Fig. 3

Non-canonical imprinted H3K4me3 in ExE demarcates imprinted ERVK LTR elements with extra-embryonic-specific imprinted expression. a Allelic ratio for H3K4me3 at canonical maternally regulated imprinted H3K4me3 peaks (N = 49) canonical paternally regulated imprinted H3K4me3 peaks (N = 3), and non-canonical imprinted H3K4me3 peaks (N = 17) in B6/CAST, CAST/B6, and matDKO/CAST E6.5 ExE. Informative H3K4me3 peaks were quantitated using read counts corrected for library size, and relative allelic ratios were calculated (allelic ratio = mat/(mat + pat)). b The percentage of non-canonical imprinted H3K4me3 peaks with paternal allelic bias (N = 15) and canonical imprinted H3K4me3 peaks (N = 52) that were overlapping each category of genomic feature, including CpG islands (CGIs) and classes of repetitive elements. Each pair-wise comparison was done using chi-square statistic, with a significance threshold adjusted for multiple comparisons using Bonferroni correction. c Allelic expression of transcribed ERVK LTRs within a non-canonical imprinted paternal H3K4me3 peak (N = 8, Additional file 2: Table S5) is shown in extra-embryonic tissues at E12.5 (placenta and visceral endoderm (VE)). Reciprocal hybrids are denoted as F/C (FvB/CAST) and C/F (CAST/FvB). White boxes indicate where there was insufficient data (< 5 SNP-spanning reads in all replicates). d Heatmap showing expression levels across extra-embryonic and embryonic tissues of transcriptionally active ERVK LTR elements within a non-canonical imprinted paternal H3K4me3 peak (N = 8). The nearest gene is denoted in brackets next to the ERVK LTR identifier