J Integr Plant Biol. ›› 2023, Vol. 65 ›› Issue (8): 1966-1982.DOI: 10.1111/jipb.13502

• Functional Omics and Systems Biology • Previous Articles     Next Articles

Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants

Linhua Sun1,2†, Yuxin Cao2†, Zhu Li1,3†, Yi Liu2, Xiaochang Yin2, Xing Wang Deng1,2*, Hang He1,2* and Weiqiang Qian1,2*   

  1. 1. National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China;
    2. School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China;
    3. School of Plant Science and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel
    Linhua Sun, Yuxin Cao, and Zhu Li contributed equally to this work.
    *Correspondences: Xing Wang Deng (deng@pku.edu.cn); Hang He (hehang@pku.edu.cn); Weiqiang Qian (wqqian@pku.edu.cn, Dr. Qian is fully responsible for the distribution of the materials associated with this article)
  • Received:2023-02-23 Accepted:2023-05-06 Online:2023-05-08 Published:2023-08-01

Abstract: Higher-order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome. We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG-medicated chromatin loops are stable, many of these loops are tissue-specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max, indicating that these long-range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.

Key words: Arabidopsis, gene clusters, Hi-C, long-range chromatin loops, H3K27me3

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