Although mammalian genomes are diploid, previous studies extensively investigated the average chromatin architectures without considering the differences between homologous chromosomes. We generated Hi-C, ChIP-seq, and RNA-seq data sets from CD4 T cells of B6, Cast, and hybrid mice, to investigate the diploid chromatin organization and epigenetic regulation. Our data indicate that inter-chromosomal interaction patterns between homologous chromosomes are similar, and the similarity is highly correlated with their allelic coexpression levels. Reconstruction of the 3D nucleus revealed that distances of the homologous chromosomes to the center of nucleus are almost the same. The inter-chromosomal interactions at centromere ends are significantly weaker than those at telomere ends, suggesting that they are located in different regions within the chromosome territories. The majority of A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments owing to cis effect. About 95% of the trans-effected B6/Cast divergent compartments converge to the same compartment status potentially because of a shared cellular environment. We showed the differentially expressed genes between the two haploids in hybrid were associated with either genetic or epigenetic effects. In summary, our multi-omics data from the hybrid mice provided haploid-specific information on the 3D nuclear architecture and a rich resource for further understanding the epigenetic regulation of haploid-specific gene expression.

中文翻译：

---

杂种小鼠的多组学数据揭示的二倍体基因组结构。

尽管哺乳动物基因组是二倍体，但之前的研究广泛研究了平均染色质结构，而没有考虑同源染色体之间的差异。我们从 B6、Cast 和杂交小鼠的 CD4 T 细胞生成 Hi-C、ChIP-seq 和 RNA-seq 数据集，以研究二倍体染色质组织和表观遗传调控。我们的数据表明同源染色体之间的染色体间相互作用模式相似，并且相似性与其等位基因共表达水平高度相关。3D 细胞核的重建显示同源染色体到细胞核中心的距离几乎相同。着丝粒末端的染色体间相互作用明显弱于端粒末端的相互作用，表明它们位于染色体区域内的不同区域。大多数 A|B 区室或拓扑关联域 (TAD) 在 B6 和 Cast 之间是一致的。我们发现杂种中 58% 的单倍体在 B6/Cast 发散区室中保持其亲本区室状态，原因是顺效应。由于共享的细胞环境，大约 95% 的反式影响的 B6/Cast 发散区室会聚到相同的区室状态。我们发现杂种中两个单倍体之间的差异表达基因与遗传或表观遗传效应有关。总之，我们来自杂交小鼠的多组学数据提供了关于 3D 核结构的单倍体特异性信息，并为进一步了解单倍体特异性基因表达的表观遗传调控提供了丰富的资源。