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PrimeDesign software for rapid and simplified design of prime editing guide RNAs

Author

Listed:
  • Jonathan Y. Hsu

    (Department of Biological Engineering, Massachusetts Institute of Technology
    Molecular Pathology Unit, Massachusetts General Hospital
    Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital)

  • Julian Grünewald

    (Molecular Pathology Unit, Massachusetts General Hospital
    Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital
    Department of Pathology, Harvard Medical School)

  • Regan Szalay

    (Molecular Pathology Unit, Massachusetts General Hospital
    Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital)

  • Justine Shih

    (Molecular Pathology Unit, Massachusetts General Hospital
    Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital)

  • Andrew V. Anzalone

    (Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Kin Chung Lam

    (Molecular Pathology Unit, Massachusetts General Hospital
    Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital
    Department of Pathology, Harvard Medical School)

  • Max W. Shen

    (Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT
    Harvard University
    Harvard University
    Computational and Systems Biology Program, Massachusetts Institute of Technology)

  • Karl Petri

    (Molecular Pathology Unit, Massachusetts General Hospital
    Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital
    Department of Pathology, Harvard Medical School)

  • David R. Liu

    (Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • J. Keith Joung

    (Molecular Pathology Unit, Massachusetts General Hospital
    Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital
    Department of Pathology, Harvard Medical School)

  • Luca Pinello

    (Molecular Pathology Unit, Massachusetts General Hospital
    Department of Pathology, Harvard Medical School
    Broad Institute of Harvard and MIT)

Abstract

Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.

Suggested Citation

  • Jonathan Y. Hsu & Julian Grünewald & Regan Szalay & Justine Shih & Andrew V. Anzalone & Kin Chung Lam & Max W. Shen & Karl Petri & David R. Liu & J. Keith Joung & Luca Pinello, 2021. "PrimeDesign software for rapid and simplified design of prime editing guide RNAs," Nature Communications, Nature, vol. 12(1), pages 1-6, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21337-7
    DOI: 10.1038/s41467-021-21337-7
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    Citations

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    Cited by:

    1. Monica Rengifo-Gonzalez & Maria-Vittoria Mazzuoli & Axel B. Janssen & Anne-Stéphanie Rueff & Jessica Burnier & Xue Liu & Jan-Willem Veening, 2025. "Make-or-break prime editing for genome engineering in Streptococcus pneumoniae," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    2. Sébastien Levesque & Diana Mayorga & Jean-Philippe Fiset & Claudia Goupil & Alexis Duringer & Andréanne Loiselle & Eva Bouchard & Daniel Agudelo & Yannick Doyon, 2022. "Marker-free co-selection for successive rounds of prime editing in human cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. J. Ferreira da Silva & G. P. Oliveira & E. A. Arasa-Verge & C. Kagiou & A. Moretton & G. Timelthaler & J. Jiricny & J. I. Loizou, 2022. "Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Yidian Fu & Xiaoyu He & Liang Ma & Xin D. Gao & Pengpeng Liu & Hanhan Shi & Peiwei Chai & Shengfang Ge & Renbing Jia & David R. Liu & Xianqun Fan & Zhi Yang, 2025. "In vivo prime editing rescues photoreceptor degeneration in nonsense mutant retinitis pigmentosa," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    5. Xiaosa Li & Lina Zhou & Bao-Qing Gao & Guangye Li & Xiao Wang & Ying Wang & Jia Wei & Wenyan Han & Zixian Wang & Jifang Li & Runze Gao & Junjie Zhu & Wenchao Xu & Jing Wu & Bei Yang & Xiaodong Sun & L, 2022. "Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    6. Qichen Yuan & Xue Gao, 2022. "Multiplex base- and prime-editing with drive-and-process CRISPR arrays," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Qichen Yuan & Hongzhi Zeng & Tyler C. Daniel & Qingzhuo Liu & Yongjie Yang & Emmanuel C. Osikpa & Qiaochu Yang & Advaith Peddi & Liliana M. Abramson & Boyang Zhang & Yong Xu & Xue Gao, 2024. "Orthogonal and multiplexable genetic perturbations with an engineered prime editor and a diverse RNA array," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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