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Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data

Author

Listed:
  • Matteo Ciciani

    (Cellular and Integrative Biology, University of Trento)

  • Michele Demozzi

    (Cellular and Integrative Biology, University of Trento)

  • Eleonora Pedrazzoli

    (Cellular and Integrative Biology, University of Trento)

  • Elisabetta Visentin

    (Cellular and Integrative Biology, University of Trento)

  • Laura Pezzè

    (Alia Therapeutics)

  • Lorenzo Federico Signorini

    (Cellular and Integrative Biology, University of Trento
    Tel Aviv University)

  • Aitor Blanco-Miguez

    (Cellular and Integrative Biology, University of Trento)

  • Moreno Zolfo

    (Cellular and Integrative Biology, University of Trento)

  • Francesco Asnicar

    (Cellular and Integrative Biology, University of Trento)

  • Antonio Casini

    (Alia Therapeutics)

  • Anna Cereseto

    (Cellular and Integrative Biology, University of Trento)

  • Nicola Segata

    (Cellular and Integrative Biology, University of Trento)

Abstract

The identification of the protospacer adjacent motif (PAM) sequences of Cas9 nucleases is crucial for their exploitation in genome editing. Here we develop a computational pipeline that was used to interrogate a massively expanded dataset of metagenome and virome assemblies for accurate and comprehensive PAM predictions. This procedure allows the identification and isolation of sequence-tailored Cas9 nucleases by using the target sequence as bait. As proof of concept, starting from the disease-causing mutation P23H in the RHO gene, we find, isolate and experimentally validate a Cas9 which uses the mutated sequence as PAM. Our PAM prediction pipeline will be instrumental to generate a Cas9 nuclease repertoire responding to any PAM requirement.

Suggested Citation

  • Matteo Ciciani & Michele Demozzi & Eleonora Pedrazzoli & Elisabetta Visentin & Laura Pezzè & Lorenzo Federico Signorini & Aitor Blanco-Miguez & Moreno Zolfo & Francesco Asnicar & Antonio Casini & Anna, 2022. "Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34213-9
    DOI: 10.1038/s41467-022-34213-9
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    1. F. Ann Ran & Le Cong & Winston X. Yan & David A. Scott & Jonathan S. Gootenberg & Andrea J. Kriz & Bernd Zetsche & Ophir Shalem & Xuebing Wu & Kira S. Makarova & Eugene V. Koonin & Phillip A. Sharp & , 2015. "In vivo genome editing using Staphylococcus aureus Cas9," Nature, Nature, vol. 520(7546), pages 186-191, April.
    2. Giedrius Gasiunas & Joshua K. Young & Tautvydas Karvelis & Darius Kazlauskas & Tomas Urbaitis & Monika Jasnauskaite & Mantvyda M. Grusyte & Sushmitha Paulraj & Po-Hao Wang & Zhenglin Hou & Shane K. Do, 2020. "A catalogue of biochemically diverse CRISPR-Cas9 orthologs," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    3. Daphne Collias & Chase L. Beisel, 2021. "CRISPR technologies and the search for the PAM-free nuclease," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Josiane E. Garneau & Marie-Ève Dupuis & Manuela Villion & Dennis A. Romero & Rodolphe Barrangou & Patrick Boyaval & Christophe Fremaux & Philippe Horvath & Alfonso H. Magadán & Sylvain Moineau, 2010. "The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA," Nature, Nature, vol. 468(7320), pages 67-71, November.
    5. Metin Balaban & Niema Moshiri & Uyen Mai & Xingfan Jia & Siavash Mirarab, 2019. "TreeCluster: Clustering biological sequences using phylogenetic trees," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-20, August.
    6. Keiichiro Suzuki & Yuji Tsunekawa & Reyna Hernandez-Benitez & Jun Wu & Jie Zhu & Euiseok J. Kim & Fumiyuki Hatanaka & Mako Yamamoto & Toshikazu Araoka & Zhe Li & Masakazu Kurita & Tomoaki Hishida & Mo, 2016. "In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration," Nature, Nature, vol. 540(7631), pages 144-149, December.
    7. Jennifer A. Doudna, 2020. "The promise and challenge of therapeutic genome editing," Nature, Nature, vol. 578(7794), pages 229-236, February.
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