Search
Close this search box.

Comparison of Cas12a and Cas9-mediated mutagenesis in tomato cells – Scientific Reports

  • Jaganathan, D., Ramasamy, K., Sellamuthu, G., Jayabalan, S. & Venkataraman, G. CRISPR for crop improvement: An update review. Front. Plant Sci. 9, 1–17 (2018).


    Google Scholar
     

  • Chen, K., Wang, Y., Zhang, R., Zhang, H. & Gao, C. CRISPR/Cas genome editing and precision plant breeding in agriculture. Annu. Rev. Plant Biol. 70, 667–697 (2019).

    CAS 
    PubMed 

    Google Scholar
     

  • Zhu, H., Li, C. & Gao, C. Applications of CRISPR–Cas in agriculture and plant biotechnology. Nat. Rev. Mol. Cell. Biol. 21, 661–677 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Lemmon, Z. H. et al. Rapid improvement of domestication traits in an orphan crop by genome editing. Nat. Plants 4, 766–770 (2018).

    CAS 
    PubMed 

    Google Scholar
     

  • Kwon, C. T. et al. Rapid customization of Solanaceae fruit crops for urban agriculture. Nat. Biotechnol. 38, 182–188 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Zsögön, A. et al. De novo domestication of wild tomato using genome editing. Nat. Biotechnol. https://doi.org/10.1038/nbt.4272 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-cas system. Cell 163, 759–771 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sage, F. & Geijsen, N. Ligation-assisted homologous recombination enables precise genome editing by deploying both MMEJ and HDR. Nucl. Acids Res. 50(11), e62–e62 (2022).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 1979(337), 816–821 (2012).


    Google Scholar
     

  • Fonfara, I., Richter, H., BratoviÄ, M., Le Rhun, A. & Charpentier, E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532, 517–521 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Zetsche, B. et al. Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array. Nat. Biotechnol. 35, 31–34 (2016).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hur, J. K. et al. Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins. Nat. Biotechnol. 34, 807–808 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Kim, Y. et al. Generation of knockout mice by Cpf1-mediated gene targeting. Nat. Biotechnol. 34, 808–810 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Kim, H. K. et al. In vivo high-throughput profiling of CRISPR-Cpf1 activity. Nat. Methods 14, 153–159 (2017).

    CAS 
    PubMed 

    Google Scholar
     

  • Kleinstiver, B. P. et al. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat. Biotechnol. 34, 869–874 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, D. et al. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat. Biotechnol. 34, 863–868 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Hu, X., Wang, C., Liu, Q., Fu, Y. & Wang, K. Targeted mutagenesis in rice using CRISPR-Cpf1 system. J. Genetics Genomics 44, 71–73 (2017).

    CAS 

    Google Scholar
     

  • Xu, R. et al. Generation of targeted mutant rice using a CRISPR-Cpf1 system. Plant Biotechnol. J. 15, 713–717 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tang, X. et al. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat. Plants 3, 1–5 (2017).


    Google Scholar
     

  • Schindele, P. & Puchta, H. Engineering CRISPR/LbCas12a for highly efficient, temperature-tolerant plant gene editing. Plant Biotechnol. J. 18, 1118–1120 (2020).

    PubMed 

    Google Scholar
     

  • Wang, M. et al. Multiplex gene editing in rice with simplified CRISPR-Cpf1 and CRISPR-Cas9 systems. J. Integr. Plant Biol. 60, 1–11 (2018).


    Google Scholar
     

  • Xia, X. et al. Advances in application of genome editing in tomato and recent development of genome editing technology. Theor. Appl. Genetics 134, 2727–2747 (2021).


    Google Scholar
     

  • Chandrasekaran, M., Boopathi, T. & Paramasivan, M. A status-quo review on CRISPR-Cas9 gene editing applications in tomato. Int. J. Biol. Macromol. 190, 120–129 (2021).

    CAS 
    PubMed 

    Google Scholar
     

  • Vu, T. V. et al. Highly efficient homology-directed repair using CRISPR/Cpf1-geminiviral replicon in tomato. Plant Biotechnol. J. 18, 2133–2143 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vu, T. V. et al. Improvement of the LbCas12a-crRNA system for efficient gene targeting in tomato. Front. Plant Sci. 12, 722552 (2021).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bernabé-Orts, J. M. et al. Assessment of Cas12a-mediated gene editing efficiency in plants. Plant Biotechnol. J. 17, 1971–1984 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • van Roekel, J. S. C., Damm, B., Melchers, L. S. & Hoekema, A. Factors influencing transformation frequency of tomato (Lycopersicon esculentum). Plant Cell Rep. 12, 644–647 (1993).

    PubMed 

    Google Scholar
     

  • Slaman, E., Lammers, M., Angenent, G. C. & de Maagd, R. A. High-throughput sgRNA testing reveals rules for Cas9 specificity and DNA repair in tomato cells. Front. Genome Ed 5, 1196763 (2023).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Concordet, J. P. & Haeussler, M. CRISPOR: Intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucl. Acids Res. 46, W242–W245 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Guo, A. Y. et al. PlantTFDB: A comprehensive plant transcription factor database. Nucl. Acids Res. 36, 966–969 (2008).


    Google Scholar
     

  • Bae, S., Park, J. & Kim, J.-S. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473–1475 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ali, S. K. & Al-Koofee, D. A. F. BatchPrimer3: A free web application for allele specific (SBE and allele flanking) primer design for SNPs genotyping in molecular diagnostics: A bioinformatics study. Gene Rep. 17, 100524 (2019).


    Google Scholar
     

  • Weber, E., Engler, C., Gruetzner, R., Werner, S. & Marillonnet, S. A modular cloning system for standardized assembly of multigene constructs. PLoS One 6, 1–11 (2011).


    Google Scholar
     

  • Engler, C. et al. A golden gate modular cloning toolbox for plants. ACS Synth. Biol. 3, 839–843 (2014).

    CAS 
    PubMed 

    Google Scholar
     

  • Labun, K. et al. Accurate analysis of genuine CRISPR editing events with ampliCan. Genome Res. 29, 843–847 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lin, Y. et al. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucl. Acids Res. 42, 7473–7485 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fusi, N., Smith, I., Doench, J. & Listgarten, J. In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency. bioRxiv 021568 (2015) doi:https://doi.org/10.1101/021568.

  • Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, J., Chen, W., Xue, L. & Tang, B. Prediction of activity and specificity of CRISPR-Cpf1 using convolutional deep learning neural networks. BMC Bioinf. 20, 332 (2019).


    Google Scholar
     

  • Wang, M., Mao, Y., Lu, Y., Tao, X. & Zhu, J. K. Multiplex gene editing in rice using the CRISPR-Cpf1 system. Mol. Plant 10, 1011–1013 (2017).

    CAS 
    PubMed 

    Google Scholar
     

  • Kim, H. et al. CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat. Commun. 8, 1–7 (2017).


    Google Scholar
     

  • Moreno-Mateos, M. A. et al. CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nat. Commun. 8, 2024 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • LeBlanc, C. et al. Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress. Plant J. 12, 3218–3221 (2017).


    Google Scholar
     

  • Malzahn, A. A. et al. Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis. BMC Biol. 17, 9 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Horlbeck, M. A. et al. Nucleosomes impede cas9 access to DNA in vivo and in vitro. Elife 5, 1–21 (2016).


    Google Scholar
     

  • Yarrington, R. M., Verma, S., Schwartz, S., Trautman, J. K. & Carroll, D. Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo. Proc. Natl. Acad. Sci. 115, 201810062 (2018).


    Google Scholar
     

  • Graf, R., Li, X., Chu, V. T. & Rajewsky, K. sgRNA Sequence motifs blocking efficient CRISPR/Cas9-mediated gene editing. Cell Rep. 26, 1098-1103.e3 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lei, Y. et al. CRISPR-P: A web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol. Plant 7, 1494–1496 (2014).

    CAS 
    PubMed 

    Google Scholar
     

  • Moreno-Mateos, M. A. et al. CRISPRscan: Designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat. Methods 12, 982–988 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zuo, Z. & Liu, J. Cas9-catalyzed DNA cleavage generates staggered ends: evidence from molecular dynamics simulations. Sci. Rep. 5, 1–9 (2016).


    Google Scholar
     

  • Shou, J., Li, J., Liu, Y. & Wu, Q. Precise and predictable CRISPR chromosomal rearrangements reveal principles of cas9-mediated nucleotide insertion. Mol. Cell. 71, 498-509.e4 (2018).

    CAS 
    PubMed 

    Google Scholar
     

  • Allen, F. et al. Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nat. Biotechnol. 37, 64–82 (2019).

    CAS 

    Google Scholar
     

  • Chen, W. et al. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucl. Acids Res. 47, 7989–8003 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shi, X. et al. Cas9 has no exonuclease activity resulting in staggered cleavage with overhangs and predictable di- and tri-nucleotide CRISPR insertions without template donor. Cell. Discov. 5, 4–7 (2019).


    Google Scholar
     

  • Lemos, B. R. et al. CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles. Proc. Natl. Acad. Sci. U.S.A. 115, E2010–E2047 (2018).


    Google Scholar
     

  • Wolter, F. & Puchta, H. In planta gene targeting can be enhanced by the use of CRISPR /Cas12a. Plant J. TPJ https://doi.org/10.1111/tpj.14488 (2019).

    Article 

    Google Scholar
     

  • Van, T. V. et al. Highly efficient homology-directed repair using CRISPR/Cpf1-geminiviral replicon in tomato. Plant Biotechnol. J. 18, 2133–2143 (2020).


    Google Scholar
     

  • Truong, L. N. et al. Microhomology-mediated end joining and homologous recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 110, 7720–7725 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ceccaldi, R., Rondinelli, B. & D’Andrea, A. D. Repair pathway choices and consequences at the double-strand break. Trends Cell. Biol. 26, 52–64 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Puchta, H. The repair of double-strand breaks in plants: Mechanisms and consequences for genome evolution. J. Exp. Bot. 56, 1–14 (2005).

    CAS 
    PubMed 

    Google Scholar
     

  • Manova, V. & Gruszka, D. DNA damage and repair in plants–from models to crops. Front. Plant Sci. 6, 1–26 (2015).


    Google Scholar
     

  • Rodríguez-Leal, D., Lemmon, Z. H., Man, J., Bartlett, M. E. & Lippman, Z. B. Engineering quantitative trait variation for crop improvement by genome editing. Cell 171, 470-480.e8 (2017).

    PubMed 

    Google Scholar
     

  • Wang, X. et al. Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nat. Plants 7, 419–427 (2021).

    CAS 
    PubMed 

    Google Scholar
     

  • Tang, X. et al. A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biol. 19, 84 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, K. et al. Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize. Plant Biotechnol. J. https://doi.org/10.1111/pbi.12982 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raitskin, O., Schudoma, C., West, A. & Patron, N. J. Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering. PLoS One 14, e0211598 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hsu, P. D. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827–832 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar