Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation

Abstract

Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease susceptibility, but maps of this phenomenon using stringent criteria in disease-relevant tissues remain sparse. Here we apply array-based and Methyl-Seq approaches to multiple human tissues and cell types, including brain, purified neurons and glia, T lymphocytes, and placenta, and identify 795 hap-ASM differentially methylated regions (DMRs) and 3,082 strong methylation quantitative trait loci (mQTLs), most not previously reported. More than half of these DMRs have cell type-restricted ASM, and among them are 188 hap-ASM DMRs and 933 mQTLs located near GWAS signals for immune and neurological disorders. Targeted bis-seq confirmed hap-ASM in 12/13 loci tested, including CCDC155, CD69, FRMD1, IRF1, KBTBD11, and S100A(∗)-ILF2, associated with immune phenotypes, MYT1L, PTPRN2, CMTM8 and CELF2, associated with neurological disorders, NGFR and HLA-DRB6, associated with both immunological and brain disorders, and ZFP57, a trans-acting regulator of genomic imprinting. Polymorphic CTCF and transcription factor (TF) binding sites were over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to macaques, indicated that CTCF and TF binding likelihood predicts the strength and direction of the allelic methylation asymmetry. These results show that hap-ASM is highly tissue specific; an important trans-acting regulator of genomic imprinting is regulated by this phenomenon; and variation in CTCF and TF binding sites is an underlying mechanism, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supra- and sub-threshold GWAS peaks in immunological and neurological disorders.

Nutriepigenomics Advances into Personalized Nutrition

“…The relationship between sequence variants and DNA methylation patterns in different sets of individuals may also provide insight into complex traits in which a particular environmental exposure associates with a trait only if incurred at a particular developmental window [4]. Mapping hap-ASM and mQTLs and superimposing these maps on GWAS data can support the biological relevance of GWAS peaks, the hypothesis being that detection of hap-ASM or an mQTL near a GWAS peak suggests the presence of a valid regulatory SNP or haplotype, which associates a physical asymmetry between the two alleles in heterozygotes [5]. A major finding in the field of nutrition is discovering that dietary components may reshape the genome in utero and that epigenetic changes induced during early life may permanently alter the phenotype in the adult organism ( Figure 1).…”

“…The epigenetic state that is set during the reprogramming stages persists at some loci for the lifetime of an individual. Evidence to support a role of epigenetics in developmental programming of disease demonstrated the impact of a suboptimal intrauterine nutritional environment on the epigenome and phenotype of the offspring [1][2][3][4][5][6].…”

“…The concept of inheritance is especially important to understanding how the nutritional environments of the parents can influence the epigenome of future generations. Haplotype-dependent allelespecific methylations (hap-ASM) can impact disease susceptibility, however maps of this phenomenon using stringent criteria in disease-relevant tissues are few in number [5]. In order to understand how hap-ASM contributes to disease, a short review is needed.…”

“…Therefore, methods to provide biological validity to both supra-and sub-threshold variants are a high priority. Moreover, multiple statistical comparisons demand stringent thresholds for significance, p < 5 × 10 −8 for a GWAS 1 and this level probably leads to the rejection of many biological true positives with sub-threshold p values [4,5].…”

“…ASM is a combination of two different phenomena: genomic imprinting, where the methylation of an allele is determined by its parent-oforigin, and (non-imprinted) hap-ASM, in which the local sequence context acts in cis to dictate the methylation status of local CpGs. Hap-ASM can be assessed either directly by bisulfite sequencing (bis-seq) in heterozygotes or by methylation quantitative trait loci (mQTL) analysis, which correlates net methylation of single CpGs with genotypes at nearby SNPs [5]. The ability to detect anmQTL is influenced by statistical power, which may depend on SNP allele frequency and linkage disequilibrium (LD) structure, which vary based on ancestry, or the variance of methylation at a specific CpG site, which may differ across stages of development or tissue type.…”