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

Abstract

Background 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. Results 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. Conclusions Our data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.

Stress Conditions Modulate the Chromatin Interactions Network in Arabidopsis

“…The stress condition leads to establishment of 896 and 2789 new interactions and loss of 1222 and 1104 interactions in SA and HT treatment, respectively, as compared to native conditions (Supplementary Figure S5). The chromosomal reorganization in response to heat stress is consistent with the previous studies in Arabidopsis and rice (Sun et al, 2020;Liang et al, 2021). Our data show that the chromosomal contact increased in response to heat stress compared with the control (Supplementary Table S1).…”

“…Further, our analysis of correlation heat map showing the visual transition of chromatin compartment in HT condition (Figure 1C; Supplementary Figure S3). Similar observations have recently been reported for Arabidopsis and rice (Sun et al, 2020;Liang et al, 2021), suggesting that the compartment transition might be conserved among different species. We have uncovered several interactions in the heterochromatic and euchromatic regions that established physical communication with the different regions of the genome, which will provide a new mechanistic way of gene regulation in plants (Figure 1).…”

Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription

“…It was then of interest to examine whether genomic regions at sequences detected by the BG4 assay are associated with any specific in vivo marks. To this end, we integrated dG4 data with existing omics data, including R-loop (DRIP-seq, GSE111944) (Fang et al, 2019), DHSs (DNase I hypersensitive sites, DNase-seq, GSE26734) (Zhang et al, 2012), ATAC-seq (GSE144564) (Liang et al, 2021) and 12 histone marks (Supplemental Table S5) (Zhang et al, 2012;Lu et al, 2015;Fang et al, 2016;Tan et al, 2016). We performed a fold enrichment assay by comparing each mark distributed in promoter, gene body, terminal and intergenic regions with dG4s relative to udG4s (Figure 7A).…”

Harnessing Current Knowledge of DNA N6-Methyladenosine From Model Plants for Non-model Crops

“…Contrastingly, the well-known 5mC is correlated with transcription repression. In addition, 6mA has been shown to associate with accessible chromatin regions, 3D chromatin structures and other types of epigenetic modifications (e.g., histone modifications, non-coding RNAs) to regulate gene transcription in plants ( Liang et al, 2021 ; Zhou et al, 2021 ). Thus, it needs more investigation on what molecular role of 6mA has during transcription in plants.…”