Both genetic and epigenetic regulations shape the gene expression in hybrid mouse. (A) GO enrichment for differentially expressed genes between B6 and Cast. (B) Relative expressions in parents and haploids of differentially expressed genes between Fb6 and Fcast. Dot size represents average expression level of Fb6 + Fcast. Blue to red represents average expression level of B6 + Cast. (C) Allele-specific H3K4me3 is positively correlated with allele-specific gene expression in the hybrid. Each point represents a biased ChIP-seq peak and its regulated gene (R = 0.85, P-value = 1.2 × 10−13). (D) Cast/Fcast-specific epigenetic modifications and expression near Gzma. (E) B6/Fb6-specific epigenetic modification and expression near Ly6e. (F) Maternal imprinted gene Peg13 only showed paternal-specific active epigenetic modifications in the hybrid.
