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Enhancement of prime editing via xrRNA motif-joined pegRNA

Author

Listed:
  • Guiquan Zhang

    (Model Animal Research Center at Medical School of Nanjing University)

  • Yao Liu

    (Northwest A&F University)

  • Shisheng Huang

    (ShanghaiTech University)

  • Shiyuan Qu

    (ShanghaiTech University)

  • Daolin Cheng

    (Model Animal Research Center at Medical School of Nanjing University)

  • Yuan Yao

    (Zhejiang University)

  • Quanjiang Ji

    (ShanghaiTech University)

  • Xiaolong Wang

    (Northwest A&F University)

  • Xingxu Huang

    (ShanghaiTech University
    Zhejiang Laboratory)

  • Jianghuai Liu

    (Model Animal Research Center at Medical School of Nanjing University)

Abstract

The prime editors (PEs) have shown great promise for precise genome modification. However, their suboptimal efficiencies present a significant technical challenge. Here, by appending a viral exoribonuclease-resistant RNA motif (xrRNA) to the 3′-extended portion of pegRNAs for their increased resistance against degradation, we develop an upgraded PE platform (xrPE) with substantially enhanced editing efficiencies in multiple cell lines. A pan-target average enhancement of up to 3.1-, 4.5- and 2.5-fold in given cell types is observed for base conversions, small deletions, and small insertions, respectively. Additionally, xrPE exhibits comparable edit:indel ratios and similarly minimal off-target editing as the canonical PE3. Of note, parallel comparison of xrPE to the most recently developed epegRNA-based PE system shows their largely equivalent editing performances. Our study establishes a highly adaptable platform of improved PE that shall have broad implications.

Suggested Citation

  • Guiquan Zhang & Yao Liu & Shisheng Huang & Shiyuan Qu & Daolin Cheng & Yuan Yao & Quanjiang Ji & Xiaolong Wang & Xingxu Huang & Jianghuai Liu, 2022. "Enhancement of prime editing via xrRNA motif-joined pegRNA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29507-x
    DOI: 10.1038/s41467-022-29507-x
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    References listed on IDEAS

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    1. Yoav Benjamini & Abba M. Krieger & Daniel Yekutieli, 2006. "Adaptive linear step-up procedures that control the false discovery rate," Biometrika, Biometrika Trust, vol. 93(3), pages 491-507, September.
    2. Andrea MacFadden & Zoe O’Donoghue & Patricia A. G. C. Silva & Erich G. Chapman & René C. Olsthoorn & Mark G. Sterken & Gorben P. Pijlman & Peter J. Bredenbeek & Jeffrey S. Kieft, 2018. "Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    3. Luke W. Koblan & Michael R. Erdos & Christopher Wilson & Wayne A. Cabral & Jonathan M. Levy & Zheng-Mei Xiong & Urraca L. Tavarez & Lindsay M. Davison & Yantenew G. Gete & Xiaojing Mao & Gregory A. Ne, 2021. "In vivo base editing rescues Hutchinson–Gilford progeria syndrome in mice," Nature, Nature, vol. 589(7843), pages 608-614, January.
    4. Kiran Musunuru & Alexandra C. Chadwick & Taiji Mizoguchi & Sara P. Garcia & Jamie E. DeNizio & Caroline W. Reiss & Kui Wang & Sowmya Iyer & Chaitali Dutta & Victoria Clendaniel & Michael Amaonye & Aar, 2021. "In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in primates," Nature, Nature, vol. 593(7859), pages 429-434, May.
    5. Andrew V. Anzalone & Peyton B. Randolph & Jessie R. Davis & Alexander A. Sousa & Luke W. Koblan & Jonathan M. Levy & Peter J. Chen & Christopher Wilson & Gregory A. Newby & Aditya Raguram & David R. L, 2019. "Search-and-replace genome editing without double-strand breaks or donor DNA," Nature, Nature, vol. 576(7785), pages 149-157, December.
    6. Alexis C. Komor & Yongjoo B. Kim & Michael S. Packer & John A. Zuris & David R. Liu, 2016. "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage," Nature, Nature, vol. 533(7603), pages 420-424, May.
    7. Xiaolin Niu & Qiuhan Liu & Zhonghe Xu & Zhifeng Chen & Linghui Xu & Lilei Xu & Jinghong Li & Xianyang Fang, 2020. "Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    8. Antonio Suma & Lucia Coronel & Giovanni Bussi & Cristian Micheletti, 2020. "Directional translocation resistance of Zika xrRNA," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
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    Cited by:

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    2. Jianli Tao & Daniel E. Bauer & Roberto Chiarle, 2023. "Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Ronghao Chen & Yu Cao & Yajing Liu & Dongdong Zhao & Ju Li & Zhihui Cheng & Changhao Bi & Xueli Zhang, 2023. "Enhancement of a prime editing system via optimal recruitment of the pioneer transcription factor P65," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    4. Youcai Xiong & Yinyu Su & Ruigao He & Xiaosong Han & Sheng Li & Minghuan Liu & Xiaoning Xi & Zijia Liu & Heng Wang & Shengsong Xie & Xuewen Xu & Kui Li & Jifeng Zhang & Jie Xu & Xinyun Li & Shuhong Zh, 2025. "EXPERT expands prime editing efficiency and range of large fragment edits," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    5. Jidong Fei & Dongdong Zhao & Caiyi Pang & Ju Li & Siwei Li & Wentao Qiao & Juan Tan & Changhao Bi & Xueli Zhang, 2025. "Mismatch prime editing gRNA increased efficiency and reduced indels," Nature Communications, Nature, vol. 16(1), pages 1-10, December.

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