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Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C]

ABSTRACT: Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C]

PROVIDER: PRJNA879086 | ENA |

REPOSITORIES: ENA

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Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C]

Project description: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.

2022-09-15 | GSE213090 | GEO

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq]

2022-09-15 | GSE213089 | GEO

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [RNA-Seq]

2022-09-15 | GSE213093 | GEO

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq]

2022-09-15 | GSE213226 | GEO

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice

| PRJNA879786 | ENA

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [RNA-Seq]

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [RNA-Seq]

| PRJNA879083 | ENA

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq]

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq]

| PRJNA879791 | ENA

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq]

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq]

| PRJNA879081 | ENA

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [Hi-C]

Project description:Circadian gene expression is essential for organisms to adjust cellular responses and anticipate daily changes in the environment. In addition to its physiological importance, the clock circuit represents an ideal, temporally resolved, system to study transcription regulation. Here, we analysed changes in spatial mouse liver chromatin conformation using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription in mouse liver. We found circadian topologically associated domains switched assignments to the transcriptionally active, open chromatin compartment and the inactive compartment at different hours of the day while their boundaries stably maintain their structure over time. Individual circadian gene promoters displayed maximal chromatin contacts at times of peak transcriptional output and the expression of circadian genes and contacted transcribed regulatory elements, or other circadian genes, was phase-coherent. Anchor sites of promoter chromatin loops were enriched in binding sites for liver nuclear receptors and transcription factors, some exclusively present in either rhythmic or stable contacts. The circadian 3D chromatin maps provided here identify the scales of chromatin conformation that parallel oscillatory gene expression and protein factors specifically associated with circadian or stable chromatin configurations.

2021-05-04 | GSE155158 | GEO

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [Hi-C]

Project description:The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [Hi-C]

| PRJNA648874 | ENA