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Multiplex base editing to convert TAG into TAA codons in the human genome

Author

Listed:
  • Yuting Chen

    (Harvard Medical School
    Wyss Institute for Biologically Inspired Engineering
    Chinese Academy of Sciences)

  • Eriona Hysolli

    (Harvard Medical School
    Wyss Institute for Biologically Inspired Engineering)

  • Anlu Chen

    (Harvard Medical School)

  • Stephen Casper

    (Harvard Medical School)

  • Songlei Liu

    (Harvard Medical School
    Wyss Institute for Biologically Inspired Engineering)

  • Kevin Yang

    (Harvard Medical School)

  • Chenli Liu

    (Chinese Academy of Sciences)

  • George Church

    (Harvard Medical School
    Wyss Institute for Biologically Inspired Engineering)

Abstract

Whole-genome recoding has been shown to enable nonstandard amino acids, biocontainment and viral resistance in bacteria. Here we take the first steps to extend this to human cells demonstrating exceptional base editing to convert TAG to TAA for 33 essential genes via a single transfection, and examine base-editing genome-wide (observing ~40 C-to-T off-target events in essential gene exons). We also introduce GRIT, a computational tool for recoding. This demonstrates the feasibility of recoding, and highly multiplex editing in mammalian cells.

Suggested Citation

  • Yuting Chen & Eriona Hysolli & Anlu Chen & Stephen Casper & Songlei Liu & Kevin Yang & Chenli Liu & George Church, 2022. "Multiplex base editing to convert TAG into TAA codons in the human genome," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31927-8
    DOI: 10.1038/s41467-022-31927-8
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    References listed on IDEAS

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    1. Nicholas S. McCarty & Alicia E. Graham & Lucie Studená & Rodrigo Ledesma-Amaro, 2020. "Multiplexed CRISPR technologies for gene editing and transcriptional regulation," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    2. Alexis J. Rovner & Adrian D. Haimovich & Spencer R. Katz & Zhe Li & Michael W. Grome & Brandon M. Gassaway & Miriam Amiram & Jaymin R. Patel & Ryan R. Gallagher & Jesse Rinehart & Farren J. Isaacs, 2015. "Correction: Corrigendum: Recoded organisms engineered to depend on synthetic amino acids," Nature, Nature, vol. 527(7577), pages 264-264, November.
    3. Julius Fredens & Kaihang Wang & Daniel Torre & Louise F. H. Funke & Wesley E. Robertson & Yonka Christova & Tiongsun Chia & Wolfgang H. Schmied & Daniel L. Dunkelmann & Václav Beránek & Chayasith Utta, 2019. "Total synthesis of Escherichia coli with a recoded genome," Nature, Nature, vol. 569(7757), pages 514-518, May.
    4. Yajing Liu & Changyang Zhou & Shisheng Huang & Lu Dang & Yu Wei & Jun He & Yingsi Zhou & Shaoshuai Mao & Wanyu Tao & Yu Zhang & Hui Yang & Xingxu Huang & Tian Chi, 2020. "A Cas-embedding strategy for minimizing off-target effects of DNA base editors," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    5. Krishanu Saha & Erik J. Sontheimer & P. J. Brooks & Melinda R. Dwinell & Charles A. Gersbach & David R. Liu & Stephen A. Murray & Shengdar Q. Tsai & Ross C. Wilson & Daniel G. Anderson & Aravind Asoka, 2021. "The NIH Somatic Cell Genome Editing program," Nature, Nature, vol. 592(7853), pages 195-204, April.
    6. Beverly Y. Mok & Marcos H. de Moraes & Jun Zeng & Dustin E. Bosch & Anna V. Kotrys & Aditya Raguram & FoSheng Hsu & Matthew C. Radey & S. Brook Peterson & Vamsi K. Mootha & Joseph D. Mougous & David R, 2020. "A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing," Nature, Nature, vol. 583(7817), pages 631-637, July.
    7. 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.
    8. 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.
    9. Alexis J. Rovner & Adrian D. Haimovich & Spencer R. Katz & Zhe Li & Michael W. Grome & Brandon M. Gassaway & Miriam Amiram & Jaymin R. Patel & Ryan R. Gallagher & Jesse Rinehart & Farren J. Isaacs, 2015. "Recoded organisms engineered to depend on synthetic amino acids," Nature, Nature, vol. 518(7537), pages 89-93, February.
    10. Jessica S. Dymond & Sarah M. Richardson & Candice E. Coombes & Timothy Babatz & Héloïse Muller & Narayana Annaluru & William J. Blake & Joy W. Schwerzmann & Junbiao Dai & Derek L. Lindstrom & Annabel , 2011. "Synthetic chromosome arms function in yeast and generate phenotypic diversity by design," Nature, Nature, vol. 477(7365), pages 471-476, September.
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