How 3D DNA structure, gene regulation, and gene activity work together to control the daily biological clock in rice

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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