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Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL

Author

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  • Linhua Sun

    (Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang
    Peking University)

  • Jingru Zhou

    (Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang)

  • Xiao Xu

    (Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang)

  • Yi Liu

    (Peking University)

  • Ni Ma

    (Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang
    Peking University)

  • Yutong Liu

    (Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang)

  • Wenchao Nie

    (Wuhan Frasergen Bioinformatics Co., Ltd.)

  • Ling Zou

    (Wuhan Frasergen Bioinformatics Co., Ltd.)

  • Xing Wang Deng

    (Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang
    Peking University)

  • Hang He

    (Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang
    Peking University)

Abstract

Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.

Suggested Citation

  • Linhua Sun & Jingru Zhou & Xiao Xu & Yi Liu & Ni Ma & Yutong Liu & Wenchao Nie & Ling Zou & Xing Wang Deng & Hang He, 2024. "Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-023-44347-z
    DOI: 10.1038/s41467-023-44347-z
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    1. Anna-Maria Göbel & Sida Zhou & Zhidan Wang & Sofia Tzourtzou & Axel Himmelbach & Shiwei Zheng & Mónica Pradillo & Chang Liu & Hua Jiang, 2024. "Mutations of PDS5 genes enhance TAD-like domain formation in Arabidopsis thaliana," Nature Communications, Nature, vol. 15(1), pages 1-8, December.

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