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Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors
Open accessAbstract
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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“they create new formats of off-target effects such as RNA editing and sgRNA-independent DNA editing”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Grünewald et al., 2019
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“While these methods have been used in cultured cells, they are not yet ready for clinical use until matters of specificity 33,34 and delivery are addressed.”
From The promise and challenge of therapeutic genome editing (2020) · cites this paper as [33]
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“The RNA off-target effects can be detected by RNA-seq”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Grünewald et al., 2019
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“Although CBE and ABE greatly reduce the classic off-target effects of CRISPR/Cas9 systems”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Grünewald et al., 2019
Experimental — accuracy not yet measuredIn the citing paper
“These systems induce transient conversions, potentially minimising undesired physiological changes compared to DNA editing. 90”
From Innovative therapies for inherited retinal dystrophies: navigating DNA, RNA, and protein approaches (2025) · cites this paper as [90]
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Citations
Cites
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
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
CRISPResso2 provides accurate and rapid genome editing sequence analysis
Clement, K., Rees, H. A., Canver, M. C., Gehrke, J. M., Farouni, R., Hsu, J. Y., Cole, M. A., Liu, D. R., Joung, J. K., Bauer, D. E., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0032-3 · Cited by 1,656
Self-citationSimplified mammalian DNA isolation procedure
Laird, P. W., Zijderveld, A., Linders, K., Rudnicki, M. A., Jaenisch, R., & Berns, A. J. M. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.15.4293 · Cited by 1,497
Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capturePreprint
Rohland, N., & Reich, D. (2012) · Genome Research · doi:10.1101/gr.128124.111 · Cited by 1,153
A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine
Powell, L. M., Wallis, S. C., Pease, R. J., Edwards, Y. H., Knott, T. J., & Scott, J. (1987) · Cell · doi:10.1016/0092-8674(87)90510-1 · Cited by 1,039
Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction
Koblan, L. W., Doman, J. L., Wilson, C., Levy, J. M., Tay, T., Newby, G. A., Maianti, J. P., Raguram, A., & Liu, D. R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4172 · Cited by 944
Komor, A. C., Zhao, K. T., Packer, M. S., Gaudelli, N. M., Waterbury, A. L., Koblan, L. W., Kim, Y. B., Badran, A. H., & Liu, D. R. (2017) · Science Advances · doi:10.1126/sciadv.aao4774 · Cited by 783
Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos
Zuo, E., Sun, Y., Wei, W., Yuan, T., Ying, W., Sun, H., Yuan, L., Steinmetz, L. M., Li, Y., & Yang, H. (2019) · Science · doi:10.1126/science.aav9973 · Cited by 782
Apolipoprotein B-48 Is the Product of a Messenger RNA with an Organ-Specific In-Frame Stop Codon
Chen, S. H., Habib, G. M., Yang, C., Gu, Z.-W., Lee, B. R., Weng, S. A., Silberman, S. R., Cai, S.-J., Deslypère, J. P., Rosseneu, M., et al. (1987) · Science · doi:10.1126/science.3659919 · Cited by 756
RNA Editing Enzyme APOBEC1 and Some of Its Homologs Can Act as DNA Mutators
Harris, R. S., Petersen‐Mahrt, S. K., & Neuberger, M. S. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00742-6 · Cited by 609
The APOBEC Protein Family: United by Structure, Divergent in Function
Salter, J. D., Bennett, R. P., & Smith, H. C. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2016.05.001 · Cited by 408
tadA, an essential tRNA‐specific adenosine deaminase from Escherichia coli
Wolf, J., Gerber, A. P., & Keller, W. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf362 · Cited by 288
Genome-wide target specificities of CRISPR RNA-guided programmable deaminases
Kim, D., Lim, K., Kim, S., Yoon, S.-H., Kim, K., Ryu, S.-M., & Kim, J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3852 · Cited by 281
Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs
Rosenberg, B. R., Hamilton, C. E., Mwangi, M. M., Dewell, S., & Papavasiliou, F. N. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1975 · Cited by 232
Navaratnam, N., Bhattacharya, S., Fujino, T., Patel, D., Jarmuz, A., & Scott, J. (1995) · Cell · doi:10.1016/0092-8674(95)90328-3 · Cited by 180
MacGinnitie, A. J., Anant, S., & Davidson, N. O. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.24.14768 · Cited by 130
The Neurofibromatosis Type I Messenger RNA Undergoes Base-Modification RNA Editing
Skuse, G. R., Cappione, A., Sowden, M. P., Metheny, L. J., & Smith, H. C. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.3.478 · Cited by 126
Olarerin-George, A. O., & Hogenesch, J. B. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv136 · Cited by 121
Yamanaka, S., Poksay, K. S., Balestra, M. E., Zeng, G., & Innerarity, T. L. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)31865-3 · Cited by 111
Structural and Kinetic Characterization of Escherichia coli TadA, the Wobble-Specific tRNA Deaminase
Kim, J., Malashkevich, V. N., Roday, S., Lisbin, M. J., Schramm, V. L., & Almo, S. C. (2006) · Biochemistry · doi:10.1021/bi0522394 · Cited by 97
Boström, K. B., Garcia, Z. C., Poksay, K. S., Johnson, D. F., Lusis, A. J., & Innerarity, T. L. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)45725-0 · Cited by 85
Lau, P. P., Chen, S. H., Wang, J. C., & Chan, L. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.19.5817 · Cited by 68
Overexpression of APOBEC-1 Results in Mooring Sequence-dependent Promiscuous RNA Editing
Sowden, M., Hamm, J. K., & Smith, H. C. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.6.3011 · Cited by 68
Yamanaka, S., Poksay, K. S., Driscoll, D. M., & Innerarity, T. L. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.19.11506 · Cited by 58
Teng, B.-B., Ochsner, S. A., Zhang, Q., Soman, K. V., Lau, P. P., & Chan, L. (1999) · Journal of Lipid Research · doi:10.1016/s0022-2275(20)32141-6 · Cited by 51
Hypermutation induced by APOBEC-1 overexpression can be eliminated
Chen, Z., Eggerman, T. L., Bocharov, A. V., Baranova, I. N., Vishnyakova, T. G., Csákó, G., & Patterson, A. P. (2010) · RNA · doi:10.1261/rna.1863010 · Cited by 27
Towards therapeutic base editing
Seo, H., & Kim, J. (2018) · Nature Medicine · doi:10.1038/s41591-018-0215-3 · Cited by 7
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The promise and challenge of therapeutic genome editing
Doudna, J. A. (2020) · Nature · doi:10.1038/s41586-020-1978-5 · Cited by 1,126
CRISPR technology: A decade of genome editing is only the beginning
Wang, J. Y., & Doudna, J. A. (2023) · Science · doi:10.1126/science.add8643 · Cited by 1,105
Richter, M. F., Zhao, K. T., Eton, E., Lapinaite, A., Newby, G. A., Thuronyi, B. W., Wilson, C., Koblan, L. W., Zeng, J., Bauer, D. E., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0453-z · Cited by 1,020
In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in primates
Musunuru, K., Chadwick, A. C., Mizoguchi, T., Garcia, S. P., DeNizio, J. E., Reiss, C. W., Wang, K., Iyer, S., Dutta, C., Clendaniel, V., et al. (2021) · Nature · doi:10.1038/s41586-021-03534-y · Cited by 793
Self-citation
Metadata
- 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
- Venue
- Nature
- Published
- 2019-04-17
- Volume
- 569
- Issue
- 7756
- Pages
- 433-437
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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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