State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
Genome Biol. 2023 Jan 19;24(1):12. doi: 10.1186/s13059-023-02854-8.
High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported.
Here, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations (SVs) as well as gene expression. We find that intersection regions between A/B compartments largely contribute to compartment divergence. Topologically associating domain (TAD) boundaries in A compartments exhibit significantly higher density compared to those in B compartments. Pan-3D genome analysis shows that core TAD boundaries have the highest transcription start site (TSS) density and lowest GC content and repeat percentage. Further investigation shows that non-long terminal repeat (non-LTR) retrotransposons play important roles in maintaining TAD boundaries, while Gypsy elements and satellite repeats are associated with private TAD boundaries. Moreover, presence and absence variation (PAV) is found to be the major contributor to 3D genome variations. Nevertheless, approximately 55% of 3D genome variations are not associated with obvious genetic variations, and half of them affect the flanking gene expression. In addition, we find that the 3D genome may also undergo selection during soybean domestication.
Our study sheds light on the role of 3D genomes in plant genetic diversity and provides a valuable resource for studying gene regulation and genome evolution.
高级染色质结构在基因调控中起着重要作用。然而，植物品系之间的三维（3D）基因组多样性很少有报道。
在这里，我们使用来自 27 个大豆品系的 Hi-C 测序数据进行泛 3D 基因组分析，并全面研究了 3D 基因组变异与结构变异（SVs）以及基因表达之间的关系。我们发现 A/B 区室之间的交集区域在很大程度上导致了区室的分化。A 区室的拓扑关联域（TAD）边界的密度明显高于 B 区室的密度。泛 3D 基因组分析表明，核心 TAD 边界具有最高的转录起始位点（TSS）密度和最低的 GC 含量和重复百分比。进一步的研究表明，非长末端重复（non-LTR）逆转座子在维持 TAD 边界方面起着重要作用，而 Gypsy 元件和卫星重复序列与特有的 TAD 边界有关。此外，存在和缺失变异（PAV）被发现是 3D 基因组变异的主要贡献者。然而，大约 55%的 3D 基因组变异与明显的遗传变异无关，其中一半影响侧翼基因的表达。此外，我们发现 3D 基因组在大豆驯化过程中也可能经历选择。
我们的研究揭示了 3D 基因组在植物遗传多样性中的作用，并为研究基因调控和基因组进化提供了有价值的资源。
Zotero 插件
