Pairwise combinations of allelic chromatin states that result in observed allelic skew of a chromatin mark.

<p>Allelic promoters are shown as points in the space of K4me3 and K27me3 densities. <b>A,</b> Schematic of major types of allelic chromatin states and their possible combinations on two alleles. Regions 1, 2, and 3 correspond to silent, bivalent, and active alleles, respectively. Combinations observed in larger numbers of genes (“observed”) are shown as cyan lines. Combination observed in fewer genes (“unobserved”) is shown as orange line. <b>B,</b> Scatter plot of K4me3 vs. K27me3 promoter densities on maternal (M) <i>mus</i> allele of all autosomal genes shown as gray points; genes with allelic skew in K4me3 are highlighted in blue. Regions 1, 2, and 3 are marked by dashed lines. <b>C-E,</b> Scatter plots of K4me3 vs. K27me3 promoter densities on paternal (P) <i>cas</i> allele, shown as gray points. Red points in these three plots highlight three subgroups of genes shown in <b>B</b>: genes whose maternal allele belongs to silent, bivalent, or active type (regions 1, 2, and 3 in <b>B</b>, marked for the reference by a blue rectangle in each corresponding plot <b>C-E</b>). Hue indicates the local density of paternal alleles with similar K4me3/K27me3 densities. <b>C,</b> Among genes with K4me3 skew whose maternal allele is in a silent state (region 1 in <b>B,</b> <i>n</i> = 24), paternal allele (P) generally has medium to high K4me3 density and low K27me3 density. <b>D,</b> Among genes with K4me3 skew whose maternal allele is in a bivalent state (region 2 in <b>B,</b> <i>n</i> = 66), paternal allele (P) generally also resides in a bivalent state. <b>E,</b> Among genes with K4me3 skew whose maternal allele is in an active state (region 3 in <b>B,</b> <i>n</i> = 281), paternal allele (P) most often resides in an active or bivalent state; there are much fewer cases of a fully silent paternal allele.</p>