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A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects

Nature Methods volume 17, pages 600–604 (2020)Cite this article

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Abstract

Cytosine base editors (CBEs) offer a powerful tool for correcting point mutations, yet their DNA and RNA off-target activities have caused concerns in biomedical applications. We describe screens of 23 rationally engineered CBE variants, which reveal mutation residues in the predicted DNA-binding site can dramatically decrease the Cas9-independent off-target effects. Furthermore, we obtained a CBE variant—YE1-BE3-FNLS—that retains high on-target editing efficiency while causing extremely low off-target edits and bystander edits.

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Fig. 1: On-target efficiency of engineered CBEs.
Fig. 2: DNA and RNA off-target evaluation of engineered CBEs.
Fig. 3: Activities of engineered BE3-FNLS and BE3-hA3A.

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Data availability

All the sequencing data were deposited in NCBI Sequence Read Archive (SRA) under project accession PRJNA527003 and https://www.biosino.org/node/project/detail/OEP000272. The data that support the findings of this study are available from the corresponding author upon request.

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Acknowledgements

We thank the FACS facility staff H. Wu, L. Quan and S. Qian at ION, M. Zhang at IPS, and L. Yuan at Big Data Platform (SIBS, CAS). This study was supported by the R&D Program of China (2018YFC2000100 and 2017YFC1001302, 2017YFC0909701), the CAS Strategic Priority Research Program (XDB32060000, XDBS01060100), the National Natural Science Foundation of China (31871502, 31522037, 31822035, 31922048, 31925016, 91957122), the Basic Frontier Scientific Research Program of Chinese Academy of Sciences From 0 to 1 original innovation project (ZDBS-LY-SM001), the Shanghai Municipal Science and Technology Major Project (2018SHZDZX05), the Shanghai City Committee of science and technology project (18411953700, 18JC1410100, 16JC1420202), the National Science and Technology Major Project (2015ZX10004801-005), the National Key Research and Development Program of China (2017YFA0505500, 2016YFC0901704) the Agricultural Science and Technology Innovation Program to E.Z. and the International Partnership Program of Chinese Academy of Sciences (153D31KYSB20170059).

Author information

Author notes

  1. These authors contributed equally to this work: Erwei Zuo, Yidi Sun, Tanglong Yuan, Bingbing He, Changyang Zhou.

Authors and Affiliations

  1. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

    Erwei Zuo, Tanglong Yuan & Jing Liu

  2. Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

    Erwei Zuo, Bingbing He, Changyang Zhou, Wenqin Ying & Hui Yang

  3. CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China

    Yidi Sun & Rong Zeng

  4. Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China

    Yidi Sun, Wu Wei & Yixue Li

  5. Center for Biomedical Informatics, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China

    Wu Wei

  6. Department of Life Sciences, Shanghai Tech University, 100 Haike Road, Shanghai, China

    Rong Zeng & Yixue Li

  7. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China

    Yixue Li

  8. Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China

    Yixue Li

  9. Shanghai Center for Bioinformation Technology, Shanghai Academy of Science & Technology, Shanghai, China

    Hui Yang

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  1. Erwei Zuo
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Contributions

E.Z. designed and performed experiments. Y.S., W.W., R.Z. and Y.L. performed data analysis. T.Y., B.H. and J.L. performed PCR analysis. W.Y. performed mouse embryo transfer. C.Z. performed cell transfection experiments. H.Y. and Y.L. supervised the project and designed experiments. Y.S. and H.Y. wrote the paper.

Corresponding authors

Correspondence to Erwei Zuo, Yixue Li or Hui Yang.

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Competing interests

The authors disclose a patent application relating to aspects of this work (engineered base editors).

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Peer review information Lei, Tang was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 The on-target editing ofthe BE3 and BE3 variants in different target sites.

a, The mutated residues are highlighted in the predicted structure of rAPOBEC1. Green and yellow colors indicate residues in the helix and the loop of the structure, respectively. b, The crystal structure of APOBEC3G. c, The on-target efficiency and indel frequencies of different versions of engineered CBEs for additional 11 target sites. d, The C-to-T editing efficiency for the engineered variants at each C of the 21 target sites. n = 21 independent experiments for each group. All values are presented as mean ± s.e.m. e, The indel frequency comparison among the engineered variants for the 21 target sites. n = 21 independent experiments for each group. P value was calculated by two-sided Student’s t-tests. Box-and-whisker plots: center line indicates median, the bottom and top lines of the box represents the first quartile and third quartile of the values, respectively. The bottom and top of the vertical line represent the minimum and maximum value. f, The on-target C-to-T editing efficiency of engineered BE3 variants at each target site. n = 3 biologically independent samples for each group. P value was calculated by two-sided Student’s t-tests. Sequences of the on-target protospacers and primers were shown in Extended Data Table 5. The data for BE3 and YE1-BE3 are also used in Figs. 3a and 3d-g.

Extended Data Fig. 2 The embryonicdevelopment rates for BE3 and BE3 variants.

a, The blastocyst rate of BE3 and BE3 variants with sgRNA-D. All values are presented as mean ± s.e.m. b, The blastocyst rate for BE3-hA3A and BE3-FNLSwith additional sgRNAs. All values are presented as mean ± s.e.m. n = 3 biologically independent samples for each group.

Extended Data Fig. 3 On-target editing efficiency and characteristics of off-target SNVs of engineered CBEs.

a, On-target editing efficiency of BE3 and CBE variants from WGS data. Two BE3 embryos without sgRNAs were not shown as they have no target site. b, Comparison of C-to-T and G-to-A conversions between CBE variants-treated and Cre or BE3 groups. n = 3 biologically independent samples for Cre, n = 6 biologically independent samples for BE3, n = 12 biologically independent samples for BE3R126E, n = 3 biologically independent samples for BE3R132E, n = 8 biologically independent samples for YE1-BE3, and n = 3 biologically independent samples for FE1-BE3. Two Cre samples and six BE3 samples were derived from Zuo et al.22 and one Cre sample was newly generated in this study. All values are presented as mean ± s.e.m. P value was calculated by two-sided Student’s t-test.

Extended Data Fig. 4 Venn diagrams of SNVs detected in each embryo by WGS data using the indicated software tools.

a, SNVs identified in BE3R126E-treated embryos. b, SNVs identified in BE3R132E-treated embryos. c, SNVs identified in YE1-BE3-treated embryos. d, SNVs identified in FE1-BE3-treated embryos. e, SNVs identified in the newly generated Cre-treated embryo.

Extended Data Fig. 5 Characteristics of off-target SNVs of engineered CBEs.

a, The overlap among SNVs detected from our analysis with predicted off-targets sites by Cas-OFFinder and CRISPOR.

Extended Data Fig. 6 Editing rate of RNA off-targets for BE3 variants at 36 h post-transfection.

Editing rate of each variant across the chromosomes for each sample.

Extended Data Fig. 7 RNA off-target evaluation of engineered CBEs at 72h post-transfection.

a, The comparison of the total number of detected RNA off-target SNVs at 72 h post-transfection. n = 6 biologically independent samples for GFP, n = 9 biologically independent samples for BE3, n = 7 biologically independent samples for BE3R126E and n = 2 biologically independent samples for YE1-BE3 groups. All values are presented as mean ± s.e.m. P values above each bar were calculated by comparing with GFP group with two-sided Student’s t-tests. b, The distribution of mutation types for GFP, BE3, and BE3 variants-treated groups. c, Editing rate of RNA off-targets for BE3 variants at 72 h post-transfection.

Extended Data Fig. 8 On-target editing efficiency and off-target effects of BE3-FNLS and BE3-hA3A.

a, The C-to-T editing efficiency for the engineered variants at each C of the 21 target sites. n = 21 independent experiments for each group. All values are presented as mean ± s.e.m. The data for BE3 are also used in Fig. 3d. b, SNVs identified in BE3-hA3AY130F and YE1-BE3-FNLS-treated embryos. c, The overlap among SNVs detected from our analysis with predicted off-targets sites by Cas-OFFinder and CRISPOR. d, The distribution of mutation types of DNA off-target SNVs for BE3-hA3AY130F and YE1-BE3-FNLS-treated embryos. e, The distribution of mutation types of RNA off-target SNVs for BE3-hA3AY130F and YE1-BE3-FNLS-treated embryos. f, The expression level of APOBEC1 in BE3 and BE3-FNLS variants. n = 3 biologically independent samples for each group. Box-and-whisker plots: center line indicates median, the bottom and top lines of the box represents the first quartile and third quartile of the values, respectively. The bottom and top of the vertical line represent the minimum and maximum value. g, Editing rate of RNA off-targets for BE3 and BE3-FNLS variants at 36 h post-transfection. n = 3 biological replicates for each group. P value was calculated by two-sided Student’s t-test.

Extended Data Fig. 9 The comparation of BE3-FNLS, YE1-BE3-FNLS and BE4max.

a, The C-to-T editing efficiency for BE3-FNLS, YE1-BE3-FNLS and BE4max at indicated target sites. b, Indel frequency for BE3-FNLS, YE1-BE3-FNLS and BE4max at indicated target sites. Data are shown as mean values ± SEM for n = 3 biological replicates performed at the same time. P value was calculated by two-sided Student’s t-test.

Extended Data Fig. 10 Activities of CBE and CBE variants at the indicated Cas9-dependent off-target sites.

a, The Cas9-dependent off-target effects of the CBE and CBE variants. b, The comparison of editing frequencies of CBE and CBE variants at 34 potential off-target sites. P values were calculated by two sided Student’s t-tests, compared with YE1-BE3-FNLS group. Each cell represents the percentage of total sequencing reads with C to T conversion. n = 21 independent experiments for each group. Box-and-whisker plots: center line indicates median, the bottom and top lines of the box represents the first quartile and third quartile of the values, respectively. The bottom and top of the vertical line represent the minimum and maximum value. HEK293T cells were transfected with plasmids expressing BE3, BE3R126E, BE3R132E, YE1-BE3, FE1-BE3, BE3-hA3A, BE3-hA3AY130F, BE3-FNLS and YE1-BE3-FNLS and sgRNAs matching the indicated on-target sequence using Lipofectamine 3000. Three days after transfection, genomic DNA was extracted, amplified by PCR, and analyzed by high-throughput DNA sequencing at the on-target loci, plus the top ten known Cas9 off-target loci for these sgRNAs, as previously determined using the GUIDE-seq method23, 24 and ChIP-seq method25. Sequences of the on-target and off-target protospacers and primers were shown in Extended Data Table 5.

Supplementary information

Supplementary Information

Supplementary Figure 1, Supplementary Tables 1–3, 5 and 6, and Supplementary Sequence 1

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Supplementary Table

Allele sequence

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Zuo, E., Sun, Y., Yuan, T. et al. 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 (2020). https://doi.org/10.1038/s41592-020-0832-x

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