Reorganization of the 3D chromatin architecture of rice genomes during heat stress

BMC Biology

Guihua Hu¹  Yifan Wang¹  Qian Zhang¹  Liwen Yang¹  Pingxian Zhang¹  Xiaofeng Gu¹  Zhe Liang²  Changmian Ji³ 

[1] Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany;Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, China;

关键词: Hi-C;    Rice;    Heat stress;    TAD;    Plant;    Chromatin organization;    ATAC-seq;    A/B compartment;   

DOI  :  10.1186/s12915-021-00996-4

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere 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.ConclusionsOur data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.

【 授权许可】

CC BY