The DOI matches its Crossref record; 65 of the 65 references it cites were found in a registry or an index.
Continuous evolution of base editors with expanded target compatibility and improved activity
Open accessAbstract
Base editors use DNA-modifying enzymes targeted with a catalytically impaired CRISPR protein to precisely install point mutations. Here, we develop phage-assisted continuous evolution of base editors (BE-PACE) to improve their editing efficiency and target sequence compatibility. We used BE-PACE to evolve cytosine base editors (CBEs) that overcome target sequence context constraints of canonical CBEs. One evolved CBE, evoAPOBEC1-BE4max, is up to 26-fold more efficient at editing cytosine in the GC context, a disfavored context for wild-type APOBEC1 deaminase, while maintaining efficient editing in all other sequence contexts tested. Another evolved deaminase, evoFERNY, is 29% smaller than APOBEC1 and edits efficiently in all tested sequence contexts. We also evolved a CBE based on CDA1 deaminase with much higher editing efficiency at difficult target sites. Finally, we used data from evolved CBEs to illuminate the relationship between deaminase activity, base editing efficiency, editing window width and byproduct formation. These findings establish a system for rapid evolution of base editors and inform their use and improvement.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The evolved variants such as EvoFERNY and CBE6-variants do no longer have this sequence context.”
From Protocol to create isogenic disease models from adult stem cell-derived organoids using next-generation CRISPR tools (2024) · cites this paper as [25]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“For this reason, make sure to always be updated with the literature and find editors that do not have such a sequence context, such as CBE6b or EvoFERNY.25,53”
From Protocol to create isogenic disease models from adult stem cell-derived organoids using next-generation CRISPR tools (2024) · cites this paper as [25]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
Notredame, C., Higgins, D. G., & Heringa, J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4042 · Cited by 6,964
I-TASSER: a unified platform for automated protein structure and function prediction
Roy, A., Küçükural, A., & Zhang, Y. (2010) · Nature Protocols · doi:10.1038/nprot.2010.5 · Cited by 6,212
Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016) · Nature · doi:10.1038/nature17946 · Cited by 5,437
Self-citationProgrammable base editing of A•T to G•C in genomic DNA without DNA cleavage
Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R. (2017) · Nature · doi:10.1038/nature24644 · Cited by 4,184
Self-citationApolipoprotein E and Alzheimer disease: risk, mechanisms and therapy
Liu, C.-C., Kanekiyo, T., Xu, H., & Bu, G. (2013) · Nature Reviews Neurology · doi:10.1038/nrneurol.2012.263 · Cited by 3,459
A One Pot, One Step, Precision Cloning Method with High Throughput Capability
Engler, C., Kandzia, R., & Marillonnet, S. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003647 · Cited by 2,434
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3117 · Cited by 2,268
Base editing: precision chemistry on the genome and transcriptome of living cells
Rees, H. A., & Liu, D. R. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0059-1 · Cited by 1,675
Self-citation
Cited by
Sorted by citations
Items 301–346 of 346
神先先生の古稀及び定年を迎えられるにあたって (神先秀雄・薄田桂・友松芳郎三教授古稀記念特輯)
井上, 宏. (1981) · 関西大学社会学部紀要
Extension and Improvement of CRISPR-Based Technology
Zhang, Z., Wang, P., & Liu, J. (2022) · Springer eBooks · doi:10.1007/978-981-16-8504-0_3
How to increase precision in Xenopus gene editing and base editing experimentsPreprint
Smith, S. J. (2021) · OSF Preprints (OSF Preprints) · doi:10.31219/osf.io/2tvjp
Roadmap for the use of Base Editors to Decipher Drug Mechanism of ActionPreprint
Aparicio-Prat, E., Yan, D., Mariotti, M., Bassik, M. C., Hess, G. T., Fortin, J., Weston, A. D., Xi, H. S., & Stanton, R. V. (2020) · doi:10.21203/rs.3.rs-119015/v1
A self-inactivating system for AAV-mediated in vivo base editingPreprint
Zuo, Y., Wang, P., Gao, Y., Zhang, C., Zhou, Y., Li, H., Chen, Z., Yang, Z., Xu, J., Zhang, J., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1663604/v1
CRISPR base editing of cis -regulatory elements enables target gene perturbationsPreprint
Lim, C. K. W., McCallister, T. X., Saporito-Magriñá, C., McPheron, G. D., Krishnan, R., C., M. A. Z., Powell, J. E., Clark, L. V., Pérez‐Piñera, P., & Gaj, T. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.26.493649
Modelling and Analysis of Cascade Digital Circuit System Based on DNA Strand Displacement
Lv, H., Sun, T., & Zhang, Q. (2022) · Lecture notes in computer science · doi:10.1007/978-3-031-09726-3_21
Genome Editing with CRISPR‐Cas Systems
Lotfy, P., & Hsu, P. D. (2022) · Wiley eBooks · doi:10.1002/9781683673798.ch11
Engineering Nme2Cas9 Adenine Base Editors with Improved Activity and Targeting ScopePreprint
Bamidele, N., Zhang, H., Dong, X., Gaston, N., Cheng, H., Kelly, K. L., Watts, J. K., Xie, J., Gao, G., & Sontheimer, E. J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.14.536905
Programmable Chemical Evolution with Natural/Non‐Natural Building Blocks
Liu, P., Jannatul, R., Chen, J., Hou, L., Gao, M., Wang, P., Wang, L., Jin, D., Chen, H., Liu, R., et al. (2024) · Angewandte Chemie · doi:10.1002/ange.202409746
Becerra, B., Wittibschlager, S., Patel, Z. M., Kutschat, A. P., Delano, J., Che, E., Karjalainen, A., Wu, T., Starrs, M., Jankowiak, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.09.612085
Patinios, C., Gupta, D., Bassett, H. V., Collins, S. P., Kamm, C., Kibe, A., Wang, Y., Zhao, C., Vollen, K., Toussaint, C., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.17.623984
TadA-Derived Cytosine Base Editor for Precise Genome Editing in ZebrafishPreprint
Qin, W., Lin, S., Petree, C., Varshney, P., & Varshney, G. K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.28.635338
Accelerated evolution of whole gene clusters by an engineered lytic phage system in E. coliPreprint
Ong, S., Ghode, P. B., Narenderan, A., Willenborg, F., Eden, T. V., Lao, S., Marsh, C. O., Yew, W. S., & Fredens, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.21.649713
Srinivasan, S., Huhle, V. H., Bippes, C. C., Tanner, N., Frank, S., Killer, H. E., Kohler, C., & Neutzner, A. (2025) · Advanced Science · doi:10.1002/advs.202417141
Protocol for assessment of CRISPR base editors and their components in Escherichia coli
Shelake, R. M., & Kim, J. (2025) · STAR Protocols · doi:10.1016/j.xpro.2025.103973
Advancing cell therapy manufacturing through precision genome engineering
Flugel, C. L., Cadiñanos-Garai, A., & Abou‐El‐Enein, M. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-14064-8.00052-7
Huang, C., Li, G., Wu, J., Liang, J., & Wang, X. (2021) · Figshare · doi:10.6084/m9.figshare.14196480
Gaillochet, C., Fernández, A. P., Goossens, V., D’Halluin, K., Drozdzecki, A., Shafie, M., Van Duyse, J., Isterdael, G. V., Gonzalez, C., Vermeersch, M., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22611368
Huang, C., Li, G., Wu, J., Liang, J., & Wang, X. (2021) · Figshare · doi:10.6084/m9.figshare.14196477
Gaillochet, C., Fernández, A. P., Goossens, V., D’Halluin, K., Drozdzecki, A., Shafie, M., Van Duyse, J., Isterdael, G. V., Gonzalez, C., Vermeersch, M., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22611395
Huang, C., Li, G., Wu, J., Liang, J., & Wang, X. (2021) · Figshare · doi:10.6084/m9.figshare.14196474
Jang, W., & Jang, H. (2025) · KSBB Journal · doi:10.7841/ksbbj.2025.40.4.343
Simpson, A., Hung, S. S. C., Somasiri, P., Rajendra, K. C., Guinan, T., Barnett, A., Hewitt, A. W., & Fairfax, K. A. (2026) · Research Square · doi:10.21203/rs.3.rs-8370034/v1
Hu, Y., Wang, Y., Wang, S., Jiao, Y., Tao, R., & Yao, S. (2026) · New Biotechnology · doi:10.1016/j.nbt.2026.02.002
An autonomous system for multi-objective continuous evolution at scalePreprint
Boileau, R. M., Golas, S. M., Ma, Q., Jiang, B., Aradhana, Jia, M. S., Ilieva, N., Baydush, A., Fu, H., & Chory, E. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.02.709196
An efficient C-to-U RNA recorder as a tool for profiling targets of RNA-binding proteins
Li, C., Jia, Y., Ye, T., Zheng, L., Song, W., Piao, W., Qi, C., & Jin, H. (2026) · New Biotechnology · doi:10.1016/j.nbt.2026.03.004
Base editing approaches for the treatment of β-hemoglobinopathies
Antoniou, P. (2021) · theses.fr (ABES) · doi:10.70675/c4dddb32zf8aez4bc3z8cf8zce9a4e808265
Genome and epigenome editing approaches to treat β-hemoglobinopathies
Fontana, L. (2024) · theses.fr (ABES) · doi:10.70675/f1623d8bz5529z4d2dzb255z45ed273f643c
Inducible, split base editors for in vivo cancer functional genomics
Ren, D., Wang, S., Yamada, K., Liu, Y., Hapke, R., Alpsoy, A., Ho, Y., Zhang, C., Lan, Y., Zhang, S., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03077-5 · Cited by 1
Base editing of Artemis mutations ex vivo sheds light on gene therapy for Artemis-deficient SCID
Huang, Z., Cai, Z., Yan, P., Hu, Y., Wang, Y., Zhou, G., Deng, L., Wang, X., Li, Z., Chen, W., et al. (2026) · Advanced Biotechnology · doi:10.1007/s44307-026-00115-w
Protein Engineering and Directed Evolution
Abey, E. E., Mathew, A. E., Veettil, A. H. S., & Arivarasan, V. K. (2026) · Springer eBooks · doi:10.1007/978-981-95-3957-4_18
Synthetic Phage for the Evolution of Biomolecules
Abdi, G., Dave, K., & Gautam, S. (2026) · Springer eBooks · doi:10.1007/978-981-95-3957-4_36
Chuang, J.-N., Purcell, J., Sangalli, L., Rosenbluh, J., Knott, G. J., Corrie, S. R., & Garnier, G. (2026) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2026.1829373
Hwang, H., Mariam, N., Kweon, J., Yi, H., Jang, G., Roh, J., Lim, K., Park, J.-H., Kim, Y., & Kim, D. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag737
Smart Design: Integrating Artificial Intelligence and Gene Editing for Advanced mRNA Therapeutics
Shi, H., Liu, S., Dai, D., Jiang, S., Tian, T., Niu, Z., Xiang, Z., Zou, C., Liu, F., Tang, X., et al. (2026) · MedComm – Biomaterials and Applications · doi:10.1002/mba2.70062
Interplay Between Base Editing and DNA repair: From Molecular Mechanisms to Clinical Translation
Tao, R., Li, M., Luo, T., & Yao, S. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.109018
Advancements in CRISPR-based in vivo gene therapy for hemophilia
Zhang, X., Xu, K., Zou, S., Zhu, Z., Teng, S., & Huang, P. (2026) · Frontiers in Genome Editing · doi:10.3389/fgeed.2026.1924733
Islam, M. N., Islam, M. M., Feng, H., Bellah, S. F., Miah, M. M. Z., & Hossain, M. (2026) · Molecular Biology Reports · doi:10.1007/s11033-026-12771-1
An Electroporation-Based Protocol for Ex Vivo Base Editing: From Design to Quantitative Assessment
Peña-Gutiérrez, I., Mazzeo, D., Bassons-Bascuñana, A., Haider, S., García‐García, L., Olalla-Sastre, B., Río, P., López-Manzaneda, S., & Mataix, M. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5547-4_19
From base transitions to expanded editing tools: development and applications of plant base editors
Sui, N., Zhang, J., Xu, W., 庞美新, Zhang, R., Chai, N., Wen, J., Liu, T., Zheng, Z., Huang, J., et al. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.109074
Beyond prediction: The evolving role of artificial intelligence in genome editing
Shin, S., Uhm, H., Kim, Y.-W., Im, H. W., & Bae, S. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.08.025
Techniques and applications of directed evolution
Dhananjaya, G., Naik, Y., Jana, S., & Mahanta, N. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-44536-1.00009-2
Role of Chromatin-Associated RNAs in Eye Physiology and Pathology
Savickyte, I., & Lapinaitė, A. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5627-3_1
Metadata
- Authors
- Thuronyi, B. W., Koblan, L. W., Levy, J. M., Yeh, W.-H., Zheng, C., Newby, G. A., Wilson, C., Bhaumik, M., Shubina-Oleinik, O., Holt, J. R., & Liu, D. R.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- Boston Children's Hospital (US)
- Corresponding author
- Liu, David R.
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2019-07-22
- Volume
- 37
- Issue
- 9
- Pages
- 1070-1079
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC6728210
- OpenAlex
- W2963629338
- Cited by
- 347
- References
- 65
- Citations by year
- 2026: 31 · 2025: 56 · 2024: 55 · 2023: 51 · 2022: 46 · 2021: 45 · 2020: 53 · 2019: 9
- FWCI
- 12.65
- Type
- journal article
- Language
- en
- Update notices
- correction (2019-08-12)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (U01 AI142756)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (RM1 HG009490)
- U.S. Department of Health & Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (R01 EB022376)
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R35 GM118062)
- United States Department of Defense | Defense Advanced Research Projects Agency (HR0011-17-2-0049)
- Howard Hughes Medical Institute (Liu Investigatorship)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme Catalysis and Immobilization
- Keywords
- base editors, phage-assisted continuous evolution, cytosine base editors, editing efficiency, deaminase activity, by-product formation
- MeSH terms
- Gene Editing, Adenosine Deaminase, Animals, Base Sequence, Cell Line, Humans, Gene Expression Regulation, Enzymologic, Gene Targeting, Directed Molecular Evolution, Mice, INDEL Mutation, CRISPR-Cas Systems
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
