Both cis and trans effects of hybrid genomes influence the status of chromatin compartment and gene expression. The compartment analyses were conducted at 100-kb resolution. (A) Correlation of genome-wide A|B compartment scores among parents and the haploids from hybrid. Heatmap (left) and bar plot (right) of correlation coefficient between different genomes. (B) GO analysis of genes in B6 and Cast divergent A|B compartments. (C) A|B compartment status of Fb6, Fcast, B6, and Cast at B6/Cast divergent A|B compartments: (Cis) compartment status is consistent between haploid and parent of origin; (Trans) compartment status is different between haploid and parent of origin. (D) A|B compartments and gene expression in B6, Cast, Fb6, and Fcast around cis-regulated Plxdc2. (E) A|B compartments and gene expression in B6, Cast, Fb6, and Fcast around trans-regulated Dlg5.
