Tissue-specific plasticity of DNA methylation across intertidal microhabitats in juvenile mussels (Mytilus californianus)

Epigenetic modifications to DNA are proposed to underpin plastic responses to environmental change, and the manner in which DNA methylation contributes to plasticity likely differs among tissues. However, few studies have investigated tissue-specific DNA methylation responses to ecologically relevant environmental stressors in natural settings. Here, we used reduced representation bisulfite sequencing on foot and gill to examine the influence of in situ microhabitats on DNA methylation in juvenile California mussels (Mytilus californianus), a foundation species with widespread dispersal and little evidence of genetic population structure. We examined mussels from a one-month reciprocal transplant experiment between a cool, wave-exposed and a warm, wave-protected microhabitat. These manipulations, which were previously shown to alter juvenile mussels heat tolerance, led to significant and highly tissue-specific changes in CpG methylation, including within a number of genes with roles in stress response pathways. Differentially methylated genes were involved in processes including heat shock response, proteolysis, DNA repair, and temperature sensing. In gill, differentially methylated CpGs were more likely to occur in introns relative to other inter- and intragenic features. This study expands on previous research that examined environmentally driven shifts in DNA methylation by documenting plastic and tissue-specific changes in DNA methylation between microhabitats in a natural setting.