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Yuan YG, Liu SZ, Farhab M, Lv MY, Zhang T, Cao SX. Genome editing: An insight into disease resistance, production efficiency, and biomedical applications in livestock. Funct Integr Genomics 2024; 24:81. [PMID: 38709433 DOI: 10.1007/s10142-024-01364-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/07/2024]
Abstract
One of the primary concerns for the survival of the human species is the growing demand for food brought on by an increasing global population. New developments in genome-editing technology present promising opportunities for the growth of wholesome and prolific farm animals. Genome editing in large animals is used for a variety of purposes, including biotechnology to improve food production, animal health, and pest management, as well as the development of animal models for fundamental research and biomedicine. Genome editing entails modifying genetic material by removing, adding, or manipulating particular DNA sequences from a particular locus in a way that does not happen naturally. The three primary genome editors are CRISPR/Cas 9, TALENs, and ZFNs. Each of these enzymes is capable of precisely severing nuclear DNA at a predetermined location. One of the most effective inventions is base editing, which enables single base conversions without the requirement for a DNA double-strand break (DSB). As reliable methods for precise genome editing in studies involving animals, cytosine and adenine base editing are now well-established. Effective zygote editing with both cytosine and adenine base editors (ABE) has resulted in the production of animal models. Both base editors produced comparable outcomes for the precise editing of point mutations in somatic cells, advancing the field of gene therapy. This review focused on the principles, methods, recent developments, outstanding applications, the advantages and disadvantages of ZFNs, TALENs, and CRISPR/Cas9 base editors, and prime editing in diverse lab and farm animals. Additionally, we address the methodologies that can be used for gene regulation, base editing, and epigenetic alterations, as well as the significance of genome editing in animal models to better reflect real disease. We also look at methods designed to increase the effectiveness and precision of gene editing tools. Genome editing in large animals is used for a variety of purposes, including biotechnology to improve food production, animal health, and pest management, as well as the development of animal models for fundamental research and biomedicine. This review is an overview of the existing knowledge of the principles, methods, recent developments, outstanding applications, the advantages and disadvantages of zinc finger nucleases (ZFNs), transcription-activator-like endonucleases (TALENs), and clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR/Cas 9), base editors and prime editing in diverse lab and farm animals, which will offer better and healthier products for the entire human race.
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Affiliation(s)
- Yu-Guo Yuan
- College of Veterinary Medicine/Key Laboratory of Animal Genetic Engineering, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Song-Zi Liu
- College of Veterinary Medicine/Key Laboratory of Animal Genetic Engineering, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Muhammad Farhab
- College of Veterinary Medicine/Key Laboratory of Animal Genetic Engineering, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Mei-Yun Lv
- College of Veterinary Medicine/Key Laboratory of Animal Genetic Engineering, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ting Zhang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212499, China
| | - Shao-Xiao Cao
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Jiangsu Provincial Engineering Research Center for Precision animal Breeding, Nanjing, 210014, China
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Jose B, Punetha M, Tripathi MK, Khanna S, Yadav V, Singh AK, Kumar B, Singh K, Chouhan VS, Sarkar M. CRISPR/Cas mediated disruption of BMPR-1B gene and introduction of FecB mutation into the Caprine embryos using Easi-CRISPR strategy. Theriogenology 2023; 211:125-133. [PMID: 37619525 DOI: 10.1016/j.theriogenology.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Bone Morphogenetic Proteins play a significant role in ovarian physiology and contribute to the reproductive fitness of mammals. The BMPR-1B/FecB mutation, a loss of function mutation increases litter size by 1-2 with each number of mutated alleles in sheep. Considering demand-supply gap of the meat industry, and low replacement rate of indigenous caprine species, the conservative BMPR-1B locus can be explored, and FecB mutated goats can be produced. The experiment one produced CRISPR/Cas mediated KO transferable caprine embryos, and experiment two generated caprine embryos with desired FecB mutation using Easi-CRISPR strategy. In the KO experiment, Cas9 and BMPR-1B guide RNA (100:100ng/ul) were electroporated into single stage caprine zygotes at 750V, 10 ms and 1pulse using Neon transfection system. In the second experiment, phosphorothioate (PS) modified single-stranded oligodeoxynucleotide (ssODN) was used as an HDR template along with CRISPR components (100:100ng/ul, ssODN 100ng/ul). The precise time and method of electroporation, RNP format of CRISPR components and PS modified asymmetric ssODN were the factors that affected the production of mosaicism free BMPR-1B edited caprine embryos. The editing efficiency of KO and KI experiments was 68.52 and 63.16% respectively, and successful production of goats with higher mean ovulation rate can be realized with addition of embryo transfer technology to these experiments.
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Affiliation(s)
- Bosco Jose
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Meeti Punetha
- Division of Animal Physiology and Reproduction, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India.
| | - Manoj Kumar Tripathi
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Shivani Khanna
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Vijay Yadav
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Amit Kumar Singh
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Brijesh Kumar
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Kiranjeet Singh
- Division of Surgery, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Vikrant Singh Chouhan
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Mihir Sarkar
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
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Wang M, Ding F, Wang H, Li L, Dai Y, Sun Z, Li N. Versatile generation of precise gene edits in bovines using SEGCPN. BMC Biol 2023; 21:226. [PMID: 37864194 PMCID: PMC10589966 DOI: 10.1186/s12915-023-01677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/07/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Gene knockout and knock-in have been widely performed in large farm animals based on genome editing systems. However, many types of precise gene editing, including targeted deletion, gene tagging, and large gene fragment replacement, remain a challenge in large farm animals. RESULTS Here, we established versatile self-excising gene-targeting technology in combination with programmable nucleases (SEGCPN) to efficiently generate various types of precise gene editing in bovine. First, we used this versatile method to successfully generate bovine embryos with point mutations and 11-bp deletions at the MSTN locus. Second, we successfully generated bulls with EGFP labeling at the SRY locus. Finally, we successfully generated humanized cows in which the endogenous 18-kb α-casein gene was replaced with a 2.6-kb human α-lactalbumin gene. CONCLUSIONS In summary, our new SEGCPN method offers unlimited possibilities for various types of precise gene editing in large animals for application both in agriculture and disease models.
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Affiliation(s)
- Ming Wang
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China
| | - Fangrong Ding
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Haiping Wang
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Ling Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Yunping Dai
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
| | - ZhaoLin Sun
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China.
| | - Ning Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China.
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Popova J, Bets V, Kozhevnikova E. Perspectives in Genome-Editing Techniques for Livestock. Animals (Basel) 2023; 13:2580. [PMID: 37627370 PMCID: PMC10452040 DOI: 10.3390/ani13162580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Genome editing of farm animals has undeniable practical applications. It helps to improve production traits, enhances the economic value of livestock, and increases disease resistance. Gene-modified animals are also used for biomedical research and drug production and demonstrate the potential to be used as xenograft donors for humans. The recent discovery of site-specific nucleases that allow precision genome editing of a single-cell embryo (or embryonic stem cells) and the development of new embryological delivery manipulations have revolutionized the transgenesis field. These relatively new approaches have already proven to be efficient and reliable for genome engineering and have wide potential for use in agriculture. A number of advanced methodologies have been tested in laboratory models and might be considered for application in livestock animals. At the same time, these methods must meet the requirements of safety, efficiency and availability of their application for a wide range of farm animals. This review aims at covering a brief history of livestock animal genome engineering and outlines possible future directions to design optimal and cost-effective tools for transgenesis in farm species.
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Affiliation(s)
- Julia Popova
- Laboratory of Bioengineering, Novosibirsk State Agrarian University, 630039 Novosibirsk, Russia; (J.P.); (V.B.)
| | - Victoria Bets
- Laboratory of Bioengineering, Novosibirsk State Agrarian University, 630039 Novosibirsk, Russia; (J.P.); (V.B.)
- Center of Technological Excellence, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Elena Kozhevnikova
- Laboratory of Bioengineering, Novosibirsk State Agrarian University, 630039 Novosibirsk, Russia; (J.P.); (V.B.)
- Laboratory of Experimental Models of Cognitive and Emotional Disorders, Scientific-Research Institute of Neurosciences and Medicine, 630117 Novosibirsk, Russia
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Introduction of the FecG F mutation in GDF9 gene via CRISPR/Cas9 system with single-stranded oligodeoxynucleotide. Theriogenology 2023; 197:177-185. [PMID: 36525857 DOI: 10.1016/j.theriogenology.2022.11.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 11/21/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) 9 system has been a recent focus of breeders owing to its potential to improve economically significant traits of livestock. The introduction of defined point mutations into the ovine genome via CRISPR/Cas9-mediated homology-directed repair has been reported; however, indel and mosaic events observed in genetically modified animals limit the practical application of this system in sheep breeding. The FecGF mutation (g. G1111A, p. V371 M) in the growth differentiation factor 9 (GDF9) gene is strongly associated with litter size in Belclare and Norwegian White Sheep. In the present study, we introduced the FecGF mutation in GDF9 by co-injecting the CRISPR/Cas9 system, single-stranded oligodeoxynucleotide (ssODN), and Scr7 into ovine zygotes. Scr7 at various concentrations (0 μM, 1 μM, and 2 μM) had no adverse effects on embryonic development in vitro. No significant differences in total mutation, point mutation, and indel rates in embryos were observed among groups treated with different concentrations of Scr7. However, the mosaicism rates of embryos from zygotes microinjected with 1 and 2 μM Scr7 were significantly lower than that for 0 μM Scr7 (7.7% and 7.5% vs. 19.7%). We successfully obtained lambs with defined nucleotide substitutions by the coinjection of Cas9 mRNA, sgRNA, ssODN, and 1 μM Scr7 into Altay sheep zygotes. The single nucleotide mutation efficiency was 7.69% (3/39) in newborn lambs, with one mosaic. Our findings provide evidence that Scr7 could improve the specificity of the CRISPR/Cas9 system for the introduction of a defined point mutation in livestock to some extent.
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Jiang P, Iqbal A, Cui Z, Yu H, Zhao Z. Bta-miR-33a affects gene expression and lipid levels in Chinese Holstein mammary epithelial cells. Arch Anim Breed 2022; 65:357-370. [PMID: 36304442 PMCID: PMC9594864 DOI: 10.5194/aab-65-357-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 08/29/2022] [Indexed: 11/07/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules of about 19-25 nucleotides in length that regulate different biological processes, including lipid metabolism. In this study, we explored the effect of bta-miR-33a on lipid metabolism in bovine mammary epithelial cells (BMECs) of Chinese Holstein for the first time. For this purpose, the plasmids of bta-miR-33a mimic, bta-miR-33a inhibitor and bta-miR-33a negative control were constructed to overexpress or repress bta-miR-33a in BMECs. The effects of plasmid transfection were analysed by examining the mRNA and protein expression levels of ELOVL6 and the intracellular triglycerides. The results showed that bta-miR-33a directly inhibited the expression of ELOVL6 in BMECs; decreased the mRNA levels of ELOVL5, HACD2, CPT1A and MSMO1; and increased the mRNA level of ALOX15. Sequence bta-miR-33a also increased the contents of triglycerides in the cells, presumably as a consequence of these gene expression changes. In summary, the results of the present study suggest that bta-miR-33a regulates lipid metabolism by targeting ELOVL6, which might be a potential molecular marker of milk fat composition.
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Affiliation(s)
- Ping Jiang
- Department of Animal Breeding and Genetics, College of Coastal
Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong,
524088, PR China
| | - Ambreen Iqbal
- Department of Animal Breeding and Genetics, College of Coastal
Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong,
524088, PR China
| | - Zhiqian Cui
- College of Animal Science, Jilin University,
Changchun, 130062, PR China
| | - Haibin Yu
- Department of Animal Breeding and Genetics, College of Coastal
Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong,
524088, PR China
| | - Zhihui Zhao
- Department of Animal Breeding and Genetics, College of Coastal
Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong,
524088, PR China
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Wei J, Brophy B, Cole SA, Moormann J, Boch J, Laible G. Cytoplasmic Injection of Zygotes to Genome Edit Naturally Occurring Sequence Variants Into Bovine Embryos. Front Genet 2022; 13:925913. [PMID: 35899192 PMCID: PMC9310181 DOI: 10.3389/fgene.2022.925913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022] Open
Abstract
Genome editing provides opportunities to improve current cattle breeding strategies through targeted introduction of natural sequence variants, accelerating genetic gain. This can be achieved by harnessing homology-directed repair mechanisms following editor-induced cleavage of the genome in the presence of a repair template. Introducing the genome editors into zygotes and editing in embryos has the advantage of uncompromised development into live animals and alignment with contemporary embryo-based improvement practices. In our study, we investigated the potential to introduce sequence variants, known from the pre-melanosomal protein 17 (PMEL) and prolactin receptor (PRLR) genes, and produce non-mosaic, edited embryos, completely converted into the precision genotype. Injection of gRNA/Cas9 editors into bovine zygotes to introduce a 3 bp deletion variant into the PMEL gene produced up to 11% fully converted embryos. The conversion rate was increased to up to 48% with the use of TALEN but only when delivered by plasmid. Testing three gRNA/Cas9 editors in the context of several known PRLR sequence variants, different repair template designs and delivery as DNA, RNA or ribonucleoprotein achieved full conversion rates up to 8%. Furthermore, we developed a biopsy-based screening strategy for non-mosaic embryos which has the potential for exclusively producing non-mosaic animals with intended precision edits.
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Affiliation(s)
- Jingwei Wei
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Brigid Brophy
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Sally-Ann Cole
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
| | - Jannis Moormann
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Gӧtz Laible
- Animal Biotechnology, Ruakura Research Centre, AgResearch Ltd, Hamilton, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
- *Correspondence: Gӧtz Laible,
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Enhancing Animal Disease Resistance, Production Efficiency, and Welfare through Precise Genome Editing. Int J Mol Sci 2022; 23:ijms23137331. [PMID: 35806334 PMCID: PMC9266401 DOI: 10.3390/ijms23137331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 12/03/2022] Open
Abstract
The major goal of animal breeding is the genetic enhancement of economic traits. The CRISPR/Cas system, which includes nuclease-mediated and base editor mediated genome editing tools, provides an unprecedented approach to modify the mammalian genome. Thus, farm animal genetic engineering and genetic manipulation have been fundamentally revolutionized. Agricultural animals with traits of interest can be obtained in just one generation (and without long time selection). Here, we reviewed the advancements of the CRISPR (Clustered regularly interspaced short palindromic repeats)/Cas (CRISPR associated proteins) genome editing tools and their applications in animal breeding, especially in improving disease resistance, production performance, and animal welfare. Additionally, we covered the regulations on genome-edited animals (GEAs) and ways to accelerate their use. Recommendations for how to produce GEAs were also discussed. Despite the current challenges, we believe that genome editing breeding and GEAs will be available in the near future.
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Lin Y, Li J, Li C, Tu Z, Li S, Li XJ, Yan S. Application of CRISPR/Cas9 System in Establishing Large Animal Models. Front Cell Dev Biol 2022; 10:919155. [PMID: 35656550 PMCID: PMC9152178 DOI: 10.3389/fcell.2022.919155] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
The foundation for investigating the mechanisms of human diseases is the establishment of animal models, which are also widely used in agricultural industry, pharmaceutical applications, and clinical research. However, small animals such as rodents, which have been extensively used to create disease models, do not often fully mimic the key pathological changes and/or important symptoms of human disease. As a result, there is an emerging need to establish suitable large animal models that can recapitulate important phenotypes of human diseases for investigating pathogenesis and developing effective therapeutics. However, traditional genetic modification technologies used in establishing small animal models are difficultly applied for generating large animal models of human diseases. This difficulty has been overcome to a great extent by the recent development of gene editing technology, especially the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). In this review, we focus on the applications of CRISPR/Cas9 system to establishment of large animal models, including nonhuman primates, pigs, sheep, goats and dogs, for investigating disease pathogenesis and treatment. We also discuss the limitations of large animal models and possible solutions according to our current knowledge. Finally, we sum up the applications of the novel genome editing tool Base Editors (BEs) and its great potential for gene editing in large animals.
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Xu X, Zhang X, Peng X, Liu C, Li W, Liu M. Comparison of the efficiency and precision of Base editor and CRISPR/Cas9 for inducing defined point mutation(S395F) in ovine embryos. Reprod Domest Anim 2022; 57:829-838. [DOI: 10.1111/rda.14124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/10/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Xin Xu
- College of Life Science and Technology Xinjiang University Urumqi 830046 Xinjiang China
| | - Xuemei Zhang
- Institute of animal biotechnology Xinjiang Academy of Animal Science Urumqi 830026 Xinjiang China
| | - Xinrong Peng
- Institute of animal biotechnology Xinjiang Academy of Animal Science Urumqi 830026 Xinjiang China
| | - Chunjie Liu
- College of Animal Science Tarim University Alar 843300 Xinjiang China
| | - Wenrong Li
- Institute of animal biotechnology Xinjiang Academy of Animal Science Urumqi 830026 Xinjiang China
| | - Mingjun Liu
- Institute of animal biotechnology Xinjiang Academy of Animal Science Urumqi 830026 Xinjiang China
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Karavolias NG, Horner W, Abugu MN, Evanega SN. Application of Gene Editing for Climate Change in Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.685801] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Climate change imposes a severe threat to agricultural systems, food security, and human nutrition. Meanwhile, efforts in crop and livestock gene editing have been undertaken to improve performance across a range of traits. Many of the targeted phenotypes include attributes that could be beneficial for climate change adaptation. Here, we present examples of emerging gene editing applications and research initiatives that are aimed at the improvement of crops and livestock in response to climate change, and discuss technical limitations and opportunities therein. While only few applications of gene editing have been translated to agricultural production thus far, numerous studies in research settings have demonstrated the potential for potent applications to address climate change in the near future.
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Perisse IV, Fan Z, Singina GN, White KL, Polejaeva IA. Improvements in Gene Editing Technology Boost Its Applications in Livestock. Front Genet 2021; 11:614688. [PMID: 33603767 PMCID: PMC7885404 DOI: 10.3389/fgene.2020.614688] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 12/18/2022] Open
Abstract
Accelerated development of novel CRISPR/Cas9-based genome editing techniques provides a feasible approach to introduce a variety of precise modifications in the mammalian genome, including introduction of multiple edits simultaneously, efficient insertion of long DNA sequences into specific targeted loci as well as performing nucleotide transitions and transversions. Thus, the CRISPR/Cas9 tool has become the method of choice for introducing genome alterations in livestock species. The list of new CRISPR/Cas9-based genome editing tools is constantly expanding. Here, we discuss the methods developed to improve efficiency and specificity of gene editing tools as well as approaches that can be employed for gene regulation, base editing, and epigenetic modifications. Additionally, advantages and disadvantages of two primary methods used for the production of gene-edited farm animals: somatic cell nuclear transfer (SCNT or cloning) and zygote manipulations will be discussed. Furthermore, we will review agricultural and biomedical applications of gene editing technology.
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Affiliation(s)
- Iuri Viotti Perisse
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Zhiqiang Fan
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Galina N. Singina
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Kenneth L. White
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Irina A. Polejaeva
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
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Zhou S, Ding Y, Liu J, Liu Y, Zhao X, Li G, Zhang C, Li C, Wang Y, Kalds P, Gao Y, Zong B, Huang X, Huang S, Yu H, Kou Q, Petersen B, Huang X, Wang X, Ma B, Chen Y. Highly efficient generation of sheep with a defined FecB B mutation via adenine base editing. Genet Sel Evol 2020; 52:35. [PMID: 32611306 PMCID: PMC7328262 DOI: 10.1186/s12711-020-00554-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/18/2020] [Indexed: 02/08/2023] Open
Abstract
Base editing has the potential to improve important economic traits in agriculture and can precisely convert single nucleotides in DNA or RNA sequences into minimal double-strand DNA breaks (DSB). Adenine base editors (ABE) have recently emerged as a base editing tool for the conversion of targeted A:T to G:C, but have not yet been used in sheep. ABEmax is one of the latest versions of ABE, which consists of a catalytically-impaired nuclease and a laboratory-evolved DNA-adenosine deaminase. The Booroola fecundity (FecBB) mutation (g.A746G, p.Q249R) in the bone morphogenetic protein receptor 1B (BMPR1B) gene influences fecundity in many sheep breeds. In this study, by using ABEmax we successfully obtained lambs with defined point mutations that result in an amino acid substitution (p.Gln249Arg). The efficiency of the defined point mutations was 75% in newborn lambs, since six lambs were heterozygous at the FecBB mutation site (g.A746G, p.Q249R), and two lambs were wild-type. We did not detect off-target mutations in the eight edited lambs. Here, we report the validation of the first gene-edited sheep generated by ABE and highlight its potential to improve economically important traits in livestock.
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Affiliation(s)
- Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yige Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoe Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Guanwei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chenguang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bo Zong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyu Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Honghao Yu
- College of Biotechnology, Guilin Medical University, Guilin, China
| | - Qifang Kou
- Ningxia Tianyuan Tan Sheep Farm, Hongsibu, China
| | - Bjoern Petersen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Baohua Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
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14
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Menchaca A, Dos Santos-Neto PC, Mulet AP, Crispo M. CRISPR in livestock: From editing to printing. Theriogenology 2020; 150:247-254. [PMID: 32088034 PMCID: PMC7102594 DOI: 10.1016/j.theriogenology.2020.01.063] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022]
Abstract
Precise genome editing of large animals applied to livestock and biomedicine is nowadays possible since the CRISPR revolution. This review summarizes the latest advances and the main technical issues that determine the success of this technology. The pathway from editing to printing, from engineering the genome to achieving the desired animals, does not always imply an easy, fast and safe journey. When applied in large animals, CRISPR involves time- and cost-consuming projects, and it is mandatory not only to choose the best approach for genome editing, but also for embryo production, zygote microinjection or electroporation, cryopreservation and embryo transfer. The main technical refinements and most frequent questions to improve this disruptive biotechnology in large animals are presented. In addition, we discuss some CRISPR applications to enhance livestock production in the context of a growing global demand of food, in terms of increasing efficiency, reducing the impact of farming on the environment, enhancing pest control, animal welfare and health. The challenge is no longer technical. Controversies and consensus, opportunities and threats, benefits and risks, ethics and science should be reconsidered to enter into the CRISPR era.
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Affiliation(s)
- A Menchaca
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Cruz del Sur 2350, Montevideo, Uruguay.
| | - P C Dos Santos-Neto
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Cruz del Sur 2350, Montevideo, Uruguay
| | - A P Mulet
- Unidad de Animales Transgénicos y de Experimentación (UATE), Institut Pasteur de Montevideo, Mataojo, 2020, Montevideo, Uruguay
| | - M Crispo
- Unidad de Animales Transgénicos y de Experimentación (UATE), Institut Pasteur de Montevideo, Mataojo, 2020, Montevideo, Uruguay
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15
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Menchaca A, Dos Santos-Neto PC, Souza-Neves M, Cuadro F, Mulet AP, Tesson L, Chenouard V, Guiffès A, Heslan JM, Gantier M, Anegón I, Crispo M. Otoferlin gene editing in sheep via CRISPR-assisted ssODN-mediated Homology Directed Repair. Sci Rep 2020; 10:5995. [PMID: 32265471 PMCID: PMC7138848 DOI: 10.1038/s41598-020-62879-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/21/2020] [Indexed: 11/20/2022] Open
Abstract
Different mutations of the OTOF gene, encoding for otoferlin protein expressed in the cochlear inner hair cells, induces a form of deafness that is the major cause of nonsyndromic recessive auditory neuropathy spectrum disorder in humans. We report the generation of the first large animal model of OTOF mutations using the CRISPR system associated with different Cas9 components (mRNA or protein) assisted by single strand oligodeoxynucleotides (ssODN) to induce homology-directed repair (HDR). Zygote microinjection was performed with two sgRNA targeting exon 5 and 6 associated to Cas9 mRNA or protein (RNP) at different concentrations in a mix with an ssODN template targeting HDR in exon 5 containing two STOP sequences. A total of 73 lambs were born, 13 showing indel mutations (17.8%), 8 of which (61.5%) had knock-in mutations by HDR. Higher concentrations of Cas9-RNP induced targeted mutations more effectively, but negatively affected embryo survival and pregnancy rate. This study reports by the first time the generation of OTOF disrupted sheep, which may allow better understanding and development of new therapies for human deafness related to genetic disorders. These results support the use of CRISPR/Cas system assisted by ssODN as an effective tool for gene editing in livestock.
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Affiliation(s)
- A Menchaca
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay.
| | - P C Dos Santos-Neto
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - M Souza-Neves
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - F Cuadro
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - A P Mulet
- Unidad de Animales Transgénicos y de Experimentación (UATE), Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - L Tesson
- Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France.,Transgenesis Rat ImmunoPhenomic facility (TRIP), F-44000, Nantes, France
| | - V Chenouard
- Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France.,Transgenesis Rat ImmunoPhenomic facility (TRIP), F-44000, Nantes, France
| | - A Guiffès
- Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France.,Transgenesis Rat ImmunoPhenomic facility (TRIP), F-44000, Nantes, France
| | - J M Heslan
- Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France.,GenoCellEdit facility, F-44000, Nantes, France
| | - M Gantier
- Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France.,GenoCellEdit facility, F-44000, Nantes, France
| | - I Anegón
- Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France. .,Transgenesis Rat ImmunoPhenomic facility (TRIP), F-44000, Nantes, France. .,GenoCellEdit facility, F-44000, Nantes, France.
| | - M Crispo
- Unidad de Animales Transgénicos y de Experimentación (UATE), Institut Pasteur de Montevideo, Montevideo, Uruguay.
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16
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Redesigning small ruminant genomes with CRISPR toolkit: Overview and perspectives. Theriogenology 2020; 147:25-33. [PMID: 32086048 DOI: 10.1016/j.theriogenology.2020.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/24/2020] [Accepted: 02/08/2020] [Indexed: 12/11/2022]
Abstract
Genetic modification is a rapidly developing field in which numerous significant breakthroughs have been achieved. Over the last few decades, genetic modification has evolved from insertional transgenesis to gene targeting and editing and, more recently, to base and prime editing using CRISPR-derived systems. Currently, CRISPR-based genome editing systems are showing great potential for generating gene-edited offspring with defined genetic characteristics. Domestic small ruminants (sheep and goats) have shown great potential as large animal models for genome engineering. Ovine and caprine genomes have been engineered using CRISPR-based systems for numerous purposes. These include generating superior agricultural breeds, expression of therapeutic agents in mammary glands, and developing animal models to be used in the study of human genetic disorders and regenerative medicine. The creation of these models has been facilitated by the continuous emergence and development of genetic modification tools. In this review, we provide an overview on how CRISPR-based systems have been used in the generation of gene-edited small ruminants through the two main pathways (embryonic microinjection and somatic cell nuclear transfer) and highlight the ovine and caprine genes that have been targeted via knockout, knockin, HDR-mediated point mutation, and base editing approaches, as well as the aims of these specific manipulations.
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17
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Bishop TF, Van Eenennaam AL. Genome editing approaches to augment livestock breeding programs. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb207159. [PMID: 32034040 DOI: 10.1242/jeb.207159] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The prospect of genome editing offers a number of promising opportunities for livestock breeders. Firstly, these tools can be used in functional genomics to elucidate gene function, and identify causal variants underlying monogenic traits. Secondly, they can be used to precisely introduce useful genetic variation into structured livestock breeding programs. Such variation may include repair of genetic defects, the inactivation of undesired genes, and the moving of useful alleles and haplotypes between breeds in the absence of linkage drag. Editing could also be used to accelerate the rate of genetic progress by enabling the replacement of the germ cell lineage of commercial breeding animals with cells derived from genetically elite lines. In the future, editing may also provide a useful complement to evolving approaches to decrease the length of the generation interval through in vitro generation of gametes. For editing to be adopted, it will need to seamlessly integrate with livestock breeding schemes. This will likely involve introducing edits into multiple elite animals to avoid genetic bottlenecks. It will also require editing of different breeds and lines to maintain genetic diversity, and enable structured cross-breeding. This requirement is at odds with the process-based trigger and event-based regulatory approach that has been proposed for the products of genome editing by several countries. In the absence of regulatory harmony, researchers in some countries will have the ability to use genome editing in food animals, while others will not, resulting in disparate access to these tools, and ultimately the potential for global trade disruptions.
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18
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Lee K, Uh K, Farrell K. Current progress of genome editing in livestock. Theriogenology 2020; 150:229-235. [PMID: 32000993 DOI: 10.1016/j.theriogenology.2020.01.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 12/12/2022]
Abstract
Historically, genetic engineering in livestock proved to be challenging. Without stable embryonic stem cell lines to utilize, somatic cell nuclear transfer (SCNT) had to be employed to produce many of the genetically engineered (GE) livestock models. Through the genetic engineering of somatic cells followed by SCNT, GE livestock models could be generated carrying site-specific modifications. Although successful, only a few GE livestock models were generated because of low efficiency and associated birth defects. Recently, there have been major strides in the development of genome editing tools: Zinc-Finger Nucleases (ZFNs), Transcription activator-like effector nucleases (TALENS), and Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated 9 (Cas9) system. These tools rely on the generation of a double strand DNA break, followed by one of two repair pathways: non-homologous end joining (NHEJ) or homology directed repair (HDR). Compared to the traditional approaches, these tools dramatically reduce time and effort needed to establish a GE animal. Another benefit of utilizing genome editing tools is the application of direct injection into developing embryos to induce targeted mutations, therefore, eliminating side effects associated with SCNT. Emerging technological advancements of genome editing systems have dramatically improved efficiency to generate GE livestock models for both biomedical and agricultural purposes. Although the efficiency of genome editing tools has revolutionized GE livestock production, improvements for safe and consistent application are desired. This review will provide an overview of genome editing techniques, as well as examples of GE livestock models for agricultural and biomedical purposes.
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Affiliation(s)
- Kiho Lee
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, USA.
| | - Kyungjun Uh
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Kayla Farrell
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, USA
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19
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Kalds P, Zhou S, Cai B, Liu J, Wang Y, Petersen B, Sonstegard T, Wang X, Chen Y. Sheep and Goat Genome Engineering: From Random Transgenesis to the CRISPR Era. Front Genet 2019; 10:750. [PMID: 31552084 PMCID: PMC6735269 DOI: 10.3389/fgene.2019.00750] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Sheep and goats are valuable livestock species that have been raised for their production of meat, milk, fiber, and other by-products. Due to their suitable size, short gestation period, and abundant secretion of milk, sheep and goats have become important model animals in agricultural, pharmaceutical, and biomedical research. Genome engineering has been widely applied to sheep and goat research. Pronuclear injection and somatic cell nuclear transfer represent the two primary procedures for the generation of genetically modified sheep and goats. Further assisted tools have emerged to enhance the efficiency of genetic modification and to simplify the generation of genetically modified founders. These tools include sperm-mediated gene transfer, viral vectors, RNA interference, recombinases, transposons, and endonucleases. Of these tools, the four classes of site-specific endonucleases (meganucleases, ZFNs, TALENs, and CRISPRs) have attracted wide attention due to their DNA double-strand break-inducing role, which enable desired DNA modifications based on the stimulation of native cellular DNA repair mechanisms. Currently, CRISPR systems dominate the field of genome editing. Gene-edited sheep and goats, generated using these tools, provide valuable models for investigations on gene functions, improving animal breeding, producing pharmaceuticals in milk, improving animal disease resistance, recapitulating human diseases, and providing hosts for the growth of human organs. In addition, more promising derivative tools of CRISPR systems have emerged such as base editors which enable the induction of single-base alterations without any requirements for homology-directed repair or DNA donor. These precise editors are helpful for revealing desirable phenotypes and correcting genetic diseases controlled by single bases. This review highlights the advances of genome engineering in sheep and goats over the past four decades with particular emphasis on the application of CRISPR/Cas9 systems.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bjoern Petersen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | | | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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20
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Li G, Zhou S, Li C, Cai B, Yu H, Ma B, Huang Y, Ding Y, Liu Y, Ding Q, He C, Zhou J, Wang Y, Zhou G, Li Y, Yan Y, Hua J, Petersen B, Jiang Y, Sonstegard T, Huang X, Chen Y, Wang X. Base pair editing in goat: nonsense codon introgression into FGF5 results in longer hair. FEBS J 2019; 286:4675-4692. [PMID: 31276295 DOI: 10.1111/febs.14983] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/21/2019] [Accepted: 07/03/2019] [Indexed: 12/26/2022]
Abstract
The ability to alter single bases without homology directed repair (HDR) of double-strand breaks provides a potential solution for editing livestock genomes for economic traits, which are often multigenic. Progress toward multiplex editing in large animals has been hampered by the costly inefficiencies of HDR via microinjection of in vitro manipulated embryos. Here, we designed sgRNAs to induce nonsense codons (C-to-T transitions) at four target sites in caprine FGF5, which is a crucial regulator of hair length in mammals. Initial transfections of the third generation Base Editor (BE3) plasmid and four different sgRNAs into caprine fibroblasts were ineffective in altering FGF5. In contrast, all five progenies produced from microinjected single-cell embryos had alleles with a targeted nonsense mutation. The effectiveness of BE3 to make single base changes varied considerably based on sgRNA design. In addition, the rate of mosaicism differed between animals, target sites, and tissue type. The phenotypic effects on hair fiber were characterized by hematoxylin and eosin, immunofluorescence staining, and western blotting. Differences in morphology were detectable, even though mosaicism was probably affecting the levels of FGF5 expression. PCR amplicon and whole-genome resequencing analyses for off-target changes caused by BE3 were low at a genome-wide scale. This study provided the first evidence of base editing in large mammals produced from microinjected single-cell embryos. Our results support further optimization of BEs for introgressing complex human disease alleles into large animal models, to evaluate potential genetic improvement of complex health and production traits in a single generation.
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Affiliation(s)
- Guanwei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Honghao Yu
- College of Biotechnology, Guilin Medical University, China
| | - Baohua Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yu Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yige Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiang Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chong He
- College of Information and Engineering, Northwest A&F University, Yangling, China
| | - Jiankui Zhou
- School of Life Science and Technology, ShanghaiTech University, China
| | - Ying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guangxian Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuan Yan
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jinlian Hua
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Bjoern Petersen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | | | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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21
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Zhou S, Cai B, He C, Wang Y, Ding Q, Liu J, Liu Y, Ding Y, Zhao X, Li G, Li C, Yu H, Kou Q, Niu W, Petersen B, Sonstegard T, Ma B, Chen Y, Wang X. Programmable Base Editing of the Sheep Genome Revealed No Genome-Wide Off-Target Mutations. Front Genet 2019; 10:215. [PMID: 30930940 PMCID: PMC6428697 DOI: 10.3389/fgene.2019.00215] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/27/2019] [Indexed: 12/23/2022] Open
Abstract
Since its emergence, CRISPR/Cas9-mediated base editors (BEs) with cytosine deaminase activity have been used to precisely and efficiently introduce single-base mutations in genomes, including those of human cells, mice, and crop species. Most production traits in livestock are induced by point mutations, and genome editing using BEs without homology-directed repair of double-strand breaks can directly alter single nucleotides. The p.96R > C variant of Suppressor cytokine signaling 2 (SOCS2) has profound effects on body weight, body size, and milk production in sheep. In the present study, we successfully obtained lambs with defined point mutations resulting in a p.96R > C substitution in SOCS2 by the co-injection of BE3 mRNA and a single guide RNA (sgRNA) into sheep zygotes. The observed efficiency of the single nucleotide exchange in newborn animals was as high as 25%. Observations of body size and body weight in the edited group showed that gene modification contributes to enhanced growth traits in sheep. Moreover, targeted deep sequencing and unbiased family trio-based whole genome sequencing revealed undetectable off-target mutations in the edited animals. This study demonstrates the potential for the application of BE-mediated point mutations in large animals for the improvement of production traits in livestock species.
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Affiliation(s)
- Shiwei Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bei Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chong He
- College of Information Engineering, Northwest A&F University, Yangling, China
| | - Ying Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiang Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yige Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoe Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Guanwei Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Honghao Yu
- Guilin Medical University, Guilin, China
| | - Qifang Kou
- Ningxia Tianyuan Tan Sheep Farm, Hongsibu, China
| | - Wenzhi Niu
- Ningxia Tianyuan Tan Sheep Farm, Hongsibu, China
| | - Bjoern Petersen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | | | - Baohua Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Williams DK, Pinzón C, Huggins S, Pryor JH, Falck A, Herman F, Oldeschulte J, Chavez MB, Foster BL, White SH, Westhusin ME, Suva LJ, Long CR, Gaddy D. Genetic engineering a large animal model of human hypophosphatasia in sheep. Sci Rep 2018; 8:16945. [PMID: 30446691 PMCID: PMC6240114 DOI: 10.1038/s41598-018-35079-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/24/2018] [Indexed: 12/02/2022] Open
Abstract
The availability of tools to accurately replicate the clinical phenotype of rare human diseases is a key step toward improved understanding of disease progression and the development of more effective therapeutics. We successfully generated the first large animal model of a rare human bone disease, hypophosphatasia (HPP) using CRISPR/Cas9 to introduce a single point mutation in the tissue nonspecific alkaline phosphatase (TNSALP) gene (ALPL) (1077 C > G) in sheep. HPP is a rare inherited disorder of mineral metabolism that affects bone and tooth development, and is associated with muscle weakness. Compared to wild-type (WT) controls, HPP sheep have reduced serum alkaline phosphatase activity, decreased tail vertebral bone size, and metaphyseal flaring, consistent with the mineralization deficits observed in human HPP patients. Computed tomography revealed short roots and thin dentin in incisors, and reduced mandibular bone in HPP vs. WT sheep, accurately replicating odonto-HPP. Skeletal muscle biopsies revealed aberrant fiber size and disorganized mitochondrial cristae structure in HPP vs. WT sheep. These genetically engineered sheep accurately phenocopy human HPP and provide a novel large animal platform for the longitudinal study of HPP progression, as well as other rare human bone diseases.
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Affiliation(s)
- Diarra K Williams
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Carlos Pinzón
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Shannon Huggins
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Jane H Pryor
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Alyssa Falck
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Forrest Herman
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - James Oldeschulte
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michael B Chavez
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Brian L Foster
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Sarah H White
- Department of Animal Science, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Mark E Westhusin
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Larry J Suva
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Charles R Long
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Dana Gaddy
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, 43210, USA.
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23
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Zhou S, Yu H, Zhao X, Cai B, Ding Q, Huang Y, Li Y, Li Y, Niu Y, Lei A, Kou Q, Huang X, Petersen B, Ma B, Chen Y, Wang X. Generation of gene-edited sheep with a defined Booroola fecundity gene (FecB B) mutation in bone morphogenetic protein receptor type 1B (BMPR1B) via clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) 9. Reprod Fertil Dev 2018; 30:1616-1621. [PMID: 31039970 DOI: 10.1071/rd18086] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/03/2018] [Indexed: 12/15/2022] Open
Abstract
Since its emergence, the clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated (Cas) 9 system has been increasingly used to generate animals for economically important traits. However, most CRISPR/Cas9 applications have been focused on non-homologous end joining, which results in base deletions and insertions, leading to a functional knockout of the targeted gene. The Booroola fecundity gene (FecBB) mutation (p.Q249R) in bone morphogenetic protein receptor type 1B (BMPR1B) has been demonstrated to exert a profound effect on fecundity in many breeds of sheep. In the present study, we successfully obtained lambs with defined point mutations resulting in a p.249Q>R substitution through the coinjection of Cas9 mRNA, a single guide RNA and single-stranded DNA oligonucleotides into Tan sheep zygotes. In the newborn lambs, the observed efficiency of the single nucleotide exchange was as high as 23.8%. We believe that our findings will contribute to improved reproduction traits in sheep, as well as to the generation of defined point mutations in other large animals.
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Affiliation(s)
- Shiwei Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Honghao Yu
- Guilin Medical University, Guilin 541004, China
| | - Xiaoe Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Bei Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Qiang Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yu Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yaxin Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yiyuan Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Anmin Lei
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Qifang Kou
- Ningxia Tianyuan Sheep Farm, Hongsibu, 751999, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Björn Petersen
- Institute of Farm Animal Genetics, Friedrich Loeffler Institute, Neustadt 31535, Germany
| | - Baohua Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
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24
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Polkoff K, Piedrahita JA. The transformational impact of site-specific DNA modifiers on biomedicine and agriculture. Anim Reprod 2018; 15:171-179. [PMID: 34178139 PMCID: PMC8202236 DOI: 10.21451/1984-3143-ar2018-0065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The development of genetically modified livestock has been dependent on incremental technological
advances such as embryo transfer, homologous recombination, and somatic cell nuclear transfer
(SCNT). This development rate has increased exponentially with the advent of targeted gene
modifiers such as zinc finger nucleases, TAL-effector nucleases (TALENs) and clustered
regularly interspaced short palindromic repeats (CRISPR-Cas). CRISPR-Cas based systems
in particular have broad applicability, and have low technical and economic barriers for
their implementation. As a result, they are having, and will continue to have, a transformational
impact in the field of gene editing in domestic animals. With these advances also comes the
responsibility to properly apply this technology so it has a beneficial effect throughout
all levels of society.
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Affiliation(s)
- Kathryn Polkoff
- Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA.,Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - Jorge A Piedrahita
- Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA.,Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
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25
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Abstract
Prokaryotic type II adaptive immune systems have been developed into the versatile CRISPR technology, which has been widely applied in site-specific genome editing and has revolutionized biomedical research due to its superior efficiency and flexibility. Recent studies have greatly diversified CRISPR technologies by coupling it with various DNA repair mechanisms and targeting strategies. These new advances have significantly expanded the generation of genetically modified animal models, either by including species in which targeted genetic modification could not be achieved previously, or through introducing complex genetic modifications that take multiple steps and cost years to achieve using traditional methods. Herein, we review the recent developments and applications of CRISPR-based technology in generating various animal models, and discuss the everlasting impact of this new progress on biomedical research.
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Affiliation(s)
- Xun Ma
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Avery Sum-Yu Wong
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Hei-Yin Tam
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Samuel Yung-Kin Tsui
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Dittman Lai-Shun Chung
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Bo Feng
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Guangdong 510530, China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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