Fig. 2: Joint genetic/epigenetic analysis across 202 samples from 135 donors identifies parental allele-specific methylation.
From: Atlas of imprinted and allele-specific DNA methylation in the human body
A A computational algorithm identifies bimodal regions (n = 324,759), by analyzing deeply sequenced methylomes from 39 cell types. Shown is a bimodal region (chr19:54039871-54043130, hg19, highlighted) where 51% of DNA fragments are methylated (black), and 46% are unmethylated, in a colon macrophage sample purified from a single donor. B Similarly, DNA fragments from Adipocytes were split by a common T/G SNP (rs2071094, chr11:2021164) to show allele-specific methylation. Fragments carrying the T allele are unmethylated (white), whereas G allele fragments are methylated. (C) Contingency table of alleles by methylation, as shown in (B). All 29 unmethylated fragments are from the G genotype, whereas all 22 methylated ones carry the T genotype (adj. p 7.1E-19 ≤ 7.1E-19, Fisher’s exact). D Genetic/Epigenetic table across multiple samples/cell types (rs9330298, chr1:153590254, hg19). Here, for all samples (homozygous or heterozygous), unmethylated fragments (U) have the G genotype, whereas the methylated fragments (M) are associated with the alternative T genotype, consistent with sequence-dependent allele-specific methylation (SD-ASM). E A similar table for rs80269905 (chr11:2720873), is consistent with parental allele-specific methylation. All samples are bimodal (showing both U and M fragments), and heterozygous samples are associated with allele-specific bimodal patterns but switch across different donors.
