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Sirohi U, Kumar M, Sharma VR, Teotia S, Singh D, Chaudhary V, Yadav MK. CRISPR/Cas9 System: A Potential Tool for Genetic Improvement in Floricultural Crops. Mol Biotechnol 2022; 64:1303-1318. [PMID: 35751797 PMCID: PMC9244459 DOI: 10.1007/s12033-022-00523-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022]
Abstract
Demand of flowers is increasing with time worldwide. Floriculture has become one of the most important commercial trades in agriculture. Although traditional breeding methods like hybridization and mutation breeding have contributed significantly to the development of important flower varieties, flower production and quality of flowers can be significantly improved by employing modern breeding approaches. Novel traits of significance have interest to consumers and producers, such as fragrance, new floral color, change in floral architecture and morphology, vase life, aroma, and resistance to biotic and abiotic stresses, have been introduced by genetic manipulation. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has recently emerged as a powerful genome-editing tool for accurately changing DNA sequences at specific locations. It provides excellent means of genetically improving floricultural crops. CRISPR/Cas system has been utilized in gene editing in horticultural cops. There are few reports on the utilization of the CRISPR/Cas9 system in flowers. The current review summarizes the research work done by employing the CRISPR/Cas9 system in floricultural crops including improvement in flowering traits such as color modification, prolonging the shelf life of flowers, flower initiation, and development, changes in color of ornamental foliage by genome editing. CRISPR/Cas9 gene editing could be useful in developing novel cultivars with higher fragrance and enhanced essential oil and many other useful traits. The present review also highlights the basic mechanism and key components involved in the CRISPR/Cas9 system.
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Affiliation(s)
- Ujjwal Sirohi
- Present Address: National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
- Department of Agricultural Biotechnology, College of Agriculture, SVPUAT, Meerut, Uttar Pradesh 250110 India
| | - Mukesh Kumar
- Department of Horticulture, College of Agriculture, SVPUAT, Meerut, Uttar Pradesh 250110 India
| | - Vinukonda Rakesh Sharma
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001 India
| | - Sachin Teotia
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh 201306 India
| | - Deepali Singh
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh 201308 India
| | - Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, Uttar Pradesh 250003 India
| | - Manoj Kumar Yadav
- Department of Agricultural Biotechnology, College of Agriculture, SVPUAT, Meerut, Uttar Pradesh 250110 India
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Lainšček D, Forstnerič V, Mikolič V, Malenšek Š, Pečan P, Benčina M, Sever M, Podgornik H, Jerala R. Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing. Nat Commun 2022; 13:3604. [PMID: 35739111 PMCID: PMC9226073 DOI: 10.1038/s41467-022-31386-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
The CRISPR/Cas system has emerged as a powerful and versatile genome engineering tool, revolutionizing biological and biomedical sciences, where an improvement of efficiency could have a strong impact. Here we present a strategy to enhance gene editing based on the concerted action of Cas9 and an exonuclease. Non-covalent recruitment of exonuclease to Cas9/gRNA complex via genetically encoded coiled-coil based domains, termed CCExo, recruited the exonuclease to the cleavage site and robustly increased gene knock-out due to progressive DNA strand recession at the cleavage site, causing decreased re-ligation of the nonedited DNA. CCExo exhibited increased deletion size and enhanced gene inactivation efficiency in the context of several DNA targets, gRNA selection, Cas variants, tested cell lines and type of delivery. Targeting a sequence-specific oncogenic chromosomal translocation using CCExo in cells of chronic myelogenous leukemia patients and in an animal model led to the reduction or elimination of cancer, establishing it as a highly specific tool for treating CML and potentially other appropriate diseases with genetic etiology.
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Affiliation(s)
- Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
| | - Veronika Mikolič
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Špela Malenšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Peter Pečan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia
| | - Matjaž Sever
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana, 1000, Slovenia
| | - Helena Podgornik
- Department of Hematology, Division of Internal Medicine, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana, 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, 1000, Slovenia.
- EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana, 1000, Slovenia.
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Development of Genome Editing Approaches against Herpes Simplex Virus Infections. Viruses 2021; 13:v13020338. [PMID: 33671590 PMCID: PMC7926879 DOI: 10.3390/v13020338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) is a herpesvirus that may cause cold sores or keratitis in healthy or immunocompetent individuals, but can lead to severe and potentially life-threatening complications in immune-immature individuals, such as neonates or immune-compromised patients. Like all other herpesviruses, HSV-1 can engage in lytic infection as well as establish latent infection. Current anti-HSV-1 therapies effectively block viral replication and infection. However, they have little effect on viral latency and cannot completely eliminate viral infection. These issues, along with the emergence of drug-resistant viral strains, pose a need to develop new compounds and novel strategies for the treatment of HSV-1 infection. Genome editing methods represent a promising approach against viral infection by modifying or destroying the genetic material of human viruses. These editing methods include homing endonucleases (HE) and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated protein (Cas) RNA-guided nuclease system. Recent studies have showed that both HE and CRISPR/Cas systems are effective in inhibiting HSV-1 infection in cultured cells in vitro and in mice in vivo. This review, which focuses on recently published progress, suggests that genome editing approaches could be used for eliminating HSV-1 latent and lytic infection and for treating HSV-1 associated diseases.
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Adames NR, Gallegos JE, Peccoud J. Yeast genetic interaction screens in the age of CRISPR/Cas. Curr Genet 2019; 65:307-327. [PMID: 30255296 PMCID: PMC6420903 DOI: 10.1007/s00294-018-0887-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 12/21/2022]
Abstract
The ease of performing both forward and reverse genetics in Saccharomyces cerevisiae, along with its stable haploid state and short generation times, has made this budding yeast the consummate model eukaryote for genetics. The major advantage of using budding yeast for reverse genetics is this organism's highly efficient homology-directed repair, allowing for precise genome editing simply by introducing DNA with homology to the chromosomal target. Although plasmid- and PCR-based genome editing tools are quite efficient, they depend on rare spontaneous DNA breaks near the target sequence. Consequently, they can generate only one genomic edit at a time, and the edit must be associated with a selectable marker. However, CRISPR/Cas technology is efficient enough to permit markerless and multiplexed edits in a single step. These features have made CRISPR/Cas popular for yeast strain engineering in synthetic biology and metabolic engineering applications, but it has not been widely employed for genetic screens. In this review, we critically examine different methods to generate multi-mutant strains in systematic genetic interaction screens and discuss the potential of CRISPR/Cas to supplement or improve on these methods.
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Affiliation(s)
- Neil R Adames
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jenna E Gallegos
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jean Peccoud
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA.
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Guha TK, Edgell DR. Applications of Alternative Nucleases in the Age of CRISPR/Cas9. Int J Mol Sci 2017; 18:ijms18122565. [PMID: 29186020 PMCID: PMC5751168 DOI: 10.3390/ijms18122565] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 01/10/2023] Open
Abstract
Breakthroughs in the development of programmable site-specific nucleases, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), meganucleases (MNs), and most recently, the clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (including Cas9) have greatly enabled and accelerated genome editing. By targeting double-strand breaks to user-defined locations, the rates of DNA repair events are greatly enhanced relative to un-catalyzed events at the same sites. However, the underlying biology of each genome-editing nuclease influences the targeting potential, the spectrum of off-target cleavages, the ease-of-use, and the types of recombination events at targeted double-strand breaks. No single genome-editing nuclease is optimized for all possible applications. Here, we focus on the diversity of nuclease domains available for genome editing, highlighting biochemical properties and the potential applications that are best suited to each domain.
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Affiliation(s)
- Tuhin K Guha
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada.
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada.
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6
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Wolfs JM, Hamilton TA, Lant JT, Laforet M, Zhang J, Salemi LM, Gloor GB, Schild-Poulter C, Edgell DR. Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease. Proc Natl Acad Sci U S A 2016; 113:14988-14993. [PMID: 27956611 PMCID: PMC5206545 DOI: 10.1073/pnas.1616343114] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The CRISPR/Cas9 nuclease is commonly used to make gene knockouts. The blunt DNA ends generated by cleavage can be efficiently ligated by the classical nonhomologous end-joining repair pathway (c-NHEJ), regenerating the target site. This repair creates a cycle of cleavage, ligation, and target site regeneration that persists until sufficient modification of the DNA break by alternative NHEJ prevents further Cas9 cutting, generating a heterogeneous population of insertions and deletions typical of gene knockouts. Here, we develop a strategy to escape this cycle and bias events toward defined length deletions by creating an RNA-guided dual active site nuclease that generates two noncompatible DNA breaks at a target site, effectively deleting the majority of the target site such that it cannot be regenerated. The TevCas9 nuclease, a fusion of the I-TevI nuclease domain to Cas9, functions robustly in HEK293 cells and generates 33- to 36-bp deletions at frequencies up to 40%. Deep sequencing revealed minimal processing of TevCas9 products, consistent with protection of the DNA ends from exonucleolytic degradation and repair by the c-NHEJ pathway. Directed evolution experiments identified I-TevI variants with broadened targeting range, making TevCas9 an easy-to-use reagent. Our results highlight how the sequence-tolerant cleavage properties of the I-TevI homing endonuclease can be harnessed to enhance Cas9 applications, circumventing the cleavage and ligation cycle and biasing genome-editing events toward defined length deletions.
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Affiliation(s)
- Jason M Wolfs
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Thomas A Hamilton
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Jeremy T Lant
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Marcon Laforet
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Jenny Zhang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Louisa M Salemi
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - Gregory B Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Caroline Schild-Poulter
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada;
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7
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Stella S, Montoya G. The genome editing revolution: A CRISPR-Cas TALE off-target story. Bioessays 2016; 38 Suppl 1:S4-S13. [DOI: 10.1002/bies.201670903] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/26/2015] [Accepted: 10/29/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Stefano Stella
- Novo Nordisk Foundation Center for Protein Research, Protein Structure and Function Programme, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research, Protein Structure and Function Programme, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
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8
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Salient Features of Endonuclease Platforms for Therapeutic Genome Editing. Mol Ther 2016; 24:422-9. [PMID: 26796671 DOI: 10.1038/mt.2016.21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/07/2016] [Indexed: 12/11/2022] Open
Abstract
Emerging gene-editing technologies are nearing a revolutionary phase in genetic medicine: precisely modifying or repairing causal genetic defects. This may include any number of DNA sequence manipulations, such as knocking out a deleterious gene, introducing a particular mutation, or directly repairing a defective sequence by site-specific recombination. All of these edits can currently be achieved via programmable rare-cutting endonucleases to create targeted DNA breaks that can engage and exploit endogenous DNA repair pathways to impart site-specific genetic changes. Over the past decade, several distinct technologies for introducing site-specific DNA breaks have been developed, yet the different biological origins of these gene-editing technologies bring along inherent differences in parameters that impact clinical implementation. This review aims to provide an accessible overview of the various endonuclease-based gene-editing platforms, highlighting the strengths and weakness of each with respect to therapeutic applications.
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Crispo M, Mulet AP, Tesson L, Barrera N, Cuadro F, dos Santos-Neto PC, Nguyen TH, Crénéguy A, Brusselle L, Anegón I, Menchaca A. Efficient Generation of Myostatin Knock-Out Sheep Using CRISPR/Cas9 Technology and Microinjection into Zygotes. PLoS One 2015; 10:e0136690. [PMID: 26305800 PMCID: PMC4549068 DOI: 10.1371/journal.pone.0136690] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 08/05/2015] [Indexed: 01/01/2023] Open
Abstract
While CRISPR/Cas9 technology has proven to be a valuable system to generate gene-targeted modified animals in several species, this tool has been scarcely reported in farm animals. Myostatin is encoded by MSTN gene involved in the inhibition of muscle differentiation and growth. We determined the efficiency of the CRISPR/Cas9 system to edit MSTN in sheep and generate knock-out (KO) animals with the aim to promote muscle development and body growth. We generated CRISPR/Cas9 mRNAs specific for ovine MSTN and microinjected them into the cytoplasm of ovine zygotes. When embryo development of CRISPR/Cas9 microinjected zygotes (n = 216) was compared with buffer injected embryos (n = 183) and non microinjected embryos (n = 173), cleavage rate was lower for both microinjected groups (P<0.05) and neither was affected by CRISPR/Cas9 content in the injected medium. Embryo development to blastocyst was not affected by microinjection and was similar among the experimental groups. From 20 embryos analyzed by Sanger sequencing, ten were mutant (heterozygous or mosaic; 50% efficiency). To obtain live MSTN KO lambs, 53 blastocysts produced after zygote CRISPR/Cas9 microinjection were transferred to 29 recipient females resulting in 65.5% (19/29) of pregnant ewes and 41.5% (22/53) of newborns. From 22 born lambs analyzed by T7EI and Sanger sequencing, ten showed indel mutations at MSTN gene. Eight showed mutations in both alleles and five of them were homozygous for indels generating out-of frame mutations that resulted in premature stop codons. Western blot analysis of homozygous KO founders confirmed the absence of myostatin, showing heavier body weight than wild type counterparts. In conclusion, our results demonstrate that CRISPR/Cas9 system was a very efficient tool to generate gene KO sheep. This technology is quick and easy to perform and less expensive than previous techniques, and can be applied to obtain genetically modified animal models of interest for biomedicine and livestock.
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Affiliation(s)
- M. Crispo
- Unidad de Animales Transgénicos y de Experimentación (UATE), Institut Pasteur de Montevideo, Montevideo, Uruguay
- * E-mail: (MC); (IA); (AM)
| | - A. P. Mulet
- Unidad de Animales Transgénicos y de Experimentación (UATE), Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - L. Tesson
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
| | - N. Barrera
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - F. Cuadro
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | | | - T. H. Nguyen
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
| | - A. Crénéguy
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
| | - L. Brusselle
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
| | - I. Anegón
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
- * E-mail: (MC); (IA); (AM)
| | - A. Menchaca
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
- * E-mail: (MC); (IA); (AM)
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10
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Ni W, Qiao J, Hu S, Zhao X, Regouski M, Yang M, Polejaeva IA, Chen C. Efficient gene knockout in goats using CRISPR/Cas9 system. PLoS One 2014; 9:e106718. [PMID: 25188313 PMCID: PMC4154755 DOI: 10.1371/journal.pone.0106718] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/10/2014] [Indexed: 11/19/2022] Open
Abstract
The CRISPR/Cas9 system has been adapted as an efficient genome editing tool in laboratory animals such as mice, rats, zebrafish and pigs. Here, we report that CRISPR/Cas9 mediated approach can efficiently induce monoallelic and biallelic gene knockout in goat primary fibroblasts. Four genes were disrupted simultaneously in goat fibroblasts by CRISPR/Cas9-mediated genome editing. The single-gene knockout fibroblasts were successfully used for somatic cell nuclear transfer (SCNT) and resulted in live-born goats harboring biallelic mutations. The CRISPR/Cas9 system represents a highly effective and facile platform for targeted editing of large animal genomes, which can be broadly applied to both biomedical and agricultural applications.
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Affiliation(s)
- Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Jun Qiao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Shengwei Hu
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
- * E-mail: (SH); (IP); (CC)
| | - Xinxia Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Misha Regouski
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Min Yang
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Irina A. Polejaeva
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
- * E-mail: (SH); (IP); (CC)
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
- * E-mail: (SH); (IP); (CC)
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11
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Wolfs JM, DaSilva M, Meister SE, Wang X, Schild-Poulter C, Edgell DR. MegaTevs: single-chain dual nucleases for efficient gene disruption. Nucleic Acids Res 2014; 42:8816-29. [PMID: 25013171 PMCID: PMC4117789 DOI: 10.1093/nar/gku573] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Targeting gene disruptions in complex genomes relies on imprecise repair by the non-homologous end-joining DNA pathway, creating mutagenic insertions or deletions (indels) at the break point. DNA end-processing enzymes are often co-expressed with genome-editing nucleases to enhance the frequency of indels, as the compatible cohesive ends generated by the nucleases can be precisely repaired, leading to a cycle of cleavage and non-mutagenic repair. Here, we present an alternative strategy to bias repair toward gene disruption by fusing two different nuclease active sites from I-TevI (a GIY-YIG enzyme) and I-OnuI E2 (an engineered meganuclease) into a single polypeptide chain. In vitro, the MegaTev enzyme generates two double-strand breaks to excise an intervening 30-bp fragment. In HEK 293 cells, we observe a high frequency of gene disruption without co-expression of DNA end-processing enzymes. Deep sequencing of disrupted target sites revealed minimal processing, consistent with the MegaTev sequestering the double-strand breaks from the DNA repair machinery. Off-target profiling revealed no detectable cleavage at sites where the I-TevI CNNNG cleavage motif is not appropriately spaced from the I-OnuI binding site. The MegaTev enzyme represents a small, programmable nuclease platform for extremely specific genome-engineering applications.
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Affiliation(s)
- Jason M Wolfs
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Matthew DaSilva
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Sarah E Meister
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Xu Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
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12
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Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology. Nat Commun 2014; 5:3831. [PMID: 24871200 DOI: 10.1038/ncomms4831] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 04/08/2014] [Indexed: 02/07/2023] Open
Abstract
Diatoms, a major group of photosynthetic microalgae, have a high biotechnological potential that has not been fully exploited because of the paucity of available genetic tools. Here we demonstrate targeted and stable modifications of the genome of the marine diatom Phaeodactylum tricornutum, using both meganucleases and TALE nucleases. When nuclease-encoding constructs are co-transformed with a selectable marker, high frequencies of genome modifications are readily attained with 56 and 27% of the colonies exhibiting targeted mutagenesis or targeted gene insertion, respectively. The generation of an enhanced lipid-producing strain (45-fold increase in triacylglycerol accumulation) through the disruption of the UDP-glucose pyrophosphorylase gene exemplifies the power of genome engineering to harness diatoms for biofuel production.
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Abstract
Current technology enables the production of highly specific genome modifications with excellent efficiency and specificity. Key to this capability are targetable DNA cleavage reagents and cellular DNA repair pathways. The break made by these reagents can produce localized sequence changes through inaccurate nonhomologous end joining (NHEJ), often leading to gene inactivation. Alternatively, user-provided DNA can be used as a template for repair by homologous recombination (HR), leading to the introduction of desired sequence changes. This review describes three classes of targetable cleavage reagents: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas RNA-guided nucleases (RGNs). As a group, these reagents have been successfully used to modify genomic sequences in a wide variety of cells and organisms, including humans. This review discusses the properties, advantages, and limitations of each system, as well as the specific considerations required for their use in different biological systems.
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Affiliation(s)
- Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112;
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Stoddard BL. Homing endonucleases from mobile group I introns: discovery to genome engineering. Mob DNA 2014; 5:7. [PMID: 24589358 PMCID: PMC3943268 DOI: 10.1186/1759-8753-5-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 02/13/2014] [Indexed: 12/20/2022] Open
Abstract
Homing endonucleases are highly specific DNA cleaving enzymes that are encoded within genomes of all forms of microbial life including phage and eukaryotic organelles. These proteins drive the mobility and persistence of their own reading frames. The genes that encode homing endonucleases are often embedded within self-splicing elements such as group I introns, group II introns and inteins. This combination of molecular functions is mutually advantageous: the endonuclease activity allows surrounding introns and inteins to act as invasive DNA elements, while the splicing activity allows the endonuclease gene to invade a coding sequence without disrupting its product. Crystallographic analyses of representatives from all known homing endonuclease families have illustrated both their mechanisms of action and their evolutionary relationships to a wide range of host proteins. Several homing endonucleases have been completely redesigned and used for a variety of genome engineering applications. Recent efforts to augment homing endonucleases with auxiliary DNA recognition elements and/or nucleic acid processing factors has further accelerated their use for applications that demand exceptionally high specificity and activity.
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Affiliation(s)
- Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, N, A3-025, Seattle, WA 98109, USA.
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In vitro Inactivation of Latent HSV by Targeted Mutagenesis Using an HSV-specific Homing Endonuclease. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e146. [PMID: 24496438 PMCID: PMC3951911 DOI: 10.1038/mtna.2013.75] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 12/26/2013] [Indexed: 12/21/2022]
Abstract
Following acute infection, herpes simplex virus (HSV) establishes latency in sensory neurons, from which it can reactivate and cause recurrent disease. Available antiviral therapies do not affect latent viral genomes; therefore, they do not prevent reactivation following therapy cessation. One possible curative approach involves the introduction of DNA double strand breaks in latent HSV genomes by rare-cutting endonucleases, leading to mutagenesis of essential viral genes. We tested this approach in an in vitro HSV latency model using the engineered homing endonuclease (HE) HSV1m5, which recognizes a sequence in the HSV-1 gene UL19, encoding the virion protein VP5. Coexpression of the 3'-exonuclease Trex2 with HEs increased HE-mediated mutagenesis frequencies up to sixfold. Following HSV1m5/Trex2 delivery with adeno-associated viral (AAV) vectors, the target site was mutated in latent HSV genomes with no detectable cell toxicity. Importantly, HSV production by latently infected cells after reactivation was decreased after HSV1m5/Trex2 exposure. Exposure to histone deacetylase inhibitors prior to HSV1m5/Trex2 treatment increased mutagenesis frequencies of latent HSV genomes another two- to fivefold, suggesting that chromatin modification may be a useful adjunct to gene-targeting approaches. These results support the continuing development of HEs and other nucleases (ZFNs, TALENs, CRISPRs) for cure of chronic viral infections.Molecular Therapy-Nucleic Acids (2014) 3, e1; doi:10.1038/mtna.2013.75; published online 4 February 2014.
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16
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Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D, Scharenberg AM. megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. Nucleic Acids Res 2014; 42:2591-601. [PMID: 24285304 PMCID: PMC3936731 DOI: 10.1093/nar/gkt1224] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/04/2013] [Accepted: 11/05/2013] [Indexed: 01/13/2023] Open
Abstract
Rare-cleaving endonucleases have emerged as important tools for making targeted genome modifications. While multiple platforms are now available to generate reagents for research applications, each existing platform has significant limitations in one or more of three key properties necessary for therapeutic application: efficiency of cleavage at the desired target site, specificity of cleavage (i.e. rate of cleavage at 'off-target' sites), and efficient/facile means for delivery to desired target cells. Here, we describe the development of a single-chain rare-cleaving nuclease architecture, which we designate 'megaTAL', in which the DNA binding region of a transcription activator-like (TAL) effector is used to 'address' a site-specific meganuclease adjacent to a single desired genomic target site. This architecture allows the generation of extremely active and hyper-specific compact nucleases that are compatible with all current viral and nonviral cell delivery methods.
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Affiliation(s)
- Sandrine Boissel
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Jordan Jarjour
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Alexander Astrakhan
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Andrew Adey
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Agnès Gouble
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Philippe Duchateau
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Barry L. Stoddard
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Michael T. Certo
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Andrew M. Scharenberg
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA, Pregenen, Inc., Seattle, WA 98103, USA, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA, Cellectis S.A., Paris, 75013, France, Division of Basic Sciences, Fred Hutch Cancer Research Center, Seattle, WA 98109, USA, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA and Department of Immunology, University of Washington, Seattle, WA 98195, USA
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17
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Beurdeley M, Bietz F, Li J, Thomas S, Stoddard T, Juillerat A, Zhang F, Voytas DF, Duchateau P, Silva GH. Compact designer TALENs for efficient genome engineering. Nat Commun 2013; 4:1762. [PMID: 23612303 PMCID: PMC3644105 DOI: 10.1038/ncomms2782] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 03/20/2013] [Indexed: 01/29/2023] Open
Abstract
Transcription activator-like effector nucleases are readily targetable 'molecular scissors' for genome engineering applications. These artificial nucleases offer high specificity coupled with simplicity in design that results from the ability to serially chain transcription activator-like effector repeat arrays to target individual DNA bases. However, these benefits come at the cost of an appreciably large multimeric protein complex, in which DNA cleavage is governed by the nonspecific FokI nuclease domain. Here we report a significant improvement to the standard transcription activator-like effector nuclease architecture by leveraging the partially specific I-TevI catalytic domain to create a new class of monomeric, DNA-cleaving enzymes. In vivo yeast, plant and mammalian cell assays demonstrate that the half-size, single-polypeptide compact transcription activator-like effector nucleases exhibit overall activity and specificity comparable to currently available designer nucleases. In addition, we harness the catalytic mechanism of I-TevI to generate novel compact transcription activator-like effector nuclease-based nicking enzymes that display a greater than 25-fold increase in relative targeted gene correction efficacy.
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Affiliation(s)
- Marine Beurdeley
- Cellectis, Research and Development, 8 rue de la Croix Jarry, 75013 Paris, France
| | - Fabian Bietz
- Cellectis, Research and Development, 8 rue de la Croix Jarry, 75013 Paris, France
| | - Jin Li
- Cellectis Plant Sciences, 600 County Road D West Suite 8, New Brighton, Minnesota 55112, USA
| | - Severine Thomas
- Cellectis, Research and Development, 8 rue de la Croix Jarry, 75013 Paris, France
| | - Thomas Stoddard
- Cellectis Plant Sciences, 600 County Road D West Suite 8, New Brighton, Minnesota 55112, USA
| | - Alexandre Juillerat
- Cellectis, Research and Development, 8 rue de la Croix Jarry, 75013 Paris, France
| | - Feng Zhang
- Cellectis Plant Sciences, 600 County Road D West Suite 8, New Brighton, Minnesota 55112, USA
| | - Daniel F. Voytas
- Cellectis Plant Sciences, 600 County Road D West Suite 8, New Brighton, Minnesota 55112, USA
| | - Philippe Duchateau
- Cellectis, Research and Development, 8 rue de la Croix Jarry, 75013 Paris, France
| | - George H. Silva
- Cellectis, Research and Development, 8 rue de la Croix Jarry, 75013 Paris, France
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