An unbiased genome-wide analysis of zinc-finger nuclease specificity
Abstract
Zinc-finger nucleases (ZFNs) allow gene editing in live cells by inducing a targeted DNA double-strand break (DSB) at a specific genomic locus. However, strategies for characterizing the genome-wide specificity of ZFNs remain limited. We show that nonhomologous end-joining captures integrase-defective lentiviral vectors at DSBs, tagging these transient events. Genome-wide integration site analysis mapped the actual in vivo cleavage activity of four ZFN pairs targeting CCR5 or IL2RG. Ranking loci with repeatedly detectable nuclease activity by deep-sequencing allowed us to monitor the degree of ZFN specificity in vivo at these positions. Cleavage required binding of ZFNs in specific spatial arrangements on DNA bearing high homology to the intended target site and only tolerated mismatches at individual positions of the ZFN binding sites. Whereas the consensus binding sequence derived in vivo closely matched that obtained in biochemical experiments, the ranking of in vivo cleavage sites could not be predicted in silico. Comprehensive mapping of ZFN activity in vivo will facilitate the broad application of these reagents in translational research.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
An integrase-deficient lentivirus capture assay measures genome wide integration as a way to detect off-target effects in an unbiased manner.
“Another study used an integrase-deficient lentivirus capture (IDL genome gets inserted at DSBs created by ZFN) assay to measure genome wide integration as a way to detect off-target effects in an unbiased manner.”
From Newer Gene Editing Technologies toward HIV Gene Therapy (2013) · cites this paper as [65]
Proper evaluation of the specificity of any particular ZFN pair will require the use of the relevant cell type, the intended ZFN dose and the delivery method for that specific application.
“Taken together, these studies highlight the fact that proper evaluation of the specificity of any particular ZFN pair will require the use of the relevant cell type, the intended ZFN dose and the delivery method for that specific application.”
From Newer Gene Editing Technologies toward HIV Gene Therapy (2013) · cites this paper as [65]
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 · see citing works
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works
In Vivo Gene Delivery and Stable Transduction of Nondividing Cells by a Lentiviral Vector
Naldini, L., Blömer, U., Gallay, P., Ory, D., Mulligan, R., Gage, F. H., Verma, I. M., & Trono, D. (1996) · Science · doi:10.1126/science.272.5259.263 · Cited by 4,903 · see citing works
Self-citationGenome editing with engineered zinc finger nucleases
Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S., & Gregory, P. D. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2842 · Cited by 2,285 · see citing works
Self-citationHybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain.
Kim, Y. G., Cha, J., & Chandrasegaran, S. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.3.1156 · Cited by 2,099 · see citing works
HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots
Schröder, A. R. W., Shinn, P., Chen, H., Berry, C., Ecker, J. R., & Bushman, F. (2002) · Cell · doi:10.1016/s0092-8674(02)00864-4 · Cited by 1,832 · see citing works
Highly efficient endogenous human gene correction using designed zinc-finger nucleases
Urnov, F. D., Miller, J. C., Lee, Y.-L., Beausejour, C. M., Rock, J. M., Augustus, S., Jamieson, A. C., Porteus, M. H., Gregory, P. D., & Holmes, M. C. (2005) · Nature · doi:10.1038/nature03556 · Cited by 1,642 · see citing works
Self-citationDistinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions
Goldberg, A. D., Banaszynski, L. A., Noh, K., Lewis, P. W., Elsässer, S. J., Stadler, S. C., Dewell, S. B., Law, M. J., Guo, X., Li, X., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.003 · Cited by 1,281 · see citing works
Self-citationAn improved zinc-finger nuclease architecture for highly specific genome editing
Miller, J. C., Holmes, M. C., Wang, J., Guschin, D. Y., Lee, Y.-L., Rupniewski, I., Beausejour, C. M., Waite, A. J., Wang, N. S., Kim, K. A., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1319 · Cited by 1,051 · see citing works
Self-citationHockemeyer, D. F., Soldner, F., Beard, C., Gao, Q., Mitalipova, M. M., DeKelver, R. C., Katibah, G. E., Amora, R., Boydston, E. A., Zeitler, B., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1562 · Cited by 1,035 · see citing works
Self-citationRetroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences
Mitchell, R., Beitzel, B., Schroder, A. R. W., Shinn, P., Chen, H., Berry, C., Ecker, J., & Bushman, F. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020234 · Cited by 1,024 · see citing works
Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases
Perez, E. E., Wang, J., Miller, J. C., Jouvenot, Y., Kim, K. A., Liu, O., Wang, N., Lee, G., Bartsevich, V. V., Lee, Y.-L., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1410 · Cited by 999 · see citing works
Self-citationKnockout Rats via Embryo Microinjection of Zinc-Finger Nucleases
Geurts, A. M., Cost, G. J., Freyvert, Y., Zeitler, B., Miller, J. C., Choi, V. M., Jenkins, S. S., Wood, A. J., Cui, X., Meng, X., et al. (2009) · Science · doi:10.1126/science.1172447 · Cited by 924 · see citing works
Self-citationTargeted Chromosomal Cleavage and Mutagenesis in Drosophila Using Zinc-Finger Nucleases
Bibikova, M., Golic, M., Golic, K. G., & Carroll, D. (2002) · Genetics · doi:10.1093/genetics/161.3.1169 · Cited by 860 · see citing works
Lombardo, A., Genovese, P., Beausejour, C. M., Colleoni, S., Lee, Y.-L., Kim, K. A., Ando, D., Urnov, F. D., Galli, C., Gregory, P. D., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1353 · Cited by 845 · see citing works
Self-citationEnhancing Gene Targeting with Designed Zinc Finger Nucleases
Bibikova, M. V., Beumer, K. J., Trautman, J. K., & Carroll, D. (2003) · Science · doi:10.1126/science.1079512 · Cited by 824 · see citing works
The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation
Klug, A. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-010909-095056 · Cited by 710 · see citing works
Maeder, M. L., Thibodeau-Beganny, S., Osiak, A., Wright, D. A., Anthony, R. M., Eichtinger, M., Jiang, T., Foley, J. E., Winfrey, R. J., Townsend, J. A., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.06.016 · Cited by 708 · see citing works
Stimulation of Homologous Recombination through Targeted Cleavage by Chimeric Nucleases
Bibikova, M. V., Carroll, D., Segal, D. J., Trautman, J. K., Smith, J., Kim, Y., & Chandrasegaran, S. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.1.289-297.2001 · Cited by 614 · see citing works
A Rapid and General Assay for Monitoring Endogenous Gene Modification
Guschin, D. Y., Waite, A. J., Katibah, G. E., Miller, J. C., Holmes, M. C., & Rebar, E. J. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-753-2_15 · Cited by 500 · see citing works
Self-citationFok I dimerization is required for DNA cleavage
Bitinaite, J., Wah, D. A., Aggarwal, A. K., & Schildkraut, I. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.18.10570 · Cited by 490 · see citing works
Smith, J. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.17.3361 · Cited by 425 · see citing works
Role of the non‐homologous DNA end joining pathway in the early steps of retroviral infection
Li, L., Olvera, J. M., Yoder, K., Mitchell, R., Butler, S., Lieber, M., Martin, S. L., & Bushman, F. D. (2001) · EMBO Journal · doi:10.1093/emboj/20.12.3272 · Cited by 386 · see citing works
Moehle, E. A., Rock, J. M., Lee, Y.-L., Jouvenot, Y., DeKelver, R. C., Gregory, P. D., Urnov, F. D., & Holmes, M. C. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611478104 · Cited by 371 · see citing works
Self-citationTargeted gene knockout in mammalian cells by using engineered zinc-finger nucleases
Santiago, Y., Chan, E. M., Liu, P., Orlando, S., Zhang, L., Urnov, F. D., Holmes, M. C., Guschin, D. Y., Waite, A. J., Miller, J. C., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800940105 · Cited by 358 · see citing works
Self-citationHigh-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR)
Schmidt, M., Schwarzwaelder, K., Bartholomae, C., Zaoui, K., Ball, C., Pilz, I., Braun, S., Glimm, H., & von Kalle, C. (2007) · Nature Methods · doi:10.1038/nmeth1103 · Cited by 328 · see citing works
DeKelver, R. C., Choi, V. M., Moehle, E. A., Paschon, D. E., Hockemeyer, D. F., Meijsing, S. H., Sancak, Y., Cui, X., Steine, E. J., Miller, J. C., et al. (2010) · Genome Research · doi:10.1101/gr.106773.110 · Cited by 310 · see citing works
Self-citationAdeno-associated virus vectors integrate at chromosome breakage sites
Miller, D. G., Petek, L. M., & Russell, D. W. (2004) · Nature Genetics · doi:10.1038/ng1380 · Cited by 266 · see citing works
Deichmann, A., Hacein‐Bey‐Abina, S., Schmidt, M., Garrigue, A., Brugman, M. H., Hu, J., Glimm, H., Gyapay, G., Prum, B., Fraser, C. C., et al. (2007) · Journal of Clinical Investigation · doi:10.1172/jci31659 · Cited by 257 · see citing works
Self-citationRapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells
Doyon, J., Zeitler, B., Cheng, J., Cheng, A. T., Cherone, J. M., Santiago, Y., Lee, A. H., Vo, T. D., Doyon, Y., Miller, J. C., et al. (2011) · Nature Cell Biology · doi:10.1038/ncb2175 · Cited by 244 · see citing works
Self-citationTransient Gene Expression by Nonintegrating Lentiviral Vectors
Nightingale, S. J., Hollis, R. P., Pepper, K. A., Petersen, D., Yu, X.-J., Yang, C., Bahner, I., & Kohn, D. B. (2006) · Molecular Therapy · doi:10.1016/j.ymthe.2006.01.008 · Cited by 192 · see citing works
Comprehensive genomic access to vector integration in clinical gene therapy
Gabriel, R., Eckenberg, R., Paruzynski, A., Bartholomae, C. C., Nowrouzi, A., Arens, A., Howe, S. J., Recchia, A., Cattoglio, C., Wang, W., et al. (2009) · Nature Medicine · doi:10.1038/nm.2057 · Cited by 182 · see citing works
Self-citationGenome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing
Paruzynski, A., Arens, A., Gabriel, R., Bartholomae, C., Scholz, S. J., Wang, W., Wolf, S., Glimm, H., Schmidt, M., & von Kalle, C. (2010) · Nature Protocols · doi:10.1038/nprot.2010.87 · Cited by 179 · see citing works
Self-citationFokI requires two specific DNA sites for cleavage
Vanamee, É. S., Santagata, S., & Aggarwal, A. K. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4635 · Cited by 178 · see citing works
Novel Integrase-Defective Lentiviral Episomal Vectors for Gene Transfer
Vargas, J. J., Gusella, G., Najfeld, V., Klotman, M., & Cara, A. (2004) · Human Gene Therapy · doi:10.1089/104303404322959515 · Cited by 143 · see citing works
Mátrai, J., Cantore, A., Bartholomae, C. C., Annoni, A., Wang, W., Acosta-Sanchez, A., Samara-Kuko, E., De Waele, L., Ma, L., Genovese, P., et al. (2011) · Hepatology · doi:10.1002/hep.24230 · Cited by 139 · see citing works
Self-citationHändel, E.-M., Alwin, S., & Cathomen, T. (2008) · Molecular Therapy · doi:10.1038/mt.2008.233 · Cited by 138 · see citing works
Capture of DNA Sequences at Double-Strand Breaks in Mammalian Chromosomes
Lin, Y., & Waldman, A. S. (2001) · Genetics · doi:10.1093/genetics/158.4.1665 · Cited by 113 · see citing works
Generation of a triple-gene knockout mammalian cell line using engineered zinc-finger nucleases
Liu, P., Chan, E. M., Cost, G. J., Zhang, L., Wang, J., Miller, J. C., Guschin, D. Y., Reik, A., Holmes, M. C., Mott, J. E., et al. (2010) · Biotechnology and Bioengineering · doi:10.1002/bit.22654 · Cited by 107 · see citing works
Self-citationTargeted Genome Modifications Using Integrase-deficient Lentiviral Vectors
Cornu, T. I., & Cathomen, T. (2007) · Molecular Therapy · doi:10.1038/sj.mt.6300345 · Cited by 105 · see citing works
Mani, M., Smith, J., Kandavelou, K., Berg, J. M., & Chandrasegaran, S. (2005) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2005.07.021 · Cited by 94 · see citing works
Non-homologous end-joining for repairing I-SceI-induced DNA double strand breaks in human cells
Honma, M., Sakuraba, M., Koizumi, T., Takashima, Y., Sakamoto, H., & Hayashi, M. (2007) · DNA repair · doi:10.1016/j.dnarep.2007.01.004 · Cited by 66 · see citing works
Frequent Endonuclease Cleavage at Off-target Locations In Vivo
Petek, L. M., Russell, D. W., & Miller, D. G. (2010) · Molecular Therapy · doi:10.1038/mt.2010.35 · Cited by 53 · see citing works
Promiscuous patching of broken chromosomes in mammalian cells with extrachromosomal DNA
Lin, Y., & Waldman, A. S. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.19.3975 · Cited by 53 · see citing works
Gaur, M., & Leavitt, A. D. (1998) · Journal of Virology · doi:10.1128/jvi.72.6.4678-4685.1998 · Cited by 52 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Development and Applications of CRISPR-Cas9 for Genome Engineering
Hsu, P. D., Lander, E. S., & Zhang, F. (2014) · Cell · doi:10.1016/j.cell.2014.05.010 · Cited by 5,762 · 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
High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292 · see citing works
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 · see citing works
Kim, S., Kim, D., Cho, S. W., Kim, J., & Kim, J.-S. (2014) · Genome Research · doi:10.1101/gr.171322.113 · Cited by 1,856 · see citing works
Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L., & Church, G. M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2675 · Cited by 1,752 · see citing works
Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
Cho, S. W., Kim, S., Kim, Y., Kweon, J., Kim, H. S., Bae, S., & Kim, J.-S. (2014) · Genome Research · doi:10.1101/gr.162339.113 · Cited by 1,356 · see citing works
Off-target Effects in CRISPR/Cas9-mediated Genome Engineering
Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., & Yang, S.-H. (2015) · Molecular Therapy - Nucleic Acids · doi:10.1038/mtna.2015.37 · Cited by 1,273 · see citing works
Gene therapy returns to centre stage
Naldini, L. (2015) · Nature · doi:10.1038/nature15818 · Cited by 1,184 · 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
Digenome-seq: Genome-wide profiling of CRISPR-cas9 off-target effects in human cells
Kim, D., Bae, S., Park, J., Kim, E., Kim, S., Yu, H. R., Hwang, J., Kim, J.-I., & Kim, J.-S. (2015) · Nature Methods · doi:10.1038/nmeth.3284 · Cited by 992 · see citing works
CIRCLE-Seq: A highly sensitive in vitro screen for genome-wide CRISPR-cas9 nuclease off-targets
Tsai, S. Q., Nguyen, N. T., Malagon-Lopez, J., Topkar, V. V., Aryee, M. J., & Joung, J. K. (2017) · Nature Methods · doi:10.1038/nmeth.4278 · Cited by 814 · see citing works
Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
Frock, R. L., Hu, J., Meyers, R. M., Ho, Y.-J., Kii, E., & Alt, F. W. (2015) · Nature Biotechnology · doi:10.1038/nbt.3101 · Cited by 673 · 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).”
BackgroundInfluentialDelivery 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
CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity
Cradick, T. J., Fine, E. J., Antico, C. J., & Bao, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt714 · Cited by 590 · 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-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 SSN design, organism, and cell type and have already been to some extent implemented in hPSCs. Understanding the frequency and impact of off-targets is highly relevant to develop the use of SSN for clinical applications as well as for their reliable use in basic research (Gabriel et al., 2011).”
BackgroundRNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection
Hu, W., Kaminski, R., Yang, F., Zhang, Y., Cosentino, L., Li, F., Luo, B., Alvarez-Carbonell, D., Garcia-Mesa, Y., Karn, J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405186111 · Cited by 527 · see citing works
Wang, X., Wang, Y., Wu, X., Wang, J., Wang, Y., Qiu, Z., Chang, T., Huang, H., Lin, R.-J., & Yee, J.-K. (2015) · Nature Biotechnology · doi:10.1038/nbt.3127 · Cited by 442 · see citing works
Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing
Naeem, M., Majeed, S., Hoque, M. Z., & Ahmad, I. (2020) · Cells · doi:10.3390/cells9071608 · Cited by 457 · see citing works
Correction of the sickle cell disease mutation in human hematopoietic stem/progenitor cells
Hoban, M. D., Cost, G. J., Mendel, M. C., Romero, Z., Kaufman, M. L., Joglekar, A. V., Ho, M., Lumaquin, D., Gray, D., Lill, G. R., et al. (2015) · Blood · doi:10.1182/blood-2014-12-615948 · Cited by 320 · see citing works
Self-citationTargeted gene knockout by direct delivery of zinc-finger nuclease proteins
Gaj, T., Guo, J., Kato, Y., Sirk, S. J., & Barbas, C. F. (2012) · Nature Methods · doi:10.1038/nmeth.2030 · Cited by 306 · see citing works
DNA Breaks and End Resection Measured Genome-wide by End Sequencing
Canela, A., Sridharan, S., Sciascia, N., Tubbs, A., Meltzer, P., Sleckman, B. P., & Nussenzweig, A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.06.034 · Cited by 284 · 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-citationPartial DNA-guided Cas9 enables genome editing with reduced off-target activity
Yin, H., Song, C.-Q., Suresh, S., Kwan, S.-Y., Wu, Q., Walsh, S., Ding, J., Bogorad, R. L., Zhu, L. J., Wolfe, S. A., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2559 · Cited by 240 · see citing works
CRISPR/Cas9-Mediated Correction of the Sickle Mutation in Human CD34+ cells
Hoban, M. D., Lumaquin, D., Kuo, C. Y., Romero, Z., Long, J., Ho, M., Young, C. S., Mojadidi, M., Fitz-Gibbon, S., Cooper, A. R., et al. (2016) · Molecular Therapy · doi:10.1038/mt.2016.148 · Cited by 220 · see citing works
Evaluation of TCR Gene Editing Achieved by TALENs, CRISPR/Cas9, and megaTAL Nucleases
Osborn, M. J., Webber, B. R., Knipping, F., Lonetree, C.-L., Tennis, N., DeFeo, A. P., McElroy, A. N., Starker, C. G., Lee, C., Merkel, S., et al. (2016) · Molecular Therapy · doi:10.1038/mt.2015.197 · Cited by 201 · see citing works
Self-citationDe Ravin, S. S., Reik, A., Liu, P.-Q., Li, L., Wu, X., Su, L., Raley, C., Theobald, N., Choi, U., Song, A. H., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3513 · Cited by 195 · see citing works
Self-citationGenetic treatment of a molecular disorder: gene therapy approaches to sickle cell disease
Hoban, M. D., Orkin, S. H., & Bauer, D. E. (2016) · Blood · doi:10.1182/blood-2015-09-618587 · Cited by 194 · see citing works
Hultquist, J. F., Schumann, K., Woo, J. M., Manganaro, L., McGregor, M. J., Doudna, J., Simon, V., Krogan, N. J., & Marson, A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.09.080 · Cited by 170 · see citing works
Li, L., Krymskaya, L., Wang, J., Henley, J., Rao, A., Cao, L.-F., Tran, C.-A., Torres-Coronado, M., Gardner, A., Gonzalez, N., et al. (2013) · Molecular Therapy · doi:10.1038/mt.2013.65 · Cited by 181 · see citing works
Self-citationEvaluating and enhancing target specificity of gene-editing nucleases and deaminases
Kim, D., Luk, K., Wolfe, S. A., & Kim, J.-S. (2019) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-013118-111730 · Cited by 171 · see citing works
Suzuki, K., Yu, C., Qu, J., Li, M., Yao, X., Yuan, T., Goebl, A., Tang, S., Ren, R., Aizawa, E., et al. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.06.016 · Cited by 169 · see citing works
Adenoviral vector DNA for accurate genome editing with engineered nucleases
Holkers, M., Maggio, I., Henriques, S. F. D., Janssen, J. M., Cathomen, T., & Gonçalves, M. A. F. V. (2014) · Nature Methods · doi:10.1038/nmeth.3075 · Cited by 138 · see citing works
Wang, J., DeClercq, J. J., Hayward, S. B., Li, P. W.-L., Shivak, D. A., Gregory, P. D., Lee, G., & Holmes, M. C. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1121 · Cited by 128 · see citing works
Self-citationFerrari, S., Jacob, A., Cesana, D., Laugel, M., Beretta, S., Varesi, A., Unali, G., Conti, A., Canarutto, D., Albano, L., et al. (2022) · Cell stem cell · doi:10.1016/j.stem.2022.09.001 · Cited by 133 · see citing works
Self-citationMaier, D. A., Brennan, A. L., Jiang, S., Binder-Scholl, G. K., Lee, G., Plesa, G., Zheng, Z., Cotte, J., Carpenito, C., Wood, T., et al. (2013) · Human Gene Therapy · doi:10.1089/hum.2012.172 · Cited by 126 · see citing works
Self-citationWake-up Sleepy Gene: Reactivating Fetal Globin for β-Hemoglobinopathies
Wienert, B., Martyn, G. E., Funnell, A. P. W., Quinlan, K. G. R., & Crossley, M. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.09.004 · Cited by 115 · see citing works
VSV-G-Enveloped Vesicles for Traceless Delivery of CRISPR-Cas9
Montagna, C., Petris, G., Casini, A., Maule, G., Franceschini, G. M., Zanella, I., Conti, L., Arnoldi, F., Burrone, O. R., Zentilin, L., et al. (2018) · Molecular Therapy Nucleic Acids · doi:10.1016/j.omtn.2018.05.010 · Cited by 117 · see citing works
Tools for experimental and computational analyses of off-target editing by programmable nucleases
Bao, X. R., Pan, Y., Lee, C. M., Davis, T. H., & Bao, G. (2021) · Nature Protocols · doi:10.1038/s41596-020-00431-y · Cited by 106 · see citing works
Biased and unbiased methods for the detection of off-target cleavage by CRISPR/Cas9: An overview
Martin, F., Sánchez-Hernández, S., Gutiérrez-Guerrero, A., Pinedo-Gomez, J., & Benabdellah, K. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17091507 · Cited by 92 · see citing works
“[27] as a tool to develop the first unbiased approach to detecting off-target sites generated by ZFNs (Figure 3, right).”
BackgroundMethodInfluentialNewer Gene Editing Technologies toward HIV Gene Therapy
Manjunath, N., Yi, G., Dang, Y., & Shankar, P. (2013) · Viruses · doi:10.3390/v5112748 · Cited by 77 · see citing works
Towards a new era in medicine: therapeutic genome editing
Porteus, M. H. (2015) · Genome Biology · doi:10.1186/s13059-015-0859-y · Cited by 69 · see citing works
Concerns regarding ‘off-target’activity of genome editing endonucleases
Kadam, U. S., Shelake, R. M., Chavhan, R. L., & Suprasanna, P. (2018) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2018.03.027 · Cited by 47 · see citing works
Adeno-associated virus inverted terminal repeats stimulate gene editing
Hirsch, M. L. (2015) · Gene Therapy · doi:10.1038/gt.2014.109 · Cited by 32 · see citing works
Detection of CRISPR/Cas9-Generated off-target effect by integration-defective lentiviral vector
Wang, X., Wu, Y., & Yee, J.-K. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-0687-2_14 · Cited by 5 · see citing works
- Authors
- Gabriel, R., Lombardo, A., Arens, A., Miller, J. C., Genovese, P., Kaeppel, C., Nowrouzi, A., Bartholomae, C. C., Wang, J., Friedman, G., Holmes, M. C., Gregory, P. D., Glimm, H., Schmidt, M., Naldini, L., & von Kalle, C.
- Affiliations
- German Cancer Research Center (DE)
- Vita-Salute San Raffaele University (IT)
- Sangamo BioSciences (United States) (US)
- Corresponding author
- Naldini, Luigi
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2011-08-07
- Volume
- 29
- Issue
- 9
- Pages
- 816-823
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2148050025
- Cited by
- 526
- References
- 45
- Citations by year
- 2026: 4 · 2025: 6 · 2024: 14 · 2023: 11 · 2022: 21 · 2021: 21 · 2020: 27 · 2019: 22 · 2018: 33 · 2017: 41 · 2016: 61 · 2015: 61 · 2014: 70 · 2013: 59 · 2012: 54
- FWCI
- 26.07
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Archivio Istituzionale della Ricerca - Università Vita-Salute San Raffaele (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- zinc finger nucleases, off-target effects, nuclease specificity, non-homologous end joining, integrase-defective lentiviral vectors, CCR5, IL2RG, DNA double-strand breaks, in vivo gene editing
- MeSH terms
- Binding Sites, Endodeoxyribonucleases, Genetic Vectors, Humans, Protein Binding, Substrate Specificity, Cluster Analysis, Lentivirus, Zinc Fingers, Sequence Analysis, DNA, Gene Targeting, HIV Integrase, Cell Line, Tumor, DNA Breaks, Double-Stranded, Genetic Loci
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
