General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)

Abstract

<jats:title>Abstract</jats:title><jats:p>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 (<jats:italic>Crassostrea virginica</jats:italic>) gonad tissue, oysters were cultured in the laboratory under control (491 ± 49 μatm) or high (2550 ± 211 μatm) <jats:italic>p</jats:italic>CO<jats:sub>2</jats:sub> conditions for four 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 <jats:italic>C. virginica</jats:italic> genome predicted to be methylated. In response to elevated <jats:italic>p</jats:italic>CO<jats:sub>2</jats:sub>, 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.</jats:p>

Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases

“…This is expected and is consistent with previous reports applying MBDBS in other marine invertebrates where unmethylated CpGs actually represent the highest proportion of loci in the data, attributable to the nature of the methylation landscape and enrichment protocol (e.g. (Gavery & Roberts, 2013; Venkataraman et al, 2020)). The base pair resolution of methylation revealed by MBDBS is a benefit over MBD-Seq alone because it enables a fine-scale examination of specific genomic features (e.g.…”

Ocean Acidification Induces Subtle Shifts in Gene Expression and DNA Methylation in Mantle Tissue of the Eastern Oyster (Crassostrea virginica)

“…Both types of genes are involved in cell apoptosis and possibly reflect a stress response to OA. Similar OA-induced responses in protein-ubiquitination genes were found in the gonadal tissue of C. virginica (Venkataraman et al, 2020), suggesting OA can induce parallel shifts in DNA methylation in the methylome of different tissues. However, general overlap of OA-induced DNA methylation was low among tissues (2 OA-induced DMLs among 85 identified in the mantle were also induced in the gonadal tissue; Supplementary Figure 3.4).…”

“…Files were then processed by performing a median based normalization of methylation counts among samples, destranding CpGs loci, and filtering loci that did not have at least 5x coverage for each sample using the R package methylKit (v1.10.0; Akalin et al, 2012). Finally, CpG loci were annotated by feature (e.g., introns, exons, and intergenic regions) and genomic coordinates using feature tracks created based on methods outlined in Venkataraman et al (2020) and gene annotation file available on NCBI (Accession: GCA_002022765.4). Hereafter, "gene body" is used to reference the transcriptional region of the gene, which includes exons, introns, and untranslated regions, but not promoters.…”

Inference of DNA methylation patterns in molluscs

“…DNA methylation has been directly investigated by bisulfite sequencing or immunoprecipitation in a total of only 16 species of molluscs: eight gastropods, seven bivalves and one cephalopod. The analysis of an eighth bivalve was published later [26]. Genome-wide analyses are restricted to the freshwater gastropod B. glabrata [27,28] and the congeneric marine bivalves C. gigas and C. virginica [20,26,29,30].…”

“…The analysis of an eighth bivalve was published later [26]. Genome-wide analyses are restricted to the freshwater gastropod B. glabrata [27,28] and the congeneric marine bivalves C. gigas and C. virginica [20,26,29,30]. In addition, the normalized dinucleotide CG content has been analysed in the marine limpet Lottia gigantea [24].…”