Allele-specific methylation occurs at genetic variants associated with complex disease.

John N Hutchinson,Andrew Chess,Robert Plenge,Mark Daly,Towfique Raj,Fernando T Viloria,Alexander Gimelbrant,Johanna Seddon,Eli Stahl,Jes Fagerness

doi:10.1371/journal.pone.0098464

Abstract

We hypothesize that the phenomenon of allele-specific methylation (ASM) may underlie the phenotypic effects of multiple variants identified by Genome-Wide Association studies (GWAS). We evaluate ASM in a human population and document its genome-wide patterns in an initial screen at up to 380,678 sites within the genome, or up to 5% of the total genomic CpGs. We show that while substantial inter-individual variation exists, 5% of assessed sites show evidence of ASM in at least six samples; the majority of these events (81%) are under genetic influence. Many of these cis-regulated ASM variants are also eQTLs in peripheral blood mononuclear cells and monocytes and/or in high linkage-disequilibrium with variants linked to complex disease. Finally, focusing on autoimmune phenotypes, we extend this initial screen to confirm the association of cis-regulated ASM with multiple complex disease-associated variants in an independent population using next-generation bisulfite sequencing. These four variants are implicated in complex phenotypes such as ulcerative colitis and AIDS progression disease (rs10491434), Celiac disease (rs2762051), Crohn's disease, IgA nephropathy and early-onset inflammatory bowel disease (rs713875) and height (rs6569648). Our results suggest cis-regulated ASM may provide a mechanistic link between the non-coding genetic changes and phenotypic variation observed in these diseases and further suggests a route to integrating DNA methylation status with GWAS results.

Highlights

In recent years, Genome Wide Association Studies (GWASs) have unearthed thousands of disease associated DNA sequence variants
Using Affymetrix SNP 6.0 arrays we looked for allelic ratio changes of these methylation sensitive restriction enzyme (MSRE) positive regions (MPRs) after MSRE digestion of genomic DNA derived from whole blood
We adjusted for both probe-specific and sample specific biases by adjusting for the variation observed for individual SNP probes within HapMap samples and the variation observed for MSRE negative regions within an individual sample, respectively (Figure 1)

Summary

Introduction

Genome Wide Association Studies (GWASs) have unearthed thousands of disease associated DNA sequence variants. Recent evidence showing enrichment of expression Quantitative Trait Loci (eQTLs) within these uncategorized groups of variants [1] suggests they can affect phenotype by regulating gene expression levels, likely through their effects on regulatory mediators. Evidence suggests that DNA methylation [5], an epigenetic process that can regulate gene expression [6], may mediate genetic variants’ phenotypic effects [7]. As ASM is associated with expression changes in nearby genes, this genetic control of cis-regulated differential methylation has the potential to affect phenotypic variation [10,11,12,13]

Methods

Results

Conclusion