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Series GSE213089 Query DataSets for GSE213089
Status Public on Sep 15, 2022
Title Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq]
Organism Oryza sativa Indica Group
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Plants are extremely sensitive to and can re-output rhythm by light signals during photoperiod cues. The circadian transcriptome and epigenetically modified rice genome exhibited distinct circadian behavioural outputs under three light signals during the photoperiod.By comparing and analysing the output circadian genes under different light signals, we detected that constant light (LL) shortens the day-night cycle, while constant night (DD) suppresses the oscillation amplitude. The circadian changing lncRNAs at the genome-wide level that were temporally correlated with oscillating genes at proximal loci and accompanied by synchronised circadian oscillations of H3K9ac modifications. We used the Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to profile the open chromatin regions and transcription factor (TF) footprints in rice at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20). The regulation of circadian gene expression occurs, not through temporal regulation of chromatin opening but through time-dependent binding of transcription factors in cis-regulatory elements. We mapped the 4D genome architecture of rice by employing BL-Hi-C, to capture oscillating chromatin interactions at ZT8 and ZT20. Circadian genes within the same peak phases of expression were preferentially coordinated transcription with non-circadian genes. Circadian genes at the ZT8 circadian phase tended to be enriched in ZT8-speific spatial clusters to orchestrate gene expression. Our findings contribute significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways in rice.
Overall design Timing specificity of transcription factors binding may underlie circadian gene expression in rice
Contributor(s) Zhang Y, Chen G
Citation(s) 37572350
Submission date Sep 10, 2022
Last update date Sep 27, 2023
Contact name guoting chen
Phone +86 13212791520
Organization name National Key Laboratory of Crop Genetic Improvement
Street address 1 Shizishan Street, Hongshan District
City Wuhan
ZIP/Postal code 430000
Country China
Platforms (1)
GPL26667 HiSeq X Ten (Oryza sativa Indica Group)
Samples (12)
GSM7152967 ATAC-Seq_LL-ZT0-rep1
GSM7152968 ATAC-Seq_LL-ZT0-rep2
GSM7152969 ATAC-Seq_LL-ZT4-rep1
This SubSeries is part of SuperSeries:
GSE213227 Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice
BioProject PRJNA879081

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

Supplementary file Size Download File type/resource
GSE213089_RAW.tar 2.7 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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