Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany.
BMC Biol. 2021 Mar 19;19(1):53. doi: 10.1186/s12915-021-00996-4.
The three-dimensional spatial organization of the genome plays important roles in chromatin accessibility and gene expression in multiple biological processes and has been reported to be altered in response to environmental stress. However, the functional changes in spatial genome organization during environmental changes in crop plants are poorly understood.
Here we perform Hi-C, ATAC-seq, and RNA-seq in two agronomically important rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica), to report a comprehensive profile of nuclear dynamics during heat stress (HS). We show that heat stress affects different levels of chromosome organization, including A/B compartment transition, increase in the size of topologically associated domains, and loss of short-range interactions. The chromatin architectural changes were associated with chromatin accessibility and gene expression changes. Comparative analysis revealed that 93-11 exhibited more dynamic gene expression and chromatin accessibility changes, including HS-related genes, consistent with observed higher HS tolerance in this cultivar.
Our data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.
基因组的三维空间组织在多个生物学过程中的染色质可及性和基因表达中发挥重要作用，并已被报道在响应环境胁迫时发生改变。然而，作物植物在环境变化过程中空间基因组组织的功能变化仍知之甚少。
本研究中，我们在两个重要的农业水稻品种 Nipponbare（Nip；粳稻）和 93-11（籼稻）中进行 Hi-C、ATAC-seq 和 RNA-seq，以报告热应激（HS）过程中核动态的综合情况。结果表明，热应激影响不同水平的染色体组织，包括 A/B 区室转换、拓扑关联域大小增加和短距离相互作用丧失。染色质结构变化与染色质可及性和基因表达变化相关。比较分析表明，93-11 表现出更高的基因表达和染色质可及性变化，包括与热应激相关的基因，与该品种观察到的更高的热应激耐受性一致。
本研究揭示了高级染色质结构作为理解水稻响应热应激转录调控的新层面。
