Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
Nat Plants. 2019 Aug;5(8):822-832. doi: 10.1038/s41477-019-0479-8. Epub 2019 Aug 5.
The non-random three-dimensional (3D) organization of the genome in the nucleus is critical to gene regulation and genome function. Using high-throughput chromatin conformation capture, we generated chromatin interaction maps for Brassica rapa and Brassica oleracea at a high resolution and characterized the conservation and divergence of chromatin organization in these two species. Large-scale chromatin structures, including A/B compartments and topologically associating domains, are notably conserved between B. rapa and B. oleracea, yet their KNOT structures are highly divergent. We found that genes retained in less fractionated subgenomes exhibited stronger interaction strengths, and diploidization-resistant duplicates retained in pairs or triplets are more likely to be colocalized in both B. rapa and B. oleracea. These observations suggest that spatial constraint in duplicated genes is correlated to their biased retention in the diploidization process. In addition, we found strong similarities in the epigenetic modification and Gene Ontology terms of colocalized paralogues, which were largely conserved across B. rapa and B. oleracea, indicating functional constraints on their 3D positioning in the nucleus. This study presents an investigation of the spatial organization of genomes in Brassica and provides insights on the role of 3D organization in the genome evolution of this genus.
基因组在核内的非随机三维（3D）组织对于基因调控和基因组功能至关重要。我们使用高通量染色质构象捕获技术，以高分辨率生成了芸薹属植物芸薹和甘蓝的染色质互作图谱，并对这两个物种的染色质组织的保守性和分化进行了分析。大规模染色质结构，包括 A/B 区室和拓扑关联域，在芸薹和甘蓝之间显著保守，但它们的 KNOT 结构高度分化。我们发现，在较少分裂的亚基因组中保留的基因表现出更强的相互作用强度，并且在成对或成组保留的二倍体化抗性重复基因更有可能在芸薹和甘蓝中共同定位。这些观察结果表明，空间约束与基因在二倍体化过程中的偏向保留有关。此外，我们还发现，共同定位的同源基因在表观遗传修饰和基因本体论术语方面具有很强的相似性，这在芸薹和甘蓝中大部分是保守的，表明它们在核内 3D 定位受到功能限制。本研究对芸薹属植物基因组的空间组织进行了研究，为 3D 组织在该属基因组进化中的作用提供了见解。
