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BEAR reveals that increased fidelity variants can successfully reduce the mismatch tolerance of adenine but not cytosine base editors

Author

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  • András Tálas

    (Research Centre for Natural Sciences
    Semmelweis University)

  • Dorottya A. Simon

    (Research Centre for Natural Sciences
    Gene Design Ltd.)

  • Péter I. Kulcsár

    (Research Centre for Natural Sciences
    Semmelweis University
    Biospiral-2006 Ltd.)

  • Éva Varga

    (Research Centre for Natural Sciences
    University of Szeged)

  • Sarah L. Krausz

    (Research Centre for Natural Sciences
    Semmelweis University)

  • Ervin Welker

    (Research Centre for Natural Sciences
    Biological Research Centre)

Abstract

Adenine and cytosine base editors (ABE, CBE) allow for precision genome engineering. Here, Base Editor Activity Reporter (BEAR), a plasmid-based fluorescent tool is introduced, which can be applied to report on ABE and CBE editing in a virtually unrestricted sequence context or to label base edited cells for enrichment. Using BEAR-enrichment, we increase the yield of base editing performed by nuclease inactive base editors to the level of the nickase versions while maintaining significantly lower indel background. Furthermore, by exploiting the semi-high-throughput potential of BEAR, we examine whether increased fidelity SpCas9 variants can be used to decrease SpCas9-dependent off-target effects of ABE and CBE. Comparing them on the same target sets reveals that CBE remains active on sequences, where increased fidelity mutations and/or mismatches decrease the activity of ABE. Our results suggest that the deaminase domain of ABE is less effective to act on rather transiently separated target DNA strands, than that of CBE explaining its lower mismatch tolerance.

Suggested Citation

  • András Tálas & Dorottya A. Simon & Péter I. Kulcsár & Éva Varga & Sarah L. Krausz & Ervin Welker, 2021. "BEAR reveals that increased fidelity variants can successfully reduce the mismatch tolerance of adenine but not cytosine base editors," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26461-y
    DOI: 10.1038/s41467-021-26461-y
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    1. Péter István Kulcsár & András Tálas & Zoltán Ligeti & Eszter Tóth & Zsófia Rakvács & Zsuzsa Bartos & Sarah Laura Krausz & Ágnes Welker & Vanessza Laura Végi & Krisztina Huszár & Ervin Welker, 2023. "A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets," Nature Communications, Nature, vol. 14(1), pages 1-20, December.

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