Bisulfite sequencing highlights a role for epigenetics in regulating stress response

Over the last decade, it has become clear that epigenetic mechanisms could play a role in the toxicity of environmental toxicants. Epigenetic mechanisms are mechanisms that alter the DNA strands without changing the DNA itself. For example, the most well-known epigenetic mechanism is DNA methylation, which refers to the addition of a methyl group to the DNA bases.

In this study, we focus on the DNA methylation patterns in the waterflea Daphnia magna when exposed to a toxic blue green algae called Microcystis.  We studied the methylation patterns in exposed and unexposed animals and found significant differences between the two treatments. First, we observed that some amino acid codons were more susceptible than others. Second, we observed differences in genes involved in protein degradation and transport. Third, we observed a potential relationship between DNA methylation and alternative splicing. Overall, this study suggests that DNA methylation plays an important role in the toxicity response.

Scientific abstract

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.

Full reference (link)

Asselman J, De Coninck DIM, Beert E, Janssen CR, Orsinill L, Pfrender ME, Decaestecker E, De Schamphelaere KAC. 2017. 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. Environmental Science & Technology 51 (2), pp 924–931.