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You B, Li L, Li Z, Wang W, Yang Y, Cheng W, Luo X, Qian Y. Imaging of zinc ions across diverse biological samples with a quinoline-based tris(2-pyridylmethyl)amine fluorescent probe. Talanta 2025; 284:127267. [PMID: 39586214 DOI: 10.1016/j.talanta.2024.127267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 11/12/2024] [Accepted: 11/21/2024] [Indexed: 11/27/2024]
Abstract
Zinc ions (Zn2⁺) is actively involved in diverse biological processes. Therefore, the precise detection of Zn2⁺ ion is an important object of increasing investigation. Although numerous fluorescent zinc ion detection probes have been developed, simple, biocompatible, and sensitive probes are still urgently needed. Herein, we reported two novel fluorescent probes, ZnTP1 and ZnTP2, by incorporating a quinoline fluorophore into a membrane-permeable zinc chelator tris(2-pyridylmethyl)amine. ZnTP1 exhibited a significant fluorescence enhancement in the presence of zinc ions through chelation-enhanced fluorescence (CHEF) processes, whereas probe ZnTP2 did not show any significant change in fluorescence due to the insertion of the carbonyl group. Further investigations revealed that ZnTP1 can effectively penetrate cell membranes and detect Zn2+ with high sensitivity in diverse biological samples, including living cells, plant tissues, and animal model zebrafish. This work suggests that ZnTP1 as a simple and efficient chemical probe has great potential for zinc ions detection in various biological contexts, thus providing a new tool for probing zinc ions in biosystems.
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Affiliation(s)
- Binghui You
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China
| | - Ling Li
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China
| | - Zheng Li
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China
| | - Wei Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China
| | - Yanli Yang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China
| | - Wei Cheng
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China
| | - Xiangjie Luo
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Yong Qian
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China; Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom.
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2
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Phan HTL, Kim K, Lee H, Seong JK. Progress in and Prospects of Genome Editing Tools for Human Disease Model Development and Therapeutic Applications. Genes (Basel) 2023; 14:483. [PMID: 36833410 PMCID: PMC9957140 DOI: 10.3390/genes14020483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Programmable nucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas, are widely accepted because of their diversity and enormous potential for targeted genomic modifications in eukaryotes and other animals. Moreover, rapid advances in genome editing tools have accelerated the ability to produce various genetically modified animal models for studying human diseases. Given the advances in gene editing tools, these animal models are gradually evolving toward mimicking human diseases through the introduction of human pathogenic mutations in their genome rather than the conventional gene knockout. In the present review, we summarize the current progress in and discuss the prospects for developing mouse models of human diseases and their therapeutic applications based on advances in the study of programmable nucleases.
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Affiliation(s)
- Hong Thi Lam Phan
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
- Laboratory of Developmental Biology and Genomics, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology, BIO-MAX/N-Bio Institute, Seoul National University, Seoul 08826, Republic of Korea
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3
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Fujii W. Generation of Knock-In Mouse by Genome Editing. Methods Mol Biol 2023; 2637:99-109. [PMID: 36773141 DOI: 10.1007/978-1-0716-3016-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Knock-in mice are useful for evaluating endogenous gene expressions and functions in vivo. Instead of the conventional gene-targeting method using embryonic stem cells, an exogenous DNA sequence can be inserted into the target locus in the zygote using genome-editing technology. In this chapter, I describe the generation of epitope-tagged mice using engineered endonuclease and single-strand oligodeoxynucleotide through the mouse zygote as an example of how to generate a knock-in mouse by genome editing.
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Affiliation(s)
- Wataru Fujii
- Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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4
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Ou-Yang H, Yang SH, Chen W, Yang SH, Cidem A, Sung LY, Chen CM. Cruciform DNA Structures Act as Legible Templates for Accelerating Homologous Recombination in Transgenic Animals. Int J Mol Sci 2022; 23:3973. [PMID: 35409332 PMCID: PMC9000021 DOI: 10.3390/ijms23073973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Inverted repeat (IR) DNA sequences compose cruciform structures. Some genetic disorders are the result of genome inversion or translocation by cruciform DNA structures. The present study examined whether exogenous DNA integration into the chromosomes of transgenic animals was related to cruciform DNA structures. Large imperfect cruciform structures were frequently predicted around predestinated transgene integration sites in host genomes of microinjection-based transgenic (Tg) animals (αLA-LPH Tg goat, Akr1A1eGFP/eGFP Tg mouse, and NFκB-Luc Tg mouse) or CRISPR/Cas9 gene-editing (GE) animals (αLA-AP1 GE mouse). Transgene cassettes were imperfectly matched with their predestinated sequences. According to the analyzed data, we proposed a putative model in which the flexible cruciform DNA structures acted as a legible template for DNA integration into linear DNAs or double-strand break (DSB) alleles. To demonstrate this model, artificial inverted repeat knock-in (KI) reporter plasmids were created to analyze the KI rate using the CRISPR/Cas9 system in NIH3T3 cells. Notably, the KI rate of the 5′ homologous arm inverted repeat donor plasmid (5′IR) with the ROSA gRNA group (31.5%) was significantly higher than the knock-in reporter donor plasmid (KIR) with the ROSA gRNA group (21.3%, p < 0.05). However, the KI rate of the 3′ inverted terminal repeat/inverted repeat donor plasmid (3′ITRIR) group was not different from the KIR group (23.0% vs. 22.0%). These results demonstrated that the legibility of the sequence with the cruciform DNA existing in the transgene promoted homologous recombination (HR) with a higher KI rate. Our findings suggest that flexible cruciform DNAs folded by IR sequences improve the legibility and accelerate DNA 3′-overhang integration into the host genome via homologous recombination machinery.
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Affiliation(s)
- Huan Ou-Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Shiao-Hsuan Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Reproductive Medicine Center, Department of Gynecology, Changhua Christian Hospital, Changhua 515, Taiwan
| | - Wei Chen
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shang-Hsun Yang
- Department of Physiology, National Cheng Kung University, Tainan 701, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Abdulkadir Cidem
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25250, Turkey
| | - Li-Ying Sung
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chuan-Mu Chen
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Rong-Hsing Translational Medicine Research Center, Taichung Veterans General Hospital, Taichung 407, Taiwan
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5
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Establishment of a Cre-rat resource for creating conditional and physiological relevant models of human diseases. Transgenic Res 2021; 30:91-104. [PMID: 33481207 PMCID: PMC7854434 DOI: 10.1007/s11248-020-00226-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/28/2020] [Indexed: 10/25/2022]
Abstract
The goal of this study is to establish a Cre/loxP rat resource for conditional and physiologically predictive rat models of human diseases. The laboratory rat (R. norvegicus) is a central experimental animal in several fields of biomedical research, such as cardiovascular diseases, aging, infectious diseases, autoimmunity, cancer models, transplantation biology, inflammation, cancer risk assessment, industrial toxicology, pharmacology, behavioral and addiction studies, and neurobiology. Up till recently, the ability of creating genetically modified rats has been limited compared to that in the mouse mainly due to lack of genetic manipulation tools and technologies in the rat. Recent advances in nucleases, such as CRISPR/Cas9 (clustered regularly-interspaced short palindromic repeats/CRISPR associated protein 9), as well as TARGATT™ integrase system enables fast, efficient and site-specific introduction of exogenous genetic elements into the rat genome. Here, we report the generation of a collection of tissue-specific, inducible transgenic Cre rats as tool models using TARGATT™, CRISPR/Cas9 and random transgenic approach. More specifically, we generated Cre driver rat models that allow controlled gene expression or knockout (conditional models) both temporally and spatially through the Cre-ERT2/loxP system. A total of 10 Cre rat lines and one Cre reporter/test line were generated, including eight (8) Cre lines for neural specific and two (2) lines for cardiovascular specific Cre expression. All of these lines have been deposited with the Rat Resource and Research Center and provide a much-needed resource for the bio-medical community who employ rat models for their studies of human diseases.
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Yanik M, Ponnam SPG, Wimmer T, Trimborn L, Müller C, Gambert I, Ginsberg J, Janise A, Domicke J, Wende W, Lorenz B, Stieger K. Development of a Reporter System to Explore MMEJ in the Context of Replacing Large Genomic Fragments. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 11:407-415. [PMID: 29858075 PMCID: PMC5992787 DOI: 10.1016/j.omtn.2018.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/13/2018] [Accepted: 03/20/2018] [Indexed: 01/21/2023]
Abstract
Common genome-editing strategies are either based on non-homologous end joining (NHEJ) or, in the presence of a template DNA, based on homologous recombination with long (homology-directed repair [HDR]) or short (microhomology-mediated end joining [MMEJ]) homologous sequences. In the current study, we aim to develop a model system to test the activity of MMEJ after CRISPR/Cas9-mediated cleavage in cell culture. Following successful proof of concept in an episomally based reporter system, we tested template plasmids containing a promoter-less luciferase gene flanked by microhomologous sequences (mhs) of different length (5, 10, 15, 20, 30, and 50 bp) that are complementary to the mouse retinitis pigmentosa GTPase regulator (RPGR)-ORF15, which is under the control of a CMV promoter stably integrated into a HEK293 cell line. Luciferase signal appearance represented successful recombination events and was highest when the mhs were 5 bp long, while longer mhs revealed lower luciferase signal. In addition, presence of Csy4 RNase was shown to increase luciferase signaling. The luciferase reporter system is a valuable tool to study the input of the different DNA repair mechanisms in the replacement of large DNA sequences by mhs.
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Affiliation(s)
- Mert Yanik
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Surya Prakash Goud Ponnam
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany; Department of Molecular Biology & Biotechnology, Tezpur University, Napaam, Assam 784028, India
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Lennart Trimborn
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Carina Müller
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Isabel Gambert
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Johanna Ginsberg
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Annabella Janise
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Janina Domicke
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Wolfgang Wende
- Institute for Biochemistry, Justus-Liebig-University, Giessen 35392, Germany
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany.
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7
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Abstract
Knock-in mice are useful for evaluating endogenous gene expressions and functions in vivo. Instead of the conventional gene-targeting method using embryonic stem cells, an exogenous DNA sequence can be inserted into the target locus in the zygote using genome editing technology. In this chapter, I describe the generation of epitope-tagged mice using engineered endonuclease and single-stranded oligodeoxynucleotide through the mouse zygote as an example of how to generate a knock-in mouse by genome editing.
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Affiliation(s)
- Wataru Fujii
- Laboratory of Applied Genetics, Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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8
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Sakuma T, Yamamoto T. Magic wands of CRISPR—lots of choices for gene knock-in. Cell Biol Toxicol 2017; 33:501-505. [DOI: 10.1007/s10565-017-9409-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 12/18/2022]
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9
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Abstract
Genome integration is a powerful tool in both basic and applied biological research. However, traditional genome integration, which is typically mediated by homologous recombination, has been constrained by low efficiencies and limited host range. In recent years, the emergence of homing endonucleases and programmable nucleases has greatly enhanced integration efficiencies and allowed alternative integration mechanisms such as nonhomologous end joining and microhomology-mediated end joining, enabling integration in hosts deficient in homologous recombination. In this review, we will highlight recent advances and breakthroughs in genome integration methods made possible by programmable nucleases, and their new applications in synthetic biology and metabolic engineering.
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Affiliation(s)
- Zihe Liu
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Youyun Liang
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Ee Lui Ang
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Huimin Zhao
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Fitness Assays Reveal Incomplete Functional Redundancy of the HoxA1 and HoxB1 Paralogs of Mice. Genetics 2016; 201:727-36. [PMID: 26447130 DOI: 10.1534/genetics.115.178079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Gene targeting techniques have led to the phenotypic characterization of numerous genes; however, many genes show minimal to no phenotypic consequences when disrupted, despite many having highly conserved sequences. The standard explanation for these findings is functional redundancy. A competing hypothesis is that these genes have important ecological functions in natural environments that are not needed under laboratory settings. Here we discriminate between these hypotheses by competing mice (Mus musculus) whose Hoxb1 gene has been replaced by Hoxa1, its highly conserved paralog, against matched wild-type controls in seminatural enclosures. This Hoxb1(A1) swap was reported as a genetic manipulation resulting in no discernible embryonic or physiological phenotype under standard laboratory tests. We observed a transient decline in first litter size for Hoxb1(A1) homozygous mice in breeding cages, but their fitness was consistently and more dramatically reduced when competing against controls within seminatural populations. Specifically, males homozygous for the Hoxb1(A1) swap acquired 10.6% fewer territories and the frequency of the Hoxb1(A1) allele decreased from 0.500 in population founders to 0.419 in their offspring. The decrease in Hoxb1(A1) frequency corresponded with a deficiency of both Hoxb1(A1) homozygous and heterozygous offspring. These data suggest that Hoxb1 and Hoxa1 are more phenotypically divergent than previously reported and support that sub- and/or neofunctionalization has occurred in these paralogous genes leading to a divergence of gene function and incomplete redundancy. Furthermore, this study highlights the importance of obtaining fitness measures of mutants in ecologically relevant conditions to better understand gene function and evolution.
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The Development and Use of Zinc-Finger Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Cellular Engineering and Disease Modeling with Gene-Editing Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Abstract
Programmable nucleases enable engineering of the genome by utilizing endogenous DNA double-strand break (DSB) repair pathways. Although homologous recombination (HR)-mediated gene knock-in is well established, it cannot necessarily be applied in every cell type and organism because of variable HR frequencies. We recently reported an alternative method of gene knock-in, named the PITCh (Precise Integration into Target Chromosome) system, assisted by microhomology-mediated end-joining (MMEJ). MMEJ harnesses independent machinery from HR, and it requires an extremely short homologous sequence (5-25 bp) for DSB repair, resulting in precise gene knock-in with a more easily constructed donor vector. Here we describe a streamlined protocol for PITCh knock-in, including the design and construction of the PITCh vectors, and their delivery to either human cell lines by transfection or to frog embryos by microinjection. The construction of the PITCh vectors requires only a few days, and the entire process takes ∼ 1.5 months to establish knocked-in cells or ∼ 1 week from injection to early genotyping in frog embryos.
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14
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Induced Pluripotency and Gene Editing in Disease Modelling: Perspectives and Challenges. Int J Mol Sci 2015; 16:28614-34. [PMID: 26633382 PMCID: PMC4691066 DOI: 10.3390/ijms161226119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/13/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023] Open
Abstract
Embryonic stem cells (ESCs) are chiefly characterized by their ability to self-renew and to differentiate into any cell type derived from the three main germ layers. It was demonstrated that somatic cells could be reprogrammed to form induced pluripotent stem cells (iPSCs) via various strategies. Gene editing is a technique that can be used to make targeted changes in the genome, and the efficiency of this process has been significantly enhanced by recent advancements. The use of engineered endonucleases, such as homing endonucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and Cas9 of the CRISPR system, has significantly enhanced the efficiency of gene editing. The combination of somatic cell reprogramming with gene editing enables us to model human diseases in vitro, in a manner considered superior to animal disease models. In this review, we discuss the various strategies of reprogramming and gene targeting with an emphasis on the current advancements and challenges of using these techniques to model human diseases.
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15
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Efficient genome engineering by targeted homologous recombination in mouse embryos using transcription activator-like effector nucleases. Nat Commun 2015; 5:3045. [PMID: 24413636 DOI: 10.1038/ncomms4045] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/02/2013] [Indexed: 02/06/2023] Open
Abstract
Generation of mouse models by introducing transgenes using homologous recombination is critical for understanding fundamental biology and pathology of human diseases. Here we investigate whether artificial transcription activator-like effector nucleases (TALENs)-powerful tools that induce DNA double-strand breaks at specific genomic locations-can be combined with a targeting vector to induce homologous recombination for the introduction of a transgene in embryonic stem cells and fertilized murine oocytes. We describe the generation of a conditional mouse model using TALENs, which introduce double-strand breaks at the genomic locus of the special AT-rich sequence-binding protein-1 in combination with a large 14.4 kb targeting template vector. We report successful germline transmission of this allele and demonstrate its recombination in primary cells in the presence of Cre-recombinase. These results suggest that TALEN-assisted induction of DNA double-strand breaks can facilitate homologous recombination of complex targeting constructs directly in oocytes.
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Tobita T, Guzman-Lepe J, Collin de l'Hortet A. From hacking the human genome to editing organs. Organogenesis 2015; 11:173-82. [PMID: 26588350 DOI: 10.1080/15476278.2015.1120047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies.
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Affiliation(s)
- Takamasa Tobita
- a Department of Pathology ; University of Pittsburgh ; Pittsburgh ; PA USA
| | - Jorge Guzman-Lepe
- a Department of Pathology ; University of Pittsburgh ; Pittsburgh ; PA USA
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17
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Controlled delivery of β-globin-targeting TALENs and CRISPR/Cas9 into mammalian cells for genome editing using microinjection. Sci Rep 2015; 5:16031. [PMID: 26558999 PMCID: PMC4642230 DOI: 10.1038/srep16031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/09/2015] [Indexed: 12/25/2022] Open
Abstract
Tal-effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated (Cas) proteins are genome editing tools with unprecedented potential. However, the ability to deliver optimal amounts of these nucleases into mammalian cells with minimal toxicity poses a major challenge. Common delivery approaches are transfection- and viral-based methods; each associated with significant drawbacks. An alternative method for directly delivering genome-editing reagents into single living cells with high efficiency and controlled volume is microinjection. Here, we characterize a glass microcapillary-based injection system and demonstrate controlled co-injection of TALENs or CRISPR/Cas9 together with donor template into single K562 cells for targeting the human β-globin gene. We quantified nuclease induced insertions and deletions (indels) and found that, with β-globin-targeting TALENs, similar levels of on- and off-target activity in cells could be achieved by microinjection compared with nucleofection. Furthermore, we observed 11% and 2% homology directed repair in single K562 cells co-injected with a donor template along with CRISPR/Cas9 and TALENs respectively. These results demonstrate that a high level of targeted gene modification can be achieved in human cells using glass-needle microinjection of genome editing reagents.
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18
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Ménoret S, De Cian A, Tesson L, Remy S, Usal C, Boulé JB, Boix C, Fontanière S, Crénéguy A, Nguyen TH, Brusselle L, Thinard R, Gauguier D, Concordet JP, Cherifi Y, Fraichard A, Giovannangeli C, Anegon I. Homology-directed repair in rodent zygotes using Cas9 and TALEN engineered proteins. Sci Rep 2015; 5:14410. [PMID: 26442875 PMCID: PMC4595769 DOI: 10.1038/srep14410] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/26/2015] [Indexed: 12/20/2022] Open
Abstract
The generation of genetically-modified organisms has been revolutionized by the development of new genome editing technologies based on the use of gene-specific nucleases, such as meganucleases, ZFNs, TALENs and CRISPRs-Cas9 systems. The most rapid and cost-effective way to generate genetically-modified animals is by microinjection of the nucleic acids encoding gene-specific nucleases into zygotes. However, the efficiency of the procedure can still be improved. In this work we aim to increase the efficiency of CRISPRs-Cas9 and TALENs homology-directed repair by using TALENs and Cas9 proteins, instead of mRNA, microinjected into rat and mouse zygotes along with long or short donor DNAs. We observed that Cas9 protein was more efficient at homology-directed repair than mRNA, while TALEN protein was less efficient than mRNA at inducing homology-directed repair. Our results indicate that the use of Cas9 protein could represent a simple and practical methodological alternative to Cas9 mRNA in the generation of genetically-modified rats and mice as well as probably some other mammals.
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Affiliation(s)
- Séverine Ménoret
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France.,Platform Rat Transgenesis Immunophenomic, SFR François Bonamy, CNRS UMS3556 Nantes, F44093, France
| | - Anne De Cian
- INSERM U1154, CNRS UMR7196, Structure and Instability of Genomes, Sorbonne Universités, Museum National d'Histoire Naturelle; CP26 57 rue Cuvier, F75005 Paris, France
| | - Laurent Tesson
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France.,Platform Rat Transgenesis Immunophenomic, SFR François Bonamy, CNRS UMS3556 Nantes, F44093, France
| | - Séverine Remy
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France.,Platform Rat Transgenesis Immunophenomic, SFR François Bonamy, CNRS UMS3556 Nantes, F44093, France
| | - Claire Usal
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France.,Platform Rat Transgenesis Immunophenomic, SFR François Bonamy, CNRS UMS3556 Nantes, F44093, France
| | - Jean-Baptiste Boulé
- INSERM U1154, CNRS UMR7196, Structure and Instability of Genomes, Sorbonne Universités, Museum National d'Histoire Naturelle; CP26 57 rue Cuvier, F75005 Paris, France
| | - Charlotte Boix
- INSERM U1154, CNRS UMR7196, Structure and Instability of Genomes, Sorbonne Universités, Museum National d'Histoire Naturelle; CP26 57 rue Cuvier, F75005 Paris, France
| | | | | | - Tuan H Nguyen
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
| | | | - Reynald Thinard
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France.,Platform Rat Transgenesis Immunophenomic, SFR François Bonamy, CNRS UMS3556 Nantes, F44093, France
| | - Dominique Gauguier
- Sorbonne Universities, University Pierre &Marie Curie, University Paris Descartes, Sorbonne Paris Cité, INSERM UMR_S 1138, Cordeliers Research Centre, 75006 Paris, France.,Institute of Cardiometabolism and Nutrition, University Pierre &Marie Curie, Boulevard de l'Hopital, 75013 Paris, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, Structure and Instability of Genomes, Sorbonne Universités, Museum National d'Histoire Naturelle; CP26 57 rue Cuvier, F75005 Paris, France
| | | | | | - Carine Giovannangeli
- INSERM U1154, CNRS UMR7196, Structure and Instability of Genomes, Sorbonne Universités, Museum National d'Histoire Naturelle; CP26 57 rue Cuvier, F75005 Paris, France
| | - Ignacio Anegon
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France.,Platform Rat Transgenesis Immunophenomic, SFR François Bonamy, CNRS UMS3556 Nantes, F44093, France
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19
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Efficient introgression of allelic variants by embryo-mediated editing of the bovine genome. Sci Rep 2015; 5:11735. [PMID: 26156133 PMCID: PMC4496724 DOI: 10.1038/srep11735] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/12/2015] [Indexed: 12/29/2022] Open
Abstract
The recent development of designer nucleases allows for the efficient and precise introduction of genetic change into livestock genomes. Most studies so far have focused on the introduction of random mutations in cultured cells and the use of nuclear transfer to generate animals with edited genotypes. To circumvent the intrinsic uncertainties of random mutations and the inefficiencies of nuclear transfer we directed our efforts to the introduction of specific genetic changes by homology-driven repair directly in in vitro produced embryos. Initially, we injected zinc finger nuclease (ZFN)-encoding mRNA or DNA into bovine zygotes to verify cleavage activity at their target site within the gene for beta-lactoglobulin (LGB) and detected ZFN-induced random mutations in 30% to 80% of embryos. Next, to precisely change the LGB sequence, we co-injected ZFNs or transcription activator-like effector nucleases (TALENs) with DNA oligonucleotides (ODNs). Analysis of co-injected embryos showed targeted changes in up to 33% (ZFNs) and 46% (TALENs) of blastocysts. Deep sequence analysis of selected embryos revealed contributions of the targeted LGB allele can reach 100% which implies that genome editing by zygote injections can facilitate the one-step generation of non-mosaic livestock animals with pre-designed biallelic modifications.
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20
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Chen F, Pruett-Miller SM, Davis GD. Gene editing using ssODNs with engineered endonucleases. Methods Mol Biol 2015; 1239:251-65. [PMID: 25408411 DOI: 10.1007/978-1-4939-1862-1_14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Gene editing using engineered endonucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nucleases, requires the creation of a targeted, chromosomal DNA double-stranded break (DSB). In mammalian cells, these DSBs are typically repaired by one of the two major DNA repair pathways: nonhomologous end joining (NHEJ) or homology-directed repair (HDR). NHEJ is an error-prone repair process that can result in a wide range of end-joining events that leads to somewhat random mutations at the site of DSB. HDR is a precise repair pathway that can utilize either an endogenous or exogenous piece of homologous DNA as a template or "donor" for repair. Traditional gene editing via HDR has relied on the co-delivery of a targeted, engineered endonuclease and a circular plasmid donor construct. More recently, it has been shown that single-stranded oligodeoxynucleotides (ssODNs) can also serve as DNA donors and thus obviate the more laborious and time-consuming plasmid vector construction process. Here we describe the use of ssODNs for making defined genome modifications in combination with engineered endonucleases.
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Affiliation(s)
- Fuqiang Chen
- Sigma-Aldrich Biotechnology, 2909 Laclede Ave., St. Louis, MO, 63103, USA
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21
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Truong DJJ, Kühner K, Kühn R, Werfel S, Engelhardt S, Wurst W, Ortiz O. Development of an intein-mediated split-Cas9 system for gene therapy. Nucleic Acids Res 2015; 43:6450-8. [PMID: 26082496 PMCID: PMC4513872 DOI: 10.1093/nar/gkv601] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 05/26/2015] [Indexed: 11/14/2022] Open
Abstract
Using CRISPR/Cas9, it is possible to target virtually any gene in any organism. A major limitation to its application in gene therapy is the size of Cas9 (>4 kb), impeding its efficient delivery via recombinant adeno-associated virus (rAAV). Therefore, we developed a split–Cas9 system, bypassing the packaging limit using split-inteins. Each Cas9 half was fused to the corresponding split-intein moiety and, only upon co-expression, the intein-mediated trans-splicing occurs and the full Cas9 protein is reconstituted. We demonstrated that the nuclease activity of our split-intein system is comparable to wild-type Cas9, shown by a genome-integrated surrogate reporter and by targeting three different endogenous genes. An analogously designed split-Cas9D10A nickase version showed similar activity as Cas9D10A. Moreover, we showed that the double nick strategy increased the homologous directed recombination (HDR). In addition, we explored the possibility of delivering the repair template accommodated on the same dual-plasmid system, by transient transfection, showing an efficient HDR. Most importantly, we revealed for the first time that intein-mediated split–Cas9 can be packaged, delivered and its nuclease activity reconstituted efficiently, in cells via rAAV.
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Affiliation(s)
- Dong-Jiunn Jeffery Truong
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany Institute of Developmental Genetics,Technische Universität München, Freising-Weihenstephan 85354, Germany
| | - Karin Kühner
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany
| | - Ralf Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany Max Delbrück Center for Molecular Medicine (MDC), Berlin 13125, Germany
| | - Stanislas Werfel
- Institute of Pharmacology and Toxicology. Technische Universität München, Munich 80802, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology. Technische Universität München, Munich 80802, Germany German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich 80802, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany Institute of Developmental Genetics,Technische Universität München, Freising-Weihenstephan 85354, Germany Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Munich 80336, Germany Munich Cluster for Systems Neurology (SyNergy) Adolf-Butenandt-Institut Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Oskar Ortiz
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 85764, Germany
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22
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Flister MJ, Prokop JW, Lazar J, Shimoyama M, Dwinell M, Geurts A. 2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research. J Cardiovasc Transl Res 2015; 8:269-77. [PMID: 25920443 PMCID: PMC4475456 DOI: 10.1007/s12265-015-9626-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/15/2015] [Indexed: 12/24/2022]
Abstract
The rat has long been a key physiological model for cardiovascular research, most of the inbred strains having been previously selected for susceptibility or resistance to various cardiovascular diseases (CVD). These CVD rat models offer a physiologically relevant background on which candidates of human CVD can be tested in a more clinically translatable experimental setting. However, a diverse toolbox for genetically modifying the rat genome to test molecular mechanisms has only recently become available. Here, we provide a high-level description of several strategies for developing genetically modified rat models of CVD.
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Affiliation(s)
- Michael J Flister
- Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, 53226, WI, USA,
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23
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Proetzel G, Wiles MV, Roopenian DC. Genetically engineered humanized mouse models for preclinical antibody studies. BioDrugs 2015; 28:171-80. [PMID: 24150980 DOI: 10.1007/s40259-013-0071-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The use of genetic engineering has vastly improved our capabilities to create animal models relevant in preclinical research. With the recent advances in gene-editing technologies, it is now possible to very rapidly create highly tunable mouse models as needs arise. Here, we provide an overview of genetic engineering methods, as well as the development of humanized neonatal Fc receptor (FcRn) models and their use for monoclonal antibody in vivo studies.
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24
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New Transgenic Technologies. Mov Disord 2015. [DOI: 10.1016/b978-0-12-405195-9.00003-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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25
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Pruett-Miller SM, Davis GD. Donor plasmid design for codon and single base genome editing using zinc finger nucleases. Methods Mol Biol 2015; 1239:219-229. [PMID: 25408408 DOI: 10.1007/978-1-4939-1862-1_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In recent years, CompoZr zinc finger nuclease (ZFN) technology has matured to the point that a user-defined double strand break (DSB) can be placed at virtually any location in the human genome within 50 bp of a desired site. Such high resolution ZFN engineering is well within the conversion tract limitations demarcated by the mammalian DNA repair machinery, resulting in a nearly universal ability to create point mutations throughout the human genome. Additionally, new architectures for targeted nuclease engineering have been rapidly developed, namely transcription activator like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems, further expanding options for placement of DSBs. This new capability has created a need to explore the practical limitations of delivering plasmid-based information to the sites of chromosomal double strand breaks so that nuclease-donor methods can be widely deployed in fundamental and therapeutic research. In this chapter, we explore a ZFN-compatible donor design in the context of codon changes at an endogenous locus encoding the human RSK2 kinase.
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Affiliation(s)
- Shondra M Pruett-Miller
- Department of Genetics, Genome Engineering and iPSC Center, Washington University School of Medicine, St. Louis, MO, USA
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26
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Brandl C, Ortiz O, Röttig B, Wefers B, Wurst W, Kühn R. Creation of targeted genomic deletions using TALEN or CRISPR/Cas nuclease pairs in one-cell mouse embryos. FEBS Open Bio 2014; 5:26-35. [PMID: 25685662 PMCID: PMC4309836 DOI: 10.1016/j.fob.2014.11.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/25/2014] [Accepted: 11/27/2014] [Indexed: 12/26/2022] Open
Abstract
Targeted genomic deletions can be generated directly in one-cell mouse embryos using sequence-specific nucleases. Deletions occur by end ligation repair and are not supported by homologous recombination. TALEN as well as CRISPR/Cas nucleases can be used. Homozygous mutants exhibiting phenotypes can be obtained in a single step.
The use of TALEN and CRISPR/CAS nucleases is becoming increasingly popular as a means to edit single target sites in one-cell mouse embryos. Nevertheless, an area that has received less attention concerns the engineering of structural genome variants and the necessary religation of two distant double-strand breaks. Herein, we applied pairs of TALEN or sgRNAs and Cas9 to create deletions in the Rab38 gene. We found that the deletion of 3.2 or 9.3 kb, but not of 30 kb, occurs at a frequency of 6–37%. This is sufficient for the direct production of mutants by embryo microinjection. Therefore, deletions up to ∼10 kb can be readily achieved for modeling human disease alleles. This work represents an important step towards the establishment of new protocols that support the ligation of remote DSB ends to achieve even larger rearrangements.
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Affiliation(s)
- Christina Brandl
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Oskar Ortiz
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Bernhard Röttig
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Benedikt Wefers
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), 80336 Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany ; Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), 80336 Munich, Germany ; Max-Planck-Institute of Psychiatry, 80804 Munich, Germany ; Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Ralf Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany ; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
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27
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Yao J, Huang J, Hai T, Wang X, Qin G, Zhang H, Wu R, Cao C, Xi JJ, Yuan Z, Zhao J. Efficient bi-allelic gene knockout and site-specific knock-in mediated by TALENs in pigs. Sci Rep 2014; 4:6926. [PMID: 25370805 PMCID: PMC4220281 DOI: 10.1038/srep06926] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/17/2014] [Indexed: 12/31/2022] Open
Abstract
Pigs are ideal organ donors for xenotransplantation and an excellent model for studying human diseases, such as neurodegenerative disease. Transcription activator-like effector nucleases (TALENs) are used widely for gene targeting in various model animals. Here, we developed a strategy using TALENs to target the GGTA1, Parkin and DJ-1 genes in the porcine genome using Large White porcine fibroblast cells without any foreign gene integration. In total, 5% (2/40), 2.5% (2/80), and 22% (11/50) of the obtained colonies of fibroblast cells were mutated for GGTA1, Parkin, and DJ-1, respectively. Among these mutant colonies, over 1/3 were bi-allelic knockouts (KO), and no off-target cleavage was detected. We also successfully used single-strand oligodeoxynucleotides to introduce a short sequence into the DJ-1 locus. Mixed DJ-1 mutant colonies were used as donor cells for somatic cell nuclear transfer (SCNT), and three female piglets were obtained (two were bi-allelically mutated, and one was mono-allelically mutated). Western blot analysis showed that the expression of the DJ-1 protein was disrupted in KO piglets. These results imply that a combination of TALENs technology with SCNT can efficiently generate bi-allelic KO pigs without the integration of exogenous DNA. These DJ-1 KO pigs will provide valuable information for studying Parkinson's disease.
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Affiliation(s)
- Jing Yao
- State Key laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
| | - Jiaojiao Huang
- State Key laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
| | - Tang Hai
- State Key laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
| | - Xianlong Wang
- State Key laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
| | - Guosong Qin
- State Key laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
| | - Hongyong Zhang
- State Key laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
| | - Rong Wu
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China, 100101
| | - Chunwei Cao
- State Key laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
| | - Jianzhong Jeff Xi
- Biomedical Engineering Department, College of Engineering, Peking University, Beijing, P. R. China, 100871
| | - Zengqiang Yuan
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China, 100101
| | - Jianguo Zhao
- State Key laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, P. R. China, 100101
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28
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Remy S, Tesson L, Menoret S, Usal C, De Cian A, Thepenier V, Thinard R, Baron D, Charpentier M, Renaud JB, Buelow R, Cost GJ, Giovannangeli C, Fraichard A, Concordet JP, Anegon I. Efficient gene targeting by homology-directed repair in rat zygotes using TALE nucleases. Genome Res 2014; 24:1371-83. [PMID: 24989021 PMCID: PMC4120090 DOI: 10.1101/gr.171538.113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The generation of genetically modified animals is important for both research and commercial purposes. The rat is an important model organism that until recently lacked efficient genetic engineering tools. Sequence-specific nucleases, such as ZFNs, TALE nucleases, and CRISPR/Cas9 have allowed the creation of rat knockout models. Genetic engineering by homology-directed repair (HDR) is utilized to create animals expressing transgenes in a controlled way and to introduce precise genetic modifications. We applied TALE nucleases and donor DNA microinjection into zygotes to generate HDR-modified rats with large new sequences introduced into three different loci with high efficiency (0.62%–5.13% of microinjected zygotes). Two of these loci (Rosa26 and Hprt1) are known to allow robust and reproducible transgene expression and were targeted for integration of a GFP expression cassette driven by the CAG promoter. GFP-expressing embryos and four Rosa26 GFP rat lines analyzed showed strong and widespread GFP expression in most cells of all analyzed tissues. The third targeted locus was Ighm, where we performed successful exon exchange of rat exon 2 for the human one. At all three loci we observed HDR only when using linear and not circular donor DNA. Mild hypothermic (30°C) culture of zygotes after microinjection increased HDR efficiency for some loci. Our study demonstrates that TALE nuclease and donor DNA microinjection into rat zygotes results in efficient and reproducible targeted donor integration by HDR. This allowed creation of genetically modified rats in a work-, cost-, and time-effective manner.
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Affiliation(s)
- Séverine Remy
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Laurent Tesson
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Séverine Menoret
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Claire Usal
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Anne De Cian
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | - Virginie Thepenier
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Reynald Thinard
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Daniel Baron
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France
| | - Marine Charpentier
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | - Jean-Baptiste Renaud
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | - Roland Buelow
- Open Monoclonal Technologies, Palo Alto, California 94303, USA
| | | | - Carine Giovannangeli
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | | | - Jean-Paul Concordet
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | - Ignacio Anegon
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
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29
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Wijshake T, Baker DJ, van de Sluis B. Endonucleases: new tools to edit the mouse genome. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1942-1950. [PMID: 24794718 DOI: 10.1016/j.bbadis.2014.04.020] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/16/2014] [Accepted: 04/18/2014] [Indexed: 12/26/2022]
Abstract
Mouse transgenesis has been instrumental in determining the function of genes in the pathophysiology of human diseases and modification of genes by homologous recombination in mouse embryonic stem cells remains a widely used technology. However, this approach harbors a number of disadvantages, as it is time-consuming and quite laborious. Over the last decade a number of new genome editing technologies have been developed, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas). These systems are characterized by a designed DNA binding protein or RNA sequence fused or co-expressed with a non-specific endonuclease, respectively. The engineered DNA binding protein or RNA sequence guides the nuclease to a specific target sequence in the genome to induce a double strand break. The subsequent activation of the DNA repair machinery then enables the introduction of gene modifications at the target site, such as gene disruption, correction or insertion. Nuclease-mediated genome editing has numerous advantages over conventional gene targeting, including increased efficiency in gene editing, reduced generation time of mutant mice, and the ability to mutagenize multiple genes simultaneously. Although nuclease-driven modifications in the genome are a powerful tool to generate mutant mice, there are concerns about off-target cleavage, especially when using the CRISPR/Cas system. Here, we describe the basic principles of these new strategies in mouse genome manipulation, their inherent advantages, and their potential disadvantages compared to current technologies used to study gene function in mouse models. This article is part of a Special Issue entitled: From Genome to Function.
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Affiliation(s)
- Tobias Wijshake
- Molecular Genetics, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Darren J Baker
- Department of Pediatric and Adolescent Medicine, Mayo Clinic College of Medicine, 200 First St SW, Rochester, MN 55905, USA
| | - Bart van de Sluis
- Molecular Genetics, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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30
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Abstract
Transgenic mice carrying site-specific genome modifications (knockout, knock-in) are of vital importance for dissecting complex biological systems as well as for modeling human diseases and testing therapeutic strategies. Recent advances in the use of designer nucleases such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 system for site-specific genome engineering open the possibility to perform rapid targeted genome modification in virtually any laboratory species without the need to rely on embryonic stem (ES) cell technology. A genome editing experiment typically starts with identification of designer nuclease target sites within a gene of interest followed by construction of custom DNA-binding domains to direct nuclease activity to the investigator-defined genomic locus. Designer nuclease plasmids are in vitro transcribed to generate mRNA for microinjection of fertilized mouse oocytes. Here, we provide a protocol for achieving targeted genome modification by direct injection of TALEN mRNA into fertilized mouse oocytes.
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Affiliation(s)
- Mario Hermann
- Institute of Laboratory Animal Science, University of Zurich
| | - Tomas Cermak
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota
| | - Daniel F Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota
| | - Pawel Pelczar
- Institute of Laboratory Animal Science, University of Zurich;
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31
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Low BE, Krebs MP, Joung JK, Tsai SQ, Nishina PM, Wiles MV. Correction of the Crb1rd8 allele and retinal phenotype in C57BL/6N mice via TALEN-mediated homology-directed repair. Invest Ophthalmol Vis Sci 2014; 55:387-95. [PMID: 24346171 DOI: 10.1167/iovs.13-13278] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE We directly corrected the mouse Crb1(rd8) gene mutation, which is present in many inbred laboratory strains derived from C57BL/6N and complicates genetic studies of retinal disease in mice. METHODS Fertilized C57BL/6NJ oocytes were coinjected with mRNAs encoding a transcription activator-like effector nuclease (TALEN) targeting the Crb1(rd8) allele plus single-stranded oligonucleotides to correct the allele. The oligonucleotides included additional nucleotide changes to distinguish the corrected allele (Crb1(em1Mvw)) from wild-type Crb1 and to minimize TALEN recutting. Oligonucleotide length, concentration of injected oligonucleotides and TALEN mRNAs were varied to optimize homology-directed repair of the locus. Following microinjection, embryos were carried to term in pseudopregnant females. Correction efficiency was assessed by PCR analysis of the Crb1(em1Mvw) allele. Phenotypic correction was demonstrated by fundus imaging and optical coherence tomography of live mice, and by confocal fluorescence microscopy of retinal flat mounts. RESULTS Under optimal conditions, homology-directed repair was observed in 27% (8/30) of live-born animals and showed minimal illegitimate recombination of donor DNA. However, extensive founder mosaicism was evident, emphasizing the need to analyze offspring of founder animals. Unlike C57BL/6NJ mice, which exhibited external limiting membrane fragmentation and regional retinal dysplasia, heterozygous Crb1(em1Mvw)/Crb1(rd8) mice showed a normal retinal phenotype. CONCLUSIONS The C57BL/6NJ-Crb1(rd8) mutation and its associated retinal phenotypes were corrected efficiently by TALEN-mediated homology-directed repair. The C57BL/6NJ-Crb1(em1Mvw) mice generated by this strategy will enhance ocular phenotyping efforts based on the C57BL/6N background, such as those implemented by the International Mouse Phenotyping Consortium (IMPC) project.
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Sakuma T, Woltjen K. Nuclease-mediated genome editing: At the front-line of functional genomics technology. Dev Growth Differ 2014; 56:2-13. [PMID: 24387662 DOI: 10.1111/dgd.12111] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/18/2013] [Accepted: 11/18/2013] [Indexed: 12/26/2022]
Abstract
Genome editing with engineered endonucleases is rapidly becoming a staple method in developmental biology studies. Engineered nucleases permit random or designed genomic modification at precise loci through the stimulation of endogenous double-strand break repair. Homology-directed repair following targeted DNA damage is mediated by co-introduction of a custom repair template, allowing the derivation of knock-out and knock-in alleles in animal models previously refractory to classic gene targeting procedures. Currently there are three main types of customizable site-specific nucleases delineated by the source mechanism of DNA binding that guides nuclease activity to a genomic target: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Among these genome engineering tools, characteristics such as the ease of design and construction, mechanism of inducing DNA damage, and DNA sequence specificity all differ, making their application complementary. By understanding the advantages and disadvantages of each method, one may make the best choice for their particular purpose.
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Affiliation(s)
- Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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33
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Abstract
Genome editing is a cutting-edge technology that enables to modify the target gene using programmable site-specific nucleases, such as TALENs and CRISPR/Cas9. Currently, cell and animal models of human diseases have been competitively created throughout the world, because genome editing technology paved the way for genetic modifications even in cells and organisms that had been difficult to manipulate the genome. In this review, we introduce the basic principles and current situations of genome editing with programmable nucleases.
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TALEN-mediated single-base-pair editing identification of an intergenic mutation upstream of BUB1B as causative of PCS (MVA) syndrome. Proc Natl Acad Sci U S A 2013; 111:1461-6. [PMID: 24344301 DOI: 10.1073/pnas.1317008111] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cancer-prone syndrome of premature chromatid separation with mosaic variegated aneuploidy [PCS (MVA) syndrome] is a rare autosomal recessive disorder characterized by constitutional aneuploidy and a high risk of childhood cancer. We previously reported monoallelic mutations in the BUB1B gene (encoding BUBR1) in seven Japanese families with the syndrome. No second mutation was found in the opposite allele of any of the families studied, although a conserved BUB1B haplotype and a decreased transcript were identified. To clarify the molecular pathology of the second allele, we extended our mutational search to a candidate region surrounding BUB1B. A unique single nucleotide substitution, G > A at ss802470619, was identified in an intergenic region 44 kb upstream of a BUB1B transcription start site, which cosegregated with the disorder. To examine whether this is the causal mutation, we designed a transcription activator-like effector nuclease-mediated two-step single-base pair editing strategy and biallelically introduced this substitution into cultured human cells. The cell clones showed reduced BUB1B transcripts, increased PCS frequency, and MVA, which are the hallmarks of the syndrome. We also encountered a case of a Japanese infant with PCS (MVA) syndrome carrying a homozygous single nucleotide substitution at ss802470619. These results suggested that the nucleotide substitution identified was the causal mutation of PCS (MVA) syndrome.
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35
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Jones JM, Meisler MH. Modeling human epilepsy by TALEN targeting of mouse sodium channel Scn8a. Genesis 2013; 52:141-8. [PMID: 24288358 DOI: 10.1002/dvg.22731] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 01/09/2023]
Abstract
To evaluate the efficiency of TALEN technology for introducing mutations into the mouse genome we targeted Scn8a, a member of a multigene family with nine closely related paralogs. Our goal was to generate a model of early onset epileptic encephalopathy by introduction of the Scn8a missense mutation p.Asn1768Asp. We used a pair of TALENs that were highly active in transfected cells. The targeting template for homologous recombination contained a 4 kb genomic fragment. Microinjection of TALENs with the targeting construct into the pronucleus of 350 fertilized mouse eggs generated 67 live-born potential founders, of which 5 were heterozygous for the pathogenic mutation, a yield of 7% correctly targeted mice. Twenty-four mice carried one or two Scn8a indels, including 12 frameshift mutations and the novel amino acid deletion p.Asn1759del. Nine off-site mutations in the paralogs sodium channel genes Scn5a and Scn4a were identified. The data demonstrate the feasibility and efficiency of targeting members of multigene families using TALENs. The Scn8a(tm) (1768DMm) mouse model will be useful for investigation of the pathogenesis and therapy of early onset seizure disorders.
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Affiliation(s)
- Julie M Jones
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
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36
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Aida T, Imahashi R, Tanaka K. Translating human genetics into mouse: The impact of ultra-rapidin vivogenome editing. Dev Growth Differ 2013; 56:34-45. [DOI: 10.1111/dgd.12101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 12/26/2022]
Affiliation(s)
- Tomomi Aida
- Laboratory of Molecular Neuroscience; Medical Research Institute; Tokyo Medical and Dental University; 1-5-45 Yushima Bunkyo-Ku Tokyo, 113-8510 Japan
| | - Risa Imahashi
- Laboratory of Molecular Neuroscience; Medical Research Institute; Tokyo Medical and Dental University; 1-5-45 Yushima Bunkyo-Ku Tokyo, 113-8510 Japan
| | - Kohichi Tanaka
- Laboratory of Molecular Neuroscience; Medical Research Institute; Tokyo Medical and Dental University; 1-5-45 Yushima Bunkyo-Ku Tokyo, 113-8510 Japan
- The Center for Brain Integration Research; Tokyo Medical and Dental University; 1-5-45 Yushima Bunkyo-Ku Tokyo, 113-8510 Japan
- JST; CREST; 4-1-8 Honcho Kawaguchi-shi Saitama 332-0012 Japan
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37
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Wefers B, Panda SK, Ortiz O, Brandl C, Hensler S, Hansen J, Wurst W, Kühn R. Generation of targeted mouse mutants by embryo microinjection of TALEN mRNA. Nat Protoc 2013; 8:2355-79. [PMID: 24177293 DOI: 10.1038/nprot.2013.142] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetically engineered mice are instrumental for the analysis of mammalian gene function in health and disease. As classical gene targeting, which is performed in embryonic stem (ES) cell cultures and generates chimeric mice, is a time-consuming and labor-intensive procedure, we recently used transcription activator-like (TAL) effector nucleases (TALENs) for mutagenesis of the mouse genome directly in one-cell embryos. Here we describe a stepwise protocol for the generation of knock-in and knockout mice, including the selection of TALEN-binding sites, the design and construction of TALEN coding regions and of mutagenic oligodeoxynucleotides (ODNs) and targeting vectors, mRNA production, embryo microinjection and the identification of modified alleles in founder mutants and their progeny. After a setup time of 2-3 weeks of hands-on work for TALEN construction, investigators can obtain first founder mutants for genes of choice within 7 weeks after embryo microinjections.
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Affiliation(s)
- Benedikt Wefers
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
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38
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Shen B, Zhang X, Du Y, Wang J, Gong J, Zhang X, Tate PH, Li H, Huang X, Zhang W. Efficient knockin mouse generation by ssDNA oligonucleotides and zinc-finger nuclease assisted homologous recombination in zygotes. PLoS One 2013; 8:e77696. [PMID: 24167580 PMCID: PMC3805579 DOI: 10.1371/journal.pone.0077696] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/03/2013] [Indexed: 11/19/2022] Open
Abstract
The generation of specific mutant animal models is critical for functional analysis of human genes. The conventional gene targeting approach in embryonic stem cells (ESCs) by homologous recombination is however laborious, slow, expensive, and limited to species with functional ESCs. It is therefore a long-sought goal to develop an efficient and simple alternative gene targeting strategy. Here we demonstrate that, by combining an efficient ZFN pair and ssODN, a restriction site and a loxP site were successfully introduced into a specific genomic locus. A targeting efficiency up to 22.22% was achieved by coinciding the insertion site and the ZFN cleavage site isogenic and keeping the length of the homology arms equal and isogenic to the endogenous target locus. Furthermore, we determine that ZFN and ssODN-assisted HR is ssODN homology arm length dependent. We further show that mutant alleles generated by ZFN and ssODN-assisted HR can be transmitted through the germline successfully. This study establishes an efficient gene targeting strategy by ZFN and ssODN-assisted HR in mouse zygotes, and provides a potential avenue for genome engineering in animal species without functional ES cell lines.
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Affiliation(s)
- Bin Shen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing, China
| | - Xin Zhang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yinan Du
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing, China
| | - Jianying Wang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing, China
| | - Jun Gong
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaodong Zhang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Peri H. Tate
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hongliang Li
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Xingxu Huang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing, China
- * E-mail: (WZ); (XH)
| | - Wensheng Zhang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail: (WZ); (XH)
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39
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Andréasson C, Schick AJ, Pfeiffer SM, Sarov M, Stewart F, Wurst W, Schick JA. Direct cloning of isogenic murine DNA in yeast and relevance of isogenicity for targeting in embryonic stem cells. PLoS One 2013; 8:e74207. [PMID: 24058528 PMCID: PMC3772885 DOI: 10.1371/journal.pone.0074207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/30/2013] [Indexed: 12/25/2022] Open
Abstract
Efficient gene targeting in embryonic stem cells requires that modifying DNA sequences are identical to those in the targeted chromosomal locus. Yet, there is a paucity of isogenic genomic clones for human cell lines and PCR amplification cannot be used in many mutation-sensitive applications. Here, we describe a novel method for the direct cloning of genomic DNA into a targeting vector, pRTVIR, using oligonucleotide-directed homologous recombination in yeast. We demonstrate the applicability of the method by constructing functional targeting vectors for mammalian genes Uhrf1 and Gfap. Whereas the isogenic targeting of the gene Uhrf1 showed a substantial increase in targeting efficiency compared to non-isogenic DNA in mouse E14 cells, E14-derived DNA performed better than the isogenic DNA in JM8 cells for both Uhrf1 and Gfap. Analysis of 70 C57BL/6-derived targeting vectors electroporated in JM8 and E14 cell lines in parallel showed a clear dependence on isogenicity for targeting, but for three genes isogenic DNA was found to be inhibitory. In summary, this study provides a straightforward methodological approach for the direct generation of isogenic gene targeting vectors.
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Affiliation(s)
- Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anna J. Schick
- Physiologisches Institut, Ludwig-Maximilians-Universität, Munich, Germany
| | - Susanne M. Pfeiffer
- Institute of Developmental Genetics, Helmholtz Zentrum Munich, Munich-Neuherberg, Germany
- Technische Universität München, Freising-Weihenstephan, Germany
| | - Mihail Sarov
- The TransgeneOme Project Group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Francis Stewart
- Genomics, BioInnovationZentrum, Technische Universität Dresden, Dresden, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum Munich, Munich-Neuherberg, Germany
- Technische Universität München, Freising-Weihenstephan, Germany
| | - Joel A. Schick
- Institute of Developmental Genetics, Helmholtz Zentrum Munich, Munich-Neuherberg, Germany
- Technische Universität München, Freising-Weihenstephan, Germany
- * E-mail:
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40
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Deussing JM. Targeted mutagenesis tools for modelling psychiatric disorders. Cell Tissue Res 2013; 354:9-25. [PMID: 24078022 DOI: 10.1007/s00441-013-1708-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/16/2013] [Indexed: 12/15/2022]
Abstract
In the 1980s, the basic principles of gene targeting were discovered and forged into sharp tools for efficient and precise engineering of the mouse genome. Since then, genetic mouse models have substantially contributed to our understanding of major neurobiological concepts and are of utmost importance for our comprehension of neuropsychiatric disorders. The "domestication" of site-specific recombinases and the continuous creative technological developments involving the implementation of previously identified biological principles such as transcriptional and posttranslational control now enable conditional mutagenesis with high spatial and temporal resolution. The initiation and successful accomplishment of large-scale efforts to annotate functionally the entire mouse genome and to build strategic resources for the research community have significantly accelerated the rapid proliferation and broad propagation of mouse genetic tools. Addressing neurobiological processes with the assistance of genetic mouse models is a routine procedure in psychiatric research and will be further extended in order to improve our understanding of disease mechanisms. In light of the highly complex nature of psychiatric disorders and the current lack of strong causal genetic variants, a major future challenge is to model of psychiatric disorders more appropriately. Humanized mice, and the recently developed toolbox of site-specific nucleases for more efficient and simplified tailoring of the genome, offer the perspective of significantly improved models. Ultimately, these tools will push the limits of gene targeting beyond the mouse to allow genome engineering in any model organism of interest.
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Affiliation(s)
- Jan M Deussing
- Max Planck Institute of Psychiatry, Molecular Neurogenetics, Kraepelinstrasse 2-10, 80804, Munich, Germany,
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41
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Efficient nonmeiotic allele introgression in livestock using custom endonucleases. Proc Natl Acad Sci U S A 2013; 110:16526-31. [PMID: 24014591 DOI: 10.1073/pnas.1310478110] [Citation(s) in RCA: 191] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We have expanded the livestock gene editing toolbox to include transcription activator-like (TAL) effector nuclease (TALEN)- and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-stimulated homology-directed repair (HDR) using plasmid, rAAV, and oligonucleotide templates. Toward the genetic dehorning of dairy cattle, we introgressed a bovine POLLED allele into horned bull fibroblasts. Single nucleotide alterations or small indels were introduced into 14 additional genes in pig, goat, and cattle fibroblasts using TALEN mRNA and oligonucleotide transfection with efficiencies of 10-50% in populations. Several of the chosen edits mimic naturally occurring performance-enhancing or disease- resistance alleles, including alteration of single base pairs. Up to 70% of the fibroblast colonies propagated without selection harbored the intended edits, of which more than one-half were homozygous. Edited fibroblasts were used to generate pigs with knockout alleles in the DAZL and APC genes to model infertility and colon cancer. Our methods enable unprecedented meiosis-free intraspecific and interspecific introgression of select alleles in livestock for agricultural and biomedical applications.
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42
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Parker CC, Chen H, Flagel SB, Geurts AM, Richards JB, Robinson TE, Solberg Woods LC, Palmer AA. Rats are the smart choice: Rationale for a renewed focus on rats in behavioral genetics. Neuropharmacology 2013; 76 Pt B:250-8. [PMID: 23791960 DOI: 10.1016/j.neuropharm.2013.05.047] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/15/2013] [Accepted: 05/17/2013] [Indexed: 12/13/2022]
Abstract
Due in part to their rich behavioral repertoire rats have been widely used in behavioral studies of drug abuse-related traits for decades. However, the mouse became the model of choice for researchers exploring the genetic underpinnings of addiction after the first mouse study was published demonstrating the capability of engineering the mouse genome through embryonic stem cell technology. The sequencing of the mouse genome and more recent re-sequencing of numerous inbred mouse strains have further cemented the status of mice as the premier mammalian organism for genetic studies. As a result, many of the behavioral paradigms initially developed and optimized for rats have been adapted to mice. However, numerous complex and interesting drug abuse-related behaviors that can be studied in rats are very difficult or impossible to adapt for use in mice, impeding the genetic dissection of those traits. Now, technological advances have removed many of the historical limitations of genetic studies in rats. For instance, the rat genome has been sequenced and many inbred rat strains are now being re-sequenced and outbred rat stocks are being used to fine-map QTLs. In addition, it is now possible to create "knockout" rats using zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs) and related techniques. Thus, rats can now be used to perform quantitative genetic studies of sophisticated behaviors that have been difficult or impossible to study in mice. This article is part of a Special Issue entitled 'NIDA 40th Anniversary Issue'.
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Affiliation(s)
- Clarissa C Parker
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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43
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Abstract
Genome engineering--the ability to precisely alter the DNA information in living cells--is beginning to transform human genetics and genomics. Advances in tools and methods have enabled genetic modifications ranging from the "scarless" correction of a single base pair to the deletion of entire chromosomes. Targetable nucleases are leading the advances in this field, providing the tools to modify any gene in seemingly any organism with high efficiency. Targeted gene alterations have now been reported in more than 30 diverse species, ending the reign of mice as the exclusive model of mammalian genetics, and targetable nucleases have been used to modify more than 150 human genes and loci. A nuclease has also already entered clinical trials, signaling the beginning of genome engineering as therapy. The recent dramatic increase in the number of investigators using these techniques signifies a transition away from methods development toward a new age of exciting applications.
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Affiliation(s)
- David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, California 95616;
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44
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Davies B, Davies G, Preece C, Puliyadi R, Szumska D, Bhattacharya S. Site specific mutation of the Zic2 locus by microinjection of TALEN mRNA in mouse CD1, C3H and C57BL/6J oocytes. PLoS One 2013; 8:e60216. [PMID: 23555929 PMCID: PMC3610929 DOI: 10.1371/journal.pone.0060216] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 02/23/2013] [Indexed: 12/22/2022] Open
Abstract
Transcription Activator-Like Effector Nucleases (TALENs) consist of a nuclease domain fused to a DNA binding domain which is engineered to bind to any genomic sequence. These chimeric enzymes can be used to introduce a double strand break at a specific genomic site which then can become the substrate for error-prone non-homologous end joining (NHEJ), generating mutations at the site of cleavage. In this report we investigate the feasibility of achieving targeted mutagenesis by microinjection of TALEN mRNA within the mouse oocyte. We achieved high rates of mutagenesis of the mouse Zic2 gene in all backgrounds examined including outbred CD1 and inbred C3H and C57BL/6J. Founder mutant Zic2 mice (eight independent alleles, with frameshift and deletion mutations) were created in C3H and C57BL/6J backgrounds. These mice transmitted the mutant alleles to the progeny with 100% efficiency, allowing the creation of inbred lines. Mutant mice display a curly tail phenotype consistent with Zic2 loss-of-function. The efficiency of site-specific germline mutation in the mouse confirm TALEN mediated mutagenesis in the oocyte to be a viable alternative to conventional gene targeting in embryonic stem cells where simple loss-of-function alleles are required. This technology enables allelic series of mutations to be generated quickly and efficiently in diverse genetic backgrounds and will be a valuable approach to rapidly create mutations in mice already bearing one or more mutant alleles at other genetic loci without the need for lengthy backcrossing.
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Affiliation(s)
- Benjamin Davies
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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45
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Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides. Proc Natl Acad Sci U S A 2013; 110:3782-7. [PMID: 23426636 DOI: 10.1073/pnas.1218721110] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The study of genetic disease mechanisms relies mostly on targeted mouse mutants that are derived from engineered embryonic stem (ES) cells. Nevertheless, the establishment of mutant ES cells is laborious and time-consuming, restricting the study of the increasing number of human disease mutations discovered by high-throughput genomic analysis. Here, we present an advanced approach for the production of mouse disease models by microinjection of transcription activator-like effector nucleases (TALENs) and synthetic oligodeoxynucleotides into one-cell embryos. Within 2 d of embryo injection, we created and corrected chocolate missense mutations in the small GTPase RAB38; a regulator of intracellular vesicle trafficking and phenotypic model of Hermansky-Pudlak syndrome. Because ES cell cultures and targeting vectors are not required, this technology enables instant germline modifications, making heterozygous mutants available within 18 wk. The key features of direct mutagenesis by TALENs and oligodeoxynucleotides, minimal effort and high speed, catalyze the generation of future in vivo models for the study of human disease mechanisms and interventions.
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46
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Holmes N, Cooke A. Genetic analysis of type 1 diabetes: embryonic stem cells as new tools to unlock biological mechanisms in type 1 diabetes. Rev Diabet Stud 2012; 9:137-47. [PMID: 23804257 DOI: 10.1900/rds.2012.9.137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nonobese diabetic (NOD) mouse has provided an important animal model for studying the mechanism and genetics of type 1 diabetes over the past 30 years. Arguably, the bio-breeding (BB) rat model may be an even closer phenotypic mimic of the typical human disease. A large number of distinct genetic traits which influence diabetes development have been defined through an extraordinary effort, most conspicuously in the mouse model. However, in both NOD and BB models the lack of availability of robust means for experimental genetic manipulation has restricted our understanding of the mechanisms underlying this spontaneous autoimmune disease. Recent developments in the derivation of embryonic stem (ES) cells have the potential to transform this picture. We argue here that targeting of NOD strain ES cells can bring much needed certainty to our present understanding of the genetics of type 1 diabetes in the NOD mouse. In addition, ES cells can play important roles in the future, in both the NOD mouse and BB rat models, through the generation of new tools to investigate the mechanisms by which genetic variation acts to promote diabetes.
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Affiliation(s)
- Nick Holmes
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
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47
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Abstract
Phenotypic analysis of gene-specific knockout (KO) mice has revolutionized our understanding of in vivo gene functions. As the use of mouse embryonic stem (ES) cells is inevitable for conventional gene targeting, the generation of knockout mice remains a very time-consuming and expensive process. To accelerate the large-scale production and phenotype analyses of KO mice, international efforts have organized global consortia such as the International Knockout Mouse Consortium (IKMC) and International Mouse Phenotype Consortium (IMPC), and they are persistently expanding the KO mouse catalogue that is publicly available for the researches studying specific genes of interests in vivo. However, new technologies, adopting zinc-finger nucleases (ZFNs) or Transcription Activator-Like Effector (TALE) Nucleases (TALENs) to edit the mouse genome, are now emerging as valuable and effective shortcuts alternative for the conventional gene targeting using ES cells. Here, we introduce the recent achievement of IKMC, and evaluate the significance of ZFN/TALEN technology in mouse genetics.
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Affiliation(s)
- Young Hoon Sung
- Department of Biochemistry, College of Life Science and Biotechnology, Laboratory Animal Research Center, Yonsei University, Seoul 120-749, Korea
| | - In-Jeoung Baek
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Je Kyung Seong
- College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University, Korea
| | - Jin-Soo Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Han-Woong Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Laboratory Animal Research Center, Yonsei University, Seoul 120-749, Korea
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48
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Wefers B, Meyer M, Hensler S, Panda S, Ortiz O, Wurst W, Kühn R. Gene Editing in One-Cell Embryos by Zinc-Finger and TAL Nucleases. ACTA ACUST UNITED AC 2012; 2:347-64. [PMID: 26069019 DOI: 10.1002/9780470942390.mo120177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Gene targeting by sequence-specific nucleases in one-cell embryos provides an expedited mutagenesis approach in rodents. This technology has been recently established to create knockout and knockin mutants through sequence deletion or sequence insertion. This article provides protocols for the preparation and microinjection of nuclease mRNA and targeting vector DNA into fertilized mouse eggs. Furthermore, we provide guidelines for genotyping the desired mouse mutants. Curr. Protoc. Mouse Biol. 2:347-364 © 2012 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benedikt Wefers
- Helmholtz Center Munich, Institute for Developmental Genetics Munich, Germany
| | - Melanie Meyer
- Helmholtz Center Munich, Institute for Developmental Genetics Munich, Germany.,Chair for Developmental Genetics, Technische Universität München, Munich, Germany
| | - Svenja Hensler
- Helmholtz Center Munich, Institute for Developmental Genetics Munich, Germany.,Chair for Developmental Genetics, Technische Universität München, Munich, Germany
| | - Sudeepta Panda
- Helmholtz Center Munich, Institute for Developmental Genetics Munich, Germany.,Chair for Developmental Genetics, Technische Universität München, Munich, Germany
| | - Oskar Ortiz
- Helmholtz Center Munich, Institute for Developmental Genetics Munich, Germany
| | - Wolfgang Wurst
- Helmholtz Center Munich, Institute for Developmental Genetics Munich, Germany.,Chair for Developmental Genetics, Technische Universität München, Munich, Germany.,Max Planck Institute of Psychiatry, Molecular Neurogenetics, Munich, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen, Standort München, Munich, Germany
| | - Ralf Kühn
- Helmholtz Center Munich, Institute for Developmental Genetics Munich, Germany.,Chair for Developmental Genetics, Technische Universität München, Munich, Germany
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