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General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)

View ORCID ProfileYaamini R. Venkataraman, Alan M. Downey-Wall, Justin Ries, Isaac Westfield, Samuel J. White, Steven B. Roberts, Kathleen E. Lotterhos
doi: https://doi.org/10.1101/2020.01.07.897934
Yaamini R. Venkataraman
1School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
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  • ORCID record for Yaamini R. Venkataraman
  • For correspondence: yaaminiv@uw.edu
Alan M. Downey-Wall
2Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908
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Justin Ries
2Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908
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Isaac Westfield
2Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908
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Samuel J. White
1School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
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Steven B. Roberts
1School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
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Kathleen E. Lotterhos
2Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908
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Abstract

Epigenetic modification, specifically DNA methylation, is one possible mechanism for intergenerational plasticity. Before inheritance of methylation patterns can be characterized, we need a better understanding of how environmental change modifies the parental epigenome. To examine the influence of experimental ocean acidification on eastern oyster (Crassostrea virginica) gonad tissue, oysters were cultured in the laboratory under control (491 ± 49 µatm) or high (2550 ± 211 µatm) pCO2 conditions for four weeks. DNA from reproductive tissue was isolated from five oysters per treatment, then subjected to bisulfite treatment and DNA sequencing. Irrespective of treatment, DNA methylation was primarily found in gene bodies with approximately 22% of the genome predicted to be methylated In response to elevated pCO2 we found 598 differentially methylated loci primarily overlapping with gene bodies. A majority of differentially methylated loci were in exons (61.5%) with less intron overlap (31.9%). While there was though there was no evidence of a significant tendency for the genes with differentially methylated loci to be associated with distinct biological processes, the concentration of these loci in gene bodies, including genes involved in protein ubiquitination and biomineralization suggests DNA methylation may be important for transcriptional control in response to ocean acidification. Understanding how experimental ocean acidification conditions modify the oyster epigenome, and if these modifications are inherited, allows for a better understanding of how ecosystems will respond to environmental change.

Footnotes

  • https://github.com/epigeneticstoocean/paper-gonad-meth

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 08, 2020.
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General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)
Yaamini R. Venkataraman, Alan M. Downey-Wall, Justin Ries, Isaac Westfield, Samuel J. White, Steven B. Roberts, Kathleen E. Lotterhos
bioRxiv 2020.01.07.897934; doi: https://doi.org/10.1101/2020.01.07.897934
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General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)
Yaamini R. Venkataraman, Alan M. Downey-Wall, Justin Ries, Isaac Westfield, Samuel J. White, Steven B. Roberts, Kathleen E. Lotterhos
bioRxiv 2020.01.07.897934; doi: https://doi.org/10.1101/2020.01.07.897934

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