Imprinted methylation of novel placental DMRs. (A) DNA methylation was averaged across reads with ≥5 CpGs from RRBS. The proportion of reads that was completely unmethylated (black), methylated (red), or had mixed methylation (gray) is shown for oocyte, sperm, ICM, and TE for germline known (N = 40) and novel (N = 101) DMRs. The proportion of methylated alleles did not differ between known and novel DMRs (P = 0.981, χ2 test). (B) DNA methylation was averaged across reads with ≥5 CpGs from multiplexed bisulfite sequencing in 16 placental villi and 12 matched trophoblast samples. Distribution of read methylation across DMRs (binned in 10% intervals) is shown in the density plot, with a density heat map in grayscale showing the distribution at each known (orange) and novel (blue) DMR below. DMRs with a minimum read depth of ≥5 were reported. (C) Average DNA methylation is shown for the methylated and unmethylated allele at known (orange) and novel (blue) DMRs containing a heterozygous SNP. Each row corresponds to one heterozygous SNP for one individual at one DMR; for loci with more than one informative SNP, the SNP number is designated after the sample name. Parental origin was assigned where informative, with maternal (red) and paternal (blue) monoallelic methylation, alleles with no differential methylation (gray), and uninformative alleles (white) denoted.
