ArticleGenome research2012
Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
- Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.The American journal of clinical nutrition · 2016Pooled it
- Genotype-dependent DNA methylation patterns are negatively associated with allelic variation rather than heat-induced gene expression in two contrasting potato genotypes.The Plant journal : for cell and molecular biology · 2026Article
- DNA Methylation ofBiology · 2025Article
- Adaptation to Freshwater in Allis Shad Involved a Combination of Genomic and Epigenomic Changes.Journal of molecular evolution · 2025Article
- Neomorphic leukemia-derived mutations in the TET2 enzyme induce genome instability via a substrate shift from 5-methylcytosine to thymine.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Methylome profile of medaka eggs and sperm.Epigenetics · 2024Article
- Single-cell methylation analysis of brain tissue prioritizes mutations that alter transcription.Cell genomics · 2023Article
- The role of DNA methylation on gene expression in the vertebrae of ancestrally benzo[a]pyrene exposed F1 and F3 male medaka.Epigenetics · 2023Article
- Evolutionary honing in and mutational replacement: how long-term directed mutational responses to specific environmental pressures are possible.Theory in biosciences = Theorie in den Biowissenschaften · 2023Review
- Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development.Genome research · 2023Article
- Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate.Communications biology · 2020Article
- The dynamics of DNA methylation during epigenetic reprogramming of primordial germ cells in medaka (Epigenetics · 2020Article
- Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma.Genetics · 2020Article
- A Long Polymorphic GT Microsatellite within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a CpG Island in a Goldfish Inter-Strain Hybrid.International journal of molecular sciences · 2019Article
- Article
- Targeted in vivo epigenome editing of H3K27me3.Epigenetics & chromatin · 2019Article
- The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity.Genome biology and evolution · 2018Article
- Unlinking the methylome pattern from nucleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish.PLoS genetics · 2017Article
- Centromere evolution and CpG methylation during vertebrate speciation.Nature communications · 2017Article
- Simplification, Innateness, and the Absorption of Meaning from Context: How Novelty Arises from Gradual Network Evolution.Evolutionary biology · 2017Article
Corrections and comments
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
5-methyl-cytosines at CpG sites frequently mutate into thymines, accounting for a large proportion of spontaneous point mutations. The repair system would leave substantial numbers of errors in neighboring regions if the synthesis of erased gaps around deaminated 5-methyl-cytosines is error-prone. Indeed, we identified an unexpected genome-wide role of the CpG methylation state as a major determinant of proximal natural genetic variation. Specifically, 507 Mbp (∼18%) of the human genome was within 10 bp of a CpG site; in these regions, the single nucleotide polymorphism (SNP) rate significantly increased by ∼50% (P < 10(-566) by a two-proportion z-test) if the neighboring CpG sites are methylated. To reconfirm this finding in another vertebrate, we compared six single-base resolution methylomes in two inbred medaka (Oryzias latipes) strains with sufficient genetic divergence (3.4%). We found that the SNP rate also increased by ∼50% (P < 10(-2170)), and the substitution rates in all dinucleotides increased simultaneously (P < 10(-441)) around methylated CpG sites. In the hypomethylated regions, the "CGCG" motif was significantly enriched (P < 10(-680)) and evolutionarily conserved (P = ∼ 0.203%), and slow CpG deamination rather than fast CpG gain was seen, indicating a possible role of CGCG as a candidate cis-element for the hypomethylation state. In regions that were hypermethylated in germline-like tissues but were hypomethylated in somatic liver cells, the SNP rate was significantly smaller than that in hypomethylated regions in both tissues, suggesting a positive selective pressure during DNA methylation reprogramming. This is the first report of findings showing that the CpG methylation state is significantly correlated with the characteristics of evolutionary change in neighboring DNA.
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