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

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

PROVIDER: PRJNA879786 | 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:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C]

| PRJNA879086 | 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

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

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 | 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 [Hi-C]

2022-09-15 | GSE213090 | GEO

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-09-15 | GSE213227 | GEO

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [RNA-Seq]

Project description:Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. Core circadian clock genes related chromatin connectivity networks suggested they co-localized within the same ?transcriptional factory? and define a distinct nuclear landscape and circadian outputs in the AM and PM. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

2021-12-23 | GSE143718 | GEO

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