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The relationship of DNA methylation with age, gender and genotype in twins and healthy controls.

Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, Sommer IE, Kahn RS, Ophoff RA - PLoS ONE (2009)

Bottom Line: Despite the inability to detect meaningful methylation differences in the majority of CpG loci due to tissue type and locus selection issues, we found replicable significant associations of DNA methylation with age and gender.We identified associations of genetically heritable single nucleotide polymorphisms with large differences in DNA methylation levels near the polymorphism (cis effects) as well as associations with much smaller differences in DNA methylation levels elsewhere in the human genome (trans effects).Our results demonstrate the feasibility of array-based approaches in studies of DNA methylation and highlight the vast differences between individual loci.

View Article: PubMed Central - PubMed

Affiliation: Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.

ABSTRACT
Cytosine-5 methylation within CpG dinucleotides is a potentially important mechanism of epigenetic influence on human traits and disease. In addition to influences of age and gender, genetic control of DNA methylation levels has recently been described. We used whole blood genomic DNA in a twin set (23 MZ twin-pairs and 23 DZ twin-pairs, N = 92) as well as healthy controls (N = 96) to investigate heritability and relationship with age and gender of selected DNA methylation profiles using readily commercially available GoldenGate bead array technology. Despite the inability to detect meaningful methylation differences in the majority of CpG loci due to tissue type and locus selection issues, we found replicable significant associations of DNA methylation with age and gender. We identified associations of genetically heritable single nucleotide polymorphisms with large differences in DNA methylation levels near the polymorphism (cis effects) as well as associations with much smaller differences in DNA methylation levels elsewhere in the human genome (trans effects). Our results demonstrate the feasibility of array-based approaches in studies of DNA methylation and highlight the vast differences between individual loci. The identification of CpG loci of which DNA methylation levels are under genetic control or are related to age or gender will facilitate further studies into the role of DNA methylation and disease.

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Sample plot of DNA methylation levels at probe ALOX12_P223_R by genotype of SNP rs434473.
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pone-0006767-g001: Sample plot of DNA methylation levels at probe ALOX12_P223_R by genotype of SNP rs434473.

Mentions: Based on the high heritability estimate of DNA methylation profiles of multiple CpG sites, we performed association mapping using DNA methylation levels as quantitative traits. For 91 subjects of the second set, sample genotype data was available (Illumina 550K BeadChip), with a total of 437,968 SNPs genome-wide after quality control filtering. Genomic inflation factor as a measure of population stratification ranged from 0.96 to 1.05, the mean chi-square statistic ranged between 0.98 and 1.03 indicating an absence of population stratification. We observed significant associations between DNA methylation at 11 different CpG loci representing 35 cis and 5 trans effects after stringent multiple testing correction and confirmation by permutation testing (Supplementary Table S4 shows all 106 methylation probes that showed significant associations after FDR correction for multiple testing, uncorrected for the 512 phenotypes tested). It is noticeable that all significant trans effects are observed with common variants located within genes, and not positioned in regions with known micro RNA's (http://microrna.sanger.ac.uk/). We here present genetic associations of three DNA methylation loci with nine SNPs that constituted a mean difference in DNA methylation level larger or equal than 0.17 to rule out the possibility of technical artifact and survived corrections for multiple testing both for the number of SNPs as well as the 512 phenotypes employed (Table 3). An example plot of DNA methylation differences of ALOX12 (NM_000697.1), the gene locus with the most significant association of DNA methylation with genotype, is shown in Figure 1. The heritability of these CpG loci as estimated in the twin data by means of non-parametric analysis (polychoric correlations) was significant for ALOX12_E85_R (heritability: 0.48, 95% CI: 0.24–0.61) and KRAS_E82_F (heritability: 0.9 95% CI: 0.79–1), but non-significant for ALOX12_P223_R (heritability: 0.03, 95% CI: 0–0.3) or MET_E333_F (heritability: 0.07 95% CI:0–0.42). Associations of DNA methylation level of two X- chromosomal CpG loci (GRPR (Xp22.2, NM_005314.2), and PCTK1 (Xp11.3, NM_033018.2)) with the SNPs rs12743401, rs3881953, rs12734338 rendered non-significant after including gender as a covariate. The association signals are most likely from a homolog area on the Y chromosome as the association of these SNPs with male gender (p<1E-8) confirms.


The relationship of DNA methylation with age, gender and genotype in twins and healthy controls.

Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, Sommer IE, Kahn RS, Ophoff RA - PLoS ONE (2009)

Sample plot of DNA methylation levels at probe ALOX12_P223_R by genotype of SNP rs434473.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2747671&req=5

pone-0006767-g001: Sample plot of DNA methylation levels at probe ALOX12_P223_R by genotype of SNP rs434473.
Mentions: Based on the high heritability estimate of DNA methylation profiles of multiple CpG sites, we performed association mapping using DNA methylation levels as quantitative traits. For 91 subjects of the second set, sample genotype data was available (Illumina 550K BeadChip), with a total of 437,968 SNPs genome-wide after quality control filtering. Genomic inflation factor as a measure of population stratification ranged from 0.96 to 1.05, the mean chi-square statistic ranged between 0.98 and 1.03 indicating an absence of population stratification. We observed significant associations between DNA methylation at 11 different CpG loci representing 35 cis and 5 trans effects after stringent multiple testing correction and confirmation by permutation testing (Supplementary Table S4 shows all 106 methylation probes that showed significant associations after FDR correction for multiple testing, uncorrected for the 512 phenotypes tested). It is noticeable that all significant trans effects are observed with common variants located within genes, and not positioned in regions with known micro RNA's (http://microrna.sanger.ac.uk/). We here present genetic associations of three DNA methylation loci with nine SNPs that constituted a mean difference in DNA methylation level larger or equal than 0.17 to rule out the possibility of technical artifact and survived corrections for multiple testing both for the number of SNPs as well as the 512 phenotypes employed (Table 3). An example plot of DNA methylation differences of ALOX12 (NM_000697.1), the gene locus with the most significant association of DNA methylation with genotype, is shown in Figure 1. The heritability of these CpG loci as estimated in the twin data by means of non-parametric analysis (polychoric correlations) was significant for ALOX12_E85_R (heritability: 0.48, 95% CI: 0.24–0.61) and KRAS_E82_F (heritability: 0.9 95% CI: 0.79–1), but non-significant for ALOX12_P223_R (heritability: 0.03, 95% CI: 0–0.3) or MET_E333_F (heritability: 0.07 95% CI:0–0.42). Associations of DNA methylation level of two X- chromosomal CpG loci (GRPR (Xp22.2, NM_005314.2), and PCTK1 (Xp11.3, NM_033018.2)) with the SNPs rs12743401, rs3881953, rs12734338 rendered non-significant after including gender as a covariate. The association signals are most likely from a homolog area on the Y chromosome as the association of these SNPs with male gender (p<1E-8) confirms.

Bottom Line: Despite the inability to detect meaningful methylation differences in the majority of CpG loci due to tissue type and locus selection issues, we found replicable significant associations of DNA methylation with age and gender.We identified associations of genetically heritable single nucleotide polymorphisms with large differences in DNA methylation levels near the polymorphism (cis effects) as well as associations with much smaller differences in DNA methylation levels elsewhere in the human genome (trans effects).Our results demonstrate the feasibility of array-based approaches in studies of DNA methylation and highlight the vast differences between individual loci.

View Article: PubMed Central - PubMed

Affiliation: Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.

ABSTRACT
Cytosine-5 methylation within CpG dinucleotides is a potentially important mechanism of epigenetic influence on human traits and disease. In addition to influences of age and gender, genetic control of DNA methylation levels has recently been described. We used whole blood genomic DNA in a twin set (23 MZ twin-pairs and 23 DZ twin-pairs, N = 92) as well as healthy controls (N = 96) to investigate heritability and relationship with age and gender of selected DNA methylation profiles using readily commercially available GoldenGate bead array technology. Despite the inability to detect meaningful methylation differences in the majority of CpG loci due to tissue type and locus selection issues, we found replicable significant associations of DNA methylation with age and gender. We identified associations of genetically heritable single nucleotide polymorphisms with large differences in DNA methylation levels near the polymorphism (cis effects) as well as associations with much smaller differences in DNA methylation levels elsewhere in the human genome (trans effects). Our results demonstrate the feasibility of array-based approaches in studies of DNA methylation and highlight the vast differences between individual loci. The identification of CpG loci of which DNA methylation levels are under genetic control or are related to age or gender will facilitate further studies into the role of DNA methylation and disease.

Show MeSH