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

Zhe Liang,Liwen Yang,Guihua Hu,Yifan Wang,Qian Zhang,Pingxian Zhang,Xiaofeng Gu,Changmian Ji

doi:10.1186/s12915-021-00996-4

Abstract

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.

Highlights

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
We identified A/B compartments in Nip and 93-11 and found that 82% of their genomes share synteny A/B compartments and their distribution patterns were highly conserved between Nip and 93-11 (Fig. 1a)
We analyzed and compared the local level of chromatin organization represented by Topologically associating domain (TAD) and found that the number and distribution of TADs were quite similar between Nip and 93-11 (Fig. 1a and Additional file 3: Table S2)

Summary

Introduction

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. Spatial organization of the three-dimensional (3D) genome plays crucial roles in gene transcription regulation and controlling multiple biological processes in eukaryotic organisms [1,2,3]. 3D chromatin organization maps have been reported in model Arabidopsis and several crops, including rice, maize, barley, and tomato [7,8,9,10,11,12,13,14,15], and have revealed that 3D chromatin architectures are highly correlated with the functionality of the genome. Our data uncovered 3D chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in crops

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Results

Conclusion