Homologous chromosomes show similar interaction patterns and the similarity correlates with allelic coexpression level. (A) Schematic representation of the hybrid mouse model, in which male B6 and female Cast were crossbred to generate hybrid progeny. Haploid genome in the hybrid originating from B6 and Cast were called Fb6 and Fcast, respectively. (B) Box plot of chromosomal interactions between maternal–maternal (MM), maternal–paternal (MP), and paternal–paternal (PP) based on allelic specific PETs. (C) PCA analysis of chromosomal interactions. The chromosomes are projected on a 2D plot, in which short distance indicated high similarity of interaction patterns: (p) paternal chromosomes; (m) maternal chromosomes. (D) Distances between homologous chromosomes on PCA projection compared with other situations: (Homo) distance between homologous chromosome pair; (nearest) distance between a chromosome and its nearest nonhomologous chromosome; (mean) mean distance between a chromosome and the other chromosomes; (random) distance between two randomly picked chromosomes. P-values were calculated using t-test. (E) Biallelic coexpression level is correlated with the similarity of chromosomal interaction pattern between homologous chromosomes. (R = 0.7, P-value = 0.0006.)
