Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements

Abstract

Epigenetic modifications such as DNA methylation play a key role in gene regulation and disease susceptibility. However, little is known about the genome-wide frequency, localization, and function of methylation variation and how it is regulated by genetic and environmental factors. We utilized the Multiple Tissue Human Expression Resource (MuTHER) and generated Illumina 450K adipose methylome data from 648 twins. We found that individual CpGs had low variance and that variability was suppressed in promoters. We noted that DNA methylation variation was highly heritable (h(2)median = 0.34) and that shared environmental effects correlated with metabolic phenotype-associated CpGs. Analysis of methylation quantitative-trait loci (metQTL) revealed that 28% of CpGs were associated with nearby SNPs, and when overlapping them with adipose expression quantitative-trait loci (eQTL) from the same individuals, we found that 6% of the loci played a role in regulating both gene expression and DNA methylation. These associations were bidirectional, but there were pronounced negative associations for promoter CpGs. Integration of metQTL with adipose reference epigenomes and disease associations revealed significant enrichment of metQTL overlapping metabolic-trait or disease loci in enhancers (the strongest effects were for high-density lipoprotein cholesterol and body mass index [BMI]). We followed up with the BMI SNP rs713586, a cg01884057 metQTL that overlaps an enhancer upstream of ADCY3, and used bisulphite sequencing to refine this region. Our results showed widespread population invariability yet sequence dependence on adipose DNA methylation but that incorporating maps of regulatory elements aid in linking CpG variation to gene regulation and disease risk in a tissue-dependent manner.

Familial resemblances in blood leukocyte DNA methylation levels

“…9 Gruenberg et al using 648 twins of European descent also reported a genetic heritability of 19% in adipose tissue. 16 Our genetic heritability estimate is more similar to the one reported by Garvin et al, which ranges from 2 to 16% in the MHC region in CD4 C lymphocytes of healthy monozygotic and dizygotic twins. 20 In this study, genetic heritability also varies by gene region types (CpG islands, 5 0 ends of genes, conserved noncoding regions, and randomly selected regions).…”

“…More recently, studies using genome-wide DNA methylation array (Illumina 450K) have reported an average genetic heritability of 19% in peripheral blood leukocytes and 19% in adipose tissue. 9,16 Transgenerational similarity in DNA methylation levels has also been reported. 13 Several genome-wide association studies with methylation quantitative trait loci (mQTL) in both cis and trans locations have confirmed the genetic heritability of DNA methylation.…”

“…In fact, a study by Grunberg et al stated that a sample of 648 twins was not sufficient to obtain reliable heritability estimates of less than 10%. 16 Thus, our small sample size may affect the reliability of low values of heritability estimates and partly explain the large number of probes with an estimated maximal heritability of 0%. In addition, a SNP found in a probe location or nearby may cause methylation differences and impact the estimation of DNA methylation heritability.…”

Using epigenomic studies in monozygotic twins to improve our understanding of cancer

“…Subsequently, Grundberg et al performed a large-scale heritability analysis with the Illumina 450k array, including 97 MZ and 162 DZ twins and estimated the heritability for 344,092 methylation sites. In concordance with previous estimates, the overall heritability was estimated to be 19% [88].…”

Epigenomic profiling reveals an association between persistence of DNA methylation and metabolic memory in the DCCT/EDIC type 1 diabetes cohort

“…Major changes in DNA-me distribution at promoters are a hallmark of cancer (13,16). However, in chronic diseases, such as diabetes and its complications, increasing evidence suggests the importance of DNA-me in regulatory regions, including putative enhancer regions in kidney tissues from patients with diabetic kidney disease (50), intronic enhancers in blood cells type 2 diabetes patients (51), and gene bodies/intergenic regions rather than promoters in adipose tissues from twins (52). The high percentage of DMLs in intergenic regions, introns, and 3′ UTRs in our study is in line with such reports.…”