Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

Abstract

DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ∼300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915 cis methylation QTLs (meQTLs)—i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs.

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

“…About a quarter of TFs that show enrichment for SD-ASM show no bias in directionality (table S4), the lack of bias being explainable by contextual behavior at different binding loci, such as for Nuclear factor of activated T-cells 1 (41), or due to competing TFs at overlapping motifs. Our results support that transcription factor motif sequences are predictive of proximal CpG methylation levels (23, 42, 43). …”

Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk

“…Many other types of molecular-level QTLs have been mapped in LCLs, including QTLs for mRNA levels (eQTLs), chromatin accessibility (dsQTLs), DNA methylation (mQTLs), and histone modifications (Fraser and Xie 2009; Degner et al, 2012; Fraser et al, 2012; Kasowski et al, 2013; Lappalainen et al, 2013; McVicker et al, 2013; Kilpinen et al, 2013; Gutierrez-Arcelus et al, 2013; Ding et al, 2014; Banovich et al, 2014; Waszak et al., 2015; Grubert et al, 2015). To explore the relationships between TF binding and these other regulatory levels, we intersected our bQTLs with each of these other QTL types, and calculated the fold-enrichment compared to SNPs bound by our TFs but not classified as bQTLs (to control for any general characteristics of each TF’s binding sites, such as proximity to promoter regions) (see Supplemental Experimental Procedures).…”

Mendelian inheritance of trimodal CpG methylation sites suggests distal cis-acting genetic effects

“…The role of CpG methylation in the regulation of gene expression has been well established, and several studies have shown that genetic variations are linked to quantitative changes in methylation [37–39]. Many meQTLs are also reported to be associated with changes in gene expression (eQTLs) [40], but it remains unclear whether methylation changes are a cause or consequence of altered gene expression.…”