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Series GSE144566 Query DataSets for GSE144566
Status Public on Feb 26, 2021
Title Reorganization of 3D chromatin architecture of rice genomes during heat stress (RNA-Seq)
Organism Oryza sativa
Experiment type Expression profiling by high throughput sequencing
Summary Background: The three-dimensional spatial organization of the genome plays important roles in chromatin accessibility and gene expression in multiple biological process, 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 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 of 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.
 
Overall design RNA-seq with three replicates
 
Contributor(s) Liang Z, Zhang Q, Liu Q, Ji C, Zhang P, Hu G, Wang Y, Gu X
Citation(s) 33740972
Submission date Jan 30, 2020
Last update date Apr 06, 2021
Contact name Xiaofeng Gu
E-mail(s) guxiaofeng@caas.cn
Organization name Chinese Academy of Agricultrual Sciences
Street address Zhongguancun south street
City Beijing
ZIP/Postal code 100081
Country China
 
Platforms (1)
GPL24468 HiSeq X Ten (Oryza sativa)
Samples (12)
GSM4290986 Nip-Normal-1: RNA-seq
GSM4290987 Nip-Normal-2: RNA-seq
GSM4290988 Nip-Normal-3: RNA-seq
Relations
BioProject PRJNA604026
SRA SRP246186

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE144566_RAW.tar 2.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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