51
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Luo X, Li M, Su B. Application of the genome editing tool CRISPR/Cas9 in non-human primates. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2017; 37:214-9. [PMID: 27469252 DOI: 10.13918/j.issn.2095-8137.2016.4.214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In the past three years, RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system has been used to facilitate efficient genome editing in many model and non-model animals. However, its application in nonhuman primates is still at the early stage, though in view of the similarities in anatomy, physiology, behavior and genetics, closely related nonhuman primates serve as optimal models for human biology and disease studies. In this review, we summarize the current proceedings of gene editing using CRISPR/Cas9 in nonhuman primates.
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Affiliation(s)
- Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, Chin.
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52
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The potential application and challenge of powerful CRISPR/Cas9 system in cardiovascular research. Int J Cardiol 2016; 227:191-193. [PMID: 27847153 DOI: 10.1016/j.ijcard.2016.11.177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/06/2016] [Indexed: 11/23/2022]
Abstract
CRISPR/Cas9 is a precision-guided munition found in bacteria to fight against invading viruses. This technology has enormous potential applications, including altering genes in both somatic and germ cells, as well as generating knockout animals. Compared to other gene editing techniques such as zinc finger nucleases and TALENS, CRISPR/Cas9 is much easier to use and highly efficient. Importantly, the multiplex capacity of this technology allows multiple genes to be edited simultaneously. CRISPR/Cas9 also has the potential to prevent and cure human diseases. In this review, we wish to highlight some key points regarding the future prospect of using CRISPR/Cas9 as a powerful tool for cardiovascular research, and as a novel therapeutic strategy to treat cardiovascular diseases.
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53
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Vad-Nielsen J, Lin L, Bolund L, Nielsen AL, Luo Y. Golden Gate Assembly of CRISPR gRNA expression array for simultaneously targeting multiple genes. Cell Mol Life Sci 2016; 73:4315-4325. [PMID: 27178736 PMCID: PMC11108369 DOI: 10.1007/s00018-016-2271-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 04/29/2016] [Accepted: 05/06/2016] [Indexed: 12/12/2022]
Abstract
The engineered CRISPR/Cas9 technology has developed as the most efficient and broadly used genome editing tool. However, simultaneously targeting multiple genes (or genomic loci) in the same individual cells using CRISPR/Cas9 remain one technical challenge. In this article, we have developed a Golden Gate Assembly method for the generation of CRISPR gRNA expression arrays, thus enabling simultaneous gene targeting. Using this method, the generation of CRISPR gRNA expression array can be accomplished in 2 weeks, and contains up to 30 gRNA expression cassettes. We demonstrated in the study that simultaneously targeting 10 genomic loci or simultaneously inhibition of multiple endogenous genes could be achieved using the multiplexed gRNA expression array vector in human cells. The complete set of plasmids is available through the non-profit plasmid repository Addgene.
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Affiliation(s)
- Johan Vad-Nielsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark
| | - Anders Lade Nielsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark.
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54
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Zhang X, Liang P, Ding C, Zhang Z, Zhou J, Xie X, Huang R, Sun Y, Sun H, Zhang J, Xu Y, Songyang Z, Huang J. Efficient Production of Gene-Modified Mice using Staphylococcus aureus Cas9. Sci Rep 2016; 6:32565. [PMID: 27586692 PMCID: PMC5009317 DOI: 10.1038/srep32565] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/11/2016] [Indexed: 12/15/2022] Open
Abstract
The CRISPR/Cas system is an efficient genome-editing tool to modify genes in mouse zygotes. However, only the Streptococcus pyogenes Cas9 (SpCas9) has been systematically tested for generating gene-modified mice. The protospacer adjacent motif (PAM, 5'-NGG-3') recognized by SpCas9 limits the number of potential target sites for this system. Staphylococcus aureus Cas9 (SaCas9), with its smaller size and unique PAM (5'-NNGRRT-3') preferences, presents an alternative for genome editing in zygotes. Here, we showed that SaCas9 could efficiently and specifically edit the X-linked gene Slx2 and the autosomal gene Zp1 in mouse zygotes. SaCas9-mediated disruption of the tyrosinase (Tyr) gene led to C57BL/6J mice with mosaic coat color. Furthermore, multiplex targeting proved efficient multiple genes disruption when we co-injected gRNAs targeting Slx2, Zp1, and Tyr together with SaCas9 mRNA. We were also able to insert a Flag tag at the C-terminus of histone H1c, when a Flag-encoding single-stranded DNA oligo was co-introduced into mouse zygotes with SaCas9 mRNA and the gRNA. These results indicate that SaCas9 can specifically cleave the target gene locus, leading to successful gene knock-out and precise knock-in in mouse zygotes, and highlight the potential of using SaCas9 for genome editing in preimplantation embryos and producing gene-modified animal models.
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Affiliation(s)
- Xiya Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Puping Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chenhui Ding
- Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhen Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianwen Zhou
- Department of Pathology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaowei Xie
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Rui Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ying Sun
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Hongwei Sun
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jinran Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yanwen Xu
- Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhou Songyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junjiu Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou Key Laboratory of Healthy Aging Research and State Key Laboratory of Biocontrol, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
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55
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Chen Y, Niu Y, Ji W. Genome editing in nonhuman primates: approach to generating human disease models. J Intern Med 2016; 280:246-51. [PMID: 27114283 DOI: 10.1111/joim.12469] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nonhuman primates (NHPs) are superior than rodents to be animal models for the study of human diseases, due to their similarities in terms of genetics, physiology, developmental biology, social behaviour and cognition. Transgenic animals have become a key tool in functional genomics to generate models for human diseases and validate new drugs. However, until now, progress in the field of transgenic NHPs has been slow because of technological limitations. Many human diseases, including neurodegenerative disorders, are caused by mutations in endogenous genes. Fortunately, recent developments in precision gene editing have led to the generation of NHP models for human diseases. Since 2014, there have been several reports of the generation of monkey models using transcription activator-like endonucleases (TALENs) or clustered regularly interspaced short palindromic repeats (CRISPR/Cas9); some of these NHP models showed symptoms that were much closer to those of human diseases than have been seen previously in mouse models. No off-targeting was observed in the NHP models, and multiple gene knockout and biallelic mutants were feasible with low efficiency. These findings suggest that there are many possibilities to establish NHP models for human diseases that can mimic human diseases more faithfully than rodent models.
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Affiliation(s)
- Y Chen
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology and National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan, China
| | - Y Niu
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology and National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan, China
| | - W Ji
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology and National Engineering Research Center of Biomedicine and Animal Science, Kunming, Yunnan, China
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56
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Lendahl U. At the interface of stem cell research and new technologies. J Intern Med 2016; 280:232-5. [PMID: 27539905 DOI: 10.1111/joim.12513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- U Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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57
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Chin YW, Kang WK, Jang HW, Turner TL, Kim HJ. CAR1 deletion by CRISPR/Cas9 reduces formation of ethyl carbamate from ethanol fermentation by Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2016; 43:1517-1525. [PMID: 27573438 DOI: 10.1007/s10295-016-1831-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022]
Abstract
Enormous advances in genome editing technology have been achieved in recent decades. Among newly born genome editing technologies, CRISPR/Cas9 is considered revolutionary because it is easy to use and highly precise for editing genes in target organisms. CRISPR/Cas9 technology has also been applied for removing unfavorable target genes. In this study, we used CRISPR/Cas9 technology to reduce ethyl carbamate (EC), a potential carcinogen, which was formed during the ethanol fermentation process by yeast. Because the yeast CAR1 gene encoding arginase is the key gene to form ethyl carbamate, we inactivated the yeast CAR1 gene by the complete deletion of the gene or the introduction of a nonsense mutation in the CAR1 locus using CRISPR/Cas9 technology. The engineered yeast strain showed a 98 % decrease in specific activity of arginase while displaying a comparable ethanol fermentation performance. In addition, the CAR1-inactivated mutants showed reduced formation of EC and urea, as compared to the parental yeast strain. Importantly, CRISPR/Cas9 technology enabled generation of a CAR1-inactivated yeast strains without leaving remnants of heterologous genes from a vector, suggesting that the engineered yeast by CRISPR/Cas9 technology might sidestep GMO regulation.
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Affiliation(s)
- Young-Wook Chin
- Division of Nutrition and Metabolism Research, Korea Food Research Institute, Seongnam, 13539, Republic of Korea
| | - Woo-Kyung Kang
- Division of Nutrition and Metabolism Research, Korea Food Research Institute, Seongnam, 13539, Republic of Korea.,Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hae Won Jang
- Division of Strategic Food Research, Korea Food Research Institute, Seongnam, 13539, Republic of Korea
| | - Timothy L Turner
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 260 Bevier Hall, Urbana, IL, 61801, USA
| | - Hyo Jin Kim
- Division of Nutrition and Metabolism Research, Korea Food Research Institute, Seongnam, 13539, Republic of Korea. .,Department of Food Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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58
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Ke Q, Li W, Lai X, Chen H, Huang L, Kang Z, Li K, Ren J, Lin X, Zheng H, Huang W, Ma Y, Xu D, Chen Z, Song X, Lin X, Zhuang M, Wang T, Zhuang F, Xi J, Mao FF, Xia H, Lahn BT, Zhou Q, Yang S, Xiang AP. TALEN-based generation of a cynomolgus monkey disease model for human microcephaly. Cell Res 2016; 26:1048-61. [PMID: 27502025 PMCID: PMC5034111 DOI: 10.1038/cr.2016.93] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/23/2016] [Accepted: 05/27/2016] [Indexed: 12/13/2022] Open
Abstract
Gene editing in non-human primates may lead to valuable models for exploring the etiologies and therapeutic strategies of genetically based neurological disorders in humans. However, a monkey model of neurological disorders that closely mimics pathological and behavioral deficits in humans has not yet been successfully generated. Microcephalin 1 (MCPH1) is implicated in the evolution of the human brain, and MCPH1 mutation causes microcephaly accompanied by mental retardation. Here we generated a cynomolgus monkey (Macaca fascicularis) carrying biallelic MCPH1 mutations using transcription activator-like effector nucleases. The monkey recapitulated most of the important clinical features observed in patients, including marked reductions in head circumference, premature chromosome condensation (PCC), hypoplasia of the corpus callosum and upper limb spasticity. Moreover, overexpression of MCPH1 in mutated dermal fibroblasts rescued the PCC syndrome. This monkey model may help us elucidate the role of MCPH1 in the pathogenesis of human microcephaly and better understand the function of this protein in the evolution of primate brain size.
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Affiliation(s)
- Qiong Ke
- Program of Stem Cells and Regenerative Medicine, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510623, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Department of Biology, Zhongshan Medical School, Sun Yat-Sen University, Guangzhou 510080, China.,Guangdong Key Laboratory of Reproductive Medicine, Guangzhou 510080, China
| | - Weiqiang Li
- Program of Stem Cells and Regenerative Medicine, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510623, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Guangdong Key Laboratory of Reproductive Medicine, Guangzhou 510080, China.,Department of Biochemistry, Zhongshan Medical School, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xingqiang Lai
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Hong Chen
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Lihua Huang
- Program of Stem Cells and Regenerative Medicine, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510623, China
| | - Zhuang Kang
- Department of Radiology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510632, China
| | - Kai Li
- Department of Ultrasound, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510632, China
| | - Jie Ren
- Department of Ultrasound, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510632, China
| | - Xiaofeng Lin
- Department of Radiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Haiqing Zheng
- Department of Rehabilitation Medicine Science, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510632, China
| | - Weijun Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yunhan Ma
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, China
| | - Dongdong Xu
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, China
| | - Zheng Chen
- Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xinming Song
- Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xinyi Lin
- Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Min Zhuang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Tao Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Department of Biochemistry, Zhongshan Medical School, Sun Yat-Sen University, Guangzhou 510080, China
| | | | - Jianzhong Xi
- Department of Biomedical Engineering, College of Engineering, Peking University, Yannan Yuan 60, Beijing 100871, China
| | - Frank Fuxiang Mao
- State Key Laboratory of Ophthalmology, Zhong Shan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Huimin Xia
- Program of Stem Cells and Regenerative Medicine, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510623, China
| | - Bruce T Lahn
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Qi Zhou
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shihua Yang
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, China
| | - Andy Peng Xiang
- Program of Stem Cells and Regenerative Medicine, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510623, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Guangdong Key Laboratory of Reproductive Medicine, Guangzhou 510080, China.,Department of Biochemistry, Zhongshan Medical School, Sun Yat-Sen University, Guangzhou 510080, China
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59
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Shy BR, MacDougall MS, Clarke R, Merrill BJ. Co-incident insertion enables high efficiency genome engineering in mouse embryonic stem cells. Nucleic Acids Res 2016; 44:7997-8010. [PMID: 27484482 PMCID: PMC5027516 DOI: 10.1093/nar/gkw685] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 07/25/2016] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 nucleases have enabled powerful, new genome editing capabilities; however, the preponderance of non-homologous end joining (NHEJ) mediated repair events over homology directed repair (HDR) in most cell types limits the ability to engineer precise changes in mammalian genomes. Here, we increase the efficiency of isolating precise HDR-mediated events in mouse embryonic stem (ES) cells by more than 20-fold through the use of co-incidental insertion (COIN) of independent donor DNA sequences. Analysis of on:off-target frequencies at the Lef1 gene revealed that bi-allelic insertion of a PGK-Neo cassette occurred more frequently than expected. Using various selection cassettes targeting multiple loci, we show that the insertion of a selectable marker at one control site frequently coincided with an insertion at an unlinked, independently targeted site, suggesting enrichment of a sub-population of HDR-proficient cells. When individual cell events were tracked using flow cytometry and fluorescent protein markers, individual cells frequently performed either a homology-dependent insertion event or a homology-independent event, but rarely both types of insertions in a single cell. Thus, when HDR-dependent selection donors are used, COIN enriches for HDR-proficient cells among heterogeneous cell populations. When combined with a self-excising selection cassette, COIN provides highly efficient and scarless genome editing.
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Affiliation(s)
- Brian R Shy
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA Genome Editing Core, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Matthew S MacDougall
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ryan Clarke
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Bradley J Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA Genome Editing Core, University of Illinois at Chicago, Chicago, IL 60607, USA
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60
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Profile of Qi Zhou. SCIENCE CHINA. LIFE SCIENCES 2016; 59:573-575. [PMID: 27142349 DOI: 10.1007/s11427-016-5062-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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61
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Derivation and application of pluripotent stem cells for regenerative medicine. SCIENCE CHINA-LIFE SCIENCES 2016; 59:576-83. [DOI: 10.1007/s11427-016-5066-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/20/2016] [Indexed: 01/21/2023]
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62
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Shao S, Zhang W, Hu H, Xue B, Qin J, Sun C, Sun Y, Wei W, Sun Y. Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system. Nucleic Acids Res 2016; 44:e86. [PMID: 26850639 PMCID: PMC4872083 DOI: 10.1093/nar/gkw066] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/17/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022] Open
Abstract
Visualization of chromosomal dynamics is important for understanding many fundamental intra-nuclear processes. Efficient and reliable live-cell multicolor labeling of chromosomal loci can realize this goal. However, the current methods are constrained mainly by insufficient labeling throughput, efficiency, flexibility as well as photostability. Here we have developed a new approach to realize dual-color chromosomal loci imaging based on a modified single-guide RNA (sgRNA) of the CRISPR/Cas9 system. The modification of sgRNA was optimized by structure-guided engineering of the original sgRNA, consisting of RNA aptamer insertions that bind fluorescent protein-tagged effectors. By labeling and tracking telomeres, centromeres and genomic loci, we demonstrate that the new approach is easy to implement and enables robust dual-color imaging of genomic elements. Importantly, our data also indicate that the fast exchange rate of RNA aptamer binding effectors makes our sgRNA-based labeling method much more tolerant to photobleaching than the Cas9-based labeling method. This is crucial for continuous, long-term tracking of chromosomal dynamics. Lastly, as our method is complementary to other live-cell genomic labeling systems, it is therefore possible to combine them into a plentiful palette for the study of native chromatin organization and genome ultrastructure dynamics in living cells.
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Affiliation(s)
- Shipeng Shao
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Weiwei Zhang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Huan Hu
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Jinshan Qin
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Chaoying Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuao Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Wensheng Wei
- Biodynamic Optical Imaging Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
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63
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Ma Y, Li J, Wang G, Ke Q, Qiu S, Gao L, Wan H, Zhou Y, Xiang AP, Huang Q, Feng G, Zhou Q, Yang S. Efficient production of cynomolgus monkeys with a toolbox of enhanced assisted reproductive technologies. Sci Rep 2016; 6:25888. [PMID: 27173128 PMCID: PMC4865753 DOI: 10.1038/srep25888] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
The efficiency of assisted reproductive technologies (ARTs) in nonhuman primates is low due to no screening criterions for selecting sperm, oocyte, and embryo as well as its surrogate mothers. Here we analyzed 15 pairs of pregnant and non-pregnant cynomolgus monkeys, each pair of which received embryos from one batch of fertilized oocytes, and found ratio of endometrial to myometrial thicknesses in abdominal ultrasonic transverse section of uterus is a reliable indicator for selection of recipients for embryo transfer. We performed 305 ovarian stimulations in 128 female cynomolgus monkeys and found that ovarian stimulation can be performed in a whole year and repeated up to six times in the same monkey without deteriorating fertilization potential of eggs until a poor response to stimulation happened. Fertilization can be efficiently achieved with both conventional and piezo-driven intracytoplasmic sperm injection procedures. In semen collection, semen quality is higher with the penile robe electrical stimulus method compared with the rectal probe method. Moreover, caesarean section is an effective strategy for increasing baby survival rates of multiple pregnancies. These findings provide a practical guidance for the efficient use of ARTs, facilitating their use in genetic engineering of macaque monkeys for basic and translational neuroscience research.
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Affiliation(s)
- Yunhan Ma
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, P. R. China.,Shenzhen Key Lab of Neuropsychiatric Modulation and Collaborative Innovation Center for Brain Science, CAS Center for Excellence in Brain Science, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China
| | - Jiayu Li
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ge Wang
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Qiong Ke
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering of Ministry of Education, Sun Yat-sen University, Guangzhou 510080, P. R. China
| | - Sien Qiu
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Liang Gao
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, P. R. China.,Blooming-spring biotechnology development Co., Ltd., of Guangdong, Guangzhou 510940, P. R. China
| | - Haifeng Wan
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Yang Zhou
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering of Ministry of Education, Sun Yat-sen University, Guangzhou 510080, P. R. China
| | - Qunshan Huang
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Shihua Yang
- College of Veterinary Medicine, Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, South China Agricultural University, Guangzhou 510642, P. R. China
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64
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Miller CT, Freiwald WA, Leopold DA, Mitchell JF, Silva AC, Wang X. Marmosets: A Neuroscientific Model of Human Social Behavior. Neuron 2016; 90:219-33. [PMID: 27100195 PMCID: PMC4840471 DOI: 10.1016/j.neuron.2016.03.018] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 10/21/2022]
Abstract
The common marmoset (Callithrix jacchus) has garnered interest recently as a powerful model for the future of neuroscience research. Much of this excitement has centered on the species' reproductive biology and compatibility with gene editing techniques, which together have provided a path for transgenic marmosets to contribute to the study of disease as well as basic brain mechanisms. In step with technical advances is the need to establish experimental paradigms that optimally tap into the marmosets' behavioral and cognitive capacities. While conditioned task performance of a marmoset can compare unfavorably with rhesus monkey performance on conventional testing paradigms, marmosets' social behavior and cognition are more similar to that of humans. For example, marmosets are among only a handful of primates that, like humans, routinely pair bond and care cooperatively for their young. They are also notably pro-social and exhibit social cognitive abilities, such as imitation, that are rare outside of the Apes. In this Primer, we describe key facets of marmoset natural social behavior and demonstrate that emerging behavioral paradigms are well suited to isolate components of marmoset cognition that are highly relevant to humans. These approaches generally embrace natural behavior, which has been rare in conventional primate testing, and thus allow for a new consideration of neural mechanisms underlying primate social cognition and signaling. We anticipate that through parallel technical and paradigmatic advances, marmosets will become an essential model of human social behavior, including its dysfunction in neuropsychiatric disorders.
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Affiliation(s)
- Cory T Miller
- Cortical Systems and Behavior Laboratory, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
| | - Winrich A Freiwald
- Laboratory of Neural Systems, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
| | - David A Leopold
- Section on Cognitive Neurophysiology and Imaging, Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, 6001 Executive Blvd., Bethesda, MD 20892, USA
| | - Jude F Mitchell
- Department of Brain and Cognitive Sciences, University of Rochester, 358 Meliora Hall, Rochester, NY 14627, USA
| | - Afonso C Silva
- Section on Cerebral Microcirculation, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 6001 Executive Blvd., Bethesda, MD 20892, USA
| | - Xiaoqin Wang
- Laboratory of Auditory Neurophysiology, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 720 Rutland Ave., Baltimore, MD 21205, USA
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65
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Biallelic editing of a lamprey genome using the CRISPR/Cas9 system. Sci Rep 2016; 6:23496. [PMID: 27005311 PMCID: PMC4804306 DOI: 10.1038/srep23496] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/07/2016] [Indexed: 12/31/2022] Open
Abstract
Lampreys are extant representatives of agnathans. Descriptions of lamprey development, physiology and genome have provided critical insights into early evolution of vertebrate traits. However, efficient means for genetic manipulation in agnathan species have not been developed, hindering functional studies of genes in these important Evo-Devo models. Here, we report a CRISPR/Cas system optimized for lamprey genomes and use it to disrupt genomic loci in the Northeast Chinese lamprey (Lethenteron morii) with efficiencies ranging between 84~99%. The frequencies of indels observed in the target loci of golden (gol), kctd10, wee1, soxe2, and wnt7b, estimated from direct sequencing of genomic DNA samples of injected lamprey larvae, were 68/69, 47/56, 38/39, 36/37 and 36/42, respectively. These indels often occurred in both alleles. In the CRISPR/Cas9 treatment for gol or kctd10, 38.6% or 85.3% of the targeted larvae had the respective recessive null-like phenotypes, further confirming the disruption of both loci. The kctd10 gRNA, designed against an essential functional region of Kctd10, resulted in null-like phenotypes and in-frame mutations in alleles. We suggest that the CRISPR/Cas-based approach has the potential for efficient genetic perturbation in organisms less amenable to germ line transmission based approaches.
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66
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Cellular Engineering and Disease Modeling with Gene-Editing Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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67
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Off-target Effects in CRISPR/Cas9-mediated Genome Engineering. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e264. [PMID: 26575098 PMCID: PMC4877446 DOI: 10.1038/mtna.2015.37] [Citation(s) in RCA: 737] [Impact Index Per Article: 81.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/05/2015] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 is a versatile genome-editing technology that is widely used for studying the functionality of genetic elements, creating genetically modified organisms as well as preclinical research of genetic disorders. However, the high frequency of off-target activity (≥50%)—RGEN (RNA-guided endonuclease)-induced mutations at sites other than the intended on-target site—is one major concern, especially for therapeutic and clinical applications. Here, we review the basic mechanisms underlying off-target cutting in the CRISPR/Cas9 system, methods for detecting off-target mutations, and strategies for minimizing off-target cleavage. The improvement off-target specificity in the CRISPR/Cas9 system will provide solid genotype–phenotype correlations, and thus enable faithful interpretation of genome-editing data, which will certainly facilitate the basic and clinical application of this technology.
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68
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Serrao E, Engelman AN. Sites of retroviral DNA integration: From basic research to clinical applications. Crit Rev Biochem Mol Biol 2015; 51:26-42. [PMID: 26508664 DOI: 10.3109/10409238.2015.1102859] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One of the most crucial steps in the life cycle of a retrovirus is the integration of the viral DNA (vDNA) copy of the RNA genome into the genome of an infected host cell. Integration provides for efficient viral gene expression as well as for the segregation of viral genomes to daughter cells upon cell division. Some integrated viruses are not well expressed, and cells latently infected with human immunodeficiency virus type 1 (HIV-1) can resist the action of potent antiretroviral drugs and remain dormant for decades. Intensive research has been dedicated to understanding the catalytic mechanism of integration, as well as the viral and cellular determinants that influence integration site distribution throughout the host genome. In this review, we summarize the evolution of techniques that have been used to recover and map retroviral integration sites, from the early days that first indicated that integration could occur in multiple cellular DNA locations, to current technologies that map upwards of millions of unique integration sites from single in vitro integration reactions or cell culture infections. We further review important insights gained from the use of such mapping techniques, including the monitoring of cell clonal expansion in patients treated with retrovirus-based gene therapy vectors, or patients with acquired immune deficiency syndrome (AIDS) on suppressive antiretroviral therapy (ART). These insights span from integrase (IN) enzyme sequence preferences within target DNA (tDNA) at the sites of integration, to the roles of host cellular proteins in mediating global integration distribution, to the potential relationship between genomic location of vDNA integration site and retroviral latency.
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Affiliation(s)
- Erik Serrao
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Alan N Engelman
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA
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69
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Wang J, Li X, Zhao Y, Li J, Zhou Q, Liu Z. Generation of cell-type-specific gene mutations by expressing the sgRNA of the CRISPR system from the RNA polymerase II promoters. Protein Cell 2015; 6:689-692. [PMID: 26050089 PMCID: PMC4537475 DOI: 10.1007/s13238-015-0169-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Jiaqiang Wang
- />College of Life Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Xin Li
- />College of Life Sciences, Northeast Agricultural University, Harbin, 150030 China
- />State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yanhua Zhao
- />College of Life Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Jingyu Li
- />College of Life Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Qi Zhou
- />College of Life Sciences, Northeast Agricultural University, Harbin, 150030 China
- />State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhonghua Liu
- />College of Life Sciences, Northeast Agricultural University, Harbin, 150030 China
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70
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Tu Z, Yang W, Yan S, Guo X, Li XJ. CRISPR/Cas9: a powerful genetic engineering tool for establishing large animal models of neurodegenerative diseases. Mol Neurodegener 2015; 10:35. [PMID: 26238861 PMCID: PMC4524001 DOI: 10.1186/s13024-015-0031-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/24/2015] [Indexed: 02/07/2023] Open
Abstract
Animal models are extremely valuable to help us understand the pathogenesis of neurodegenerative disorders and to find treatments for them. Since large animals are more like humans than rodents, they make good models to identify the important pathological events that may be seen in humans but not in small animals; large animals are also very important for validating effective treatments or confirming therapeutic targets. Due to the lack of embryonic stem cell lines from large animals, it has been difficult to use traditional gene targeting technology to establish large animal models of neurodegenerative diseases. Recently, CRISPR/Cas9 was used successfully to genetically modify genomes in various species. Here we discuss the use of CRISPR/Cas9 technology to establish large animal models that can more faithfully mimic human neurodegenerative diseases.
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Affiliation(s)
- Zhuchi Tu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weili Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sen Yan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiangyu Guo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiao-Jiang Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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71
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Li J, Shou J, Guo Y, Tang Y, Wu Y, Jia Z, Zhai Y, Chen Z, Xu Q, Wu Q. Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9. J Mol Cell Biol 2015; 7:284-98. [PMID: 25757625 PMCID: PMC4524425 DOI: 10.1093/jmcb/mjv016] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/02/2015] [Indexed: 12/26/2022] Open
Abstract
The human genome contains millions of DNA regulatory elements and a large number of gene clusters, most of which have not been tested experimentally. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) programed with a synthetic single-guide RNA (sgRNA) emerges as a method for genome editing in virtually any organisms. Here we report that targeted DNA fragment inversions and duplications could easily be achieved in human and mouse genomes by CRISPR with two sgRNAs. Specifically, we found that, in cultured human cells and mice, efficient precise inversions of DNA fragments ranging in size from a few tens of bp to hundreds of kb could be generated. In addition, DNA fragment duplications and deletions could also be generated by CRISPR through trans-allelic recombination between the Cas9-induced double-strand breaks (DSBs) on two homologous chromosomes (chromatids). Moreover, junctions of combinatorial inversions and duplications of the protocadherin (Pcdh) gene clusters induced by Cas9 with four sgRNAs could be detected. In mice, we obtained founders with alleles of precise inversions, duplications, and deletions of DNA fragments of variable sizes by CRISPR. Interestingly, we found that very efficient inversions were mediated by microhomology-mediated end joining (MMEJ) through short inverted repeats. We showed for the first time that DNA fragment inversions could be transmitted through germlines in mice. Finally, we applied this CRISPR method to a regulatory element of the Pcdhα cluster and found a new role in the regulation of members of the Pcdhγ cluster. This simple and efficient method should be useful in manipulating mammalian genomes to study millions of regulatory DNA elements as well as vast numbers of gene clusters.
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Affiliation(s)
- Jinhuan Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Jia Shou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Ya Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yuanxiao Tang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yonghu Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Zhilian Jia
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yanan Zhai
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Zhifeng Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Quan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Qiang Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
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Jiang W, Marraffini LA. CRISPR-Cas: New Tools for Genetic Manipulations from Bacterial Immunity Systems. Annu Rev Microbiol 2015. [PMID: 26209264 DOI: 10.1146/annurev-micro-091014-104441] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Prokaryotic CRISPR-Cas loci encode proteins that function as an adaptive immune system against infectious viruses and plasmids. Immunity is mediated by Cas nucleases and small RNA guides, which specify a cleavage site within the genome of the invader. In type II CRISPR-Cas systems, the RNA-guided Cas9 nuclease cleaves the DNA. Cas9 can be reprogrammed to create double-strand DNA breaks in the genomes of a variety of organisms, from bacteria to human cells. Repair of Cas9 lesions by homologous recombination or nonhomologous end joining mechanisms can lead to the introduction of specific nucleotide substitutions or indel mutations, respectively. Furthermore, a nuclease-null Cas9 has been developed to regulate endogenous gene expression and to label genomic loci in living cells. Targeted genome editing and gene regulation mediated by Cas9 are easy to program, scale, and multiplex, allowing researchers to decipher the causal link between genetic and phenotypic variation. In this review, we describe the most notable applications of Cas9 in basic biology, translational medicine, synthetic biology, biotechnology, and other fields.
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Affiliation(s)
- Wenyan Jiang
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065;
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73
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Horie K, Hidema S, Hirayama T, Nishimori K. In vitro culture and in vitro fertilization techniques for prairie voles (Microtus ochrogaster). Biochem Biophys Res Commun 2015; 463:907-11. [PMID: 26071353 DOI: 10.1016/j.bbrc.2015.06.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
Prairie vole (Microtus ochrogaster) is a highly social animal and is a commonly used animal model for neuropsychopharmacological and psychiatric studies. To date, only a few reports on the development of transgenic prairie voles which was primarily due to the suboptimal development of assisted reproductive technology (ART) in prairie voles. Limitations in ART further hinder the development of genetically modified prairie voles such as the application of conventional gene targeting technologies using embryonic stem (ES) or induced pluripotent stem (iPS) cells to generate chimeric prairie voles. Moreover, recent advancement in genome-editing tools such as transcription activator-like effector nuclease (TALEN) and clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas technology provide an unprecedented opportunity to create gene targeting animal model and the development of ART in prairie voles is necessary for future development of novel transgenic prairie vole model. We have established efficient method for in vitro embryo culture and sperm cryopreservation with high fertilization rate. In G-1 PLUS and G-2 PLUS sequential culture condition, 81.0% (# of Blastocysts/total n) of one-cell embryos developed to blastocysts. In contrary, no embryos were developed to blastocyst stage in KSOM medium (0/total # of embryos in culture). In vitro fertilization rate using fresh and frozen-thawed sperm was 32.6% and 29.3%, respectively. This is the first report of IVF using cryopreserved prairie vole sperm. We employed mouse IVF methods in prairie voles and optimize culture conditions using human G-1/G-2 PLUS sequential culture method that resulted in high embryonic development rate. The development in vole reproductive technology will facilitate the generation of transgenic voles in the future.
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Affiliation(s)
- Kengo Horie
- Laboratory of Molecular Biology, Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Shizu Hidema
- Laboratory of Molecular Biology, Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Takashi Hirayama
- Department of Obstetrics and Gynecology, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Katsuhiko Nishimori
- Laboratory of Molecular Biology, Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
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74
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Abstract
Mosaic mutations and off-target effects caused by CRISPR/Cas9 have led to concerns about the efficiency and specificity of this new technique in non-human primates and other large animals. Here we discuss recent findings from primate embryos, with a focus on the technical issues CRISPR/Cas9 faces before producing non-human primate models of human diseases.
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