General DNA Methylation Patterns and Environmentally-Induced Differential Methylation in the Eastern Oyster (Crassostrea virginica)

Abstract

Epigenetic modification, specifically DNA methylation, is one possible mechanism for intergenerational plasticity. Before inheritance of methylation patterns can be characterized, we need a better understanding of how environmental change modifies the parental epigenome. To examine the influence of experimental ocean acidification on eastern oyster (Crassostrea virginica) gonad tissue, oysters were cultured in the laboratory under control (491 ± 49 µatm) or high (2550 ± 211 µatm) pCO 2 conditions for 4 weeks. DNA from reproductive tissue was isolated from five oysters per treatment, then subjected to bisulfite treatment and DNA sequencing. Irrespective of treatment, DNA methylation was primarily found in gene bodies with approximately 22% of CpGs (2.7% of total cytosines) in the C. virginica genome predicted to be methylated. In response to elevated pCO 2 , we found 598 differentially methylated loci primarily overlapping with gene bodies. A majority of differentially methylated loci were in exons (61.5%) with less intron overlap (31.9%). While there was no evidence of a significant tendency for the genes with differentially methylated loci to be associated with distinct biological processes, the concentration of these loci in gene bodies, including genes involved in protein ubiquitination and biomineralization, suggests DNA methylation may be important for transcriptional control in response to ocean acidification. Changes in gonad methylation also indicate potential for these methylation patterns to be inherited by offspring. Understanding how experimental ocean acidification conditions modify the oyster epigenome, and if these modifications are inherited, allows for a better understanding of how ecosystems will respond to environmental change.

Oyster biomineralization under ocean acidification: From genes to shell

“…The number of hypermethylated genes were higher than hypomethylated genes under OA (Figure S6ii in File S1) which is similar to the observations in an oyster Crassostrea virginica and coral ( Pocillopora damicorni s) species under OA (Putnam et al, 2016; Venkataraman et al, 2020). However, global DNA methylation levels do not always increase under stressors as hypomethylation also occurs in response to stressors (Bogan et al, 2020; Gonzalez‐Romero et al, 2017).…”

Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)

“…Crassostrea virginica exhibited a subtle genome-wide DNA methylation response to high OA, similar to the gene expression response of C. virginica . This genome-wide DNA methylation response to OA has been found in several other species of marine calcifiers, including corals, pteropods, and in the gonadal tissue of C. virginica (Putnam et al, 2016;Liew et al, 2018;Bogan et al, 2020;Venkataraman et al, 2020) . In the present study, OA was associated with a genome-wide decrease in methylation (hypomethylation), similar to the response observed in pteropods (Bogan et al, 2020) , but opposite the response observed in corals (Putnam et al, 2016;Liew et al, 2018) .…”

“…Interestingly, the overall response of individual loci to OA was quite small (85 DML across both time points) in the mantle tissue compared to the gonadal tissue (Venkataraman et al, 2020) , which exhibited hundreds of differentially methylated loci. Although the differential results amongst tissue types may arise from differences in methodologies, the distinct lack of overlap in DML suggests that a fundamental difference in responses exists amongst different tissue types.…”

“…Here, destranding involves combining the cytosine calls within a single CpG from either strand (i.e., top or bottom) and the proportion methylation was determined by dividing the number of methylated cytosine calls by the total coverage (regardless of methylation status). Finally, CpG loci were annotated by feature (e.g., introns, exons, and intergenic regions) and genomic coordinate using feature tracks created based on methods outlined in (Venkataraman et al, 2020) using the gene annotation file available on NCBI (Accession:…”

“…In marine invertebrates, DNA methylation primarily appears to occur in gene bodies (Gavery and Roberts, 2010;Dixon et al, 2018;Zhang et al, 2020) , and has been shown to respond to OA (Venkataraman et al, 2020) . Consistent with previous findings, the large majority (~94%) of all CpGs with 5x coverage and OA-induced DML were within gene bodies.…”