Genome editing with engineered zinc finger nucleases
Abstract
Reverse genetics in model organisms such as Drosophila melanogaster, Arabidopsis thaliana, zebrafish and rats, efficient genome engineering in human embryonic stem and induced pluripotent stem cells, targeted integration in crop plants, and HIV resistance in immune cells - this broad range of outcomes has resulted from the application of the same core technology: targeted genome cleavage by engineered, sequence-specific zinc finger nucleases followed by gene modification during subsequent repair. Such 'genome editing' is now established in human cells and a number of model organisms, thus opening the door to a range of new experimental and therapeutic possibilities.
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ZFNs and TALENs depend on protein engineering of DNA-binding domains to recognize and edit specific DNA sequences.
“ZFNs and TALENs depend on protein engineering of DNA-binding domains to recognize and edit specific DNA sequences.”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Urnov et al., 2010
Customizing gene disruption using either ZFNs or TALENs requires the design of specific proteins to target each dsDNA site.
“However, customizing gene disruption using either ZFNs or TALENs requires the design of specific proteins to target each dsDNA site [2], [3].”
From High-efficiency targeted editing of large viral genomes by RNA-guided nucleases (2014) · cites this paper as [2]
ZFNs have been widely utilized for genome editing in various types of cells and living organisms.
“Taking advantage of the effective and sequence-specific gene modification capability of ZFNs, the technology has been widely utilized for genome editing in various types of cells and living organisms [23,24,25,26,27,28,29].”
From Newer Gene Editing Technologies toward HIV Gene Therapy (2013) · cites this paper as [29]
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A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116 · see citing works
Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133 · see citing works
ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
Gaj, T., Gersbach, C. A., & Barbas, C. F. (2013) · Trends in Biotechnology · doi:10.1016/j.tibtech.2013.04.004 · Cited by 3,820 · see citing works
Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.04.025 · Cited by 3,495 · see citing works
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
Ran, F. A., Hsu, P. D., Lin, C.-Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.021 · Cited by 3,299 · see citing works
CRISPR-Cas systems for editing, regulating and targeting genomes
Sander, J. D., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2842 · Cited by 3,153 · see citing works
Non-viral vectors for gene-based therapy
Yin, H., Kanasty, R. L., Eltoukhy, A. A., Vegas, A. J., Dorkin, J. R., & Anderson, D. G. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3763 · Cited by 3,123 · see citing works
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937 · see citing works
RNA-guided editing of bacterial genomes using CRISPR-Cas systems
Jiang, W., Bikard, D., Cox, D., Zhang, F., & Marraffini, L. A. (2013) · Nature Biotechnology · doi:10.1038/nbt.2508 · Cited by 2,429 · see citing works
A TALE nuclease architecture for efficient genome editing
Miller, J. C., Tan, S., Qiao, G., Barlow, K. A., Wang, J., Xia, D. F., Meng, X., Paschon, D. E., Leung, E., Hinkley, S. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1755 · Cited by 2,098 · see citing works
Self-citationRNA-programmed genome editing in human cells
Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., & Doudna, J. (2013) · eLife · doi:10.7554/elife.00471 · Cited by 2,098 · see citing works
TALENs: A widely applicable technology for targeted genome editing
Joung, J. K., & Sander, J. D. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3486 · Cited by 1,650 · see citing works
Zuris, J. A., Thompson, D. B., Shu, Y., Guilinger, J. P., Bessen, J. L., Hu, J. H., Maeder, M. L., Joung, J. K., Chen, Z.-Y., & Liu, D. R. (2015) · Nature Biotechnology · doi:10.1038/nbt.3081 · Cited by 1,460 · see citing works
Dunbar, C. E., High, K. A., Joung, J. K., Kohn, D. B., Ozawa, K., & Sadelain, M. (2018) · Science · doi:10.1126/science.aan4672 · Cited by 1,410 · see citing works
Gene Editing of <i>CCR5</i> in Autologous CD4 T Cells of Persons Infected with HIV
Tebas, P., Stein, D., Tang, W. W., Frank, I., Wang, S. Q., Lee, G., Spratt, S. K., Surosky, R. T., Giedlin, M. A., Nichol, G., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1300662 · Cited by 1,357 · see citing works
Self-citationDelivering CRISPR: a review of the challenges and approaches
Lino, C. A., Harper, J. C., Carney, J. P., & Timlin, J. A. (2018) · Drug Delivery · doi:10.1080/10717544.2018.1474964 · Cited by 1,185 · see citing works
CCTop: An intuitive, flexible and reliable CRISPR/Cas9 target prediction tool
Stemmer, M., Thumberger, T., del Sol Keyer, M., Wittbrodt, J., & Mateo, J. L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124633 · Cited by 1,088 · see citing works
Koike-Yusa, H., Li, Y., Tan, E.-P., Velasco-Herrera, M. D. C., & Yusa, K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2800 · Cited by 1,064 · see citing works
Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing
Tsai, S. Q., Wyvekens, N., Khayter, C., Foden, J. A., Thapar, V., Reyon, D., Goodwin, M. J., Aryee, M. J., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2908 · Cited by 952 · see citing works
Therapeutic in vivo gene transfer for genetic disease using AAV: Progress and challenges
Mingozzi, F., & High, K. A. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2988 · Cited by 893 · see citing works
Beyond GWASs: Illuminating the Dark Road from Association to Function
Edwards, S. L., Beesley, J., French, J. D., & Dunning, A. M. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.012 · Cited by 784 · see citing works
Davenport, A. P., Hyndman, K. A., Dhaun, N., Southan, C., Kohan, D. E., Pollock, J. S., Pollock, D. M., Webb, D. J., & Maguire, J. J. (2016) · Pharmacological Reviews · doi:10.1124/pr.115.011833 · Cited by 772 · see citing works
Soldner, F., Laganière, J., Cheng, A. W., Hockemeyer, D., Gao, Q., Alagappan, R., Khurana, V., Golbe, L. I., Myers, R. H., Lindquist, S., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.019 · Cited by 728 · see citing works
Self-citationA novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity
Mussolino, C., Morbitzer, R., Lütge, F., Dannemann, N., Lahaye, T., & Cathomen, T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr597 · Cited by 714 · see citing works
Bauer, D. E., Kamran, S. C., Lessard, S., Xu, J., Fujiwara, Y., Lin, C., Shao, Z., Canver, M. C., Smith, E. C., Pinello, L., et al. (2013) · Science · doi:10.1126/science.1242088 · Cited by 653 · see citing works
Hou, Z., Zhang, Y., Propson, N. E., Howden, S. E., Chu, L.-F., Sontheimer, E. J., & Thomson, J. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313587110 · Cited by 681 · see citing works
Off-target effects in CRISPR/Cas9 gene editing
Guo, C., Ma, X., Gao, F., & Guo, Y. (2023) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.1143157 · Cited by 625 · see citing works
“Early studies utilize zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) for genome editing (Urnov et al., 2010; Joung and Sander, 2013; Shamshirgaran et al., 2022).”
BackgroundWirth, T., Parker, N., & Ylä-Herttuala, S. (2013) · Gene · doi:10.1016/j.gene.2013.03.137 · Cited by 607 · see citing works
Delivery technologies for genome editing
Yin, H., Kauffman, K. J., & Anderson, D. G. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.280 · Cited by 597 · see citing works
Targeted genome editing in human repopulating haematopoietic stem cells
Genovese, P., Schiroli, G., Escobar, G., Di Tomaso, T., Firrito, C., Calabria, A., Moi, D., Mazzieri, R., Bonini, C., Holmes, M. C., et al. (2014) · Nature · doi:10.1038/nature13420 · Cited by 555 · see citing works
Self-citationWang, H.-X., Li, M., Lee, C. M., Chakraborty, S., Kim, H.-W., Bao, G., & Leong, K. W. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00799 · Cited by 560 · see citing works
In vivo genome editing restores haemostasis in a mouse model of haemophilia
Li, H., Haurigot, V., Doyon, Y., Li, T., Wong, S. Y., Bhagwat, A. S., Malani, N., Anguela, X. M., Sharma, R., Ivanciu, L., et al. (2011) · Nature · doi:10.1038/nature10177 · Cited by 548 · see citing works
Self-citationInduced Pluripotent Stem Cells Meet Genome Editing
Hockemeyer, D., & Jaenisch, R. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.04.013 · Cited by 499 · see citing works
“The low frequency of spontaneous homology mediated gene targeting in hPSCs was dramatically increased through the development of site-specific nucleases (SSN) as a tool for their genetic engineering (reviewed in (Carroll, 2014; Hsu et al., 2014; Urnov et al., 2010)).”
MethodAn unbiased genome-wide analysis of zinc-finger nuclease specificity
Gabriel, R., Lombardo, A., Arens, A., Miller, J. C., Genovese, P., Kaeppel, C., Nowrouzi, A., Bartholomae, C. C., Wang, J., Friedman, G., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1948 · Cited by 526 · see citing works
Self-citationEfficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9
Mandal, P. K., Ferreira, L. M. R., Collins, R., Meissner, T. B., Boutwell, C. L., Friesen, M., Vrbanac, V., Garrison, B. S., Stortchevoi, A., Bryder, D., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.10.004 · Cited by 475 · see citing works
DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing
Xue, C., & Greene, E. C. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.02.008 · Cited by 431 · see citing works
Applications of the CRISPR-Cas9 system in cancer biology
Sánchez-Rivera, F. J., & Jacks, T. (2015) · Nature Reviews Cancer · doi:10.1038/nrc3950 · Cited by 405 · see citing works
Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures
Doyon, Y., Vo, T. D., Mendel, M. C., Greenberg, S. G., Wang, J., Xia, D. F., Miller, J. C., Urnov, F. D., Gregory, P. D., & Holmes, M. C. (2011) · Nature Methods · doi:10.1038/nmeth.1539 · Cited by 402 · see citing works
Self-citationChromosomal Translocations in Human Cells Are Generated by Canonical Nonhomologous End-Joining
Ghezraoui, H., Piganeau, M., Renouf, B., Renaud, J.-B., Sallmyr, A., Ruis, B., Oh, S., Tomkinson, A. E., Hendrickson, E. A., Giovannangeli, C., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.002 · Cited by 351 · see citing works
“To address the role of NHEJ pathways in the joining phase of chromosomal translocation formation, we took advantage of nucleases designed to introduce site-specific DSBs at endogenous loci in human cells (Gaj et al., 2013; Urnov et al., 2010) to induce translocations (Brunet et al.”
BackgroundA new era in functional genomics screens
Przybyla, L., & Gilbert, L. A. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-021-00409-w · Cited by 281 · see citing works
Lu, C., Napier, J. A., Clemente, T. E., & Cahoon, E. B. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.11.006 · Cited by 282 · see citing works
CRISPR-Cas9 for cancer therapy: Opportunities and challenges
Chen, M., Mao, A., Xu, M., Weng, Q., Mao, J., & Ji, J. (2019) · Cancer Letters · doi:10.1016/j.canlet.2019.01.017 · Cited by 272 · see citing works
Wang, J., Exline, C. M., DeClercq, J. J., Llewellyn, G. N., Hayward, S. B., Li, P. W.-L., Shivak, D. A., Surosky, R. T., Gregory, P. D., Holmes, M. C., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3408 · Cited by 261 · see citing works
Self-citationAdvances in therapeutic CRISPR/Cas9 genome editing
Savić, N., & Schwank, G. (2016) · Translational Research · doi:10.1016/j.trsl.2015.09.008 · Cited by 257 · see citing works
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., & Salis, H. M. (2014) · Molecular Systems Biology · doi:10.15252/msb.20134955 · Cited by 235 · see citing works
Genetic engineering of microalgae for enhanced biorefinery capabilities
Fayyaz, M., Chew, K. W., Show, P. L., Ling, T. C., Ng, I.-S., & Chang, J.-S. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107554 · Cited by 225 · see citing works
Roos, D. (2016) · British Medical Bulletin · doi:10.1093/bmb/ldw009 · Cited by 212 · see citing works
Chronic Granulomatous Disease: a Comprehensive Review
Yu, H.-H., Yang, Y.-H., & Chiang, B.-L. (2021) · Clinical Reviews in Allergy & Immunology · doi:10.1007/s12016-020-08800-x · Cited by 197 · see citing works
Bridge RNAs direct programmable recombination of target and donor DNA
Durrant, M. G., Perry, N. T., Pai, J. J., Jangid, A. R., Athukoralage, J. S., Hiraizumi, M., McSpedon, J. P., Pawluk, A., Nishimasu, H., Konermann, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07552-4 · Cited by 163 · see citing works
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Araki, M., & Ishii, T. (2014) · Reproductive Biology and Endocrinology · doi:10.1186/1477-7827-12-108 · Cited by 150 · see citing works
High-efficiency targeted editing of large viral genomes by RNA-guided nucleases
Bi, Y., Sun, L., Gao, D., Ding, C., Li, Z., Li, Y., Cun, W., & Li, Q. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004090 · Cited by 148 · see citing works
Genome-wide identification of CRISPR/Cas9 off-targets in human genome
Duan, J., Lu, G., Xie, Z., Lou, M., Luo, J., Guo, L., & Zhang, Y. (2014) · Cell Research · doi:10.1038/cr.2014.87 · Cited by 137 · see citing works
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Self-citationFunctional footprinting of regulatory DNA
Vierstra, J., Reik, A., Chang, K.-H., Stehling-Sun, S., Zhou, Y., Hinkley, S. J., Paschon, D. E., Zhang, L., Psatha, N., Bendana, Y. R., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3554 · Cited by 133 · see citing works
Self-citationBiomedical applications of mRNA nanomedicine
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Zinc-finger nuclease editing of human cxcr4 promotes HIV-1 CD4(+) T cell resistance and enrichment
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Self-citationAntibody glycoengineering strategies in mammalian cells
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Persistent repression of tau in the brain using engineered zinc finger protein transcription factors
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Self-citationNewer Gene Editing Technologies toward HIV Gene Therapy
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Genome editing and improvement of abiotic stress tolerance in crop plants
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Building a Safer and Faster CAR: Seatbelts, Airbags, and CRISPR
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A CRISPR way for accelerating cereal crop improvement: Progress and challenges
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“In-vivo, as noted above, the zinc finger nucleases function as dimers (or pairs) [54-57].”
BackgroundInfluentialEngineered retrons generate genome-independent protein-binding DNA for cellular control
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The CRISPR/Cas9 System for Crop Improvement: Progress and Prospects
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- Authors
- Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S., & Gregory, P. D.
- Affiliations
- Sangamo BioSciences (United States) (US)
- Corresponding author
- Gregory, Philip D.
- Venue
- Nature Reviews Genetics
- Published
- 2010-09
- Volume
- 11
- Issue
- 9
- Pages
- 636-646
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W1982969769
- Cited by
- 2,285
- References
- 95
- Citations by year
- 2026: 69 · 2025: 124 · 2024: 144 · 2023: 139 · 2022: 154 · 2021: 134 · 2020: 134 · 2019: 128 · 2018: 150 · 2017: 157 · 2016: 177 · 2015: 165 · 2014: 195 · 2013: 152 · 2012: 136
- FWCI
- 11.54
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- 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
- zinc finger nucleases, genome editing, gene therapy, DNA repair, reverse genetics, human embryonic stem cells, induced pluripotent stem cells, cultivated plants, HIV drug resistance, Drosophila melanogaster, Arabidopsis thaliana, zebrafish, rats
- MeSH terms
- Animals, Endonucleases, Genetic Techniques, Humans, Zinc Fingers, Genome
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