DOI QR코드

DOI QR Code

Targeted Base Editing via RNA-Guided Cytidine Deaminases in Xenopus laevis Embryos

  • Park, Dong-Seok (Department of Biomedical Sciences, University of Ulsan College of Medicine) ;
  • Yoon, Mijung (Department of Biomedical Sciences, University of Ulsan College of Medicine) ;
  • Kweon, Jiyeon (Department of Biomedical Sciences, University of Ulsan College of Medicine) ;
  • Jang, An-Hee (Department of Biomedical Sciences, University of Ulsan College of Medicine) ;
  • Kim, Yongsub (Department of Biomedical Sciences, University of Ulsan College of Medicine) ;
  • Choi, Sun-Cheol (Department of Biomedical Sciences, University of Ulsan College of Medicine)
  • Received : 2017.10.17
  • Accepted : 2017.11.06
  • Published : 2017.11.30

Abstract

Genome editing using programmable nucleases such as CRISPR/Cas9 or Cpf1 has emerged as powerful tools for gene knock-out or knock-in in various organisms. While most genetic diseases are caused by point mutations, these genome-editing approaches are inefficient in inducing single-nucleotide substitutions. Recently, Cas9-linked cytidine deaminases, named base editors (BEs), have been shown to convert cytidine to uridine efficiently, leading to targeted single-base pair substitutions in human cells and organisms. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. Injection of base editor 3 (BE3) ribonucleoprotein targeting the tyrosinase (tyr) gene in early embryos can induce site-specific base conversions with the rates of up to 20.5%, resulting in oculocutaneous albinism phenotypes without off-target mutations. We further test this base-editing system by targeting the tp53 gene with the result that the expected single-base pair substitutions are observed at the target site. Collectively, these data establish that the programmable deaminases are efficient tools for creating targeted point mutations for human disease modeling in Xenopus.

Keywords

References

  1. Aslan, Y., Tadjuidje, E., Zorn, A.M., and Cha, S.W. (2017). High-efficiency non-mosaic CRISPR-mediated knock-in and indel mutation in F0 Xenopus. Development 144, 2852-2858. https://doi.org/10.1242/dev.152967
  2. Bae, S., Park, J., and Kim, J.S. (2014). Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475. https://doi.org/10.1093/bioinformatics/btu048
  3. Blitz, I.L., Biesinger, J., Xie, X., and Cho, K.W. (2013). Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system. Genesis 51, 827-834. https://doi.org/10.1002/dvg.22719
  4. Harland, R.M., and Grainger, R.M. (2011). Xenopus research: metamorphosed by genetics and genomics. Trends Genet. 27, 507-515. https://doi.org/10.1016/j.tig.2011.08.003
  5. Kim, H., and Kim, J.S. (2014). A guide to genome engineering with programmable nucleases. Nat. Rev. Genet. 15, 321-334. https://doi.org/10.1038/nrg3686
  6. Kim, Y., Cheong, S.A., Lee, J.G., Lee, S.W., Lee, M.S., Baek, I.J. and Sung, Y.H. (2016). Generation of knockout mice by Cpf1-mediated gene targeting. Nat Biotechnol 34, 808-810. https://doi.org/10.1038/nbt.3614
  7. Kim, K., Ryu, S.M., Kim, S.T., Baek, G., Kim, D., Lim, K., Chung, E., Kim, S., and Kim, J.S. (2017a). Highly efficient RNA-guided base editing in mouse embryos. Nat. Biotechnol. 35, 435-437. https://doi.org/10.1038/nbt.3816
  8. Kim, Y.B., Komor, A.C., Levy, J.M., Packer, M.S., Zhao, K.T., and Liu, D.R. (2017b). Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat. Biotechnol. 35, 371-376. https://doi.org/10.1038/nbt.3803
  9. Komor, A.C., Kim, Y.B., Packer, M.S., Zuris, J.A., and Liu, D.R. (2016). Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420-424. https://doi.org/10.1038/nature17946
  10. Lei, Y., Guo, X., Liu, Y., Cao, Y., Deng, Y., Chen, X., Cheng, C.H., Dawid, I.B., Chen, Y., and Zhao, H. (2012). Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs). Proc. Natl. Acad. Sci. USA 109, 17484-17489. https://doi.org/10.1073/pnas.1215421109
  11. Liang, P., Sun, H., Sun, Y., Zhang, X., Xie, X., Zhang, J., Zhang, Z., Chen, Y., Ding, C., Xiong, Y., et al. (2017). Effective gene editing by high-fidelity base editor 2 in mouse zygotes. Protein Cell 8, 601-611. https://doi.org/10.1007/s13238-017-0418-2
  12. Ma, Y., Zhang, J., Yin, W., Zhang, Z., Song, Y., and Chang, X. (2016). Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nat. Methods 13, 1029-1035. https://doi.org/10.1038/nmeth.4027
  13. Nakayama, T., Fish, M.B., Fisher, M., Oomen-Hajagos, J., Thomsen, G.H., and Grainger, R.M. (2013). Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis. Genesis 51, 835-843. https://doi.org/10.1002/dvg.22720
  14. Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K.Y., et al. (2016). Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353, pii: aaf8729.
  15. Rees, H.A., Komor, A.C., Yeh, W.H., Caetano-Lopes, J., Warman, M., Edge, A.S.B., and Liu, D.R. (2017). Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. Nat. Commun. 8, 15790. https://doi.org/10.1038/ncomms15790
  16. Sakane, Y., Sakuma, T., Kashiwagi, K., Kashiwagi, A., Yamamoto, T., and Suzuki, K.T. (2014). Targeted mutagenesis of multiple and paralogous genes in Xenopus laevis using two pairs of transcription activator-like effector nucleases. Dev. Growth Differ. 56, 108-114. https://doi.org/10.1111/dgd.12105
  17. Shimatani, Z., Kashojiya, S., Takayama, M., Terada, R., Arazoe, T., Ishii, H., Teramura, H., Yamamoto, T., Komatsu, H., Miura, K., et al. (2017). Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nat. Biotechnol. 35, 441-443. https://doi.org/10.1038/nbt.3833
  18. Young, J.J., Cherone, J.M., Doyon, Y., Ankoudinova, I., Faraji, F.M., Lee, A.H., Ngo, C., Guschin, D.Y., Paschon, D.E., Miller, J.C., et al. (2011). Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases. Proc. Natl. Acad. Sci. USA 108, 7052-7057. https://doi.org/10.1073/pnas.1102030108
  19. Zhang, Y., Qin, W., Lu, X., Xu, J., Huang, H., Bai, H., Li, S., and Lin, S. (2017). Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system. Nat. Commun. 8, 118. https://doi.org/10.1038/s41467-017-00175-6
  20. Zong, Y., Wang, Y., Li, C., Zhang, R., Chen, K., Ran, Y., Qiu, J.L., Wang, D., and Gao, C. (2017). Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat. Biotechnol. 35, 438-440. https://doi.org/10.1038/nbt.3811

Cited by

  1. Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering vol.13, pp.9, 2018, https://doi.org/10.1002/biot.201700596
  2. High-throughput genetic screens using CRISPR-Cas9 system vol.41, pp.9, 2017, https://doi.org/10.1007/s12272-018-1029-z
  3. CRISPR and Target-Specific DNA Endonucleases for Efficient DNA Knock-in in Eukaryotic Genomes vol.41, pp.11, 2017, https://doi.org/10.14348/molcells.2018.0408
  4. In vivo base editing of post-mitotic sensory cells vol.9, pp.1, 2017, https://doi.org/10.1038/s41467-018-04580-3
  5. Base editing: precision chemistry on the genome and transcriptome of living cells vol.19, pp.12, 2017, https://doi.org/10.1038/s41576-018-0059-1
  6. Precise A•T to G•C base editing in the zebrafish genome vol.16, pp.1, 2017, https://doi.org/10.1186/s12915-018-0609-1
  7. A panel of eGFP reporters for single base editing by APOBEC-Cas9 editosome complexes vol.9, pp.None, 2017, https://doi.org/10.1038/s41598-018-36739-9
  8. Programmable Base Editing of the Sheep Genome Revealed No Genome-Wide Off-Target Mutations vol.10, pp.None, 2017, https://doi.org/10.3389/fgene.2019.00215
  9. Dead Cas Systems: Types, Principles, and Applications vol.20, pp.23, 2017, https://doi.org/10.3390/ijms20236041
  10. Gene Editing and Alzheimer's Disease: Is There Light at the End of the Tunnel? vol.2, pp.None, 2017, https://doi.org/10.3389/fgeed.2020.00004
  11. A CRISPR-based base-editing screen for the functional assessment of BRCA1 variants vol.39, pp.1, 2017, https://doi.org/10.1038/s41388-019-0968-2
  12. Advances in engineering CRISPR-Cas9 as a molecular Swiss Army knife vol.5, pp.1, 2020, https://doi.org/10.1093/synbio/ysaa021
  13. Simple embryo injection of long single‐stranded donor templates with the CRISPR/Cas9 system leads to homology‐directed repair in Xenopus tropicalis and Xenopus laevis vol.58, pp.6, 2020, https://doi.org/10.1002/dvg.23366
  14. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors vol.38, pp.7, 2017, https://doi.org/10.1038/s41587-020-0561-9
  15. Precision genome editing using cytosine and adenine base editors in mammalian cells vol.16, pp.2, 2021, https://doi.org/10.1038/s41596-020-00450-9