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A guide to genome engineering with programmable nucleases

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Genetic engineering of human pluripotent cells using TALE nucleases

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Genome Engineering With Zinc-Finger Nucleases

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In vivo genome editing using a high-efficiency TALEN system

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Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations

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Targeted Genome Editing Across Species Using ZFNs and TALENs

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A Multipurpose Toolkit to Enable Advanced Genome Engineering in Plants

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High-frequency, precise modification of the tomato genome

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Human Pancreatic Tumor Organoids Reveal Loss of Stem Cell Niche Factor Dependence during Disease Progression

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Genome Engineering with Targetable Nucleases

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Expanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9

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A TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models

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Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9

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Plant Genome Engineering with Sequence-Specific Nucleases

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Genome-Editing Technologies: Principles and ApplicationsPreprint

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Origins of Programmable Nucleases for Genome Engineering

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A Retrotransposon-Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes

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Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection

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Universal CARs, universal T cells, and universal CAR T cells

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In Situ Genetic Correction of the Sickle Cell Anemia Mutation in Human Induced Pluripotent Stem Cells Using Engineered Zinc Finger Nucleases

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Transcription activator‐like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing

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In vivo genome editing of the albumin locus as a platform for protein replacement therapy

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Therapeutic glycoprotein production in mammalian cells

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CRISPR-Cas9: A Preclinical and Clinical Perspective for the Treatment of Human Diseases

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MitoTALEN reduces mutant mtDNA load and restores tRNAAla levels in a mouse model of heteroplasmic mtDNA mutation

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Homology-driven genome editing in hematopoietic stem and progenitor cells using ZFN mRNA and AAV6 donors

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Synthetic nucleases for genome engineering in plants: prospects for a bright future

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Challenges and new technologies in adoptive cell therapy

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Refining strategies to translate genome editing to the clinic

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Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs

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Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs)

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Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances

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Rapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells

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Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding

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Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity

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Surrogate reporters for enrichment of cells with nuclease-induced mutations

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TALE nucleases: tailored genome engineering made easy

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Precise Editing of the Zebrafish Genome Made Simple and Efficient

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MitoTALEN: A General Approach to Reduce Mutant mtDNA Loads and Restore Oxidative Phosphorylation Function in Mitochondrial Diseases

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Characterization of Dystrophin Deficient Rats: A New Model for Duchenne Muscular Dystrophy

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Genetic and Chemical Correction of Cholesterol Accumulation and Impaired Autophagy in Hepatic and Neural Cells Derived from Niemann-Pick Type C Patient-Specific iPS Cells

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TAL effector nucleases induce mutations at a pre-selected location in the genome of primary barley transformants

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TALENs facilitate targeted genome editing in human cells with high specificity and low cytotoxicity

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Reading Frame Correction by Targeted Genome Editing Restores Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients

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Forward and Reverse Genetic Approaches for the Analysis of Vertebrate Development in the Zebrafish

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Robust ZFN-mediated genome editing in adult hemophilic mice

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Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects

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CRISPR/Cas9 and TALEN-mediated knock-in approaches in zebrafish

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TALE and TALEN genome editing technologies

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Silencing of end-joining repair for efficient site-specific gene insertion after TALEN/CRISPR mutagenesis in Aedes aegypti

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Improved Somatic Mutagenesis in Zebrafish Using Transcription Activator-Like Effector Nucleases (TALENs)

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Gene targeting, genome editing: from Dolly to editors

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Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases

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Generation of a Nonhuman Primate Model of Severe Combined Immunodeficiency Using Highly Efficient Genome Editing

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Advances in targeted genome editing

Pérez‐Piñera, P., Ousterout, D. G., & Gersbach, C. A. (2012) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.06.007 · Cited by 159 · see citing works

Transcription Activator-like Effector Nuclease (TALEN)-mediated Gene Correction in Integration-free β-Thalassemia Induced Pluripotent Stem Cells

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Simultaneous zinc-finger nuclease editing of the HIV coreceptors ccr5 and cxcr4 protects CD4+ T cells from HIV-1 infection

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Zinc-finger-nucleases mediate specific and efficient excision of HIV-1 proviral DNA from infected and latently infected human T cells

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Single-Molecule Analysis of mtDNA Replication Uncovers the Basis of the Common Deletion

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Cancer translocations in human cells induced by zinc finger and TALE nucleasesPreprint

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The potential of mitochondrial genome engineering

Silva-Pinheiro, P., & Minczuk, M. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00432-x · Cited by 139 · 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

Precision genome engineering with programmable DNA-nicking enzymesPreprint

Kim, E., Kim, S., Kim, D. H., Choi, B., Choi, I., & Kim, J. (2012) · Genome Research · doi:10.1101/gr.138792.112 · Cited by 137 · see citing works

Delivery and therapeutic applications of gene editing technologies ZFNs, TALENs, and CRISPR/Cas9

LaFountaine, J. S., Fathe, K., & Smyth, H. D. C. (2015) · International Journal of Pharmaceutics · doi:10.1016/j.ijpharm.2015.08.029 · Cited by 137 · see citing works

Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzymePreprint

Wang, J., Friedman, G., Doyon, Y., Wang, N. S., Li, C. J., Miller, J. C., Hua, K. L., Yan, J. J., Babiarz, J., Gregory, P. D., et al. (2012) · Genome Research · doi:10.1101/gr.122879.111 · Cited by 135 · see citing works

TALEN-mediated genome editing: prospects and perspectives

Wright, D. A., Li, T., Yang, B., & Spalding, M. H. (2014) · Biochemical Journal · doi:10.1042/bj20140295 · Cited by 134 · see citing works

Targeting DNA With Fingers and TALENs

Carlson, D. F., Fahrenkrug, S. C., & Hackett, P. B. (2012) · Molecular Therapy — Nucleic Acids · doi:10.1038/mtna.2011.5 · Cited by 135 · see citing works

Heritable site‐specific mutagenesis using TALEN s in maize

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Genome editing at the crossroads of delivery, specificity, and fidelity

Maggio, I., & Gonçalves, M. A. F. V. (2015) · Trends in biotechnology · doi:10.1016/j.tibtech.2015.02.011 · Cited by 132 · see citing works

An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage

Fine, E. J., Cradick, T. J., Zhao, C. L., Lin, Y., & Bao, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1326 · Cited by 132 · see citing works

Near-complete elimination of mutant mtDNA by iterative or dynamic dose-controlled treatment with mtZFNs

Gammage, P. A., Gaude, E., Haute, L. V., Rebelo‐Guiomar, P., Jackson, C. B., Rorbach, J., Pękalski, M. Ł., Robinson, A. J., Charpentier, M., Concordet, J., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw676 · Cited by 131 · see citing works

TALEN-mediated targeting of HPV oncogenes ameliorates HPV-related cervical malignancy

Hu, Z., Ding, W., Zhu, D., Yu, L., Jiang, X., Wang, X., Zhang, C., Wang, L., Ji, T., Liu, D., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci78206 · Cited by 127 · see citing works

Highly efficient homology-driven genome editing in human T cells by combining zinc-finger nuclease mRNA and AAV6 donor delivery

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

Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing

Sardo, V. L., Chubukov, P., Ferguson, W. C., Kumar, A., Teng, E. L., Duran, M., Zhang, L., Cost, G. J., Engler, A. J., Urnov, F. D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.11.014 · Cited by 126 · see citing works

Diversifying the structure of zinc finger nucleases for high-precision genome editing

Paschon, D. E., Lussier, S. J., Wangzor, T., Xia, D. F., Li, P. W., Hinkley, S. J., Scarlott, N. A., Lam, S. C., Waite, A. J., Truong, L. N., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08867-x · Cited by 128 · see citing works

Dose-dependent prevention of metabolic and neurologic disease in murine MPS II by ZFN-mediated in vivo genome editing

Laoharawee, K., DeKelver, R. C., Podetz-Pedersen, K. M., Rohde, M., Sproul, S., Nguyen, H.-O., Nguyen, T., St. Martin, S. J., Ou, L., Tom, S., et al. (2018) · Molecular Therapy · doi:10.1016/j.ymthe.2018.03.002 · Cited by 125 · see citing works

Quantifying Genome-Editing Outcomes at Endogenous Loci with SMRT Sequencing

Hendel, A., Kildebeck, E., Fine, E. J., Clark, J. T., Punjya, N., Sebastiano, V., Bao, G., & Porteus, M. H. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.040 · Cited by 126 · see citing works

A Cut above the Rest: Targeted Genome Editing Technologies in Human Pluripotent Stem Cells

Li, M., Suzuki, K., Kim, N. Y., Liu, G., & Belmonte, J. C. I. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.r113.488247 · Cited by 123 · see citing works

A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly

Chen, S., Oikonomou, G., Chiu, C. N., Niles, B. J., Liu, J., Lee, D. A., Antoshechkin, I. A., & Prober, D. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1356 · Cited by 123 · see citing works

Mitochondrial DNA heteroplasmy in disease and targeted nuclease‐based therapeutic approaches

Nissanka, N., & Moraes, C. T. (2020) · EMBO Reports · doi:10.15252/embr.201949612 · Cited by 125 · see citing works

Precision Editing of Large Animal Genomes

Tan, W. S., Carlson, D. F., Walton, M., Fahrenkrug, S. C., & Hackett, P. B. (2012) · Advances in genetics · doi:10.1016/b978-0-12-404742-6.00002-8 · Cited by 123 · see citing works

Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing

Lee, C. M., Cradick, T. J., Fine, E. J., & Bao, G. (2016) · Molecular Therapy · doi:10.1038/mt.2016.1 · Cited by 122 · see citing works

Correction of Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients Through Genomic Excision of Exon 51 by Zinc Finger Nucleases

Ousterout, D. G., Kabadi, A. M., Thakore, P. I., Pérez‐Piñera, P., Brown, M. T., Majoros, W. H., Reddy, T. E., & Gersbach, C. A. (2014) · Molecular Therapy · doi:10.1038/mt.2014.234 · Cited by 118 · see citing works

Scientific opinion addressing the safety assessment of plants developed using Zinc Finger Nuclease 3 and other Site‐Directed Nucleases with similar function

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What does our genome encode?Preprint

Stamatoyannopoulos, J. A. (2012) · Genome Research · doi:10.1101/gr.146506.112 · Cited by 116 · see citing works

Genome Editing: A New Approach to Human Therapeutics

Porteus, M. H. (2015) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124454 · Cited by 116 · see citing works

Fanconi Anemia Gene Editing by the CRISPR/Cas9 System

Osborn, M. J., Gabriel, R., Webber, B. R., DeFeo, A. P., McElroy, A. N., Jarjour, J., Starker, C. G., Wagner, J. E., Joung, J. K., Voytas, D. F., et al. (2014) · Human Gene Therapy · doi:10.1089/hum.2014.111 · Cited by 115 · see citing works

DNA Repair Mechanisms and Their Biological Roles in the Malaria Parasite Plasmodium falciparum

Lee, A. H., Symington, L. S., & Fidock, D. A. (2014) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00059-13 · Cited by 113 · see citing works

Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis

Lonowski, L. A., Narimatsu, Y., Riaz, A., Delay, C. M., Yang, Z., Niola, F., Duda, K., Ober, E. A., Clausen, H., Wandall, H. H., et al. (2017) · Nature Protocols · doi:10.1038/nprot.2016.165 · Cited by 109 · see citing works

787. Engineered Fok I Heterodimers for Enhanced Zinc Finger Nuclease Specificity

Miller, J. C., Holmes, M. C., Wang, J., Lee, Y.-L., Rupniewski, I., Waite, A., Guschin, D. Y., Gregory, P. D., Pabo, C. O., & Rebar, E. J. (2006) · Molecular Therapy · doi:10.1016/j.ymthe.2006.08.875 · Cited by 1 · see citing works

An 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

Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases

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Creating Designed Zinc-Finger Nucleases with Minimal Cytotoxicity

Ramalingam, S., Kandavelou, K., Rajenderan, R., & Chandrasegaran, S. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.10.043 · Cited by 77 · see citing works

379. New Zinc Finger Protein Nuclease Architectures for More Efficient Gene Modification Therapies

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