Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice

Localized chromatin rewiring in rice occurs within a largely stable 3D genome, with 557 dynamic compartment transitions and 35.8% of TADs linking synchronized rhythmic gene phases.

• Why it matters: Spatial genome architecture coordinating rhythmic transcription across scales in plants is poorly understood, especially how circadian changes occur without disrupting global genome structure.
• What they did: Using bridge linker Hi-C, H3K9ac ChIP-seq, and RNA-seq at six time points across a 24-h circadian cycle in rice, the study quantified compartment, TAD, and loop dynamics.
• The result: Global A/B compartments (84.5%) and TADs (>95%) were conserved, while fine-scale intradomain contacts and loops were temporally plastic; Myb motifs were enriched at dawn/early day anchors (ZT0 and ZT4).