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Dynamics of extrachromosomal circular DNA in rice

Author

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  • Jundong Zhuang

    (Shanghai Jiao Tong University
    Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yaoxin Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Congcong Zhou

    (Chinese Academy of Sciences)

  • Danlin Fan

    (Chinese Academy of Sciences)

  • Tao Huang

    (Chinese Academy of Sciences)

  • Qi Feng

    (Chinese Academy of Sciences)

  • Yiqi Lu

    (Chinese Academy of Sciences)

  • Yan Zhao

    (Chinese Academy of Sciences)

  • Qiang Zhao

    (Chinese Academy of Sciences)

  • Bin Han

    (Chinese Academy of Sciences)

  • Tingting Lu

    (Shanghai Jiao Tong University)

Abstract

The genome’s dynamic nature, exemplified by elements like extrachromosomal circular DNA (eccDNA), is crucial for biodiversity and adaptation. Yet, the role of eccDNA in plants, particularly rice, remains underexplored. Here, we identify 25,598 eccDNAs, unveiling the widespread presence of eccDNA across six rice tissues and revealing its formation as a universal and random process. Interestingly, we discover that direct repeats play a pivotal role in eccDNA formation, pointing to a unique origin mechanism. Despite eccDNA’s prevalence in coding sequences, its impact on gene expression is minimal, implying its roles beyond gene regulation. We also observe the association between eccDNA’s formation and minor chromosomal deletions, providing insights of its possible function in regulating genome stability. Further, we discover eccDNA specifically accumulated in rice leaves, which may be associated with DNA damage caused by environmental stressors like intense light. In summary, our research advances understanding of eccDNA’s role in the genomic architecture and offers valuable insights for rice cultivation and breeding.

Suggested Citation

  • Jundong Zhuang & Yaoxin Zhang & Congcong Zhou & Danlin Fan & Tao Huang & Qi Feng & Yiqi Lu & Yan Zhao & Qiang Zhao & Bin Han & Tingting Lu, 2024. "Dynamics of extrachromosomal circular DNA in rice," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46691-0
    DOI: 10.1038/s41467-024-46691-0
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    References listed on IDEAS

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    1. Panpan Zhang & Assane Mbodj & Abirami Soundiramourtty & Christel Llauro & Alain Ghesquière & Mathieu Ingouff & R. Keith Slotkin & Frédéric Pontvianne & Marco Catoni & Marie Mirouze, 2023. "Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Sihan Wu & Kristen M. Turner & Nam Nguyen & Ramya Raviram & Marcella Erb & Jennifer Santini & Jens Luebeck & Utkrisht Rajkumar & Yarui Diao & Bin Li & Wenjing Zhang & Nathan Jameson & M. Ryan Corces &, 2019. "Circular ecDNA promotes accessible chromatin and high oncogene expression," Nature, Nature, vol. 575(7784), pages 699-703, November.
    3. Fu Yang & Weijia Su & Oliver W. Chung & Lauren Tracy & Lu Wang & Dale A. Ramsden & ZZ Zhao Zhang, 2023. "Retrotransposons hijack alt-EJ for DNA replication and eccDNA biogenesis," Nature, Nature, vol. 620(7972), pages 218-225, August.
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