Population-specificity of human DNA methylation
Open accessAbstract
BACKGROUND: Ethnic differences in human DNA methylation have been shown for a number of CpG sites, but the genome-wide patterns and extent of these differences are largely unknown. In addition, whether the genetic control of polymorphic DNA methylation is population-specific has not been investigated. RESULTS: Here we measure DNA methylation near the transcription start sites of over 14, 000 genes in 180 cell lines derived from one African and one European population. We find population-specific patterns of DNA methylation at over a third of all genes. Furthermore, although the methylation at over a thousand CpG sites is heritable, these heritabilities also differ between populations, suggesting extensive divergence in the genetic control of DNA methylation. In support of this, genetic mapping of DNA methylation reveals that most of the population specificity can be explained by divergence in allele frequencies between populations, and that there is little overlap in genetic associations between populations. These population-specific genetic associations are supported by the patterns of DNA methylation in several hundred brain samples, suggesting that they hold in vivo and across tissues. CONCLUSIONS: These results suggest that DNA methylation is highly divergent between populations, and that this divergence may be due in large part to a combination of differences in allele frequencies and complex epistasis or gene × environment interactions.
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Biological confounders known to affect epigenetic patterns such as age, sex, ethnicity, body mass index, smoking behavior or nutritional aspects may introduce critical biases limiting the interpretation of epigenetic data.
“Biological confounders known to affect epigenetic patterns such as age (Xiao, Wang, & Kong, 2019), sex (Yousefi et al., 2015), ethnicity (Fraser, Lam, Neumann, & Kobor, 2012), body mass index (Sayols-Baixeras et al., 2017), smoking behavior (Li et al., 2018) or nutritional aspects (Gadecka & Bielak-Zmijewska, 2019) may introduce critical biases limiting the interpretation of epigenetic data.”
From The applied implications of epigenetics in anxiety, affective and stress-related disorders - A review and synthesis on psychosocial stress, psychotherapy and prevention (2020) · cites this paper as Fraser, Lam, Neumann, & Kobor, 2012
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- Authors
- Fraser, H. B., Lam, L. L., Neumann, S. M., & Kobor, M. S.
- Affiliations
- Stanford University (US)
- University of British Columbia (CA)
- Corresponding author
- Fraser, Hunter B
- Kobor, Michael S
- Venue
- Genome Biology
- Published
- 2012-02-09
- Volume
- 13
- Issue
- 2
- Pages
- R8-R8
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC3334571
- OpenAlex
- W2170538199
- Cited by
- 313
- References
- 31
- Citations by year
- 2026: 20 · 2025: 21 · 2024: 15 · 2023: 16 · 2022: 18 · 2021: 25 · 2020: 27 · 2019: 21 · 2018: 21 · 2017: 20 · 2016: 31 · 2015: 27 · 2014: 19 · 2013: 24 · 2012: 8
- FWCI
- 10.04
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- cIRcle (University of British Columbia) (submittedVersion, cc-by)
- Open Collections
- Funders
- Canadian Institute for Advanced Research
- National Institutes of Health (5r21hg005750-02)
- National Institute of Mental Health (R24MH081797)
- National Human Genome Research Institute (1R21HG005750-01A1, R21 HG005750)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- DNA methylation, ethnic differences, allele frequency divergence, CpG sites, transcription start sites, epistasis, gene-environment interaction
- MeSH terms
- Cell Line, Gene Frequency, Genetics, Population, Humans, Genetic Variation, Genome, Human, CpG Islands, DNA Methylation, Polymorphism, Single Nucleotide, Transcription Initiation Site, Black People, White People, Genetic Association Studies
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