Efficient and precise inversion of genomic DNA from large to chromosomal scale

  • Nat Chem Biol. 2026 Feb;22(2):328-339. doi: 10.1038/s41589-025-02033-9.
Ao Zhang  #  1 ,  Xiangkun Sun  #  1 ,  Ying Wu  #  1 ,  Pan Gao  #  1 ,  Ruiwen Zhang  1 ,  Man Zhang  1 ,  Sisi Xie  1  2 ,  Wei Fan  3 ,  Ying Zhang  1  4  5  6  7 ,  Hao Yin  8  9  10  11  12
Affiliations
  • 1. Department of Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
  • 2. Departments of Neurosurgery and Urology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
  • 3. Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China.
  • 4. TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
  • 5. State Key Laboratory of Virology and Biosafety, Wuhan University, Wuhan, China.
  • 6. RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China.
  • 7. Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
  • 8. Department of Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China. [email protected].
  • 9. Departments of Neurosurgery and Urology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China. [email protected].
  • 10. TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China. [email protected].
  • 11. State Key Laboratory of Virology and Biosafety, Wuhan University, Wuhan, China. [email protected].
  • 12. RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China. [email protected].
  • # Contributed equally.
PMID: 41062834 DOI: 10.1038/s41589-025-02033-9
Abstract

Chromosomal inversion is a key structural variation impacting cellular fitness and genomic integrity. Here we developed prime-editing-based inversion with enhanced performance (PIE) to efficiently induce large-scale inversions in mammalian cells. PIEv1 uses a prime-editing guide RNA (pegRNA) pair but yields one imprecise junction. PIEv2 and PIEv3 add a second pegRNA pair for precise inversion, with PIEv3b further enhancing coupling precise inversion through improved plasmid design. PIEv3b achieves inversion efficiencies up to 61.7% for 1 Mb and 14.2% for 50 Mb segments and shows 4-20-fold higher efficiency compared to twin prime editing with integrase, across ranges of 100 kb to 30 Mb. Additionally, PIEv3b outperforms nuclease-based approaches in both inversion efficiency and precision. Using PIE, we convert human chromosomes from metacentric to telocentric configurations by inverting 30-Mb and 100-Mb chromosomal segments. Our work represents a powerful tool for engineering chromosomal structural variations, with broad implications for medicine and biotechnology.

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