Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice
- 1Huazhong Agricultural University
Abstract
How spatial genome architecture coordinates rhythmic gene transcription across scales in plants remains poorly understood. Here, we integrated bridge linker Hi-C (BL-Hi-C), H3K9ac ChIP-seq and RNA-seq at six time points across a 24-h circadian cycle in rice. While global higher-order structure was largely invariant, with 84.5% of A/B compartments and over 95% of topologically associating domains (TADs) conserved across all time points, we identified 557 dynamic compartment transitions coupled to changes in active chromatin marks. Within this stable structural scaffold, 35.8% of TADs containing clustered loci of multiple rhythmic genes with synchronized expression phases. In contrast, fine-scale intradomain contacts and chromatin loops exhibited pronounced temporal plasticity. Chromatin interactions connected rhythmic genes with diverse expression phases. Myb-binding motifs were enriched at chromatin interaction anchors at dawn and early day (ZT0 and ZT4). Together, our findings demonstrate that localized chromatin rewiring occurs within relatively stable architectural frameworks, providing a spatiotemporal context for circadian gene regulation in rice.
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BibTeX
@misc{zhang2026localized,
title = {{Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice}},
author = {y. zhang and G. Chen and L. Guo and M. Cao and J. Zhou and X. Li and J. Yan},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.23.761304},
url = {https://www.biorxiv.org/content/10.64898/2026.10.23.761304v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice
AU - y. zhang
AU - G. Chen
AU - L. Guo
AU - M. Cao
AU - J. Zhou
AU - X. Li
AU - J. Yan
PY - 2026
DA - 2026/10/23
PB - bioRxiv
DO - 10.64898/2026.10.23.761304
UR - https://www.biorxiv.org/content/10.64898/2026.10.23.761304v1
AB - How spatial genome architecture coordinates rhythmic gene transcription across scales in plants remains poorly understood. Here, we integrated bridge linker Hi-C (BL-Hi-C), H3K9ac ChIP-seq and RNA-seq at six time points across a 24-h circadian cycle in rice. While global higher-order structure was largely invariant, with 84.5% of A/B compartments and over 95% of topologically associating domains (TADs) conserved across all time points, we identified 557 dynamic compartment transitions coupled to changes in active chromatin marks. Within this stable structural scaffold, 35.8% of TADs containing clustered loci of multiple rhythmic genes with synchronized expression phases. In contrast, fine-scale intradomain contacts and chromatin loops exhibited pronounced temporal plasticity. Chromatin interactions connected rhythmic genes with diverse expression phases. Myb-binding motifs were enriched at chromatin interaction anchors at dawn and early day (ZT0 and ZT4). Together, our findings demonstrate that localized chromatin rewiring occurs within relatively stable architectural frameworks, providing a spatiotemporal context for circadian gene regulation in rice.
ER -