CoChat
Sign Up
Cited by 35

The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.

Efficient and high-fidelity base editor with expanded PAM compatibility for cytidine dinucleotide

Liu, Zhiquan, Chen, Siyu, Jia, Yingqi, Shan, Huanhuan, Chen, Mao, Song, Yuning, Lai, Liangxue, Li, Zhanjun·2021·Science China Life Sciences
DOI 10.1007/s11427-020-1775-2
Open this paper in CoChat — free account

Abstract

Cytidine base editor (CBE), which is composed of a cytidine deaminase fused to Cas9 nickase, has been widely used to induce C-to-T conversions in a wide range of organisms. However, the targeting scope of current CBEs is largely restricted to protospacer adjacent motif (PAM) sequences containing G, T, or A bases. In this study, we developed a new base editor termed "nNme2-CBE" with excellent PAM compatibility for cytidine dinucleotide, significantly expanding the genome-targeting scope of CBEs. Using nNme2-CBE, targeted editing efficiencies of 29.0%-55.0% and 17.3%-52.5% were generated in human cells and rabbit embryos, respectively. In contrast to conventional nSp-CBE, the nNme2-CBE is a natural high-fidelity base editing platform with minimal DNA off-targeting detected in vivo. Significantly increased efficiency in GC context and precision were determined by combining nNme2Cas9 with rationally engineered cytidine deaminases. In addition, the Founder rabbits with accurate single-base substitutions at Fgf5 gene loci were successfully generated by using the nNme2-CBE system. These novel nNme2-CBEs with expanded PAM compatibility and high fidelity will expand the base editing toolset for efficient gene modification and therapeutic applications.

Overview

Integrity signals

Registry

Crossref · 10.1007/s11427-020-1775-2

Cites

11 of 11 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Citations

Cites

Flagged first, then by citations

Show all 11 references

Research works printed but not linked: 45

  1. Agudelo, D., Carter, S., Velimirovic, M., Duringer, A., Rivest, J.F., Levesque, S., Loehr, J., Mouchiroud, M., Cyr, D., Waters, P.J., et al. (2020). Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9. Genome Res 30, 107–117. · DOI
  2. Amrani, N., Gao, X.D., Liu, P., Edraki, A., Mir, A., Ibraheim, R., Gupta, A., Sasaki, K.E., Wu, T., Donohoue, P.D., et al. (2018). NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol 19, 214. · DOI
  3. Anzalone, A.V., Randolph, P.B., Davis, J.R., Sousa, A.A., Koblan, L.W., Levy, J.M., Chen, P.J., Wilson, C., Newby, G.A., Raguram, A., et al. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157. · DOI · Paper page
  4. 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. · DOI · Paper page
  5. Brinkman, E.K., Chen, T., Amendola, M., and van Steensel, B. (2014). Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res 42, e168. · DOI · Paper page
  6. Chatterjee, P., Jakimo, N., and Jacobson, J.M. (2018). Minimal PAM specificity of a highly similar SpCas9 ortholog. Sci Adv 4, eaau0766. · DOI
  7. Deng, J., Chen, M., Liu, Z., Song, Y., Sui, T., Lai, L., and Li, Z. (2019). The disrupted balance between hair follicles and sebaceous glands in Hoxc13-ablated rabbits. FASEB J 33, 1226–1234. · DOI
  8. Doman, J.L., Raguram, A., Newby, G.A., and Liu, D.R. (2020). Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors. Nat Biotechnol 38, 620–628. · DOI · Paper page
  9. Esvelt, K.M., Mali, P., Braff, J.L., Moosburner, M., Yaung, S.J., and Church, G.M. (2013). Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 10, 1116–1121. · DOI · Paper page
  10. Kluesner, M.G., Nedveck, D.A., Lahr, W.S., Garbe, J.R., Abrahante, J.E., Webber, B.R., and Moriarity, B.S. (2018). EditR: a method to quantify base editing from Sanger sequencing. CRISPR J 1, 239–250. · DOI · Paper page
  11. Gehrke, J.M., Cervantes, O., Clement, M.K., Wu, Y., Zeng, J., Bauer, D.E., Pinello, L., and Joung, J.K. (2018). An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol 36, 977–982. · DOI
  12. Housley, D.J.E., and Venta, P.J. (2006). The long and the short of it: evidence that FGF5 is a major determinant of canine ‘hair’-itability. Anim Genet 37, 309–315 · DOI
  13. Huang, T.P., Zhao, K.T., Miller, S.M., Gaudelli, N.M., Oakes, B.L., Fellmann, C., Savage, D.F., and Liu, D.R. (2019). Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nat Biotechnol 37, 626–631. · DOI
  14. Jakimo, N., Chatterjee, P., Nip, L., and Jacobson, J.M. (2018). A Cas9 with complete PAM recognition for adenine dinucleotides. bioRxiv, 429654. · DOI
  15. Kim, D., Kim, D.E., Lee, G., Cho, S.I., and Kim, J.S. (2019). Genome-wide target specificity of CRISPR RNA-guided adenine base editors. Nat Biotechnol 37, 430–435. · DOI
  16. Kim, S., Bae, T., Hwang, J., and Kim, J.S. (2017a). Rescue of high-specificity Cas9 variants using sgRNAs with matched 5′ nucleotides. Genome Biol 18, 218. · DOI
  17. 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. · DOI · Paper page
  18. Kleinstiver, B.P., Sousa, A.A., Walton, R.T., Tak, Y.E., Hsu, J.Y., Clement, K., Welch, M.M., Horng, J.E., Malagon-Lopez, J., Scarfò, I., et al. (2019). Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol 37, 276–282. · DOI
  19. Koblan, L.W., Doman, J.L., Wilson, C., Levy, J.M., Tay, T., Newby, G.A., Maianti, J.P., Raguram, A., and Liu, D.R. (2018). Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat Biotechnol 36, 843–846. · DOI · Paper page
  20. 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. · DOI · Paper page
  21. Komor, A.C., Zhao, K.T., Packer, M.S., Gaudelli, N.M., Waterbury, A.L., Koblan, L.W., Kim, Y.B., Badran, A.H., and Liu, D.R. (2017). Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci Adv 3, eaao4774. · DOI · Paper page
  22. Lee, J.K., Jeong, E., Lee, J., Jung, M., Shin, E., Kim, Y.H., Lee, K., Jung, I., Kim, D., Kim, S., et al. (2018). Directed evolution of CRISPR-Cas9 to increase its specificity. Nat Commun 9, 3048. · DOI · Paper page
  23. Levy, J.M., Yeh, W.H., Pendse, N., Davis, J.R., Hennessey, E., Butcher, R., Koblan, L.W., Comander, J., Liu, Q., and Liu, D.R. (2020). Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses. Nat Biomed Eng 4, 97–110. · DOI
  24. Li, X., Wang, Y., Liu, Y., Yang, B., Wang, X., Wei, J., Lu, Z., Zhang, Y., Wu, J., Huang, X., et al. (2018). Base editing with a Cpf1-cytidine deaminase fusion. Nat Biotechnol 36, 324–327. · DOI
  25. Liu, Z., Chen, M., Chen, S., Deng, J., Song, Y., Lai, L., and Li, Z. (2018). Highly efficient RNA-guided base editing in rabbit. Nat Commun 9, 2717. · DOI
  26. Liu, Z., Chen, S., Shan, H., Chen, M., Song, Y., Lai, L., and Li, Z. (2019a). Highly precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions. bioRxiv, 658351. · DOI
  27. Liu, Z., Chen, S., Shan, H., Jia, Y., Chen, M., Song, Y., Lai, L., and Li, Z. (2020). Efficient base editing with high precision in rabbits using YFE-BE4max. Cell Death Dis 11, 36. · DOI
  28. Liu, Z., Shan, H., Chen, S., Chen, M., Song, Y., Lai, L., and Li, Z. (2020). Highly efficient base editing with expanded targeting scope using SpCas9-NG in rabbits. FASEB J 34, 588–596. · DOI
  29. Liu, Z., Shan, H., Chen, S., Chen, M., Zhang, Q., Lai, L., and Li, Z. (2019b). Improved base editor for efficient editing in GC contexts in rabbits with an optimized AID-Cas9 fusion. FASEB J 33, 9210–9219. · DOI
  30. Martin, A.S., Salamango, D.J., Serebrenik, A.A., Shaban, N.M., Brown, W. L., and Harris, R.S. (2019). A panel of eGFP reporters for single base editing by APOBEC-Cas9 editosome complexes. Sci Rep 9, 497. · DOI
  31. Mendell, J.R., Shilling, C., Leslie, N.D., Flanigan, K.M., al-Dahhak, R., Gastier-Foster, J., Kneile, K., Dunn, D.M., Duval, B., Aoyagi, A., et al. (2012). Evidence-based path to newborn screening for Duchenne muscular dystrophy. Ann Neurol 71, 304–313. · DOI · Paper page
  32. Meng, X., Hu, X., Liu, Q., Song, X., Gao, C., Li, J., and Wang, K. (2018). Robust genome editing of CRISPR-Cas9 at NAG PAMs in rice. Sci China Life Sci 61, 122–125. · DOI
  33. Oetting, W.S., and King, R.A. (1999). Molecular basis of albinism: mutations and polymorphisms of pigmentation genes associated with albinism. Hum Mutat 13, 99–115. · DOI
  34. Rees, H.A., and Liu, D.R. (2018). Base editing: precision chemistry on the genome and transcriptome of living cells. Nat Rev Genet 19, 770–788. · DOI · Paper page
  35. Ryu, S.M., Koo, T., Kim, K., Lim, K., Baek, G., Kim, S.T., Kim, H.S., Kim, D.E., Lee, H., Chung, E., et al. (2018). Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy. Nat Biotechnol 36, 536–539. · DOI
  36. Villiger, L., Grisch-Chan, H.M., Lindsay, H., Ringnalda, F., Pogliano, C.B., Allegri, G., Fingerhut, R., Häberle, J., Matos, J., Robinson, M.D., et al. (2018). Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nat Med 24, 1519–1525. · DOI
  37. Wang, X., Li, J., Wang, Y., Yang, B., Wei, J., Wu, J., Wang, R., Huang, X., Chen, J., and Yang, L. (2018). Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotechnol 36, 946–949. · DOI
  38. Xu, Y., Liu, H., Pan, H., Wang, X., Zhang, Y., Yao, B., Li, N., Lai, L., and Li, Z. (2020). CRISPR/Cas9-mediated disruption of fibroblast growth factor 5 in rabbits results in a systemic long hair phenotype by prolonging anagen. Genes 11, 297. · DOI
  39. Xue, C., Zhang, H., Lin, Q., Fan, R., and Gao, C. (2018). Manipulating mRNA splicing by base editing in plants. Sci China Life Sci 61, 1293–1300. · DOI
  40. Yang, B., Yang, L., and Chen, J. (2019). Development and application of base editors. CRISPR J 2, 91–104. · DOI
  41. Yang, D., Xu, J., Zhu, T., Fan, J., Lai, L., Zhang, J., and Chen, Y.E. (2014). Effective gene targeting in rabbits using RNA-guided Cas9 nucleases. J Mol Cell Biol 6, 97–99. · DOI
  42. Zhang, D., Zhang, H., Li, T., Chen, K., Qiu, J.L., and Gao, C. (2017). Perfectly matched 20-nucleotide guide RNA sequences enable robust genome editing using high-fidelity SpCas9 nucleases. Genome Biol 18, 191. · DOI
  43. Zhou, C., Sun, Y., Yan, R., Liu, Y., Zuo, E., Gu, C., Han, L., Wei, Y., Hu, X., Zeng, R., et al. (2019). Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature 571, 275–278. · DOI · Paper page
  44. Zong, Y., Song, Q., Li, C., Jin, S., Zhang, D., Wang, Y., Qiu, J.L., and Gao, C. (2018). Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat Biotechnol 36, 950–953. · DOI
  45. Zuo, E., Sun, Y., Yuan, T., He, B., Zhou, C., Ying, W., Liu, J., Wei, W., Zeng, R., Li, Y., et al. (2020). A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects. Nat Methods 17, 600–604. · DOI

Cited by

Sorted by citations

See all 35

Metadata

Authors
Liu, Z., Chen, S., Jia, Y., Shan, H., Chen, M., Song, Y., Lai, L., & Li, Z.
Venue
Science China Life Sciences
Publisher
Springer Science and Business Media LLC
Published
2021-01-06
Volume
64
Issue
8
Pages
1355-1367
ISSN
  • 1674-7305
  • 1869-1889
DOI
10.1007/s11427-020-1775-2
Cited by
35
References
11
Language
en
Licence

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review