Fig. 1

Experimental design and data evaluation. a Schematic of experimental design demonstrating the collection of reciprocal hybrid post-implantation embryos for ultra low-input ChIP-seq, bisulphite-seq, and RNA-seq. Two replicates of H3K4me3, H3K27me3, and H3K36me3 ChIP-seq were each done using a pool of either E6.5 epiblasts (N = 4) or ExE (N = 8), approximating an input of ~ 2500 cells. Two 10% inputs were taken from each pool of embryos, one for a ChIP-seq input control and the other for low-coverage bisulphite-seq. RNA-seq was done on matched single E7.5 epiblast (N = 3) and ExE (N = 3). b Screenshot of E7.5 gene expression; E6.5 H3K4me3, H3K36me3, and H3K27me3; and E6.5 DNA methylation for B6/CAST epiblast and ExE. H3K4me3 is enriched at gene promoters, H3K36me3 along gene bodies of expressed genes, and H3K27me3 at transcriptionally silent promoters. The epiblast is highly methylated with exception of promoters, while ExE shows the expected lower global levels of DNA methylation. The box highlights the Sfmbt2 gene, which shows tissue-specific expression in ExE. ChIP-seq enrichment (RPKM) is shown for 1-kb running windows, with a 100-bp step (scales in square brackets), while gene expression and DNA methylation are shown using 2-kb running windows, with a 500-bp step