Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification

dc.contributor.author Venkataraman, Yaamini R.
dc.contributor.author White, Samuel J.
dc.contributor.author Roberts, Steven B.
dc.date.accessioned 2022-12-22T18:03:08Z
dc.date.available 2022-12-22T18:03:08Z
dc.date.issued 2022-08-04
dc.description © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Venkataraman, Y. R., White, S. J., & Roberts, S. B. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics, 23(1), (2022): 556, https://doi.org/10.1186/s12864-022-08781-5. en_US
dc.description.abstract Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation. en_US
dc.description.sponsorship This work was funded by National Science Foundation award 1634167 to SBR. The Hall Conservation Genetics Research Fund (YRV) supported sequencing for this project. en_US
dc.identifier.citation Venkataraman, Y. R., White, S. J., & Roberts, S. B. (2022). Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics, 23(1), 556. en_US
dc.identifier.doi 10.1186/s12864-022-08781-5
dc.identifier.uri https://hdl.handle.net/1912/29578
dc.publisher BioMed Central en_US
dc.relation.uri https://doi.org/10.1186/s12864-022-08781-5
dc.rights Attribution 4.0 International *
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ *
dc.subject Pacific oyster en_US
dc.subject Bivalve en_US
dc.subject Ocean acidification en_US
dc.subject DNA methylation en_US
dc.subject Gonad development en_US
dc.title Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification en_US
dc.type Article en_US
dspace.entity.type Publication
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relation.isAuthorOfPublication 98bd78ff-ae9a-47c9-820d-b28b2ac49c20
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relation.isAuthorOfPublication.latestForDiscovery 5ddc32ad-6613-412a-8778-61d7c02f1580
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