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

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 durin...

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Bibliographic Details
Published in:BMC biology 2021-03, Vol.19 (1), p.53-53, Article 53
Main Authors: Liang, Zhe, Zhang, Qian, Ji, Changmian, Hu, Guihua, Zhang, Pingxian, Wang, Yifan, Yang, Liwen, Gu, Xiaofeng
Format: Article
Language:English
Subjects:
Chromatin
Chromatin - chemistry
Chromatin organization
Environmental aspects
Genetic aspects
Genome, Plant - physiology
Heat stress
Heat-Shock Response - genetics
Hi-C
Oryza - genetics
Oryza - physiology
Plant
Plant Proteins - chemistry
Rice
Stress (Physiology)
TAD
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Summary: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.
ISSN:1741-7007
1741-7007
DOI:10.1186/s12915-021-00996-4