Table 1 Studies exploring methylation responses to environmental stress in Crassostrea spp (NR = not reported)
Study | Species | Stressor | Experimental Conditions | Exposure Time | Tissue | Sequencing Method | Percent CpGs Methylated | Global methylation differences | Differential methylation (hypermethylated/hypomethylated) | Genome Features Impacted | Gene Functions Enriched at Differentially Methylated Sites | Connection to Transcription |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Downey-Wall et al. 2020 [10] | Crassostrea virginica | Ocean acidification | 580 μatm (control), 2800 μatm (high OA) | 80 days (samples taken at days 9 and 80) | Mantle | MBDBS | NR | Global median methylation significantly lower in the high OA treatment than the control treatment, but increased over time | 85 DML (38 / 47) | DML predominantly in gene regions | Aminotransferase complex and biosynthetic process GOterms were enriched in hypomethylated DML | Weak but statistically significant relationship between DNA methylation and gene expression (RNA-Seq) |
Venkataraman et al. 2020 [12] | Crassostrea virginica | Ocean acidification | 491 ± 49 μatm (control), 2550 ± 211 μatm (treatment) | 28 days | Gonad | MBDBS | 22% | No global methylation differences | 598 DML (310 / 288) | Majority of DML were in exons, followed by introns | None | NR |
Chandra Rajan et al. 2021 [8] | Crassostrea hongkongensis | Ocean acidification | pH 8.0 (control), 7.4 (treatment) | 4.5 months | Mantle | MethylRAD | NR | NR | 377 DMG (214 / 163) | Loci used to identify differentially methylated genes were primarily in introns, followed by exons, intergenic regions, splice donor sites, downstream regions, and upstream regions | Top molecular function GOterms enriched in hypomethylated genes were acetoacetylco-A reductase activity and types of dehydrogenase activity, and biological process terms included cellular response to pH. Top molecular function GOterms enriched in hypermethylated genes were protein xylosyltransferase activity, translation factor activity, RNA binding, diacylglycerol kinase activity. | No direct methylation regulation of gene expression (RNA-Seq) |
Lim et al. 2020 [11] | Crassostrea hongkongensis | Ocean acidification | pH 8.0 (control), 7.4 (treatment) | 21 days | Pediveliger larvae | MethylRAD | NR | NR | 130 DMG (66 / 64) | Loci used to identify differentially methylated genes were concentrated in exons (78.5% of loci) | Enriched processes of DMG were associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis | NR |
Arredondo-Espinoza et al. 2021 [14] | Crassostrea gigas | Heat stress | No control was used, but two heat-susceptible and two heat-tolerant families were exposed to 26 °C–34 °C oscillating temperature conditions | 30 days | Gill | WGBS | 14.01–15.15% (average between four families) | No differences between phenotypes or families within phenotypes | 161 DMR (147 / 14) | DMR were concentrated in introns, followed by exons | Enriched molecular functions include binding processes, catalytic activity, and transporter activity. | NR |
Johnson et al. 2021 [17] | Crassostrea virginica | Salinity | Outplant at two sites that differed in salinity | 14 months | Gill | epiGBS/RRBS | NR | Effect of site and family on methylation | 1039 DMR (NR), 730 DMG (441/289) | Strong association with genotype but not site across genome features. Introns and TE had the highest association with genotype methylation | NR | 16 differentially methylated and differentially expressed genes (TagSeq), but this is not significantly different from what would be expected by chance. CpGO/E analysis revealed two clusters of genes, with only one cluster demonstrating an association between higher methylation, higher expression, and low expression variability |
Johnson et al. 2020 [9] | Crassostrea virginica | Perkinsus marinus infection | Outplant at Grand Isle, natural occurence of P. marinus infection | 14 months | Gill | epiGBS/RRBS | NR | NR | 913 DMR from pairwise comparisons between different levels of infection (NR) | 78.8% of DMR found in gene bodies, followed by promoters and downstream regions | None | Near-significant association of increased expression (TagSeq) and promoter methylation, significant interaction between expression and gene body methylation, and no interaction between expression and downstream methylation. Significant relationship between decreasing methylation and increasing gene expression variation. Only 2 DMR and 2 DEG overlapped and there was no significant connection between methylation and expression for those overlaps. |
Rondon et al. 2017 [18] | Crassostrea gigas | Diuron exposure | Seawater (control), 0.2-0.3 µg/L diuron (treatment) | 2 7-day periods | Spat of adult oysters exposed to diuron | WGBS | 16.6% CpGs methylated | Parental exposure did not globally modify spat DNA methylation | 236 DMR (121 / 115) | Majority of DMR (73.2%) found in genes, with 38.2% in exons and 34.8% in introns. Genic DMR were generally found at the end of coding sequences, with 36.5% of exon-specific DMR were found in the last exon of genes, and 25.5% of intron-specific DMR were found in the last introns of genes | NR | DNA methylation changes correlated directly with RNA abundance (RNA-Seq) in a small group of highly methylated genes, but did not systematically lead to splice variants (based on qPCR) |