ArticleBMC genomics2014
Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 120 citations in OpenAlex.
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- Whole genome DNA methylation atlas of the scallop Patinopecten yessoensis.Scientific data · 2026Article
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- Prior exposure to hypoxia alters DNA methylation patterns in the eastern oyster.bioRxiv : the preprint server for biology · 2025Article
- Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology (ONT).Molecular ecology resources · 2025Article
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- Genome-wide DNA methylation patterns in Daphnia magna are not significantly associated with age.Epigenetics & chromatin · 2025Article
- Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria.Genome biology · 2024Article
- Unravelling epigenetic mechanisms in Cerastoderma edule genome: a comparison of healthy and neoplastic cockles.Molecular genetics and genomics : MGG · 2024Article
- Tet-mediated DNA methylation dynamics affect chromosome organization.Nucleic acids research · 2024Article
- Transcriptomic Response of the Atlantic Surfclam (Spisula solidissima) to Acute Heat Stress.Marine biotechnology (New York, N.Y.) · 2024Article
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- Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes.Molecular biology and evolution · 2023Article
- Experimental DNA Demethylation Reduces Expression Plasticity and Thermal Tolerance in Pacific Oysters.Marine biotechnology (New York, N.Y.) · 2023Article
- Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate.Genome biology and evolution · 2023Article
- Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species.Nature communications · 2023Article
- Epigenetic machinery is functionally conserved in cephalopods.BMC biology · 2022Article
- Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions.Biochemical Society transactions · 2022Article
- Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection.Microbiome · 2022Article
- Genome-Wide Differential DNA Methylomes Provide Insights into the Infertility of Triploid Oysters.Marine biotechnology (New York, N.Y.) · 2022Article
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Authors and funding
15 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStudies of DNA methylomes in a wide range of eukaryotes have revealed both conserved and divergent characteristics of DNA methylation among phylogenetic groups. However, data on invertebrates particularly molluscs are limited, which hinders our understanding of the evolution of DNA methylation in metazoa. The sequencing of the Pacific oyster Crassostrea gigas genome provides an opportunity for genome-wide profiling of DNA methylation in this model mollusc.
resultsHomologous searches against the C. gigas genome identified functional orthologs for key genes involved in DNA methylation: DNMT1, DNMT2, DNMT3, MBD2/3 and UHRF1. Whole-genome bisulfite sequencing (BS-seq) of the oyster's mantle tissues revealed that more than 99% methylation modification was restricted to cytosines in CpG context and methylated CpGs accumulated in the bodies of genes that were moderately expressed. Young repeat elements were another major targets of CpG methylation in oysters. Comparison with other invertebrate methylomes suggested that the 5'-end bias of gene body methylation and the negative correlation between gene body methylation and gene length were the derived features probably limited to the insect lineage. Interestingly, phylostratigraphic analysis showed that CpG methylation preferentially targeted genes originating in the common ancestor of eukaryotes rather than the oldest genes originating in the common ancestor of cellular organisms.
conclusionsComparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.
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