Genome-wide allele-specific methylation is enriched at gene regulatory regions in a multi-generation pedigree from the Norfolk Island isolate

Miles C Benton,Heidi G Sutherland,Daniel Kennedy,Nicole White,Donia Macartney-Coxson,Kerry Mengersen,Lyn R Griffiths,Rodney A Lea,Larisa M Haupt

doi:10.1186/s13072-019-0304-7

Abstract

BackgroundAllele-specific methylation (ASM) occurs when DNA methylation patterns exhibit asymmetry among alleles. ASM occurs at imprinted loci, but its presence elsewhere across the human genome is indicative of wider importance in terms of gene regulation and disease risk. Here, we studied ASM by focusing on blood-based DNA collected from 24 subjects comprising a 3-generation pedigree from the Norfolk Island genetic isolate. We applied a genome-wide bisulphite sequencing approach with a genotype-independent ASM calling method to map ASM across the genome. Regions of ASM were then tested for enrichment at gene regulatory regions using Genomic Association Test (GAT) tool.ResultsIn total, we identified 1.12 M CpGs of which 147,170 (13%) exhibited ASM (P ≤ 0.05). When including contiguous ASM signal spanning ≥ 2 CpGs, this condensed to 12,761 ASM regions (AMRs). These AMRs tagged 79% of known imprinting regions and most (98.1%) co-localised with known single nucleotide variants. Notably, miRNA and lncRNA showed a 3.3- and 1.8-fold enrichment of AMRs, respectively (P < 0.005). Also, the 5′ UTR and start codons each showed a 3.5-fold enrichment of AMRs (P < 0.005). There was also enrichment of AMRs observed at subtelomeric regions of many chromosomes. Five out of 11 large AMRs localised to the protocadherin cluster on chromosome 5.ConclusionsThis study shows ASM extends far beyond genomic imprinting in humans and that gene regulatory regions are hotspots for ASM. Future studies of ASM in pedigrees should help to clarify transgenerational inheritance patterns in relation to genotype and disease phenotypes.

Highlights

Complex human disease traits are influenced by an elaborate interplay of genetic and environmental factors [1]
Characterising the CpG landscape Genome-wide bisulphite sequence data were obtained from peripheral blood mononucleocytes (PBMCs) for 24 individuals from a third-generation nuclear pedigree from the Norfolk Island cohort
We used the Roche Nimblegen SeqCapEpi CpGiant capturebased target enrichment protocol. This is an approach designed to capture the DNA methylation based around the sites interrogated by the Illumina 450K DNA methylation array, a well-recognised platform for genome-wide analysis of human DNA methylation

Summary

Introduction

Complex human disease traits are influenced by an elaborate interplay of genetic and environmental factors [1]. DNA methylation is an important epigenetic modification, which in Benton et al Epigenetics & Chromatin (2019) 12:60 potentially play an integral role in regulatory networks involved in complex disease traits [4, 5]. A study by Martos et al examined genome-wide methylation patterns using a multigenerational mouse hybrid design to reveal a new paradigm of ‘switchable allele-specific DNA methylation’ [4]. This study showed that ASM is more widespread than the known imprinted genes in mice and can occur in both a genotype-dependent and -independent manner to influence gene expression. ASM occurs at imprinted loci, but its presence elsewhere across the human genome is indicative of wider importance in terms of gene regulation and disease risk. Regions of ASM were tested for enrichment at gene regulatory regions using Genomic Association Test (GAT) tool

Methods

Results

Conclusion