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Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis

Author

Listed:
  • Linhua Sun

    (Peking University
    Peking University)

  • Yuqing Jing

    (Peking University)

  • Xinyu Liu

    (Peking University)

  • Qi Li

    (Peking University)

  • Zhihui Xue

    (Chinese Academy of Sciences)

  • Zhukuan Cheng

    (Chinese Academy of Sciences)

  • Daowen Wang

    (Henan Agricultural University, Longzi Lake Campus)

  • Hang He

    (Peking University)

  • Weiqiang Qian

    (Peking University)

Abstract

In higher eukaryotes, heterochromatin is mainly composed of transposable elements (TEs) silenced by epigenetic mechanisms. But, the silencing of certain heterochromatin-associated TEs is disrupted by heat stress. By comparing genome-wide high-resolution chromatin packing patterns under normal or heat conditions obtained through Hi-C analysis, we show here that heat stress causes global rearrangement of the 3D genome in Arabidopsis thaliana. Contacts between pericentromeric regions and distal chromosome arms, as well as proximal intra-chromosomal interactions along the chromosomes, are enhanced. However, interactions within pericentromeres and those between distal intra-chromosomal regions are decreased. Many inter-chromosomal interactions, including those within the KNOT, are also reduced. Furthermore, heat activation of TEs exhibits a high correlation with the reduction of chromosomal interactions involving pericentromeres, the KNOT, the knob, and the upstream and downstream flanking regions of the activated TEs. Together, our results provide insights into the relationship between TE activation and 3D genome reorganization.

Suggested Citation

  • Linhua Sun & Yuqing Jing & Xinyu Liu & Qi Li & Zhihui Xue & Zhukuan Cheng & Daowen Wang & Hang He & Weiqiang Qian, 2020. "Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15809-5
    DOI: 10.1038/s41467-020-15809-5
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    Cited by:

    1. Ádám Sturm & Éva Saskői & Bernadette Hotzi & Anna Tarnóci & János Barna & Ferenc Bodnár & Himani Sharma & Tibor Kovács & Eszter Ari & Nóra Weinhardt & Csaba Kerepesi & András Perczel & Zoltán Ivics & , 2023. "Downregulation of transposable elements extends lifespan in Caenorhabditis elegans," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    2. Liang Leng & Zhichao Xu & Bixia Hong & Binbin Zhao & Ya Tian & Can Wang & Lulu Yang & Zhongmei Zou & Lingyu Li & Ke Liu & Wanjun Peng & Jiangning Liu & Zhoujie An & Yalin Wang & Baozhong Duan & Zhigan, 2024. "Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Yi Liao & Juntao Wang & Zhangsheng Zhu & Yuanlong Liu & Jinfeng Chen & Yongfeng Zhou & Feng Liu & Jianjun Lei & Brandon S. Gaut & Bihao Cao & J. J. Emerson & Changming Chen, 2022. "The 3D architecture of the pepper genome and its relationship to function and evolution," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    4. 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.

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