Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.(Extended Data Fig. 5). These results show the value of large sample sizes in blood to detect trans-mQTLs regardless of the tissue. Trans-mQTL SNPs and DNAm exhibit patterned TF binding.Recent studies have uncovered multiple types of transcription factor (TF)-DNA interactions influenced by DNAm, including the binding of DNAm-sensitive TFs [26][27][28] and cooperativity between TFs 27,29 . To gain insights into how SNPs induce long-range DNAm changes, we mapped enrichments for DNAm sites and SNPs across binding sites for 171 TFs in 27 cell types 30,31 . We found strong enrichments for most TFs and cell types among DNAm sites with a trans association (cis + trans: 55%; trans only: 80%; cis only: 18%) and among cis-acting SNPs (cis only: 96%, cis + trans: 91%, trans only: 1%; Fig. 2b, Supplementary Tables 7 and 8, and Supplementary Figs. 22 and 23). Consistent with the observation that trans-only DNAm sites are enriched for CpG islands (Supplementary Fig. 13), DNAm sites that overlap TF-binding sites (TFBSs) were relatively hypomethylated (weighted mean DNAm levels = 21% versus 52%, P < 2.2 × 10 −16 ; Supplementary Fig. 24).Next, we hypothesized that, if a trans-mQTL is driven by TF activity 8,10 , then particular TF-TF pairs may exhibit preferential enrichment 32 . An mQTL has a pair of TFBS annotations 31 , one for the SNP and one for the DNAm site. We evaluated whether the annotation pairs among 18,584 interchromosomal trans-mQTLs were associated with TF binding in a nonrandom pattern (Supplementary Note and Extended Data Fig. 6a,b). We found that 6.1% (22,962 of 378,225) of possible pairwise combinations of SNP-DNAm site annotations were more over-or underrepresented than expected by chance after strict multiple testing correction (Supplementary Note, Supplementary Table 9 and Extended Data Fig. 6c).After accounting for abundance and other characteristics, the strongest pairwise enrichments involved sites close to TFBSs for proteins in the cohesin complex, ...

Most epigenome-wide association studies to date have been conducted in blood. However, metabolic syndrome is mediated by a dysregulation of adiposity and therefore it is critical to study adipose tissue in order to understand the effects of this syndrome on epigenomes. Therefore, to determine if natural variation in DNA methylation was associated with metabolic syndrome traits, we profiled global methylation levels in subcutaneous abdominal adipose tissue. We measured association with 32 clinical traits related to diabetes and obesity in 201 people from the Metabolic Syndrome In Men cohort. We performed epigenome-wide association studies between DNA methylation levels and traits, and identified significant associations for 13 clinical traits in 21 loci. We prioritized candidate genes using eQTL, and identified 18 high confidence candidate genes, including known and novel genes associated with diabetes and obesity traits. We also carried out an analysis to identify which cell types may be mediating the associations, and concluded that most of the loci we identified were specific to adipocytes. We determined whether the abundance of cell types varies with metabolic traits, and found that macrophages increased in abundance with the severity of metabolic syndrome traits. Finally, we developed a DNA methylation based biomarker to assess type II diabetes risk in adipose tissue. In conclusion, our results demonstrate that profiling DNA methylation in adipose tissue is a powerful tool for understanding the molecular effects of metabolic syndrome on adipose tissue, and can be used in conjunction with traditional genetic analyses to further characterize this disorder.. CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/223495 doi: bioRxiv preprint first posted online 3 INTRODUCTIONMetabolic syndrome traits such as obesity, dyslipidemia, insulin resistance, and hypertension underlie the common forms of atherosclerosis, type 2 diabetes (T2D) and heart failure, which together account for the majority of deaths in Western populations. Metabolic syndrome affects 44% of adults over the age of 50 in the US, and people affected with metabolic syndrome have higher risk of heart attacks, diabetes and stroke (1). Numerous studies have investigated the genetic basis of metabolic syndrome traits such as diabetes (2), and accumulating evidence suggests that epigenetics is associated with these phenotypes (3, 4).Methylation of DNA cytosine bases is evolutionarily conserved and plays important roles in development, cell differentiation, imprinting, X-chromosome inactivation, and regulation of gene expression. Aberrant DNA methylation in mammals is associated with both rare and complex traits including cancer, aging (5), and imprinting disorders such as Prader-Willi syndrome. Recent studies have demonstrated that much like ...

An 18-year-old phenotypic male who had been reported to have XX and no Y chromosome was further investigated. He had small (2.4 cm) testes and azoospermia. His testicular biopsy was markedly abnormal with dysplastic spermatic tubules and interstitial fibrosis. Cytologic studies revealed drumsticks in neutrophils and sex chromatin bodies in skin and various testicular cells. Chromosomal studies disclosed a small proportion (3/270) of XXY cells in cultures of blood and testis and no XXY cells (0/39) in culture of skin. The predominant line of cells in all these tissues had 46 chromosomes with XX and no Y chromosome. Cells with a Y chromosome were thus scarce, although as a zygote the patient presumably possessed a Y. Reference is made to the idea that sometimes selection may by unknown mechanisms work against the survival of a particular clone of cells after that clone has irrevocably influenced the course of embryonic development. The XXY cells in our patient would thus be a clone which selection has caused to nearly vanish.

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