351
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Sun N, Bao Z, Xiong X, Zhao H. SunnyTALEN: A second-generation TALEN system for human genome editing. Biotechnol Bioeng 2013; 111:683-91. [DOI: 10.1002/bit.25154] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 10/17/2013] [Accepted: 11/14/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Ning Sun
- Department of Biochemistry; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
| | - Zehua Bao
- Department of Biochemistry; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
| | - Xiong Xiong
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
| | - Huimin Zhao
- Department of Biochemistry; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
- Department of Bioengineering, Department of Chemistry; Center for Biophysics and Computational Biology and Institute for Genomic Biology; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
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352
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Abstract
Recent advances in the burgeoning field of genome engineering are accelerating the realization of personalized therapeutics for cardiovascular disease. In the postgenomic era, sequence-specific gene-editing tools enable the functional analysis of genetic alterations implicated in disease. In partnership with high-throughput model systems, efficient gene manipulation provides an increasingly powerful toolkit to study phenotypes associated with patient-specific genetic defects. Herein, this review emphasizes the latest developments in genome engineering and how applications within the field are transforming our understanding of personalized medicine with an emphasis on cardiovascular diseases.
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Affiliation(s)
- Jarryd M Campbell
- Center for Translational Science Activities, Mayo Clinic, Rochester, MN 55905, USA.
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353
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Bean AGD, Baker ML, Stewart CR, Cowled C, Deffrasnes C, Wang LF, Lowenthal JW. Studying immunity to zoonotic diseases in the natural host - keeping it real. Nat Rev Immunol 2013; 13:851-61. [PMID: 24157573 PMCID: PMC7098194 DOI: 10.1038/nri3551] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Zoonotic viruses that emerge from wildlife and domesticated animals pose a serious threat to human and animal health. In many instances, mouse models have improved our understanding of the human immune response to infection; however, when dealing with emerging zoonotic diseases, they may be of limited use. This is particularly the case when the model fails to reproduce the disease status that is seen in the natural reservoir, transmission species or human host. In this Review, we discuss how researchers are placing more emphasis on the study of the immune response to zoonotic infections in the natural reservoir hosts and spillover species. Such studies will not only lead to a greater understanding of how these infections induce variable disease and immune responses in distinct species but also offer important insights into the evolution of mammalian immune systems.
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Affiliation(s)
- Andrew G. D. Bean
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, 3220 Victoria Australia
| | - Michelle L. Baker
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, 3220 Victoria Australia
| | - Cameron R. Stewart
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, 3220 Victoria Australia
| | - Christopher Cowled
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, 3220 Victoria Australia
| | - Celine Deffrasnes
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, 3220 Victoria Australia
| | - Lin-Fa Wang
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, 3220 Victoria Australia
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, 169857 Singapore
| | - John W. Lowenthal
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, 3220 Victoria Australia
- School of Medicine, Deakin University, Waurn Ponds, 3216 Victoria Australia
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354
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Sakuma T, Ochiai H, Kaneko T, Mashimo T, Tokumasu D, Sakane Y, Suzuki KI, Miyamoto T, Sakamoto N, Matsuura S, Yamamoto T. Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity. Sci Rep 2013; 3:3379. [PMID: 24287550 PMCID: PMC3843162 DOI: 10.1038/srep03379] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/11/2013] [Indexed: 01/17/2023] Open
Abstract
Transcription activator-like effector (TALE) nuclease (TALEN) is a site-specific nuclease, which can be freely designed and easily constructed. Numerous methods of constructing TALENs harboring different TALE scaffolds and repeat variants have recently been reported. However, the functionalities of structurally different TALENs have not yet been compared. Here, we report on the functional differences among several types of TALENs targeting the same loci. Using HEK293T cell-based single-strand annealing and Cel-I nuclease assays, we found that TALENs with periodically-patterned repeat variants harboring non-repeat-variable di-residue (non-RVD) variations (Platinum TALENs) showed higher activities than TALENs without non-RVD variations. Furthermore, the efficiencies of gene disruption mediated by Platinum TALENs in frogs and rats were significantly higher than in previous reports. This study therefore demonstrated an efficient system for the construction of these highly active Platinum TALENs (Platinum Gate system), which could establish a new standard in TALEN engineering.
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Affiliation(s)
- Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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355
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Hosoi S, Sakuma T, Sakamoto N, Yamamoto T. Targeted mutagenesis in sea urchin embryos using TALENs. Dev Growth Differ 2013; 56:92-7. [DOI: 10.1111/dgd.12099] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Sayaka Hosoi
- Department of Mathematical and Life Sciences; Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima 739-8526 Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences; Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima 739-8526 Japan
| | - Naoaki Sakamoto
- Department of Mathematical and Life Sciences; Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima 739-8526 Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences; Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima 739-8526 Japan
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356
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Yang D, Zhang J, Xu J, Zhu T, Fan Y, Fan J, Chen YE. Production of apolipoprotein C-III knockout rabbits using zinc finger nucleases. J Vis Exp 2013:e50957. [PMID: 24301055 PMCID: PMC3991373 DOI: 10.3791/50957] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Apolipoprotein (Apo) C-III (ApoCIII) resides on the surface of plasma chylomicron (CM), very low density lipoprotein (VLDL) and high density lipoproteins (HDL). It has been recognized that high levels of plasma ApoCIII constitutea risk factor for cardiovascular diseases (CVD). Elevated plasma ApoCIII level often correlates with insulin resistance, obesity, and hypertriglyceridemia. Invaluable knowledge on the roles of ApoCIIIin lipid metabolisms and CVD has been obtained from transgenic mouse models including ApoCIII knockout (KO) mice; however, it is noted that the metabolism of lipoprotein in mice is different from that of humans in many aspects. It is not known until now whether elevated plasma ApoCIII is directly atherogenic. We worked to develop ApoCIII KO rabbits in the present study based on the hypothesis that rabbits can serve as a reasonablemodelfor studying human lipid metabolism and atherosclerosis. Zinc finger nuclease (ZFN) sets targeting rabbit ApoCIIIgene were subjected to in vitro validation prior to embryo microinjection. The mRNA was injected to the cytoplasm of 35 rabbit pronuclear stage embryos, and evaluated the mutation rates at the blastocyst state. Of sixteen blastocysts that were assayed, a satisfactory 50% mutation rate (8/16) at the targeting site was achieved, supporting the use of Set 1 for in vivo experiments. Next, we microinjected 145 embryos with Set 1 mRNA, and transferred these embryos to 7 recipient rabbits. After 30 days gestation, 21 kits were born, out of which five were confirmed as ApoCIII KO rabbits after PCR sequencing assays. The KO animal rate (#KO kits/total born) was 23.8%. The overall production efficiency is 3.4% (5 kits/145 embryos transferred). The present work demonstrated that ZFN is a highly efficient method to produce KO rabbits. These ApoCIII KO rabbits are novel resources to study the roles of ApoCIII in lipid metabolisms.
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Affiliation(s)
- Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical Center
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357
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Zhang Z, Zhang S, Huang X, Orwig KE, Sheng Y. Rapid assembly of customized TALENs into multiple delivery systems. PLoS One 2013; 8:e80281. [PMID: 24244669 PMCID: PMC3820630 DOI: 10.1371/journal.pone.0080281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 10/11/2013] [Indexed: 11/18/2022] Open
Abstract
Transcriptional activator-like effector nucleases (TALENs) have become a powerful tool for genome editing. Here we present an efficient TALEN assembly approach in which TALENs are assembled by direct Golden Gate ligation into Gateway(®) Entry vectors from a repeat variable di-residue (RVD) plasmid array. We constructed TALEN pairs targeted to mouse Ddx3 subfamily genes, and demonstrated that our modified TALEN assembly approach efficiently generates accurate TALEN moieties that effectively introduce mutations into target genes. We generated "user friendly" TALEN Entry vectors containing TALEN expression cassettes with fluorescent reporter genes that can be efficiently transferred via Gateway (LR) recombination into different delivery systems. We demonstrated that the TALEN Entry vectors can be easily transferred to an adenoviral delivery system to expand application to cells that are difficult to transfect. Since TALENs work in pairs, we also generated a TALEN Entry vector set that combines a TALEN pair into one PiggyBac transposon-based destination vector. The approach described here can also be modified for construction of TALE transcriptional activators, repressors or other functional domains.
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Affiliation(s)
- Zhengxing Zhang
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania, United States of America
| | - Siliang Zhang
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania, United States of America
| | - Xin Huang
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania, United States of America
- Women’s Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Kyle E. Orwig
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania, United States of America
| | - Yi Sheng
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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358
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Abstract
In this review, we discuss the repair of DNA double-strand breaks (DSBs) using a homologous DNA sequence (i.e., homologous recombination [HR]), focusing mainly on yeast and mammals. We provide a historical context for the current view of HR and describe how DSBs are processed during HR as well as interactions with other DSB repair pathways. We discuss the enzymology of the process, followed by studies on DSB repair in living cells. Whenever possible, we cite both original articles and reviews to aid the reader for further studies.
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Affiliation(s)
- Maria Jasin
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center New York, New York 10065
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359
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Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 2013; 41:e188. [PMID: 23999092 PMCID: PMC3814374 DOI: 10.1093/nar/gkt780] [Citation(s) in RCA: 681] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 08/12/2013] [Indexed: 12/18/2022] Open
Abstract
The type II CRISPR/Cas system from Streptococcus pyogenes and its simplified derivative, the Cas9/single guide RNA (sgRNA) system, have emerged as potent new tools for targeted gene knockout in bacteria, yeast, fruit fly, zebrafish and human cells. Here, we describe adaptations of these systems leading to successful expression of the Cas9/sgRNA system in two dicot plant species, Arabidopsis and tobacco, and two monocot crop species, rice and sorghum. Agrobacterium tumefaciens was used for delivery of genes encoding Cas9, sgRNA and a non-fuctional, mutant green fluorescence protein (GFP) to Arabidopsis and tobacco. The mutant GFP gene contained target sites in its 5' coding regions that were successfully cleaved by a CAS9/sgRNA complex that, along with error-prone DNA repair, resulted in creation of functional GFP genes. DNA sequencing confirmed Cas9/sgRNA-mediated mutagenesis at the target site. Rice protoplast cells transformed with Cas9/sgRNA constructs targeting the promoter region of the bacterial blight susceptibility genes, OsSWEET14 and OsSWEET11, were confirmed by DNA sequencing to contain mutated DNA sequences at the target sites. Successful demonstration of the Cas9/sgRNA system in model plant and crop species bodes well for its near-term use as a facile and powerful means of plant genetic engineering for scientific and agricultural applications.
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Affiliation(s)
- Wenzhi Jiang
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA, Deparment of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA
| | - Huanbin Zhou
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA, Deparment of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA
| | - Honghao Bi
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA, Deparment of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA
| | - Michael Fromm
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA, Deparment of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA
| | - Bing Yang
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA, Deparment of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA
| | - Donald P. Weeks
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA, Deparment of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA
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360
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Stewart CR, Keyburn AL, Deffrasnes C, Tompkins SM. Potential directions for chicken immunology research. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:463-468. [PMID: 23707787 DOI: 10.1016/j.dci.2013.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 05/15/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
The importance of poultry, particularly chicken, as a food source continues to increase globally. Moreover, zoonotic infectious diseases such as avian influenza virus not only continue to impact poultry production, but also pose an increasing threat to public health. This review discusses the importance of poultry in both agricultural and public health arenas. Recent developments in avian immunology are described, with an emphasis on host-pathogen interactions and noting differences from mammalian systems. Next generation technologies including functional genomics and targeted gene disruption (e.g. zinc finger nucleases and meganucleases) are discussed as new approaches for not only understanding immune responses in poultry, but also as novel disease intervention strategies.
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Affiliation(s)
- Cameron R Stewart
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
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361
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Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 2013. [PMID: 24157548 DOI: 10.1038/nprot.2013.143.] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.
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Affiliation(s)
- F Ann Ran
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Patrick D Hsu
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jason Wright
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - Vineeta Agarwala
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,Program in Biophysics, Harvard University, MIT, Cambridge, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts, USA
| | - David A Scott
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
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362
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Efficient targeting of FATS at a common fragile site in mice through TALEN-mediated double-hit genome modification. Biotechnol Lett 2013; 36:471-9. [PMID: 24158675 DOI: 10.1007/s10529-013-1387-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/08/2013] [Indexed: 01/08/2023]
Abstract
Transcription activator-like effector nucleases (TALENs) have emerged as a newly developed approach for genome editing. However, its application in targeting specific genomic loci susceptible to DNA damage remains obscure. Here, we report a modified approach for TALENs-based targeting of FATS, a fragile-site gene whose major introns have AT-rich sequence and di-nucleotide repeats. Two pairs of FATS-TALENs were designed to cleave two sites specifically at a coding exon of FATS. After in vitro transcription, the mRNA from FATS-TALEN pairs was microinjected into mouse zygotes. The targeting efficiency of two FATS-TALEN pairs in vivo was more than threefold higher than that of one FATS-TALEN pair. Moreover, large-size DNA deletions were detected, which were heritable and easily detectable by PCR. Our study indicates that the double-hit TALEN approach enhances targeting efficiency in vivo and provides convenience for monitoring germline transmission of mutations by PCR, which will facilitate the functional research on fragile-site genes.
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363
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Abstract
Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.
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364
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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: 1.3] [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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365
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Chen T, Wang J, Xue B, Kong Q, Liu Z, Yu B. Identification and characterization of a novel porcine endothelial cell-specific Tie1 promoter. Xenotransplantation 2013; 20:438-48. [PMID: 24112087 DOI: 10.1111/xen.12059] [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] [Received: 05/15/2013] [Accepted: 08/14/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND The use of a transgenic pig for xenotransplantation and as a cardiovascular disease model has caught much attention in the past decades. The vascular endothelial cell is the primary modification target for the application of genetically modified pigs in this field. However, the powerful porcine endothelial cell-specific promoter is still so rare that the mouse and human promoters are commonly used. In the study, the porcine Tie1 (sTie1) promoter was identified and characterized as a potential endothelial cell-specific promoter to generate a cardiovascular disease model. METHODS Tie1 promoters with different lengths of 5'-regulatory regions were cloned, and major putative DNA-binding motifs were mutated by site-directed mutagenesis. All fragments were ligated into the luciferase reporter system and were transiently transfected into endothelial cells to identify luciferase activity using a dual luciferase reporter assay. RESULTS The luciferase activities of sTie1 promoters with different lengths of the 5'-regulatory region were tested. Results showed that the luciferase activity of the 1234-bp sTie1 fragment was the strongest compared with that of others (P < 0.001). Site-directed mutagenesis in transcription-factor-binding sites, including Ets, GATA, and AP2, verified their key roles in regulating transcription, especially sites Ets (-103), GATA (-211), and AP2 (-3). The activities of Tie1 promoters from pig, human, and mouse were significantly different in pig iliac endothelial cells (PIECs) (P < 0.001), and the sTie1 promoter showed the highest activity. Moreover, sTie1 promoter activity could be detected in porcine embryo fibroblasts and skeletal muscle cells. CONCLUSIONS The sTie1 promoter shows a highly conserved sequence compared with the Tie1 promoters in human and mouse, but it has a greater activity in the porcine endothelial cell line than that of human and mouse promoters. Thus, sTie1 will be a valuable tool for generating a pig cardiovascular disease model.
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Affiliation(s)
- Tao Chen
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, Heilongjiang, China; Cardiology Division, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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366
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Liu Y, Luo D, Zhao H, Zhu Z, Hu W, Cheng CHK. Inheritable and precise large genomic deletions of non-coding RNA genes in zebrafish using TALENs. PLoS One 2013; 8:e76387. [PMID: 24130773 PMCID: PMC3794983 DOI: 10.1371/journal.pone.0076387] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 08/30/2013] [Indexed: 01/15/2023] Open
Abstract
Transcription activator-like effector nucleases (TALENs) have so far been applied to disrupt protein-coding genes which constitute only 2-3% of the genome in animals. The majority (70-90%) of the animal genome is actually transcribed as non-coding RNAs (ncRNAs), yet the lack of efficient tools to knockout ncRNA genes hinders studies on their in vivo functions. Here we have developed novel strategies using TALENs to achieve precise and inheritable large genomic deletions and knockout of ncRNA genes in zebrafish. We have demonstrated that individual miRNA genes could be disrupted using one pair of TALENs, whereas large microRNA (miRNA) gene clusters and long non-coding RNA (lncRNA) genes could be precisely deleted using two pairs of TALENs. We have generated large genomic deletions of two miRNA clusters (the 1.2 kb miR-17-92 cluster and the 79.8 kb miR-430 cluster) and one long non-coding RNA (lncRNA) gene (the 9.0 kb malat1), and the deletions are transmitted through the germline. Taken together, our results establish TALENs as a robust tool to engineer large genomic deletions and knockout of ncRNA genes, thus opening up new avenues in the application of TALENs to study the genome in vivo.
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Affiliation(s)
- Yun Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Daji Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Department of Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Hui Zhao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (WH); (CC)
| | - Christopher H. K. Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- * E-mail: (WH); (CC)
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367
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Abstract
Transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) genome editing technology enables site directed engineering of the genome. Here we demonstrate for the first time that both TALEN and ZFN injected directly into pig zygotes can produce live genome edited pigs. Monoallelic as well as heterozygous and homozygous biallelic events were identified, significantly broadening the use of genome editor technology in livestock by enabling gene knockout in zygotes from any chosen mating.
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368
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Watanabe M, Nakano K, Matsunari H, Matsuda T, Maehara M, Kanai T, Kobayashi M, Matsumura Y, Sakai R, Kuramoto M, Hayashida G, Asano Y, Takayanagi S, Arai Y, Umeyama K, Nagaya M, Hanazono Y, Nagashima H. Generation of interleukin-2 receptor gamma gene knockout pigs from somatic cells genetically modified by zinc finger nuclease-encoding mRNA. PLoS One 2013; 8:e76478. [PMID: 24130776 PMCID: PMC3793986 DOI: 10.1371/journal.pone.0076478] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/23/2013] [Indexed: 12/23/2022] Open
Abstract
Zinc finger nuclease (ZFN) is a powerful tool for genome editing. ZFN-encoding plasmid DNA expression systems have been recently employed for the generation of gene knockout (KO) pigs, although one major limitation of this technology is the use of potentially harmful genome-integrating plasmid DNAs. Here we describe a simple, non-integrating strategy for generating KO pigs using ZFN-encoding mRNA. The interleukin-2 receptor gamma (IL2RG) gene was knocked out in porcine fetal fibroblasts using ZFN-encoding mRNAs, and IL2RG KO pigs were subsequently generated using these KO cells through somatic cell nuclear transfer (SCNT). The resulting IL2RG KO pigs completely lacked a thymus and were deficient in T and NK cells, similar to human X-linked SCID patients. Our findings demonstrate that the combination of ZFN-encoding mRNAs and SCNT provides a simple robust method for producing KO pigs without genomic integration.
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Affiliation(s)
- Masahito Watanabe
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
- Meiji University International Institute for Bio-Resource Research (MUIIBR), Kawasaki, Japan
| | - Kazuaki Nakano
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Hitomi Matsunari
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
- Meiji University International Institute for Bio-Resource Research (MUIIBR), Kawasaki, Japan
| | - Taisuke Matsuda
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Miki Maehara
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Takahiro Kanai
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Mirina Kobayashi
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Yukina Matsumura
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Rieko Sakai
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Momoko Kuramoto
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Gota Hayashida
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Yoshinori Asano
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Shuko Takayanagi
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Yoshikazu Arai
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kazuhiro Umeyama
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
- Meiji University International Institute for Bio-Resource Research (MUIIBR), Kawasaki, Japan
| | - Masaki Nagaya
- Meiji University International Institute for Bio-Resource Research (MUIIBR), Kawasaki, Japan
| | - Yutaka Hanazono
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- CREST, Japan Science and Technology Agency, Tokyo, Japan
| | - Hiroshi Nagashima
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
- Meiji University International Institute for Bio-Resource Research (MUIIBR), Kawasaki, Japan
- CREST, Japan Science and Technology Agency, Tokyo, Japan
- * E-mail:
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369
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Lee K, Prather RS. Advancements in somatic cell nuclear transfer and future perspectives. Anim Front 2013. [DOI: 10.2527/af.2013-0034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Kiho Lee
- Division of Animal Science, University of Missouri, Columbia, MO, USA
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370
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Abstract
Beta cell replacement therapy has been proposed as a novel therapy for the treatment of type 1 diabetes. The proof of concept has been demonstrated with successful islet allotransplantation. Islet xenotransplantation has been proposed as an alternative, more reliable, and infinite source of beta cells. The advantages of islet xenotransplantation are the ability to transplant a well differentiated cell that is responsive to glucose and the potential for genetic modification which focuses the treatment on the donor rather than the recipient. The major hurdle remains overcoming the severe cellular rejection that affects xenografts. This review will focus on the major advances that have occurred with genetic modification and the successful therapeutic strategies that have been demonstrated in nonhuman primates. Novel approaches to overcome cell-mediated rejection including biological agents that target selectively costimulation molecules, the development of local immunosuppression through genetic manipulation, and encapsulation will be discussed. Overall, there has been considerable progress in all these areas, which eventually should lead to clinical trials.
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Affiliation(s)
- Philip J O'Connell
- Centre for Transplant and Renal Research, Westmead Millennium Institute, University of Sydney at Westmead Hospital, Westmead, NSW, 2145, Australia,
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371
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372
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Genetically engineered pig models for diabetes research. Transgenic Res 2013; 23:27-38. [PMID: 24065178 DOI: 10.1007/s11248-013-9755-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 09/13/2013] [Indexed: 12/15/2022]
Abstract
Diabetes mellitus (DM) has emerged into a steadily increasing health problem and the predicted future dimension of the global DM epidemic is alarming: an increase from currently 346 million to over 400 million affected people worldwide by the year 2030 was extrapolated. Thus concerted research efforts are imperative to gain insight into disease mechanisms and to expand the basis for development of preventive and therapeutic strategies. Diabetic rodent models have traditionally been used to follow these goals, but have limitations for translational research. The pig is another classical animal model for diabetes research. Genetic engineering now facilitates tailoring pig models which mimic human disease mechanisms at the molecular level. This article reviews the existing genetically engineered pig models for diabetes research and their current and future applications. Further, the potential role of the pig as donor of pancreatic islets for xenotransplantation or as host for growing human pancreas is outlined.
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373
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Takasu Y, Sajwan S, Daimon T, Osanai-Futahashi M, Uchino K, Sezutsu H, Tamura T, Zurovec M. Efficient TALEN construction for Bombyx mori gene targeting. PLoS One 2013; 8:e73458. [PMID: 24058473 PMCID: PMC3776831 DOI: 10.1371/journal.pone.0073458] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 07/22/2013] [Indexed: 12/13/2022] Open
Abstract
Engineered nucleases are artificial enzymes able to introduce double stranded breaks at desired genomic locations. The double stranded breaks start the error-prone repair process of non-homologous end-joining (NHEJ), which eventually leads to the induction of mutations at target sites. We showed earlier that ZFNs and TALENs are able to induce NHEJ mutations in the B. mori genome. In order to optimize our mutagenesis protocol, we modified one of the reported truncated TALEN scaffolds and optimized it for use in the B. mori embryo. We also established a novel B. mori somatic cell assay suitable for the preselection of highly efficient TALENs directly in the B. mori model system. We compared the efficiency of several TALEN pairs based on three different frameworks using the BmBLOS2 gene. The new active TALENs show one order of magnitude higher efficiency than those we used previously. We confirmed the utility of our improved protocol by mutagenesis of the autosomal gene, red egg (Bm-re) and showed that it allows obtaining homozygous mutants in G1. Our procedure minimizes the chance of failure in B. mori gene targeting experiments.
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Affiliation(s)
- Yoko Takasu
- National Institute of Agrobiological Sciences, Tsukuba, Japan
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374
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Abstract
Abstract Interest in pluripotent livestock stem cells has been with us for over 2 decades, and although much has been claimed over the years, it is only recently that real progress has been achieved. The recent developments have revolved around the ability to reprogram somatic cells to become induced pluripotent stem cells (iPSCs). Progress has been achieved in porcine, bovine, equine, and ovine species; but for each species, the extent of progress is different. I review the position of ovine iPSCs and comment on the two main drivers for this work-to produce "better" cells for nuclear transfer and to develop a good in vitro system to study the early development of ruminants.
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Affiliation(s)
- C Bruce A Whitelaw
- The Roslin Institute and R(D)SVS, University of Edinburgh , Easter Bush Campus, Edinburgh, Midlothian EH25 9RG, United Kingdom
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375
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Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino A, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 2013; 154:1380-9. [PMID: 23992846 PMCID: PMC3856256 DOI: 10.1016/j.cell.2013.08.021] [Citation(s) in RCA: 2392] [Impact Index Per Article: 217.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 12/12/2022]
Abstract
Targeted genome editing technologies have enabled a broad range of research and medical applications. The Cas9 nuclease from the microbial CRISPR-Cas system is targeted to specific genomic loci by a 20 nt guide sequence, which can tolerate certain mismatches to the DNA target and thereby promote undesired off-target mutagenesis. Here, we describe an approach that combines a Cas9 nickase mutant with paired guide RNAs to introduce targeted double-strand breaks. Because individual nicks in the genome are repaired with high fidelity, simultaneous nicking via appropriately offset guide RNAs is required for double-stranded breaks and extends the number of specifically recognized bases for target cleavage. We demonstrate that using paired nicking can reduce off-target activity by 50- to 1,500-fold in cell lines and to facilitate gene knockout in mouse zygotes without sacrificing on-target cleavage efficiency. This versatile strategy enables a wide variety of genome editing applications that require high specificity.
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Affiliation(s)
- F. Ann Ran
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrick D. Hsu
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chie-Yu Lin
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Silvana Konermann
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandro Trevino
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - David A. Scott
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Azusa Inoue
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shogo Matoba
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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376
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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: 1.2] [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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377
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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: 187] [Impact Index Per Article: 17.0] [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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378
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Menke DB. Engineering subtle targeted mutations into the mouse genome. Genesis 2013; 51:605-18. [PMID: 23913666 DOI: 10.1002/dvg.22422] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 07/25/2013] [Accepted: 07/26/2013] [Indexed: 12/13/2022]
Abstract
Homologous recombination in embryonic stem (ES) cells offers an exquisitely precise mechanism to introduce targeted modifications to the mouse genome. This ability to produce specific alterations to the mouse genome has become an essential tool for the analysis of gene function and the development of mouse models of human disease. Of the many thousands of mouse alleles that have been generated by gene targeting, the majority are designed to completely ablate gene function, to create conditional alleles that are inactivated in the presence of Cre recombinase, or to produce reporter alleles that label-specific tissues or cell populations (Eppig et al., 2012, Nucleic Acids Res 40:D881-D886). However, there is a variety of powerful motivations for the introduction of subtle targeted mutations (STMs) such as point mutations, small deletions, or small insertions into the mouse genome. The introduction of STMs allows the ablation of specific transcript isoforms, permits the functional investigation of particular domains or amino acids within a protein, provides the ability to study the role of specific sites with in cis-regulatory elements, and can result in better mouse models of human genetic disorders. In this review, I examine the current strategies that are commonly used to introduce STMs into the mouse genome and highlight new gene targeting technologies, including TALENs and CRISPR/Cas, which are likely to influence the future of gene targeting in mice.
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Affiliation(s)
- Douglas B Menke
- Department of Genetics, University of Georgia, Athens, Georgia
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379
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Targeted mutagenesis in the malaria mosquito using TALE nucleases. PLoS One 2013; 8:e74511. [PMID: 23977401 PMCID: PMC3744473 DOI: 10.1371/journal.pone.0074511] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/07/2013] [Indexed: 12/21/2022] Open
Abstract
Anopheles gambiae, the main mosquito vector of human malaria, is a challenging organism to manipulate genetically. As a consequence, reverse genetics studies in this disease vector have been largely limited to RNA interference experiments. Here, we report the targeted disruption of the immunity gene TEP1 using transgenic expression of Transcription-Activator Like Effector Nucleases (TALENs), and the isolation of several TEP1 mutant A. gambiae lines. These mutations inhibited protein production and rendered TEP1 mutants hypersusceptible to Plasmodium berghei. The TALEN technology opens up new avenues for genetic analysis in this disease vector and may offer novel biotechnology-based approaches for malaria control.
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380
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Zhu H, Lau CH, Goh SL, Liang Q, Chen C, Du S, Phang RZ, Tay FC, Tan WK, Li Z, Tay JCK, Fan W, Wang S. Baculoviral transduction facilitates TALEN-mediated targeted transgene integration and Cre/LoxP cassette exchange in human-induced pluripotent stem cells. Nucleic Acids Res 2013; 41:e180. [PMID: 23945944 PMCID: PMC3799456 DOI: 10.1093/nar/gkt721] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Safety and reliability of transgene integration in human genome continue to pose challenges for stem cell-based gene therapy. Here, we report a baculovirus-transcription activator-like effector nuclease system for AAVS1 locus-directed homologous recombination in human induced pluripotent stem cells (iPSCs). This viral system, when optimized in human U87 cells, provided a targeted integration efficiency of 95.21% in incorporating a Neo-eGFP cassette and was able to mediate integration of DNA insert up to 13.5 kb. In iPSCs, targeted integration with persistent transgene expression was achieved without compromising genomic stability. The modified iPSCs continued to express stem cell pluripotency markers and maintained the ability to differentiate into three germ lineages in derived embryoid bodies. Using a baculovirus-Cre/LoxP system in the iPSCs, the Neo-eGFP cassette at the AAVS1 locus could be replaced by a Hygro-mCherry cassette, demonstrating the feasibility of cassette exchange. Moreover, as assessed by measuring γ-H2AX expression levels, genome toxicity associated with chromosomal double-strand breaks was not detectable after transduction with moderate doses of baculoviral vectors expressing transcription activator-like effector nucleases. Given high targeted integration efficiency, flexibility in transgene exchange and low genome toxicity, our baculoviral transduction-based approach offers great potential and attractive option for precise genetic manipulation in human pluripotent stem cells.
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Affiliation(s)
- Haibao Zhu
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Department of Surgery, Program of Innovative Cancer Therapeutics, First Affiliated Hospital of Zhejiang University College of Medicine, 310009 Hangzhou, China and Institute of Bioengineering and Nanotechnology, 138669 Singapore
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381
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Ménoret S, Tesson L, Rémy S, Thinard R, Usal C, Ouisse LH, Thepenier V, Anegon I. Technical advances in the generation of transgenic animals and in their applications. Nantes, France, June 7th 2013. Transgenic Res 2013; 22:1065-72. [PMID: 23907705 DOI: 10.1007/s11248-013-9736-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Séverine Ménoret
- Transgenic Rats Nantes, INSERM, Centre National de Recherche Scientifique, 44093, Nantes, France
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382
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Xiao A, Wang Z, Hu Y, Wu Y, Luo Z, Yang Z, Zu Y, Li W, Huang P, Tong X, Zhu Z, Lin S, Zhang B. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res 2013; 41:e141. [PMID: 23748566 PMCID: PMC3737551 DOI: 10.1093/nar/gkt464] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 12/20/2022] Open
Abstract
Customized TALENs and Cas9/gRNAs have been used for targeted mutagenesis in zebrafish to induce indels into protein-coding genes. However, indels are usually not sufficient to disrupt the function of non-coding genes, gene clusters or regulatory sequences, whereas large genomic deletions or inversions are more desirable for this purpose. By injecting two pairs of TALEN mRNAs or two gRNAs together with Cas9 mRNA targeting distal DNA sites of the same chromosome, we obtained predictable genomic deletions or inversions with sizes ranging from several hundred bases to nearly 1 Mb. We have successfully achieved this type of modifications for 11 chromosomal loci by TALENs and 2 by Cas9/gRNAs with different combinations of gRNA pairs, including clusters of miRNA and protein-coding genes. Seven of eight TALEN-targeted lines transmitted the deletions and one transmitted the inversion through germ line. Our findings indicate that both TALENs and Cas9/gRNAs can be used as an efficient tool to engineer genomes to achieve large deletions or inversions, including fragments covering multiple genes and non-coding sequences. To facilitate the analyses and application of existing ZFN, TALEN and CRISPR/Cas data, we have updated our EENdb database to provide a chromosomal view of all reported engineered endonucleases targeting human and zebrafish genomes.
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Affiliation(s)
- An Xiao
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zhanxiang Wang
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Yingying Hu
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Yingdan Wu
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zhou Luo
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zhipeng Yang
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Yao Zu
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Wenyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Peng Huang
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Xiangjun Tong
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zuoyan Zhu
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Shuo Lin
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
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383
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Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ. TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol 2013; 23:390-8. [PMID: 23707478 PMCID: PMC3729746 DOI: 10.1016/j.tcb.2013.04.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/19/2022]
Abstract
Transcription activator-like (TAL) effectors are transcription factors injected into plant cells by pathogenic bacteria of the genus Xanthomonas. They function as virulence factors by activating host genes important for disease, or as avirulence factors by turning on genes that provide resistance. DNA-binding specificity is encoded by polymorphic repeats in each protein that correspond one-to-one with different nucleotides. This code has facilitated target identification and opened new avenues for engineering disease resistance. It has also enabled TAL effector customization for targeted gene control, genome editing, and other applications. This article reviews the structural basis for TAL effector-DNA specificity, the impact of the TAL effector-DNA code on plant pathology and engineered resistance, and recent accomplishments and future challenges in TAL effector-based DNA targeting.
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Affiliation(s)
- Erin L. Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. A3-025, Seattle WA 98109
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455
| | - Adam J. Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 334 Plant Science, Ithaca NY 14853
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384
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Xu L, Zhao P, Mariano A, Han R. Targeted Myostatin Gene Editing in Multiple Mammalian Species Directed by a Single Pair of TALE Nucleases. MOLECULAR THERAPY-NUCLEIC ACIDS 2013; 2:e112. [PMID: 23900226 PMCID: PMC3731890 DOI: 10.1038/mtna.2013.39] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 06/12/2013] [Indexed: 01/18/2023]
Abstract
Myostatin (MSTN) is a negative regulator of skeletal muscle mass. Strategies to block myostatin signaling pathway have been extensively pursued to increase muscle mass in various disease settings including muscular dystrophy. Here, we report a new class of reagents based on transcription activator-like effector nucleases (TALENs) to disrupt myostatin expression at the genome level. We designed a pair of MSTN TALENs to target a highly conserved sequence in the coding region of the myostatin gene. We demonstrate that codelivery of these MSTN TALENs induce highly specific and efficient gene disruption in a variety of human, cattle, and mouse cells. Based upon sequence analysis, this pair of TALENs is expected to be functional in many other mammalian species. Moreover, we demonstrate that these MSTN TALENs can facilitate targeted integration of a mCherry expression cassette or a larger muscular dystrophy gene (dysferlin) expression cassette into the MSTN locus in mouse or human cells. Therefore, targeted editing of the myostatin gene using our highly specific and efficient TALEN pair would facilitate cell engineering, allowing potential use in translational research for cell-based therapy.
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Affiliation(s)
- Li Xu
- Department of Cell and Molecular Physiology, Loyola University Chicago Health Science Division, Maywood, Illinois
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385
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Katsuyama T, Akmammedov A, Seimiya M, Hess SC, Sievers C, Paro R. An efficient strategy for TALEN-mediated genome engineering in Drosophila. Nucleic Acids Res 2013; 41:e163. [PMID: 23877243 PMCID: PMC3783190 DOI: 10.1093/nar/gkt638] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In reverse genetics, a gene’s function is elucidated through targeted modifications in the coding region or associated DNA cis-regulatory elements. To this purpose, recently developed customizable transcription activator-like effector nucleases (TALENs) have proven an invaluable tool, allowing introduction of double-strand breaks at predetermined sites in the genome. Here we describe a practical and efficient method for the targeted genome engineering in Drosophila. We demonstrate TALEN-mediated targeted gene integration and efficient identification of mutant flies using a traceable marker phenotype. Furthermore, we developed an easy TALEN assembly (easyT) method relying on simultaneous reactions of DNA Bae I digestion and ligation, enabling construction of complete TALENs from a monomer unit library in a single day. Taken together, our strategy with easyT and TALEN-plasmid microinjection simplifies mutant generation and enables isolation of desired mutant fly lines in the F1 generation.
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Affiliation(s)
- Tomonori Katsuyama
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Mattenstrasse 26, 4058 Basel, Switzerland and Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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386
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Engineering nucleases for gene targeting: safety and regulatory considerations. N Biotechnol 2013; 31:18-27. [PMID: 23851284 DOI: 10.1016/j.nbt.2013.07.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/24/2013] [Accepted: 07/03/2013] [Indexed: 12/26/2022]
Abstract
Nuclease-based gene targeting (NBGT) represents a significant breakthrough in targeted genome editing since it is applicable from single-celled protozoa to human, including several species of economic importance. Along with the fast progress in NBGT and the increasing availability of customized nucleases, more data are available about off-target effects associated with the use of this approach. We discuss how NBGT may offer a new perspective for genetic modification, we address some aspects crucial for a safety improvement of the corresponding techniques and we also briefly relate the use of NBGT applications and products to the regulatory oversight.
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387
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Generation of RAG 1- and 2-deficient rabbits by embryo microinjection of TALENs. Cell Res 2013; 23:1059-62. [PMID: 23835472 DOI: 10.1038/cr.2013.85] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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388
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Wu J, Huang Z, Ren J, Zhang Z, He P, Li Y, Ma J, Chen W, Zhang Y, Zhou X, Yang Z, Wu SQ, Chen L, Han J. Mlkl knockout mice demonstrate the indispensable role of Mlkl in necroptosis. Cell Res 2013; 23:994-1006. [PMID: 23835476 PMCID: PMC3731568 DOI: 10.1038/cr.2013.91] [Citation(s) in RCA: 456] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/07/2013] [Accepted: 05/27/2013] [Indexed: 11/09/2022] Open
Abstract
Mixed lineage kinase domain-like protein (Mlkl) was recently found to interact with receptor interacting protein 3 (Rip3) and to be essential for tumor necrosis factor (TNF)-induced programmed necrosis (necroptosis) in cultured cell lines. We have generated Mlkl-deficient mice by transcription activator-like effector nucleases (TALENs)-mediated gene disruption and found Mlkl to be dispensable for normal mouse development as well as immune cell development. Mlkl-deficient mouse embryonic fibroblasts (MEFs) and macrophages both showed resistance to necrotic but not apoptotic stimuli. Mlkl-deficient MEFs and macrophages were indistinguishable from wild-type cells in their ability to activate NF-κB, ERK, JNK, and p38 in response to TNF and lipopolysaccharides (LPS), respectively. Consistently, Mlkl-deficient macrophages and mice exhibited normal interleukin-1β (IL-1β), IL-6, and TNF production after LPS treatment. Mlkl deficiency protects mice from cerulean-induced acute pancreatitis, a necrosis-related disease, but has no effect on polymicrobial septic shock-induced animal death. Our results provide genetic evidence for the role of Mlkl in necroptosis.
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Affiliation(s)
- Jianfeng Wu
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China
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389
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Lim S, Wang Y, Yu X, Huang Y, Featherstone MS, Sampath K. A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of targeting nucleases. Genome Biol 2013; 14:R69. [PMID: 23815890 PMCID: PMC4054832 DOI: 10.1186/gb-2013-14-7-r69] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022] Open
Abstract
Precise and effective genome-editing tools are essential for functional genomics and gene therapy. Targeting nucleases have been successfully used to edit genomes. However, whole-locus or element-specific deletions abolishing transcript expression have not previously been reported. Here, we show heritable targeting of locus-specific deletions in the zebrafish nodal-related genes squint (sqt) and cyclops (cyc). Our strategy of heritable chromosomal editing can be used for disease modeling, analyzing gene clusters, regulatory regions, and determining the functions of non-coding RNAs in genomes.
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390
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Shan Q, Wang Y, Chen K, Liang Z, Li J, Zhang Y, Zhang K, Liu J, Voytas DF, Zheng X, Zhang Y, Gao C. Rapid and efficient gene modification in rice and Brachypodium using TALENs. MOLECULAR PLANT 2013; 6:1365-8. [PMID: 23288864 PMCID: PMC3968307 DOI: 10.1093/mp/sss162] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 12/20/2012] [Indexed: 05/18/2023]
Affiliation(s)
- Qiwei Shan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- These authors contributed equally to this work
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- These authors contributed equally to this work
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- These authors contributed equally to this work
| | - Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinxing Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yong Zhang
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- To whom correspondence should be addressed. C.-X.G. E-mail , tel. 86–10–64807727, fax 86–10–64807727. Y.Z. E-mail , tel. 86–28–83206556, fax 86-28-83206556
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- To whom correspondence should be addressed. C.-X.G. E-mail , tel. 86–10–64807727, fax 86–10–64807727. Y.Z. E-mail , tel. 86–28–83206556, fax 86-28-83206556
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391
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Abstract
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. These chimeric nucleases are composed of programmable, sequence-specific DNA-binding modules linked to a nonspecific DNA cleavage domain. ZFNs and TALENs enable a broad range of genetic modifications by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining or homology-directed repair at specific genomic locations. Here, we review achievements made possible by site-specific nuclease technologies and discuss applications of these reagents for genetic analysis and manipulation. In addition, we highlight the therapeutic potential of ZFNs and TALENs and discuss future prospects for the field, including the emergence of clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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392
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78495111110.1016/j.tibtech.2013.04.004" />
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393
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Weinstock MT. Keystone Symposia conference on precision genome engineering and synthetic biology brings together players from both disciplines. ACS Synth Biol 2013; 2:296-300. [PMID: 24884109 DOI: 10.1021/sb400045k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew T Weinstock
- Department of Biochemistry, University of Utah School of Medicine , Salt Lake City, Utah 84112, United States
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394
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Novel GM animal technologies and their governance. Transgenic Res 2013; 22:681-95. [DOI: 10.1007/s11248-013-9724-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 06/11/2013] [Indexed: 12/31/2022]
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395
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Pillay LM, Selland LG, Fleisch VC, Leighton PLA, Cheng CS, Famulski JK, Ritzel RG, March LD, Wang H, Allison WT, Waskiewicz AJ. Evaluating the mutagenic activity of targeted endonucleases containing a Sharkey FokI cleavage domain variant in zebrafish. Zebrafish 2013; 10:353-64. [PMID: 23781947 DOI: 10.1089/zeb.2012.0832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic targeted endonucleases such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) have recently emerged as powerful tools for targeted mutagenesis, especially in organisms that are not amenable to embryonic stem cell manipulation. Both ZFNs and TALENs consist of DNA-binding arrays that are fused to the nonspecific FokI nuclease domain. In an effort to improve targeted endonuclease mutagenesis efficiency, we enhanced their catalytic activity using the Sharkey FokI nuclease domain variant. All constructs tested display increased DNA cleavage activity in vitro. We demonstrate that one out of four ZFN arrays containing the Sharkey FokI variant exhibits a dramatic increase in mutagenesis frequency in vivo in zebrafish. The other three ZFNs exhibit no significant alteration of activity in vivo. Conversely, we demonstrate that TALENs containing the Sharkey FokI variant exhibit absent or severely reduced in vivo mutagenic activity in zebrafish. Notably, Sharkey ZFNs and TALENs do not generate increased toxicity-related defects or mortality. Our results present Sharkey ZFNs as an effective alternative to conventional ZFNs, but advise against the use of Sharkey TALENs.
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Affiliation(s)
- Laura M Pillay
- Department of Biological Sciences, University of Alberta , Edmonton, Canada
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396
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The new pig on the block: modelling cancer in pigs. Transgenic Res 2013; 22:673-80. [DOI: 10.1007/s11248-013-9720-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/30/2013] [Indexed: 01/09/2023]
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397
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Osborn MJ, Starker CG, McElroy AN, Webber BR, Riddle MJ, Xia L, DeFeo AP, Gabriel R, Schmidt M, Von Kalle C, Carlson DF, Maeder ML, Joung JK, Wagner JE, Voytas DF, Blazar BR, Tolar J. TALEN-based gene correction for epidermolysis bullosa. Mol Ther 2013; 21:1151-9. [PMID: 23546300 PMCID: PMC3677309 DOI: 10.1038/mt.2013.56] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is characterized by a functional deficit of type VII collagen protein due to gene defects in the type VII collagen gene (COL7A1). Gene augmentation therapies are promising, but run the risk of insertional mutagenesis. To abrogate this risk, we explored the possibility of using engineered transcription activator-like effector nucleases (TALEN) for precise genome editing. We report the ability of TALEN to induce site-specific double-stranded DNA breaks (DSBs) leading to homology-directed repair (HDR) from an exogenous donor template. This process resulted in COL7A1 gene mutation correction in primary fibroblasts that were subsequently reprogrammed into inducible pluripotent stem cells and showed normal protein expression and deposition in a teratoma-based skin model in vivo. Deep sequencing-based genome-wide screening established a safety profile showing on-target activity and three off-target (OT) loci that, importantly, were at least 10 kb from a coding sequence. This study provides proof-of-concept for TALEN-mediated in situ correction of an endogenous patient-specific gene mutation and used an unbiased screen for comprehensive TALEN target mapping that will cooperatively facilitate translational application.
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Affiliation(s)
- Mark J Osborn
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Colby G Starker
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amber N McElroy
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Beau R Webber
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Megan J Riddle
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lily Xia
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Anthony P DeFeo
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Richard Gabriel
- Department of Translational Oncology, National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christof Von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel F Carlson
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Morgan L Maeder
- Molecular Pathology Unit, Center for Computational & Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Computational & Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - John E Wagner
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel F Voytas
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bruce R Blazar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jakub Tolar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
- Blood and Marrow Transplantation, University of Minnesota Medical School, MMC 366, 420 Delaware Street SE, Minneapolis, Minnesota 55455, USA. E-mail:
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398
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TALENs: Customizable Molecular DNA Scissors for Genome Engineering of Plants. J Genet Genomics 2013; 40:271-9. [DOI: 10.1016/j.jgg.2013.03.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 01/07/2023]
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399
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Gupta A, Hall VL, Kok FO, Shin M, McNulty JC, Lawson ND, Wolfe SA. Targeted chromosomal deletions and inversions in zebrafish. Genome Res 2013; 23:1008-17. [PMID: 23478401 PMCID: PMC3668355 DOI: 10.1101/gr.154070.112] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/07/2013] [Indexed: 12/19/2022]
Abstract
Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) provide powerful platforms for genome editing in plants and animals. Typically, a single nuclease is sufficient to disrupt the function of protein-coding genes through the introduction of microdeletions or insertions that cause frameshifts within an early coding exon. However, interrogating the function of cis-regulatory modules or noncoding RNAs in many instances requires the excision of this element from the genome. In human cell lines and invertebrates, two nucleases targeting the same chromosome can promote the deletion of intervening genomic segments with modest efficiencies. We have examined the feasibility of using this approach to delete chromosomal segments within the zebrafish genome, which would facilitate the functional study of large noncoding sequences in a vertebrate model of development. Herein, we demonstrate that segmental deletions within the zebrafish genome can be generated at multiple loci and are efficiently transmitted through the germline. Using two nucleases, we have successfully generated deletions of up to 69 kb at rates sufficient for germline transmission (1%-15%) and have excised an entire lincRNA gene and enhancer element. Larger deletions (5.5 Mb) can be generated in somatic cells, but at lower frequency (0.7%). Segmental inversions have also been generated, but the efficiency of these events is lower than the corresponding deletions. The ability to efficiently delete genomic segments in a vertebrate developmental system will facilitate the study of functional noncoding elements on an organismic level.
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Affiliation(s)
- Ankit Gupta
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Victoria L. Hall
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Fatma O. Kok
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Masahiro Shin
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Joseph C. McNulty
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Nathan D. Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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400
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Ma AC, Lee HB, Clark KJ, Ekker SC. High efficiency In Vivo genome engineering with a simplified 15-RVD GoldyTALEN design. PLoS One 2013; 8:e65259. [PMID: 23734242 PMCID: PMC3667041 DOI: 10.1371/journal.pone.0065259] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 04/25/2013] [Indexed: 01/18/2023] Open
Abstract
Transcription activator-like effector nucleases (TALENs) enable genome engineering in cell culture and many organisms. Recently, the GoldyTALEN scaffold was shown to readily introduce mutations in zebrafish (Danio rerio) and livestock through non-homologous end joining (NHEJ) and homology-directed repair (HDR). To deploy the GoldyTALEN system for high-throughput mutagenesis in model organisms, a simple design with high efficacy is desirable. We tested the in vivo efficacy of a simplified 15-RVD GoldyTALEN design (spacer between 13–20 bp and T nucleotide preceding each TALEN binding site) in zebrafish. All 14 tested TALEN pairs (100%) introduced small insertions and deletions at somatic efficacy ranging from 24 to 86%, and mutations were inheritable at high frequencies (18–100%). By co-injecting two GoldyTALEN pairs, inheritable deletions of a large genomic fragment up to 18 kb were successfully introduced at two different loci. In conclusion, these high efficiency 15-RVD GoldyTALENs are useful for high-throughput mutagenesis in diverse application including hypothesis testing from basic science to precision medicine.
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Affiliation(s)
- Alvin C. Ma
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Han B. Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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