Bisulfite Sequencing with Daphnia Highlights a Role for Epigenetics in Regulating Stress Response to Microcystis through Preferential Differential Methylation of Serine and Threonine Amino Acids

Little is known about the influence that environmental stressors may have on genome-wide methylation patterns, and to what extent epigenetics may be involved in environmental stress response. Yet, studies of methylation patterns under stress could provide crucial insights on stress response and toxicity pathways. Here, we focus on genome-wide methylation patterns in the microcrustacean Daphnia magna, a model organism in ecotoxicology and risk assessment, exposed to the toxic cyanobacterium Microcystis aeruginosa. Bisulfite sequencing of exposed and control animals highlighted differential methylation patterns in Daphnia upon exposure to Microcystis primarily in exonic regions. These patterns are enriched for serine/threonine amino acid codons and genes related to protein synthesis, transport and degradation. Furthermore, we observed that genes with differential methylation corresponded well with genes susceptible to alternative splicing in response to Microcystis stress. Overall, our results suggest a complex mechanistic response in Daphnia characterized by interactions between DNA methylation and gene regulation mechanisms. These results underscore that DNA methylation is modulated by environmental stress and can also be an integral part of the toxicity response in our study species.

目前学界对于环境应激源对全基因组甲基化模式的影响，以及表观遗传学在环境应激响应中的参与程度仍所知有限。然而，针对应激状态下甲基化模式的研究，可为应激响应与毒性通路机制提供关键见解。本研究聚焦于暴露于产毒蓝藻铜绿微囊藻（Microcystis aeruginosa）的微甲壳类动物大型溞（Daphnia magna，生态毒理学与风险评估领域的模式生物）的全基因组甲基化模式。通过对暴露组与对照组个体的亚硫酸氢盐测序（Bisulfite sequencing）分析，本研究发现大型溞在暴露于铜绿微囊藻后，其甲基化模式出现显著差异，且差异主要集中在外显子区域。此类差异甲基化区域富集丝氨酸/苏氨酸氨基酸密码子，以及与蛋白质合成、运输及降解相关的基因。此外，本研究观察到，携带差异甲基化的基因与响应铜绿微囊藻应激时易发生可变剪接的基因高度吻合。综上，本研究结果表明大型溞存在一套复杂的应激响应机制，其核心特征为DNA甲基化与基因调控机制间的相互作用。上述结果进一步证实，DNA甲基化可受环境应激调控，同时亦是本研究物种毒性响应过程中的核心组成部分。