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Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice
How 3D DNA structure, gene regulation, and gene activity work together to control the daily biological clock in rice
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Abstract
Genome-wide analysis shows delayed gene expression phase under constant darkness and reduced amplitude under constant light in rice.
- Rhythmic gene expression in rice is influenced by photoperiods and the circadian clock.
- Synchronous oscillation of histone modifications and long non-coding RNA expression was observed at rhythmic gene loci.
- A significant number of transcription factors were identified to rhythmically associate with chromatin, though open chromatin regions did not show circadian variation.
- Core clock genes exhibited significant correlations with transcription factors involved in light and temperature signaling.
- Chromatin interactions at specific times (e.g., ZT8) suggest dynamic spatial conformation plays a role in circadian gene expression regulation.
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Key numbers
5396 (LL), 8826 (LD), 4190 (DD)
Oscillating Genes Under Light Conditions
Number of oscillating genes detected under constant light (LL), light/dark cycles (LD), and constant darkness (DD).
3943 (LL), 8332 (LD), 3253 (DD)
Oscillating Peaks
Number of peaks detected under each light condition.
1948
Oscillating Footprint-Gene Pairs
Total number of oscillating footprint-gene pairs analyzed in the study.