Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation: Methylation array data for the identification of mQTL

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 are over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to Macaca mulattamacaques, indicates 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; variation in CTCF and TF binding sites is an underlying mechanism in primary tissues, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supera- and sub-threshold GWAS peaks in immunological and neurological disorders. Bisulfite converted DNA from 54 T cells, 44 brains (temporal cortex), 18 neuron nuclei, 22 non-neuronal nuclei (referred as glia), 37 fetal placentas samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Illumina Infinium 450k Human Methylation Beadchip were performed by the Genomics Shared Resource supported by Roswell Park Cancer Institute and National Cancer Institute (NCI). The isolation of neuron and glia nuclei was performed by fluorescence-activated nuclear sorting (FANS) after incubarion with anti – NeuN- Alexa 488 conjugated antibody (Millipore MAB377X) .To identify mQTL (methylation quantitative trait loci), these methylation data were used in combination with genotyping data obtained using Illumina HumanOmni2.5-8v1.1 (Omni2.5) BeadChip.