Cited by 671CRISPR and Genetic EngineeringRNA regulation and diseaseRNA Interference and Gene Delivery

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Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

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Grünewald, Julian, Zhou, Ronghao, Garcia, Sara P., Iyer, Sowmya, Lareau, Caleb A., Aryee, Martin J., Joung, J. Keith·2019·Nature

DOI 10.1038/s41586-019-1161-zPMC PMC6657343

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Abstract

CRISPR-Cas base-editor technology enables targeted nucleotide alterations, and is being increasingly used for research and potential therapeutic applications 1,2. The most widely used cytosine base editors (CBEs) induce deamination of DNA cytosines using the rat APOBEC1 enzyme, which is targeted by a linked Cas protein-guide RNA complex 3,4. Previous studies of the specificity of CBEs have identified off-target DNA edits in mammalian cells 5,6. Here we show that a CBE with rat APOBEC1 can cause extensive transcriptome-wide deamination of RNA cytosines in human cells, inducing tens of thousands of C-to-U edits with frequencies ranging from 0.07% to 100% in 38-58% of expressed genes. CBE-induced RNA edits occur in both protein-coding and non-protein-coding sequences and generate missense, nonsense, splice site, and 5' and 3' untranslated region mutations. We engineered two CBE variants bearing mutations in rat APOBEC1 that substantially decreased the number of RNA edits (by more than 390-fold and more than 3,800-fold) in human cells. These variants also showed more precise on-target DNA editing than the wild-type CBE and, for most guide RNAs tested, no substantial reduction in editing efficiency. Finally, we show that an adenine base editor 7 can also induce transcriptome-wide RNA edits. These results have implications for the use of base editors in both research and clinical settings, illustrate the feasibility of engineering improved variants with reduced RNA editing activities, and suggest the need to more fully define and characterize the RNA off-target effects of deaminase enzymes in base editor platforms.

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Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
WebLogo: A Sequence Logo Generator: Figure 1Preprint
Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,418
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457
Enzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 10,088
The Phyre2 web portal for protein modeling, prediction and analysis
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E. (2015) · Nature Protocols · doi:10.1038/nprot.2015.053 · Cited by 9,652
The Ensembl Variant Effect Predictor
McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016) · Genome Biology · doi:10.1186/s13059-016-0974-4 · Cited by 8,099
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
Programmable 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

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Cloning and base editing of GFP transgenic rhesus monkey and off-target analysis
Kang, Y., Dai, S., Zeng, Y., Wang, F., Yang, P., Yang, Z., Pu, Y., Li, Z., Chen, X., Tian, B., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo3123 · Cited by 11
CRISPR-Based Tools for Fighting Rare Diseases
Li, Q., Gao, Y., & Wang, H. (2022) · Life · doi:10.3390/life12121968 · Cited by 11
Prime editing in hematopoietic stem cells—From ex vivo to in vivo CRISPR-based treatment of blood disorders
Wolff, J. H., & Mikkelsen, J. G. (2023) · Frontiers in Genome Editing · doi:10.3389/fgeed.2023.1148650 · Cited by 12
Modular and Flexible Molecular Device for Simultaneous Cytosine and Adenine Base Editing at Random Genomic Loci in Filamentous Fungi
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Challenges and progress related to gene editing in rare skin diseases
Hofbauer, J. P., Guttmann‐Gruber, C., Wally, V., Sharma, A. K., Gratz, I. K., & Koller, U. (2024) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2024.115294 · Cited by 13
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Roy, B., & Griggs, R. C. (2020) · Neurologic Clinics · doi:10.1016/j.ncl.2020.09.005 · Cited by 11
Sequence modification on demand: search and replace tools for precise gene editing in plants
Čermák, T. (2021) · Transgenic Research · doi:10.1007/s11248-021-00253-y · Cited by 11
The Prominent Characteristics of the Effective sgRNA for a Precise CRISPR Genome Editing
Mohammadhassan, R., Tutunchi, S., Nasehi, N., Goudarziasl, F., & Mahya, L. (2022) · IntechOpen eBooks · doi:10.5772/intechopen.106711 · Cited by 13
Advancing Precision Medicine: Recent Innovations in Gene Editing Technologies
Abhijith, K., & Thangavel, S. (2025) · Advanced Science · doi:10.1002/advs.202410237 · Cited by 13
A Molecular Glue Approach to Control the Half-Life of CRISPR-Based Technologies
Sreekanth, V., Jan, M., Zhao, K. T., Lim, D., Siriwongsup, S., Davis, J. R., McConkey, M. E., Kovalcik, V., Barkal, S., Law, B. K., et al. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.5c06230 · Cited by 12
A motif preferred adenine base editor with minimal bystander and off-targets editing
Shang, M., Li, Y., Cao, Q., Ren, J., Zeng, Y., Wang, J., Gonzalez, R. V. L., & Zhang, X. (2025) · Nature Communications · doi:10.1038/s41467-025-64203-6 · Cited by 10
C-to-U RNA Editing: From Computational Detection to Experimental Validation
Lerner, T., Kluesner, M. G., Tasakis, R. N., Moriarity, B. S., Papavasiliou, F. N., & Pecori, R. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0787-9_4 · Cited by 10
CRISPR/Cas: a potential gene-editing tool in the nervous system
Gao, Y., Gao, K., & Yang, H. (2020) · Cell Regeneration · doi:10.1186/s13619-020-00044-6 · Cited by 11
Engineering an adenine base editor in human embryonic stem cells with minimal DNA and RNA off-target activities
Zhang, Z., Tao, W., Huang, S., Sun, W., Wang, Y., Jiang, W. G., Huang, X., & Lin, C. (2022) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2022.07.026 · Cited by 11
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Li, K., Qin, L.-Y., Zhang, Z., Yan, C.-X., Gu, Y. M., Sun, X., & Huang, H. (2023) · ACS Synthetic Biology · doi:10.1021/acssynbio.3c00141 · Cited by 10
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Su, X., Chen, W., Cai, Q., Liang, P., Chen, Y., Cong, P., & Huang, J. (2020) · Science China Life Sciences · doi:10.1007/s11427-019-1611-1 · Cited by 11
Innovative Therapies for Hemoglobin Disorders
Sii-Felice, K., Nègre, O., Brendel, C., Tubsuwan, A., Morel-à-l’Huissier, E., Filardo, C., & Payen, E. (2020) · BioDrugs · doi:10.1007/s40259-020-00439-6 · Cited by 10
Early blood immune molecular alterations in cynomolgus monkeys with a PSEN1 mutation causing familial Alzheimer's disease
Li, M., Guan, M., Lin, J., Zhu, K., Zhu, J., Guo, M., Li, Y., Chen, Y., Chen, Y., Zou, Y., et al. (2024) · Alzheimer s & Dementia · doi:10.1002/alz.14046 · Cited by 12
Engineering TadA ortholog-derived cytosine base editor without motif preference and adenosine activity limitation
Li, G., Dong, X., Luo, J., Yuan, T., Li, T., Zhao, G., Zhang, H., Zhou, J., Zeng, Z., Cui, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52485-1 · Cited by 9
Bystander editing by adenine base editors impairs vision restoration in a mouse model of Leber congenital amaurosis
Lee, S., Wu, J., Im, D., Hwang, G., Jeong, Y. K., Jiang, H., Lee, S. J., Jo, D. H., Goddard, W. A., Kim, J. H., et al. (2025) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2025.101461 · Cited by 13
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Wang, J., Zhang, W., Li, S., Shi, W., Li, B., Zhang, J., Liang, Y., Teng, X., & Zhang, K. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.4c17920 · Cited by 10
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Zheng, Y., Du, F., Hang, Y., Ma, W., Yang, G., Wu, N., & Sun, X. (2025) · Biotechnology Journal · doi:10.1002/biot.70052 · Cited by 9

Authors: Grünewald, J., Zhou, R., Garcia, S. P., Iyer, S., Lareau, C. A., Aryee, M. J., & Joung, J. K.
Affiliations: Harvard University (US)
Massachusetts General Hospital (US)
Corresponding author: Joung, J. Keith
ORCID: Grünewald, Julian
Zhou, Ronghao
Garcia, Sara P.
Iyer, Sowmya
Lareau, Caleb A.
Aryee, Martin J.
Joung, J. Keith
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2019-04-17
Volume: 569
Issue: 7756
Pages: 433-437
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-019-1161-z
PMC: PMC6657343
OpenAlex: W2939749480
Cited by: 663
References: 37
Citations by year: 2026: 66 · 2025: 74 · 2024: 80 · 2023: 100 · 2022: 84 · 2021: 106 · 2020: 104 · 2019: 48
FWCI: 28.72
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: National Human Genome Research Institute (RM1HG009490)
National Institute of General Medical Sciences (R35GM118158)
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 › RNA Interference and Gene Delivery
Keywords: cytosine base editors, APOBEC1, RNA editing, off-target effects, adenine base editors, deaminase activity, human cells
MeSH terms: APOBEC-1 Deaminase, Gene Editing, Animals, Base Sequence, Cytosine, Deamination, Humans, Mutation, RNA, Substrate Specificity, RNA Editing, Rats, Hep G2 Cells, HEK293 Cells, Transcriptome, CRISPR-Cas Systems

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Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

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