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Mechanistic and genetic basis of single-strand templated repair at Cas12a-induced DNA breaks in Chlamydomonas reinhardtii

Author

Listed:
  • Aron Ferenczi

    (University of Edinburgh)

  • Yen Peng Chew

    (University of Edinburgh)

  • Erika Kroll

    (University of Edinburgh
    Rothamsted Research)

  • Charlotte Koppenfels

    (University of Edinburgh)

  • Andrew Hudson

    (University of Edinburgh)

  • Attila Molnar

    (University of Edinburgh)

Abstract

Single-stranded oligodeoxynucleotides (ssODNs) are widely used as DNA repair templates in CRISPR/Cas precision genome editing. However, the underlying mechanisms of single-strand templated DNA repair (SSTR) are inadequately understood, constraining rational improvements to precision editing. Here we study SSTR at CRISPR/Cas12a-induced DNA double-strand breaks (DSBs) in the eukaryotic model green microalga Chlamydomonas reinhardtii. We demonstrate that ssODNs physically incorporate into the genome during SSTR at Cas12a-induced DSBs. This process is genetically independent of the Rad51-dependent homologous recombination and Fanconi anemia pathways, is strongly antagonized by non-homologous end-joining, and is mediated almost entirely by the alternative end-joining enzyme polymerase θ. These findings suggest differences in SSTR between C. reinhardtii and animals. Our work illustrates the promising potentially of C. reinhardtii as a model organism for studying nuclear DNA repair.

Suggested Citation

  • Aron Ferenczi & Yen Peng Chew & Erika Kroll & Charlotte Koppenfels & Andrew Hudson & Attila Molnar, 2021. "Mechanistic and genetic basis of single-strand templated repair at Cas12a-induced DNA breaks in Chlamydomonas reinhardtii," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27004-1
    DOI: 10.1038/s41467-021-27004-1
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    References listed on IDEAS

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    1. Donghyun Lim & Vedagopuram Sreekanth & Kurt J. Cox & Benjamin K. Law & Bridget K. Wagner & Jeffrey M. Karp & Amit Choudhary, 2020. "Engineering designer beta cells with a CRISPR-Cas9 conjugation platform," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    2. Zhuobin Liang & Tzvi Tzfira, 2013. "In vivo formation of double-stranded T-DNA molecules by T-strand priming," Nature Communications, Nature, vol. 4(1), pages 1-8, October.
    3. Molly C. Kottemann & Agata Smogorzewska, 2013. "Fanconi anaemia and the repair of Watson and Crick DNA crosslinks," Nature, Nature, vol. 493(7432), pages 356-363, January.
    4. Quentin Geissmann, 2013. "OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-10, February.
    5. Samuel H. Sternberg & Sy Redding & Martin Jinek & Eric C. Greene & Jennifer A. Doudna, 2014. "DNA interrogation by the CRISPR RNA-guided endonuclease Cas9," Nature, Nature, vol. 507(7490), pages 62-67, March.
    6. Anne Bothmer & Tanushree Phadke & Luis A. Barrera & Carrie M Margulies & Christina S. Lee & Frank Buquicchio & Sean Moss & Hayat S. Abdulkerim & William Selleck & Hariharan Jayaram & Vic E. Myer & Cec, 2017. "Characterization of the interplay between DNA repair and CRISPR/Cas9-induced DNA lesions at an endogenous locus," Nature Communications, Nature, vol. 8(1), pages 1-12, April.
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