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Highly Parallel Profiling of Cas9 Variant Specificity
Open accessAbstract
Determining the off-target cleavage profile of programmable nucleases is an important consideration for any genome editing experiment, and a number of Cas9 variants have been reported that improve specificity. We describe here tagmentation-based tag integration site sequencing (TTISS), an efficient, scalable method for analyzing double-strand breaks (DSBs) that we apply in parallel to eight Cas9 variants across 59 targets. Additionally, we generated thousands of other Cas9 variants and screened for variants with enhanced specificity and activity, identifying LZ3 Cas9, a high specificity variant with a unique +1 insertion profile. This comprehensive comparison reveals a general trade-off between Cas9 activity and specificity and provides information about the frequency of generation of +1 insertions, which has implications for correcting frameshift mutations.
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“Although some Cas9 variants have comparable editing activity and specificity with SpCas9 at a few target sites, high-throughput analysis is still lacking.”
From Machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing (2024) · cites this paper as [23]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“It worth mentioning that in several previous reports, LZ3 Cas9, Sniper Cas9, and HiFi Cas9 had comparable editing activity to the SpCas9-WT in human cells or other animal embryos.”
From Machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing (2024) · cites this paper as [23]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“Although LZ3 Cas9 did not display a stable 1 bp site-directed insertion pattern, as shown in previous studies according to the DSB repair results”
From Machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing (2024) · cites this paper as [23]
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Additional file 1 of Internal initiation of reverse transcription in a Penelope-like retrotransposon
Frangieh, C. J., Wilkinson, M. E., Strebinger, D., Strecker, J. G., Walsh, M. L., Faure, G., Yushenova, I. A., Macrae, R. K., Arkhipova, I. R., & Zhang, F. (2024) · Figshare · doi:10.6084/m9.figshare.26019583
Self-citationAdditional file 4 of Internal initiation of reverse transcription in a Penelope-like retrotransposon
Frangieh, C. J., Wilkinson, M. E., Strebinger, D., Strecker, J. G., Walsh, M. L., Faure, G., Yushenova, I. A., Macrae, R. K., Arkhipova, I. R., & Zhang, F. (2024) · Figshare · doi:10.6084/m9.figshare.26732662
Self-citationAdditional file 1 of Comparison of DNA targeting CRISPR editors in human cells
Huang, H., Lv, W., Li, J., Huang, G., Tan, Z., Hu, Y., Ma, S., Zhang, X., Huang, L., & Lin, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26561671
Marinov, G. K., Kim, S. H., Bagdatli, S. T., Higashino, S. I., Trevino, A. E., Tycko, J., Wu, T., Bintu, L., Bassik, M. C., He, C., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22678208
Marinov, G. K., Kim, S. H., Bagdatli, S. T., Higashino, S. I., Trevino, A. E., Tycko, J., Wu, T., Bintu, L., Bassik, M. C., He, C., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22678205
Huang, H., Huang, G., Tan, Z., Hu, Y., Shan, L., Zhou, J., Zhang, X., Ma, S., Lv, W., Huang, T., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19654720
Additional file 2 of Comparison of DNA targeting CRISPR editors in human cells
Huang, H., Lv, W., Li, J., Huang, G., Tan, Z., Hu, Y., Ma, S., Zhang, X., Huang, L., & Lin, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26561674
Additional file 2 of Internal initiation of reverse transcription in a Penelope-like retrotransposon
Frangieh, C. J., Wilkinson, M. E., Strebinger, D., Strecker, J. G., Walsh, M. L., Faure, G., Yushenova, I. A., Macrae, R. K., Arkhipova, I. R., & Zhang, F. (2024) · Figshare · doi:10.6084/m9.figshare.26019746
Self-citationAdditional file 1 of Eukaryotic-driven directed evolution of Cas9 nucleases
Ruta, G. V., Ciciani, M., Kheir, E., Gentile, M. D., Amistadi, S., Casini, A., & Cereseto, A. (2024) · Figshare · doi:10.6084/m9.figshare.26697428
Additional file 2 of Eukaryotic-driven directed evolution of Cas9 nucleases
Ruta, G. V., Ciciani, M., Kheir, E., Gentile, M. D., Amistadi, S., Casini, A., & Cereseto, A. (2024) · Figshare · doi:10.6084/m9.figshare.26697431
Additional file 3 of Internal initiation of reverse transcription in a Penelope-like retrotransposon
Frangieh, C. J., Wilkinson, M. E., Strebinger, D., Strecker, J. G., Walsh, M. L., Faure, G., Yushenova, I. A., Macrae, R. K., Arkhipova, I. R., & Zhang, F. (2024) · Figshare · doi:10.6084/m9.figshare.26732659
Self-citationAdditional file 3 of Eukaryotic-driven directed evolution of Cas9 nucleases
Ruta, G. V., Ciciani, M., Kheir, E., Gentile, M. D., Amistadi, S., Casini, A., & Cereseto, A. (2024) · Figshare · doi:10.6084/m9.figshare.26697434
Hermantara, R., Richmond, L., Taqi, A. F., Chilaka, S., Jeantet, V., Guerrini, I., West, K. L., & West, A. G. (2024) · Figshare · doi:10.6084/m9.figshare.26698220
Huang, H., Huang, G., Tan, Z., Hu, Y., Shan, L., Zhou, J., Zhang, X., Ma, S., Lv, W., Huang, T., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19654723
A guide RNA repeat checkpoint steers CRISPR-Cas9 catalysisPreprint
Chilamkurthy, R., Sudhakar, S., Pater, A. A., Bosmeny, M. S., Stabile, F., Katolik, A., Harikrishna, S., Turk, R., Damha, M. J., Leslie, S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.02.691602
High-throughput in vitro specificity profiling of natural and high-fidelity CRISPR-Cas9 variantsPreprint
Murugan, K., Seetharam, A. S., Severin, A. J., & Sashital, D. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.12.091991 · Cited by 1
Mianné, J. (2020) · theses.fr (ABES) · doi:10.70675/179210b5z933bz4406zb297z7beef82bc3ae
Evaluating high-fidelity CRISPR-Cas nucleases in nucleosomal contexts using a quantitative framework
Handelmann, C. R., Skeens, E., Lisi, G. P., & Buck, M. J. (2026) · Frontiers in Genome Editing · doi:10.3389/fgeed.2026.1759382
CRISPR RNA architecture steers Cas9 catalysis and fidelity via a guide repeat clasp motif
Chilamkurthy, R., Sudhakar, S., Pater, A. A., Bosmeny, M. S., Stabile, F., Katolik, A., Harikrishna, S., Elazzouzi, F., Turk, R., Damha, M. J., et al. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag710
AI-guided CRISPR in crop yield enhancement
Musazade, E., Mrisho, I. I., Zhang, D., Gao, J., Cheng, Z., & Feng, X. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-44079-3.00005-x
Beyond Precision: A Multidimensional Framework for Selecting Genetic Medicine Platforms
Wieland, J., Jackson, P., Penrod, W., Nadauld, S., & Barrott, J. J. (2026) · Cells · doi:10.3390/cells15181647
Genomic splice-donor disruption rescues systemic disease in progeriaPreprint
Jin, W. Z., Ma, J., Yuan, H., Zou, Y., Zhang, Z., Zuo, J., Wong, S. K. K., Li, T., Lu, X., & Zhou, Z. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.17.752274
Metadata
- Authors
- Schmid-Burgk, J. L., Gao, L., Li, D., Gardner, Z., Strecker, J., Lash, B., & Zhang, F.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Zhang, Feng
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2020-05
- Volume
- 78
- Issue
- 4
- Pages
- 794-800.e8
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC7370240
- OpenAlex
- W3011375666
- Cited by
- 197
- References
- 29
- Citations by year
- 2026: 11 · 2025: 25 · 2024: 42 · 2023: 34 · 2022: 38 · 2021: 34 · 2020: 13
- FWCI
- 9.65
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health
- G. Harold and Leila Y. Mathers Foundation
- Howard Hughes Medical Institute
- Edward Mallinckrodt, Jr. Foundation
- 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 › DNA Repair Mechanisms
- Keywords
- Cas9 variants, off-target cleavage, DNA double-strand breaks, genome editing specificity, programmable nucleases
- MeSH terms
- Gene Editing, CRISPR-Associated Protein 9, RNA, Guide, CRISPR-Cas Systems, Humans, Genetic Variation, RNA, Guide, Kinetoplastida, K562 Cells, DNA Breaks, Double-Stranded, HEK293 Cells, CRISPR-Cas Systems
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