Fig. 2

Imprinted H3K4me3 peaks are associated with imprinted gene expression in ExE. a Scatter plots of allelic H3K4me3 enrichment at autosomal H3K4me3 peaks (N = 15,976) in B6/CAST E6.5 ExE (top) and CAST/B6 E6.5 ExE (bottom). Peaks with allelically biased H3K4me3 were identified using EdgeR statistic (p < 0.05, corrected for multiple comparisons). Significant peaks were then classified into strain-specific allelic H3K4me3 if their allelic enrichment switched in the reciprocal cross, denoted as B6-specific (green) and CAST-specific (turquoise). Significant peaks were identified as imprinted if the allelic enrichment was consistent between reciprocal crosses, denoted as paternal (blue) or maternal (red). Enrichment is quantitated as read count normalized to library size, correcting for peak length. b Heatmap showing allelic bias (log₂(pat/mat)) for E6.5 ExE H3K4me3 at H3K4me3 peaks identified in E6.5 ExE. Allelic bias (log₂(pat/mat)) for E6.5 ExE H3K36me3, E7.5 ExE gene expression, and E12.5 placenta (P) gene expression is shown for associated nearby genes (Additional file 2: Table S2). Reciprocal hybrids are denoted as B/C (B6/CAST), C/B (CAST/B6), F/C (FvB/CAST), and C/F (CAST/FvB). White boxes indicate where there was insufficient data (ChIP-seq < 20 SNP-spanning reads in all replicates, RNA-seq < 5 SNP-spanning reads in all replicates). ChIP-seq data was quantitated is as in a, RNA-seq data was quantitated as read count over exons. H3K4me3 peaks were excluded if there was no gene within 10 kb or the associated gene was uninformative in all datasets. H3K4me3 peaks overlapping more than one gene promoter are duplicated in the H3K4me3 column. Novel imprinted genes are marked with an asterisk. c Screenshot of allelic enrichment for H3K4me3 and H3K36me3 in E6.5 ExE and gene expression in E7.5 ExE for B6/CAST and CAST/B6 at the known imprinted gene Peg3. Box indicates the location of the maternal gDMR. ChIP-seq data is quantitated using enrichment normalized RPKM for autosomal 1-kb running windows with a 100-bp step (scales in square brackets); paternal (blue) and maternal (red) enrichments are shown on mirrored axes. Gene expression is quantitated as log₂(RPKM) for 500-bp running windows with a 50-bp step