylome responses may be tissue- and species-specific. To assess how ocean acidification affects the Pacific oyster (Crassostrea gigas) epigenome, we exposed oysters to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for seven weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C->T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results: Analysis of gonad methylomes revealed a total of 1,284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination: commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions: Our work suggests DNA methylation may have a regulatory role in gonad and larval development. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation.

Latitudinal variation and plasticity in response to temperature in Geukensia demissa

“…When examining partial pressures of CO 2 , it was found that exposure to elevated levels caused proteins associated with the cytoskeleton, such as actin isoforms, and oxidative stress to be upregulated (Tomanek et al, 2011). Analysis of gonad methylomes in Pacific oysters also showed genes associated with protein ubiquitination to be differentially methylated in response to differing pH levels (Venkataraman et al, 2022). Here, we found that glutathione S-transferase was upregulated in GA and MA at 20°C, and higher activity of this protein has been found in M. edulis extracted from sites with high pollution (Fitzpatrick et al, 1997), which can alter pH levels.…”