ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

Capecchi, 2005, Gene targeting in mice: functional analysis of the mammalian genome for the twenty-first century, Nat. Rev. Genet., 6, 507, 10.1038/nrg1619

McManus, 2002, Gene silencing in mammals by small interfering RNAs, Nat. Rev. Genet., 3, 737, 10.1038/nrg908

Urnov, 2010, Genome editing with engineered zinc finger nucleases, Nat. Rev. Genet., 11, 636, 10.1038/nrg2842

Carroll, 2011, Genome engineering with zinc-finger nucleases, Genetics, 188, 773, 10.1534/genetics.111.131433

Wyman, 2006, DNA double-strand break repair: all's well that ends well, Annu. Rev. Genet., 40, 363, 10.1146/annurev.genet.40.110405.090451

Beerli, 2002, Engineering polydactyl zinc-finger transcription factors, Nat. Biotechnol., 20, 135, 10.1038/nbt0202-135

Liu, 1997, Design of polydactyl zinc-finger proteins for unique addressing within complex genomes, Proc. Natl. Acad. Sci. U.S.A., 94, 5525, 10.1073/pnas.94.11.5525

Beerli, 1998, Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks, Proc. Natl. Acad. Sci. U.S.A., 95, 14628, 10.1073/pnas.95.25.14628

Beerli, 2000, Positive and negative regulation of endogenous genes by designed transcription factors, Proc. Natl. Acad. Sci. U.S.A., 97, 1495, 10.1073/pnas.040552697

Kim, 1998, Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants, Proc. Natl. Acad. Sci. U.S.A., 95, 2812, 10.1073/pnas.95.6.2812

Segal, 2006, Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA, J. Mol. Biol., 363, 405, 10.1016/j.jmb.2006.08.016

Neuteboom, 2006, Effects of different zinc finger transcription factors on genomic targets, Biochem. Biophys. Res. Commun., 339, 263, 10.1016/j.bbrc.2005.11.011

Bhakta, 2013, Highly active zinc-finger nucleases by extended modular assembly, Genome Res., 23, 530, 10.1101/gr.143693.112

Kim, 2011, Preassembled zinc-finger arrays for rapid construction of ZFNs, Nat. Methods, 8, 7, 10.1038/nmeth0111-7a

Gonzalez, 2010, Modular system for the construction of zinc-finger libraries and proteins, Nat. Protoc., 5, 791, 10.1038/nprot.2010.34

Segal, 1999, Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences, Proc. Natl. Acad. Sci. U.S.A., 96, 2758, 10.1073/pnas.96.6.2758

Maeder, 2008, Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification, Mol. Cell, 31, 294, 10.1016/j.molcel.2008.06.016

Sander, 2011, Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA), Nat. Methods, 8, 67, 10.1038/nmeth.1542

Gupta, 2012, An optimized two-finger archive for ZFN-mediated gene targeting, Nat. Methods, 9, 588, 10.1038/nmeth.1994

Boch, 2009, Breaking the code of DNA binding specificity of TAL-type III effectors, Science, 326, 1509, 10.1126/science.1178811

Moscou, 2009, A simple cipher governs DNA recognition by TAL effectors, Science, 326, 1501, 10.1126/science.1178817

Mak, 2012, The crystal structure of TAL effector PthXo1 bound to its DNA target, Science, 335, 716, 10.1126/science.1216211

Deng, 2012, Structural basis for sequence-specific recognition of DNA by TAL effectors, Science, 335, 720, 10.1126/science.1215670

Christian, 2010, Targeting DNA double-strand breaks with TAL effector nucleases, Genetics, 186, 757, 10.1534/genetics.110.120717

Mussolino, 2011, A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity, Nucleic Acids Res., 39, 9283, 10.1093/nar/gkr597

Miller, 2011, A TALE nuclease architecture for efficient genome editing, Nat. Biotechnol., 29, 143, 10.1038/nbt.1755

Zhang, 2011, Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription, Nat. Biotechnol., 29, 149, 10.1038/nbt.1775

Mercer, 2012, Chimeric TALE recombinases with programmable DNA sequence specificity, Nucleic Acids Res., 40, 11163, 10.1093/nar/gks875

Cermak, 2011, Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting, Nucleic Acids Res., 39, e82, 10.1093/nar/gkr218

Reyon, 2012, FLASH assembly of TALENs for high-throughput genome editing, Nat. Biotechnol., 30, 460, 10.1038/nbt.2170

Briggs, 2012, Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers, Nucleic Acids Res., 40, e117, 10.1093/nar/gks624

Schmid-Burgk, 2013, A ligation-independent cloning technique for high-throughput assembly of transcription activator-like effector genes, Nat. Biotechnol., 31, 76, 10.1038/nbt.2460

Kim, 2013, A library of TAL effector nucleases spanning the human genome, Nat. Biotechnol., 31, 251, 10.1038/nbt.2517

Moehle, 2007, Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases, Proc. Natl. Acad. Sci. U.S.A., 104, 3055, 10.1073/pnas.0611478104

Orlando, 2010, Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology, Nucleic Acids Res., 38, e152, 10.1093/nar/gkq512

Chen, 2011, High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases, Nat. Methods, 8, 753, 10.1038/nmeth.1653

Santiago, 2008, Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases, Proc. Natl. Acad. Sci. U.S.A., 105, 5809, 10.1073/pnas.0800940105

Lee, 2010, Targeted chromosomal deletions in human cells using zinc finger nucleases, Genome Res., 20, 81, 10.1101/gr.099747.109

Sollu, 2010, Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion, Nucleic Acids Res., 38, 8269, 10.1093/nar/gkq720

Lee, 2012, Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases, Genome Res., 22, 539, 10.1101/gr.129635.111

Brunet, 2009, Chromosomal translocations induced at specified loci in human stem cells, Proc. Natl. Acad. Sci. U.S.A., 106, 10620, 10.1073/pnas.0902076106

Cristea, 2013, In vivo cleavage of transgene donors promotes nuclease-mediated targeted integration, Biotechnol. Bioeng., 110, 871, 10.1002/bit.24733

Maresca, 2013, Obligate Ligation-Gated Recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining, Genome Res., 23, 539, 10.1101/gr.145441.112

Lombardo, 2007, Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery, Nat. Biotechnol., 25, 1298, 10.1038/nbt1353

Hockemeyer, 2009, Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases, Nat. Biotechnol., 27, 851, 10.1038/nbt.1562

Hockemeyer, 2011, Genetic engineering of human pluripotent cells using TALE nucleases, Nat. Biotechnol., 29, 731, 10.1038/nbt.1927

Ding, 2013, A TALEN genome-editing system for generating human stem cell-based disease models, Cell Stem Cell, 12, 238, 10.1016/j.stem.2012.11.011

Zou, 2009, Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells, Cell Stem Cell, 5, 97, 10.1016/j.stem.2009.05.023

Sanyal, 2012, The long-range interaction landscape of gene promoters, Nature, 489, 109, 10.1038/nature11279

Gutschner, 2011, Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases, Genome Res., 21, 1944, 10.1101/gr.122358.111

Dunham, 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247

Miller, 2007, An improved zinc-finger nuclease architecture for highly specific genome editing, Nat. Biotechnol., 25, 778, 10.1038/nbt1319

Szczepek, 2007, Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases, Nat. Biotechnol., 25, 786, 10.1038/nbt1317

Doyon, 2011, Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures, Nat. Methods, 8, 74, 10.1038/nmeth.1539

Guo, 2010, Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nucleases, J. Mol. Biol., 400, 96, 10.1016/j.jmb.2010.04.060

Sood, 2013, Efficient methods for targeted mutagenesis in zebrafish using zinc-finger nucleases: data from targeting of nine genes using CompoZr or CoDA ZFNs, PLoS ONE, 8, e57239, 10.1371/journal.pone.0057239

Perez-Pinera, 2012, Gene targeting to the ROSA26 locus directed by engineered zinc finger nucleases, Nucleic Acids Res., 40, 3741, 10.1093/nar/gkr1214

Doyon, 2010, Transient cold shock enhances zinc-finger nuclease-mediated gene disruption, Nat. Methods, 7, 459, 10.1038/nmeth.1456

Certo, 2012, Coupling endonucleases with DNA end-processing enzymes to drive gene disruption, Nat. Methods, 9, 973, 10.1038/nmeth.2177

Kim, 2011, Surrogate reporters for enrichment of cells with nuclease-induced mutations, Nat. Methods, 8, 941, 10.1038/nmeth.1733

Kim, 2012, Precision genome engineering with programmable DNA-nicking enzymes, Genome Res., 22, 1327, 10.1101/gr.138792.112

Wang, 2012, Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme, Genome Res., 22, 1316, 10.1101/gr.122879.111

Ramirez, 2012, Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects, Nucleic Acids Res., 40, 5560, 10.1093/nar/gks179

McConnell Smith, 2009, Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease, Proc. Natl. Acad. Sci. U.S.A., 106, 5099, 10.1073/pnas.0810588106

Gaj, 2012, Targeted gene knockout by direct delivery of zinc-finger nuclease proteins, Nat. Methods, 9, 805, 10.1038/nmeth.2030

Doyon, 2008, Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases, Nat. Biotechnol., 26, 702, 10.1038/nbt1409

Sander, 2011, Targeted gene disruption in somatic zebrafish cells using engineered TALENs, Nat. Biotechnol., 29, 697, 10.1038/nbt.1934

Meng, 2008, Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases, Nat. Biotechnol., 26, 695, 10.1038/nbt1398

Tesson, 2011, Knockout rats generated by embryo microinjection of TALENs, Nat. Biotechnol., 29, 695, 10.1038/nbt.1940

Geurts, 2009, Knockout rats via embryo microinjection of zinc-finger nucleases, Science, 325, 433, 10.1126/science.1172447

Bibikova, 2003, Enhancing gene targeting with designed zinc finger nucleases, Science, 300, 764, 10.1126/science.1079512

Bibikova, 2002, Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases, Genetics, 161, 1169, 10.1093/genetics/161.3.1169

Morton, 2006, Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells, Proc. Natl. Acad. Sci. U.S.A., 103, 16370, 10.1073/pnas.0605633103

Merlin, 2013, Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases, Genome Res., 23, 159, 10.1101/gr.145599.112

Young, 2011, Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases, Proc. Natl. Acad. Sci. U.S.A., 108, 7052, 10.1073/pnas.1102030108

Carlson, 2012, Efficient TALEN-mediated gene knockout in livestock, Proc. Natl. Acad. Sci. U.S.A., 109, 17382, 10.1073/pnas.1211446109

Hauschild, 2011, Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases, Proc. Natl. Acad. Sci. U.S.A., 108, 12013, 10.1073/pnas.1106422108

Wood, 2011, Targeted genome editing across species using ZFNs and TALENs, Science, 333, 307, 10.1126/science.1207773

Bedell, 2012, In vivo genome editing using a high-efficiency TALEN system, Nature, 491, 114, 10.1038/nature11537

Zu, 2013, TALEN-mediated precise genome modification by homologous recombination in zebrafish, Nat. Methods, 10, 329, 10.1038/nmeth.2374

Zhang, 2010, High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases, Proc. Natl. Acad. Sci. U.S.A., 107, 12028, 10.1073/pnas.0914991107

Shukla, 2009, Precise genome modification in the crop species Zea mays using zinc-finger nucleases, Nature, 459, 437, 10.1038/nature07992

Townsend, 2009, High-frequency modification of plant genes using engineered zinc-finger nucleases, Nature, 459, 442, 10.1038/nature07845

Li, 2012, High-efficiency TALEN-based gene editing produces disease-resistant rice, Nat. Biotechnol., 30, 390, 10.1038/nbt.2199

Urnov, 2005, Highly efficient endogenous human gene correction using designed zinc-finger nucleases, Nature, 435, 646, 10.1038/nature03556

Li, 2011, In vivo genome editing restores haemostasis in a mouse model of haemophilia, Nature, 475, 217, 10.1038/nature10177

Zou, 2011, Site-specific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease, Blood, 118, 4599, 10.1182/blood-2011-02-335554

Sebastiano, 2011, In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases, Stem Cells, 29, 1717, 10.1002/stem.718

Yusa, 2011, Targeted gene correction of alpha1-antitrypsin deficiency in induced pluripotent stem cells, Nature, 478, 391, 10.1038/nature10424

Soldner, 2011, Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations, Cell, 146, 318, 10.1016/j.cell.2011.06.019

Perez, 2008, Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases, Nat. Biotechnol., 26, 808, 10.1038/nbt1410

Holt, 2010, Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo, Nat. Biotechnol., 28, 839, 10.1038/nbt.1663

Voit, 2013, Generation of an HIV resistant T-cell line by targeted “stacking” of restriction factors, Mol. Ther., 21, 786, 10.1038/mt.2012.284

Torikai, 2012, A foundation for universal T-cell based immunotherapy: T cells engineered to express a CD19-specific chimeric-antigen-receptor and eliminate expression of endogenous TCR, Blood, 119, 5697, 10.1182/blood-2012-01-405365

Provasi, 2012, Editing T cell specificity towards leukemia by zinc finger nucleases and lentiviral gene transfer, Nat. Med., 18, 807, 10.1038/nm.2700

DeKelver, 2010, Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome, Genome Res., 20, 1133, 10.1101/gr.106773.110

Lombardo, 2011, Site-specific integration and tailoring of cassette design for sustainable gene transfer, Nat. Methods, 8, 861, 10.1038/nmeth.1674

Wiedenheft, 2012, RNA-guided genetic silencing systems in bacteria and archaea, Nature, 482, 331, 10.1038/nature10886

Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829

Jinek, 2013, RNA-programmed genome editing in human cells, eLife, 2, e00471, 10.7554/eLife.00471

Cho, 2013, Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease, Nat. Biotechnol., 31, 230, 10.1038/nbt.2507

Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143

Mali, 2013, RNA-guided human genome engineering via Cas9, Science, 339, 823, 10.1126/science.1232033

Hwang, 2013, Efficient genome editing in zebrafish using a CRISPR-Cas system, Nat. Biotechnol., 31, 227, 10.1038/nbt.2501

Jiang, 2013, RNA-guided editing of bacterial genomes using CRISPR-Cas systems, Nat. Biotechnol., 31, 233, 10.1038/nbt.2508

Gabriel, 2011, An unbiased genome-wide analysis of zinc-finger nuclease specificity, Nat. Biotechnol., 29, 816, 10.1038/nbt.1948

Holkers, 2013, Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells, Nucleic Acids Res., 41, e63, 10.1093/nar/gks1446

Ellis, 2013, Zinc-finger nuclease-mediated gene correction using single AAV vector transduction and enhancement by Food and Drug Administration-approved drugs, Gene Ther., 20, 35, 10.1038/gt.2011.211

Gaj, 2013, A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells, Nucleic Acids Res., 41, 3937, 10.1093/nar/gkt071

Gersbach, 2011, Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase, Nucleic Acids Res., 39, 7868, 10.1093/nar/gkr421

Gaj, 2011, Structure-guided reprogramming of serine recombinase DNA sequence specificity, Proc. Natl. Acad. Sci. U.S.A., 108, 498, 10.1073/pnas.1014214108

Beerli, 2000, Chemically regulated zinc finger transcription factors, J. Biol. Chem., 275, 32617, 10.1074/jbc.M005108200

Polstein, 2012, Light-inducible spatiotemporal control of gene activation by customizable zinc finger transcription factors, J. Am. Chem. Soc., 134, 16480, 10.1021/ja3065667

Perez-Pinera, 2013, Synergistic and tunable human gene activation by combinations of synthetic transcription factors, Nat. Methods, 10, 239, 10.1038/nmeth.2361

Maeder, 2013, Robust, synergistic regulation of human gene expression using TALE activators, Nat. Methods, 10, 243, 10.1038/nmeth.2366

Yant, 2007, Site-directed transposon integration in human cells, Nucleic Acids Res., 35, e50, 10.1093/nar/gkm089

Gersbach, 2010, Directed evolution of recombinase specificity by split gene reassembly, Nucleic Acids Res., 38, 4198, 10.1093/nar/gkq125

Owens, 2012, Chimeric piggyBac transposases for genomic targeting in human cells, Nucleic Acids Res., 40, 6978, 10.1093/nar/gks309

Handel, 2012, Versatile and efficient genome editing in human cells by combining zinc-finger nucleases with adeno-associated viral vectors, Hum. Gene Ther., 23, 321, 10.1089/hum.2011.140