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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

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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.
Keywords
TOXIC CYANOBACTERIUM MICROCYSTIS, DNA METHYLATION, PROTEASE INHIBITORS, SPLICING FACTORS, GENOME-WIDE, INDUCIBLE TOLERANCE, GENE-EXPRESSION, FRESH-WATER, MAGNA, AERUGINOSA

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Chicago
Asselman, Jana, Dieter De Coninck, Eline Beert, Colin Janssen, Luisa Orsini, Michael E Pfrender, Ellen Decaestecker, and Karel De Schamphelaere. 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): 924–931.
APA
Asselman, J., De Coninck, D., Beert, E., Janssen, C., Orsini, L., Pfrender, M. E., Decaestecker, E., et al. (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), 924–931.
Vancouver
1.
Asselman J, De Coninck D, Beert E, Janssen C, Orsini L, Pfrender ME, et al. 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. 2017;51(2):924–31.
MLA
Asselman, Jana, Dieter De Coninck, Eline Beert, et al. “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 (2017): 924–931. Print.
@article{8500756,
  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.},
  author       = {Asselman, Jana and De Coninck, Dieter and Beert, Eline and Janssen, Colin and Orsini, Luisa and Pfrender, Michael E and Decaestecker, Ellen and De Schamphelaere, Karel},
  issn         = {0013-936X},
  journal      = {ENVIRONMENTAL SCIENCE \& TECHNOLOGY},
  keyword      = {TOXIC CYANOBACTERIUM MICROCYSTIS,DNA METHYLATION,PROTEASE INHIBITORS,SPLICING FACTORS,GENOME-WIDE,INDUCIBLE TOLERANCE,GENE-EXPRESSION,FRESH-WATER,MAGNA,AERUGINOSA},
  language     = {eng},
  number       = {2},
  pages        = {924--931},
  title        = {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},
  url          = {http://dx.doi.org/10.1021/acs.est.6b03870},
  volume       = {51},
  year         = {2017},
}

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