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Combi-CRISPR: combination of NHEJ and HDR provides efficient and precise plasmid-based knock-ins in mice and rats. Hum Genet 2020; 140:277-287. [PMID: 32617796 PMCID: PMC7864826 DOI: 10.1007/s00439-020-02198-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022]
Abstract
CRISPR-Cas9 are widely used for gene targeting in mice and rats. The non-homologous end-joining (NHEJ) repair pathway, which is dominant in zygotes, efficiently induces insertion or deletion (indel) mutations as gene knockouts at targeted sites, whereas gene knock-ins (KIs) via homology-directed repair (HDR) are difficult to generate. In this study, we used a double-stranded DNA (dsDNA) donor template with Cas9 and two single guide RNAs, one designed to cut the targeted genome sequences and the other to cut both the flanked genomic region and one homology arm of the dsDNA plasmid, which resulted in 20–33% KI efficiency among G0 pups. G0 KI mice carried NHEJ-dependent indel mutations at one targeting site that was designed at the intron region, and HDR-dependent precise KIs of the various donor cassettes spanning from 1 to 5 kbp, such as EGFP, mCherry, Cre, and genes of interest, at the other exon site. These findings indicate that this combinatorial method of NHEJ and HDR mediated by the CRISPR-Cas9 system facilitates the efficient and precise KIs of plasmid DNA cassettes in mice and rats.
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52
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Ding W, Zhang Y, Shi S. Development and Application of CRISPR/Cas in Microbial Biotechnology. Front Bioeng Biotechnol 2020; 8:711. [PMID: 32695770 PMCID: PMC7338305 DOI: 10.3389/fbioe.2020.00711] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has been rapidly developed as versatile genomic engineering tools with high efficiency, accuracy and flexibility, and has revolutionized traditional methods for applications in microbial biotechnology. Here, key points of building reliable CRISPR/Cas system for genome engineering are discussed, including the Cas protein, the guide RNA and the donor DNA. Following an overview of various CRISPR/Cas tools for genome engineering, including gene activation, gene interference, orthogonal CRISPR systems and precise single base editing, we highlighted the application of CRISPR/Cas toolbox for multiplexed engineering and high throughput screening. We then summarize recent applications of CRISPR/Cas systems in metabolic engineering toward production of chemicals and natural compounds, and end with perspectives of future advancements.
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Affiliation(s)
- Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.,Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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53
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Alopecia areata susceptibility variant in MHC region impacts expressions of genes contributing to hair keratinization and is involved in hair loss. EBioMedicine 2020; 57:102810. [PMID: 32580135 PMCID: PMC7317227 DOI: 10.1016/j.ebiom.2020.102810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 01/08/2023] Open
Abstract
Background Alopecia areata (AA) is considered a highly heritable, T-cell-mediated autoimmune disease of the hair follicle. However, no convincing susceptibility gene has yet been pinpointed in the major histocompatibility complex (MHC), a genome region known to be associated with AA as compared to other regions. Methods We engineered mice carrying AA risk allele identified by haplotype sequencing for the MHC region using allele-specific genome editing with the CRISPR/Cas9 system. Finally, we performed functional evaluations in the mice and AA patients with and without the risk allele. Findings We identified a variant (rs142986308, p.Arg587Trp) in the coiled-coil alpha-helical rod protein 1 (CCHCR1) gene as the only non-synonymous variant in the AA risk haplotype. Furthermore, mice engineered to carry the risk allele displayed a hair loss phenotype. Transcriptomics further identified CCHCR1 as a novel component interacting with hair cortex keratin in hair shafts. Both, these alopecic mice and AA patients with the risk allele displayed morphologically impaired hair and comparable differential expression of hair-related genes, including hair keratin and keratin-associated proteins (KRTAPs). Interpretation Our results implicate CCHCR1 with the risk allele in a previously unidentified subtype of AA based on aberrant keratinization in addition to autoimmune events. Funding This work was supported by JSPS KAKENHI (JP16K10177) and the NIHR UCLH Biomedical Research center (BRC84/CN/SB/5984).
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54
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Hosur V, Skelly DA, Francis C, Low BE, Kohar V, Burzenski LM, Amiji MM, Shultz LD, Wiles MV. Improved mouse models and advanced genetic and genomic technologies for the study of neutrophils. Drug Discov Today 2020; 25:1013-1025. [PMID: 32387410 DOI: 10.1016/j.drudis.2020.03.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/16/2020] [Accepted: 03/30/2020] [Indexed: 12/31/2022]
Abstract
Mice have been excellent surrogates for studying neutrophil biology and, furthermore, murine models of human disease have provided fundamental insights into the roles of human neutrophils in innate immunity. The emergence of novel humanized mice and high-diversity mouse populations offers the research community innovative and powerful platforms for better understanding, respectively, the mechanisms by which human neutrophils drive pathogenicity, and how genetic differences underpin the variation in neutrophil biology observed among humans. Here, we review key examples of these new resources. Additionally, we provide an overview of advanced genetic engineering tools available to further improve such murine model systems, of sophisticated neutrophil-profiling technologies, and of multifunctional nanoparticle (NP)-based neutrophil-targeting strategies.
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Affiliation(s)
- Vishnu Hosur
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA.
| | - Daniel A Skelly
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Christopher Francis
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, 360 Huntington Avenue, Boston, MA 02115 USA
| | - Benjamin E Low
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Vivek Kohar
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Lisa M Burzenski
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Mansoor M Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, 360 Huntington Avenue, Boston, MA 02115 USA
| | - Leonard D Shultz
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Michael V Wiles
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
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55
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Livestock Gene Editing by One-step Embryo Manipulation. J Equine Vet Sci 2020; 89:103025. [PMID: 32563448 DOI: 10.1016/j.jevs.2020.103025] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022]
Abstract
The breakthrough and rapid advance of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has enabled the efficient generation of gene-edited animals by one-step embryo manipulation. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 delivery to the livestock embryos has been typically achieved by intracytoplasmic microinjection; however, recent studies show that electroporation may be a reliable, efficient, and practical method for CRISPR/Cas9 delivery. The source of embryos used to generate gene-edited animals varies from in vivo to in vitro produced, depending mostly on the species of interest. In addition, different Cas9 and gRNA reagents can be used for embryo editing, ranging from Cas9-coding plasmid or messenger RNA to Cas9 recombinant protein, which can be combined with in vitro transcribed or synthetic guide RNAs. Mosaicism is reported as one of the main problems with generation of animals by embryo editing. On the other hand, off-target mutations are rarely found in livestock derived from one-step editing. In this review, we discussed these and other aspects of generating gene-edited animals by single-step embryo manipulation.
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56
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Nakayama T, Grainger RM, Cha SW. Simple embryo injection of long single-stranded donor templates with the CRISPR/Cas9 system leads to homology-directed repair in Xenopus tropicalis and Xenopus laevis. Genesis 2020; 58:e23366. [PMID: 32277804 DOI: 10.1002/dvg.23366] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/24/2020] [Accepted: 03/27/2020] [Indexed: 01/05/2023]
Abstract
We report model experiments in which simple microinjection of fertilized eggs has been used to effectively perform homology-directed repair (HDR)-mediated gene editing in the two Xenopus species used most frequently for research: X. tropicalis and X. laevis. We have used long single-stranded DNAs having phosphorothioate modifications as donor templates for HDR at targeted genomic sites using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. First, X. tropicalis tyr mutant (i.e., albino) embryos were successfully rescued: partially pigmented tadpoles were seen in up to 35% of injected embryos, demonstrating the potential for efficient insertion of targeted point mutations. Second, in order to demonstrate the ability to tag genes with fluorescent proteins (FPs), we targeted the melanocyte-specific gene slc45a2.L of X. laevis to label it with the Superfolder green FP (sfGFP), seeing mosaic expression of sfGFP in melanophores in up to 20% of injected tadpoles. Tadpoles generated by these two approaches were raised to sexual maturity, and shown to successfully transmit HDR constructs through the germline with precise targeting and seamless recombination. F1 embryos showed rescue of the tyr mutation (X. tropicalis) and tagging in the appropriate pigment cell-specific manner of slc45a2.L with sfGFP (X. laevis).
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Affiliation(s)
- Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, Virginia
| | - Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, Virginia
| | - Sang-Wook Cha
- School of Natural Sciences, University of Central Missouri, Warrensburg, Missouri
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57
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Westhaus A, Cabanes-Creus M, Rybicki A, Baltazar G, Navarro RG, Zhu E, Drouyer M, Knight M, Albu RF, Ng BH, Kalajdzic P, Kwiatek M, Hsu K, Santilli G, Gold W, Kramer B, Gonzalez-Cordero A, Thrasher AJ, Alexander IE, Lisowski L. High-Throughput In Vitro, Ex Vivo, and In Vivo Screen of Adeno-Associated Virus Vectors Based on Physical and Functional Transduction. Hum Gene Ther 2020; 31:575-589. [PMID: 32000541 PMCID: PMC7232709 DOI: 10.1089/hum.2019.264] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are quickly becoming the vectors of choice for therapeutic gene delivery. To date, hundreds of natural isolates and bioengineered variants have been reported. While factors such as high production titer and low immunoreactivity are important to consider, the ability to deliver the genetic payload (physical transduction) and to drive high transgene expression (functional transduction) remains the most important feature when selecting AAV variants for clinical applications. Reporter expression assays are the most commonly used methods for determining vector fitness. However, such approaches are time consuming and become impractical when evaluating a large number of variants. Limited access to primary human tissues or challenging model systems further complicates vector testing. To address this problem, convenient high-throughput methods based on next-generation sequencing (NGS) are being developed. To this end, we built an AAV Testing Kit that allows inherent flexibility in regard to number and type of AAV variants included, and is compatible with in vitro, ex vivo, and in vivo applications. The Testing Kit presented here consists of a mix of 30 known AAVs where each variant encodes a CMV-eGFP cassette and a unique barcode in the 3′-untranslated region of the eGFP gene, allowing NGS-barcode analysis at both the DNA and RNA/cDNA levels. To validate the AAV Testing Kit, individually packaged barcoded variants were mixed at an equal ratio and used to transduce cells/tissues of interest. DNA and RNA/cDNA were extracted and subsequently analyzed by NGS to determine the physical/functional transduction efficiencies. We were able to assess the transduction efficiencies of immortalized cells, primary cells, and induced pluripotent stem cells in vitro, as well as in vivo transduction in naïve mice and a xenograft liver model. Importantly, while our data validated previously reported transduction characteristics of individual capsids, we also identified novel previously unknown tropisms for some AAV variants.
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Affiliation(s)
- Adrian Westhaus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.,Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Arkadiusz Rybicki
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Matthieu Drouyer
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Maddison Knight
- Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia
| | - Razvan F Albu
- Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia
| | - Boaz H Ng
- Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia
| | - Predrag Kalajdzic
- Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia
| | - Magdalena Kwiatek
- Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, Puławy, Poland
| | - Kenneth Hsu
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, Australia
| | - Giorgia Santilli
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Wendy Gold
- Molecular Neurobiology Research Lab, The Children's Hospital at Westmead, Westmead, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | - Belinda Kramer
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell & Organoid Facility and Stem Cell Medicine Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Adrian J Thrasher
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia.,Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, Puławy, Poland
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58
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Hao M, Wang Z, Qiao H, Yin P, Qiao J, Qi H. Dynamic Genome Editing Using In Vivo Synthesized Donor ssDNA in Escherichia coli. Cells 2020; 9:E467. [PMID: 32085579 PMCID: PMC7072734 DOI: 10.3390/cells9020467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
As a key element of genome editing, donor DNA introduces the desired exogenous sequence while working with other crucial machinery such as CRISPR-Cas or recombinases. However, current methods for the delivery of donor DNA into cells are both inefficient and complicated. Here, we developed a new methodology that utilizes rolling circle replication and Cas9 mediated (RC-Cas-mediated) in vivo single strand DNA (ssDNA) synthesis. A single-gene rolling circle DNA replication system from Gram-negative bacteria was engineered to produce circular ssDNA from a Gram-positive parent plasmid at a designed sequence in Escherichia coli. Furthermore, it was demonstrated that the desired linear ssDNA fragment could be cut out using CRISPR-associated protein 9 (CRISPR-Cas9) nuclease and combined with lambda Red recombinase as donor for precise genome engineering. Various donor ssDNA fragments from hundreds to thousands of nucleotides in length were synthesized in E. coli cells, allowing successive genome editing in growing cells. We hope that this RC-Cas-mediated in vivo ssDNA on-site synthesis system will be widely adopted as a useful new tool for dynamic genome editing.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hongyan Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Peng Yin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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59
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García-Tuñón I, Vuelta E, Lozano L, Herrero M, Méndez L, Palomero-Hernandez J, Pérez-Caro M, Pérez-García J, González-Sarmiento R, Sánchez-Martín M. Establishment of a conditional Nomo1 mouse model by CRISPR/Cas9 technology. Mol Biol Rep 2020; 47:1381-1391. [PMID: 31833031 DOI: 10.1007/s11033-019-05214-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/28/2019] [Indexed: 12/18/2022]
Abstract
The Nomo1 gene mediates a wide range of biological processes of importance in embryonic development. Accordingly, constitutive perturbation of Nomo1 function may result in myriad developmental defects that trigger embryonic lethality. To extend our understanding of Nomo1 function in postnatal stages and in a tissue-specific manner, we generated a conditional knockout mouse model of Nomo1. To achieve this, we used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology in C57Bl/6J mouse zygotes to generate a new mouse model in which exon 3 of the Nomo1 gene is specifically flanked (or floxed) by LoxP sites (Nomo1f/f). Nomo1f/f mouse embryonic fibroblasts were transduced with a Cre adenovirus and efficiently recombined between LoxP sites. Genomic and expression studies in Nomo1-transduced MEFs demonstrated that the Nomo1 exon 3 is ablated. Western blot assay showed that no protein or early truncated protein is produced. In vivo assay crossing Nomo1f/f mouse with a Msi1-CRE transgenic mouse corroborated the previous findings and it showed Nomo1 exon 3 deletion at msi1+ cell compartment. This short technical report demonstrates that CRISPR/Cas9 technology is a simple and easy method for creating conditional mouse models. The Nomo1f/f mouse will be useful to researchers who wish to explore the role of Nomo1 in any developmental stage or in a tissue-specific manner.
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Affiliation(s)
- Ignacio García-Tuñón
- IBSAL (Instituto de Investigación Biomédica de Salamanca), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Elena Vuelta
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Laura Lozano
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - María Herrero
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Lucía Méndez
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Javier Palomero-Hernandez
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - María Pérez-Caro
- Banco de ADN, Nucleus, Universidad de Salamanca, Salamanca, Spain
| | - Jessica Pérez-García
- IBSAL (Instituto de Investigación Biomédica de Salamanca), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Rogelio González-Sarmiento
- IBSAL (Instituto de Investigación Biomédica de Salamanca), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Manuel Sánchez-Martín
- IBSAL (Instituto de Investigación Biomédica de Salamanca), Salamanca, Spain.
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, Salamanca, Spain.
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain.
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60
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Hao M, Qiao J, Qi H. Current and Emerging Methods for the Synthesis of Single-Stranded DNA. Genes (Basel) 2020; 11:E116. [PMID: 31973021 PMCID: PMC7073533 DOI: 10.3390/genes11020116] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/21/2022] Open
Abstract
Methods for synthesizing arbitrary single-strand DNA (ssDNA) fragments are rapidly becoming fundamental tools for gene editing, DNA origami, DNA storage, and other applications. To meet the rising application requirements, numerous methods have been developed to produce ssDNA. Some approaches allow the synthesis of freely chosen user-defined ssDNA sequences to overcome the restrictions and limitations of different length, purity, and yield. In this perspective, we provide an overview of the representative ssDNA production strategies and their most significant challenges to enable the readers to make informed choices of synthesis methods and enhance the availability of increasingly inexpensive synthetic ssDNA. We also aim to stimulate a broader interest in the continued development of efficient ssDNA synthesis techniques and improve their applications in future research.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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Abstract
A transgenic mouse carries within its genome an artificial DNA construct (transgene) that is deliberately introduced by an experimentalist. These animals are widely used to understand gene function and protein function. When addressing the history of transgenic mouse technology, it is apparent that a number of basic science research areas laid the groundwork for success. These include reproductive science, genetics and molecular biology, and micromanipulation and microscopy equipment. From reproductive physiology came applications on how to optimize mouse breeding, how to superovulate mice to produce zygotes for DNA microinjection or preimplantation embryos for combination with embryonic stem (ES) cells, and how to return zygotes and embryos to a pseudopregnant surrogate dam for gestation and birth. From developmental biology, it was learned how to micromanipulate embryos for morula aggregation and blastocyst microinjection and how to establish germline competent ES cells. From genetics came the foundational principles governing the inheritance of genes, the interactions of gene products, and an understanding of the phenotypic consequences of genetic mutations. From molecular biology came a panoply of tools and reagents that are used to clone DNA transgenes, to detect the presence of transgenes, to assess gene expression by measuring transcription, and to detect proteins in cells and tissues. Technical advances in light microscopes, micromanipulators, micropipette pullers, and ancillary equipment made it possible for experimentalists to insert thin glass needles into zygotes or embryos under controlled conditions to inject DNA solutions or ES cells. To fully discuss the breadth of contributions of these numerous scientific disciplines to a comprehensive history of transgenic science is beyond the scope of this work. Examples will be used to illustrate scientific developments central to the foundation of transgenic technology and that are in use today.
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Affiliation(s)
- Thomas L Saunders
- Transgenic Animal Model Core, University of Michigan Medical School, Ann Arbor, MI, USA.
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
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62
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Banan M. Recent advances in CRISPR/Cas9-mediated knock-ins in mammalian cells. J Biotechnol 2020; 308:1-9. [DOI: 10.1016/j.jbiotec.2019.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 12/16/2022]
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63
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Pineault KM, Novoa A, Lozovska A, Wellik DM, Mallo M. Two CRISPR/Cas9-mediated methods for targeting complex insertions, deletions, or replacements in mouse. MethodsX 2019; 6:2088-2100. [PMID: 31667107 PMCID: PMC6812322 DOI: 10.1016/j.mex.2019.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/05/2019] [Indexed: 12/01/2022] Open
Abstract
Genetically modified model organisms are valuable tools for probing gene function, dissecting complex signaling networks, studying human disease, and more. CRISPR/Cas9 technology has significantly democratized and reduced the time and cost of generating genetically modified models to the point that small gene edits are now routinely and efficiently generated in as little as two months. However, generation of larger and more sophisticated gene-modifications continues to be inefficient. Alternative ways to provide the replacement DNA sequence, method of Cas9 delivery, and tethering the template sequence to Cas9 or the guide RNA (gRNA) have all been tested in an effort to maximize homology-directed repair for precise modification of the genome. We present two CRISPR/Cas9 methods that have been used to successfully generate large and complex gene-edits in mouse. In the first method, the Cas9 enzyme is used in conjunction with two sgRNAs and a long single-stranded DNA (lssDNA) template prepared by an alternative protocol. The second method utilizes a tethering approach to couple a biotinylated, double-stranded DNA (dsDNA) template to a Cas9-streptavidin fusion protein. Alternative method for generating long, single-stranded DNA templates for CRISPR/Cas9 editing. Demonstration that using two sgRNAs with Cas9-streptavidin/biotinylated-dsDNA is feasible for large DNA modifications.
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Affiliation(s)
- Kyriel M Pineault
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, USA.,Instituto Gulbenkian de Ciência, Portugal
| | - Ana Novoa
- Instituto Gulbenkian de Ciência, Portugal
| | | | - Deneen M Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, USA
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64
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Kanca O, Zirin J, Garcia-Marques J, Knight SM, Yang-Zhou D, Amador G, Chung H, Zuo Z, Ma L, He Y, Lin WW, Fang Y, Ge M, Yamamoto S, Schulze KL, Hu Y, Spradling AC, Mohr SE, Perrimon N, Bellen HJ. An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms. eLife 2019; 8:e51539. [PMID: 31674908 PMCID: PMC6855806 DOI: 10.7554/elife.51539] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
We previously reported a CRISPR-mediated knock-in strategy into introns of Drosophila genes, generating an attP-FRT-SA-T2A-GAL4-polyA-3XP3-EGFP-FRT-attP transgenic library for multiple uses (Lee et al., 2018a). The method relied on double stranded DNA (dsDNA) homology donors with ~1 kb homology arms. Here, we describe three new simpler ways to edit genes in flies. We create single stranded DNA (ssDNA) donors using PCR and add 100 nt of homology on each side of an integration cassette, followed by enzymatic removal of one strand. Using this method, we generated GFP-tagged proteins that mark organelles in S2 cells. We then describe two dsDNA methods using cheap synthesized donors flanked by 100 nt homology arms and gRNA target sites cloned into a plasmid. Upon injection, donor DNA (1 to 5 kb) is released from the plasmid by Cas9. The cassette integrates efficiently and precisely in vivo. The approach is fast, cheap, and scalable.
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Affiliation(s)
- Oguz Kanca
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Jonathan Zirin
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | | | - Shannon Marie Knight
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Donghui Yang-Zhou
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Gabriel Amador
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Hyunglok Chung
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Zhongyuan Zuo
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Liwen Ma
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Yuchun He
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Howard Hughes Medical Institute, Baylor College of MedicineHoustonUnited States
| | - Wen-Wen Lin
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Ying Fang
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Ming Ge
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Shinya Yamamoto
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| | - Karen L Schulze
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Howard Hughes Medical Institute, Baylor College of MedicineHoustonUnited States
| | - Yanhui Hu
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Allan C Spradling
- Department of EmbryologyHoward Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Stephanie E Mohr
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Norbert Perrimon
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Hugo J Bellen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Howard Hughes Medical Institute, Baylor College of MedicineHoustonUnited States
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
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65
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Janardhan KS, Kohnken R, Turner OC, Gurumurthy CB, Kovi RC. Looking Forward: Cutting-Edge Technologies and Skills for Pathologists in the Future. Toxicol Pathol 2019; 47:1082-1087. [DOI: 10.1177/0192623319873855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Toxicologic pathology is one of the most valuable fields contributing to the advancement of animal and human health. With the ever-changing technological and economic environment, the basic skill set that pathologists are equipped with may require refinement to address the current and future needs. Periodically, pathologists must add relevant, new skills to their toolbox. The Career Development and Outreach Committee of the Society of Toxicologic Pathology (STP) sponsored a career development workshop entitled “Looking Forward: Cutting-edge Technologies and Skills for Pathologists in the Future” in conjunction with the STP 38th Annual Symposium. Experts were chosen to speak on artificial intelligence, clustered regularly interspaced short palindromic repeats technology, microRNAs, and next-generation sequencing. This article provides a summary of the talks presented at the workshop.
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Affiliation(s)
| | | | - Oliver C. Turner
- Preclinical Safety, Novartis, Novartis Institutes for BioMedical Research, East Hanover, NJ, USA
| | | | - Ramesh C. Kovi
- Experimental Pathology Laboratories, Inc, Research Triangle Park, NC, USA
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66
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Bollen Y, Post J, Koo BK, Snippert HJG. How to create state-of-the-art genetic model systems: strategies for optimal CRISPR-mediated genome editing. Nucleic Acids Res 2019; 46:6435-6454. [PMID: 29955892 PMCID: PMC6061873 DOI: 10.1093/nar/gky571] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022] Open
Abstract
Model systems with defined genetic modifications are powerful tools for basic research and translational disease modelling. Fortunately, generating state-of-the-art genetic model systems is becoming more accessible to non-geneticists due to advances in genome editing technologies. As a consequence, solely relying on (transient) overexpression of (mutant) effector proteins is no longer recommended since scientific standards increasingly demand genetic modification of endogenous loci. In this review, we provide up-to-date guidelines with respect to homology-directed repair (HDR)-mediated editing of mammalian model systems, aimed at assisting researchers in designing an efficient genome editing strategy.
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Affiliation(s)
- Yannik Bollen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands.,Medical Cell BioPhysics, MIRA Institute, University of Twente, Enschede, The Netherlands
| | - Jasmin Post
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands
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67
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Gurumurthy CB, Sato M, Nakamura A, Inui M, Kawano N, Islam MA, Ogiwara S, Takabayashi S, Matsuyama M, Nakagawa S, Miura H, Ohtsuka M. Creation of CRISPR-based germline-genome-engineered mice without ex vivo handling of zygotes by i-GONAD. Nat Protoc 2019; 14:2452-2482. [PMID: 31341289 DOI: 10.1038/s41596-019-0187-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/01/2019] [Indexed: 01/03/2023]
Abstract
Methods to create genetically engineered mice involve three major steps: harvesting embryos from one set of females, microinjection of reagents into embryos ex vivo and their surgical transfer to another set of females. Although tedious, these methods have been used for more than three decades to create mouse models. We recently developed a method named GONAD (genome editing via oviductal nucleic acids delivery), which bypasses these steps. GONAD involves injection of CRISPR components (Cas9 mRNA and guide RNA (gRNA)) into the oviducts of pregnant females 1.5 d post conception, followed by in vivo electroporation to deliver the components into the zygotes in situ. Using GONAD, we demonstrated that target genes can be disrupted and analyzed at different stages of mouse embryonic development. Subsequently, we developed improved GONAD (i-GONAD) by delivering CRISPR ribonucleoproteins (RNPs; Cas9 protein or Cpf1 protein and gRNA) into day-0.7 pregnant mice, which made it suitable for routine generation of knockout and large-deletion mouse models. i-GONAD can also generate knock-in models containing up to 1-kb inserts when single-stranded DNA (ssDNA) repair templates are supplied. i-GONAD offers other advantages: it does not require vasectomized males and pseudo-pregnant females, the females used for i-GONAD are not sacrificed and can be used for other experiments, it can be easily adopted in laboratories lacking sophisticated microinjection equipment, and can be implemented by researchers skilled in small-animal surgery but lacking embryo-handling skills. Here, we provide a step-by-step protocol for establishing the i-GONAD method. The protocol takes ∼6 weeks to generate the founder mice.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima, Japan
| | - Ayaka Nakamura
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Masafumi Inui
- Laboratory of Animal Regeneration Systemology, Department of Life Science, School of Agriculture, Meiji University, Kanagawa, Japan
- Meiji University International Institute for Bio-Resource Research, Kanagawa, Japan
| | - Natsuko Kawano
- Laboratory of Regulatory Biology, Department of Life Science, School of Agriculture, Meiji University, Kanagawa, Japan
| | - Md Atiqul Islam
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa, Japan
- Laboratory of Laboratory Animal Science and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Sanae Ogiwara
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Shuji Takabayashi
- Laboratory for Animal Resources Development, Hamamatsu University School Of Medicine, Hamamatsu, Shizuoka, Japan
| | - Makoto Matsuyama
- Division of Molecular Genetics, Shigei Medical Research Institute, Minami-ku, Okayama, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Hokkaido, Japan
| | - Hiromi Miura
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa, Japan
| | - Masato Ohtsuka
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa, Japan.
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa, Japan.
- The Institute of Medical Sciences, Tokai University, Kanagawa, Japan.
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68
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Ahmadzadeh V, Farajnia S, Baghban R, Rahbarnia L, Zarredar H. CRISPR-Cas system: Toward a more efficient technology for genome editing and beyond. J Cell Biochem 2019; 120:16379-16392. [PMID: 31219653 DOI: 10.1002/jcb.29140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/07/2019] [Indexed: 12/26/2022]
Abstract
Genome engineering technology is of great interest for biomedical research that enables scientists to make specific manipulation in the DNA sequence. Early methods for introducing double-stranded DNA breaks relies on protein-based systems. These platforms have enabled fascinating advances, but all are costly and time-consuming to engineer, preventing these from gaining high-throughput applications. The CRISPR-Cas9 system, co-opted from bacteria, has generated considerable excitement in gene targeting. In this review, we describe gene targeting techniques with an emphasis on recent strategies to improve the specificities of CRISPR-Cas systems for nuclease and non-nuclease applications.
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Affiliation(s)
- Vahideh Ahmadzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roghayyeh Baghban
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Habib Zarredar
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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69
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Ohtsuka M, Sato M. i-GONAD: A method for generating genome-edited animals without ex vivo handling of embryos. Dev Growth Differ 2019; 61:306-315. [PMID: 31198998 DOI: 10.1111/dgd.12620] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 05/05/2019] [Indexed: 01/01/2023]
Abstract
The recent development of genome editing technologies has enabled the creation of genome-edited animals, with alterations at the desired target locus. The clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for this purpose because it is simpler and more efficient than other genome editing technologies. The conventional methods for creation of genome-edited animals involve ex vivo handling of embryos (zygotes) for microinjection or in vitro electroporation. However, this process is laborious and time-consuming, and relatively large numbers of animals are used. Furthermore, these methods require specialized skills for handling embryos. In 2015, we reported a novel method for the creation of genome-edited animals without ex vivo handling of embryos. The technology known as Genome-editing via Oviductal Nucleic Acids Delivery (GONAD) involved intraoviductal instillation of genome editing components into a pregnant female and subsequent in vivo electroporation of an entire oviduct. The genome editing components present in the oviductal lumen are transferred to preimplantation embryos in situ for introducing insertion or deletion (indel) mutations at the desired loci. This technology was further improved by optimizing several parameters to develop improved GONAD (i-GONAD) for the efficient generation of mutant or knock-in animals. In this review, we discuss the historical background, potential applications, advantages, and future challenges of GONAD/i-GONAD technology.
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Affiliation(s)
- Masato Ohtsuka
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa, Japan.,Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa, Japan.,The Institute of Medical Sciences, Tokai University, Kanagawa, Japan
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima, Japan
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70
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CRISPR/Cas9 applications in gene therapy for primary immunodeficiency diseases. Emerg Top Life Sci 2019; 3:277-287. [PMID: 33523134 DOI: 10.1042/etls20180157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 02/07/2023]
Abstract
Primary immunodeficiency diseases (PIDs) encompass a range of diseases due to mutations in genes that are critical for immunity. Haploinsufficiency and gain-of-function mutations are more complex than simple loss-of-function mutations; in addition to increased susceptibility to infections, immune dysregulations like autoimmunity and hyperinflammation are common presentations. Hematopoietic stem cell (HSC) gene therapy, using integrating vectors, provides potential cure of disease, but genome-wide transgene insertions and the lack of physiological endogenous gene regulation may yet present problems, and not applicable in PIDs where immune regulation is paramount. Targeted genome editing addresses these concerns; we discuss some approaches of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas system applicable for gene therapy in PIDs. Preclinical repair of gene mutations and insertion of complementary DNA restore endogenous gene regulation and they have shown very promising data for clinical application. However, ongoing studies to characterize off-target genotoxicity, careful donor designs to ensure physiological expression, and maneuvers to optimize engraftment potential are critical to ensure successful application of this next-gen targeted HSC gene therapy.
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71
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Ohuchi H, Sato K, Habuta M, Fujita H, Bando T. Congenital eye anomalies: More mosaic than thought? Congenit Anom (Kyoto) 2019; 59:56-73. [PMID: 30039880 DOI: 10.1111/cga.12304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022]
Abstract
The eye is a sensory organ that primarily captures light and provides the sense of sight, as well as delivering non-visual light information involving biological rhythms and neurophysiological activities to the brain. Since the early 1990s, rapid advances in molecular biology have enabled the identification of developmental genes, genes responsible for human congenital diseases, and relevant genes of mutant animals with various anomalies. In this review, we first look at the development of the eye, and we highlight seminal reports regarding archetypal gene defects underlying three developmental ocular disorders in humans: (1) holoprosencephaly (HPE), with cyclopia being exhibited in the most severe cases; (2) microphthalmia, anophthalmia, and coloboma (MAC) phenotypes; and (3) anterior segment dysgenesis (ASDG), known as Peters anomaly and its related disorders. The recently developed methods, such as next-generation sequencing and genome editing techniques, have aided the discovery of gene mutations in congenital eye diseases and gene functions in normal eye development. Finally, we discuss Pax6-genome edited mosaic eyes and propose that somatic mosaicism in developmental gene mutations should be considered a causal factor for variable phenotypes, sporadic cases, and de novo mutations in human developmental disorders.
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Affiliation(s)
- Hideyo Ohuchi
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Keita Sato
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Munenori Habuta
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hirofumi Fujita
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Tetsuya Bando
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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72
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Ge XA, Hunter CP. Efficient Homologous Recombination in Mice Using Long Single Stranded DNA and CRISPR Cas9 Nickase. G3 (BETHESDA, MD.) 2019; 9:281-286. [PMID: 30504134 PMCID: PMC6325892 DOI: 10.1534/g3.118.200758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/21/2018] [Indexed: 01/29/2023]
Abstract
The CRISPR/Cas9 nickase mutant is less prone to off-target double-strand (ds)DNA breaks than wild-type Cas9 because to produce dsDNA cleavage it requires two guide RNAs to target the nickase to nearby opposing strands. Like wild-type Cas9 lesions, these staggered lesions are repaired by either non-homologous end joining or, if a repair template is provided, by homologous recombination (HR). Here, we report very efficient (up to 100%) recovery of heterozygous insertions in Mus musculus produced by long (>300 nt), single-stranded DNA donor template-guided repair of paired-nickase lesions.
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Affiliation(s)
- Xi A Ge
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Craig P Hunter
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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73
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Gurumurthy CB, Lloyd KCK. Generating mouse models for biomedical research: technological advances. Dis Model Mech 2019; 12:dmm029462. [PMID: 30626588 PMCID: PMC6361157 DOI: 10.1242/dmm.029462] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, new methods and procedures have been developed to generate genetically engineered mouse models of human disease. This At a Glance article highlights several recent technical advances in mouse genome manipulation that have transformed our ability to manipulate and study gene expression in the mouse. We discuss how conventional gene targeting by homologous recombination in embryonic stem cells has given way to more refined methods that enable allele-specific manipulation in zygotes. We also highlight advances in the use of programmable endonucleases that have greatly increased the feasibility and ease of editing the mouse genome. Together, these and other technologies provide researchers with the molecular tools to functionally annotate the mouse genome with greater fidelity and specificity, as well as to generate new mouse models using faster, simpler and less costly techniques.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
| | - Kevin C Kent Lloyd
- Department of Surgery, School of Medicine, University of California, Davis, CA 95618, USA
- Mouse Biology Program, University of California, Davis, CA 95618, USA
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74
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Klimke A, Güttler S, Kuballa P, Janzen S, Ortmann S, Flora A. Use of CRISPR/Cas9 for the Modification of the Mouse Genome. Methods Mol Biol 2019; 1953:213-230. [PMID: 30912024 DOI: 10.1007/978-1-4939-9145-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The use of CRISPR/Cas9 to modify the mouse genome has gained immense interest in the past few years since it allows the direct modification of embryos, bypassing the need of labor-intensive procedures for the manipulation of embryonic stem cells. By shortening the overall timelines and reducing the costs for the generation of new genetically modified mouse lines (Li et al., Nat Biotechnol 31: 681-683, 2013), this technology has rapidly become a major tool for in vivo drug discovery applications.
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Affiliation(s)
| | | | | | | | | | - Adriano Flora
- PerkinElmer chemagen Technologie GmbH, Baesweiler, Germany.
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75
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Hall B, Cho A, Limaye A, Cho K, Khillan J, Kulkarni AB. Genome Editing in Mice Using CRISPR/Cas9 Technology. CURRENT PROTOCOLS IN CELL BIOLOGY 2018; 81:e57. [PMID: 30178917 PMCID: PMC9942237 DOI: 10.1002/cpcb.57] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
CRISPR/Cas9 technology has revolutionized genome editing in mice, allowing for simple and rapid development of knockouts and knockins. CRISPR relies on small guide RNAs that direct the RNA-guided nuclease Cas9 to a designated genomic site using ∼20 bp of corresponding sequence. Cas9 then creates a double-strand break in the targeted loci that is either patched in an error-prone fashion to produce a frame-shift mutation, a knockout, or is repaired by recombination with donor DNA containing homology arms, a knockin. This protocol covers the techniques needed to rapidly generate knockout and knockin mice with CRISPR via microinjection of Cas9, the guide RNA, and possible donor DNA into the mouse zygote. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Bradford Hall
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| | - Andrew Cho
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| | - Advait Limaye
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| | - Kyoungin Cho
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jaspal Khillan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ashok B Kulkarni
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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76
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Yamamoto Y, Gerbi SA. Making ends meet: targeted integration of DNA fragments by genome editing. Chromosoma 2018; 127:405-420. [PMID: 30003320 PMCID: PMC6330168 DOI: 10.1007/s00412-018-0677-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 12/27/2022]
Abstract
Targeted insertion of large pieces of DNA is an important goal of genetic engineering. However, this goal has been elusive since classical methods for homology-directed repair are inefficient and often not feasible in many systems. Recent advances are described here that enable site-specific genomic insertion of relatively large DNA with much improved efficiency. Using the preferred repair pathway in the cell of nonhomologous end-joining, DNA of up to several kb could be introduced with remarkably good precision by the methods of HITI and ObLiGaRe with an efficiency up to 30-40%. Recent advances utilizing homology-directed repair (methods of PITCh; short homology arms including ssODN; 2H2OP) have significantly increased the efficiency for DNA insertion, often to 40-50% or even more depending on the method and length of DNA. The remaining challenges of integration precision and off-target site insertions are summarized. Overall, current advances provide major steps forward for site-specific insertion of large DNA into genomes from a broad range of cells and organisms.
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Affiliation(s)
- Yutaka Yamamoto
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall room 260, 185 Meeting Street, Providence, RI, 02912, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall room 260, 185 Meeting Street, Providence, RI, 02912, USA.
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77
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Boel A, De Saffel H, Steyaert W, Callewaert B, De Paepe A, Coucke PJ, Willaert A. CRISPR/Cas9-mediated homology-directed repair by ssODNs in zebrafish induces complex mutational patterns resulting from genomic integration of repair-template fragments. Dis Model Mech 2018; 11:11/10/dmm035352. [PMID: 30355591 PMCID: PMC6215429 DOI: 10.1242/dmm.035352] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/31/2018] [Indexed: 12/30/2022] Open
Abstract
Targeted genome editing by CRISPR/Cas9 is extremely well fitted to generate gene disruptions, although precise sequence replacement by CRISPR/Cas9-mediated homology-directed repair (HDR) suffers from low efficiency, impeding its use for high-throughput knock-in disease modeling. In this study, we used next-generation sequencing (NGS) analysis to determine the efficiency and reliability of CRISPR/Cas9-mediated HDR using several types of single-stranded oligodeoxynucleotide (ssODN) repair templates for the introduction of disease-relevant point mutations in the zebrafish genome. Our results suggest that HDR rates are strongly determined by repair-template composition, with the most influential factor being homology-arm length. However, we found that repair using ssODNs does not only lead to precise sequence replacement but also induces integration of repair-template fragments at the Cas9 cut site. We observed that error-free repair occurs at a relatively constant rate of 1-4% when using different repair templates, which was sufficient for transmission of point mutations to the F1 generation. On the other hand, erroneous repair mainly accounts for the variability in repair rate between the different repair templates. To further improve error-free HDR rates, elucidating the mechanism behind this erroneous repair is essential. We show that the error-prone nature of ssODN-mediated repair, believed to act via synthesis-dependent strand annealing (SDSA), is most likely due to DNA synthesis errors. In conclusion, caution is warranted when using ssODNs for the generation of knock-in models or for therapeutic applications. We recommend the application of in-depth NGS analysis to examine both the efficiency and error-free nature of HDR events. This article has an associated First Person interview with the first author of the paper. Summary: NGS-based analysis reveals that CRISPR/Cas9-induced double-strand-break repair using single-stranded repair templates is error prone in zebrafish, resulting in complex patterns of integrated repair-template fragments.
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Affiliation(s)
- Annekatrien Boel
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Hanna De Saffel
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Anne De Paepe
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Paul J Coucke
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Andy Willaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
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78
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Gurumurthy CB, Perez-Pinera P. Technological advances in integrating multi-kilobase DNA sequences into genomes. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018. [DOI: 10.1016/j.cobme.2018.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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79
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Jun S, Lim H, Jang H, Lee W, Ahn J, Lee JH, Bang D. Straightforward Delivery of Linearized Double-Stranded DNA Encoding sgRNA and Donor DNA for the Generation of Single Nucleotide Variants Based on the CRISPR/Cas9 System. ACS Synth Biol 2018; 7:1651-1659. [PMID: 29924933 DOI: 10.1021/acssynbio.7b00345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CRISPR/Cas9 for genome editing requires delivery of a guide RNA sequence and donor DNA for targeted homologous recombination. Typically, single-stranded oligodeoxynucleotide, serving as the donor template, and a plasmid encoding guide RNA are delivered as two separate components. However, in the multiplexed generation of single nucleotide variants, this two-component delivery system is limited by difficulty of delivering a matched pair of sgRNA and donor DNA to the target cell. Here, we describe a novel codelivery system called "sgR-DNA" that uses a linearized double-stranded DNA consisting of donor DNA component and a component encoding sgRNA. Our sgR-DNA-based method is simple to implement because it does not require cloning steps. We also report the potential of our delivery system to generate multiplex genomic substitutions in Escherichia coli and human cells.
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Affiliation(s)
- Soyeong Jun
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hyeonseob Lim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Wookjae Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jinwoo Ahn
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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80
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New Turns for High Efficiency Knock-In of Large DNA in Human Pluripotent Stem Cells. Stem Cells Int 2018; 2018:9465028. [PMID: 30057628 PMCID: PMC6051061 DOI: 10.1155/2018/9465028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 04/22/2018] [Accepted: 05/13/2018] [Indexed: 12/26/2022] Open
Abstract
The groundbreaking CRISPR technology is revolutionizing biomedical research with its superior simplicity, high efficiency, and robust accuracy. Recent technological advances by a coupling CRISPR system with various DNA repair mechanisms have further opened up new opportunities to overcome existing challenges in knocking-in foreign DNA in human pluripotent stem cells, including embryonic stem cells (ESC) and induced pluripotent stem cells (iPSC). In this review, we summarized the very recent development of CRISPR-based knock-in strategies and discussed the results obtained as well as potential applications in human ESC and iPSC.
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81
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Codner GF, Mianné J, Caulder A, Loeffler J, Fell R, King R, Allan AJ, Mackenzie M, Pike FJ, McCabe CV, Christou S, Joynson S, Hutchison M, Stewart ME, Kumar S, Simon MM, Agius L, Anstee QM, Volynski KE, Kullmann DM, Wells S, Teboul L. Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants. BMC Biol 2018; 16:70. [PMID: 29925374 PMCID: PMC6011369 DOI: 10.1186/s12915-018-0530-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 01/22/2023] Open
Abstract
Background Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing have led to the use of long single-stranded DNA (lssDNA) molecules for generating conditional mutations. However, there is still limited available data on the efficiency and reliability of this method. Results We generated conditional mouse alleles using lssDNA donor templates and performed extensive characterization of the resulting mutations. We observed that the use of lssDNA molecules as donors efficiently yielded founders bearing the conditional allele, with seven out of nine projects giving rise to modified alleles. However, rearranged alleles including nucleotide changes, indels, local rearrangements and additional integrations were also frequently generated by this method. Specifically, we found that alleles containing unexpected point mutations were found in three of the nine projects analyzed. Alleles originating from illegitimate repairs or partial integration of the donor were detected in eight projects. Furthermore, additional integrations of donor molecules were identified in four out of the seven projects analyzed by copy counting. This highlighted the requirement for a thorough allele validation by polymerase chain reaction, sequencing and copy counting of the mice generated through this method. We also demonstrated the feasibility of using lssDNA donors to generate thus far problematic point mutations distant from active CRISPR cutting sites by targeting two distinct genes (Gckr and Rims1). We propose a strategy to perform extensive quality control and validation of both types of mouse models generated using lssDNA donors. Conclusion lssDNA donors reproducibly generate conditional alleles and can be used to introduce point mutations away from CRISPR/Cas9 cutting sites in mice. However, our work demonstrates that thorough quality control of new models is essential prior to reliably experimenting with mice generated by this method. These advances in genome editing techniques shift the challenge of mutagenesis from generation to the validation of new mutant models. Electronic supplementary material The online version of this article (10.1186/s12915-018-0530-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma F Codner
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Joffrey Mianné
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Jorik Loeffler
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Rachel Fell
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Ruairidh King
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Alasdair J Allan
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Matthew Mackenzie
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Fran J Pike
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | | | | | - Sam Joynson
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Marie Hutchison
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | | | - Saumya Kumar
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Michelle M Simon
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Loranne Agius
- Institute of Cellular Medicine and Ageing and Health, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Quentin M Anstee
- Institute of Cellular Medicine and Ageing and Health, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Kirill E Volynski
- UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Dimitri M Kullmann
- UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK.
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82
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Lanza DG, Gaspero A, Lorenzo I, Liao L, Zheng P, Wang Y, Deng Y, Cheng C, Zhang C, Seavitt JR, DeMayo FJ, Xu J, Dickinson ME, Beaudet AL, Heaney JD. Comparative analysis of single-stranded DNA donors to generate conditional null mouse alleles. BMC Biol 2018; 16:69. [PMID: 29925370 PMCID: PMC6011517 DOI: 10.1186/s12915-018-0529-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The International Mouse Phenotyping Consortium is generating null allele mice for every protein-coding gene in the genome and characterizing these mice to identify gene-phenotype associations. While CRISPR/Cas9-mediated null allele production in mice is highly efficient, generation of conditional alleles has proven to be more difficult. To test the feasibility of using CRISPR/Cas9 gene editing to generate conditional knockout mice for this large-scale resource, we employed Cas9-initiated homology-driven repair (HDR) with short and long single stranded oligodeoxynucleotides (ssODNs and lssDNAs). RESULTS Using pairs of single guide RNAs and short ssODNs to introduce loxP sites around a critical exon or exons, we obtained putative conditional allele founder mice, harboring both loxP sites, for 23 out of 30 targeted genes. LoxP sites integrated in cis in at least one mouse for 18 of 23 genes. However, loxP sites were mutagenized in 4 of the 18 in cis lines. HDR efficiency correlated with Cas9 cutting efficiency but was minimally influenced by ssODN homology arm symmetry. By contrast, using pairs of guides and single lssDNAs to introduce loxP-flanked exons, conditional allele founders were generated for all four genes targeted, although one founder was found to harbor undesired mutations within the lssDNA sequence interval. Importantly, when employing either ssODNs or lssDNAs, random integration events were detected. CONCLUSIONS Our studies demonstrate that Cas9-mediated HDR with pairs of ssODNs can generate conditional null alleles at many loci, but reveal inefficiencies when applied at scale. In contrast, lssDNAs are amenable to high-throughput production of conditional alleles when they can be employed. Regardless of the single-stranded donor utilized, it is essential to screen for sequence errors at sites of HDR and random insertion of donor sequences into the genome.
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Affiliation(s)
- Denise G Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Angelina Gaspero
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
| | - Isabel Lorenzo
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Lan Liao
- Department of Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
- Genetically Engineered Mouse Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Ping Zheng
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Ying Wang
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yu Deng
- Lester and Sue Smith Breast Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Chonghui Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
- Department of Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Chuansheng Zhang
- Department of Neuroscience, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
| | - Francesco J DeMayo
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Jianming Xu
- Department of Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
- Genetically Engineered Mouse Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA.
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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83
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Miyasaka Y, Uno Y, Yoshimi K, Kunihiro Y, Yoshimura T, Tanaka T, Ishikubo H, Hiraoka Y, Takemoto N, Tanaka T, Ooguchi Y, Skehel P, Aida T, Takeda J, Mashimo T. CLICK: one-step generation of conditional knockout mice. BMC Genomics 2018; 19:318. [PMID: 29720086 PMCID: PMC5930688 DOI: 10.1186/s12864-018-4713-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/23/2018] [Indexed: 02/05/2023] Open
Abstract
Background CRISPR/Cas9 enables the targeting of genes in zygotes; however, efficient approaches to create loxP-flanked (floxed) alleles remain elusive. Results Here, we show that the electroporation of Cas9, two gRNAs, and long single-stranded DNA (lssDNA) into zygotes, termed CLICK (CRISPR with lssDNA inducing conditional knockout alleles), enables the quick generation of floxed alleles in mice and rats. Conclusions The high efficiency of CLICK provides homozygous knock-ins in oocytes carrying tissue-specific Cre, which allows the one-step generation of conditional knockouts in founder (F0) mice. Electronic supplementary material The online version of this article (10.1186/s12864-018-4713-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoshiki Miyasaka
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Yoshihiro Uno
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Kazuto Yoshimi
- Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.,Mouse Genomics Resource Laboratory, National Institute of Genetics, Shizuoka, 411-8540, Japan
| | - Yayoi Kunihiro
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Takuji Yoshimura
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Tomohiro Tanaka
- Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Harumi Ishikubo
- Laboratory of Recombinant Animals, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Chiyoda, Tokyo, 101-0062, Japan
| | - Yuichi Hiraoka
- Laboratory of Recombinant Animals, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Chiyoda, Tokyo, 101-0062, Japan.,Laboratory of Molecular Neuroscience, MRI, TMDU, Tokyo, 113-8510, Japan
| | - Norihiko Takemoto
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | | | | | - Paul Skehel
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Tomomi Aida
- Laboratory of Recombinant Animals, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Chiyoda, Tokyo, 101-0062, Japan.,Laboratory of Molecular Neuroscience, MRI, TMDU, Tokyo, 113-8510, Japan.,Present address: McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Junji Takeda
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Tomoji Mashimo
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan. .,Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
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84
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Liang P, Zhang X, Chen Y, Huang J. Developmental history and application of CRISPR in human disease. J Gene Med 2018. [PMID: 28623876 DOI: 10.1002/jgm.2963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-editing tools are programmable artificial nucleases, mainly including zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeat (CRISPR). By recognizing and cleaving specific DNA sequences, genome-editing tools make it possible to generate site-specific DNA double-strand breaks (DSBs) in the genome. DSBs will then be repaired by either error-prone nonhomologous end joining or high-fidelity homologous recombination mechanisms. Through these two different mechanisms, endogenous genes can be knocked out or precisely repaired/modified. Rapid developments in genome-editing tools, especially CRISPR, have revolutionized human disease models generation, for example, various zebrafish, mouse, rat, pig, monkey and human cell lines have been constructed. Here, we review the developmental history of CRISPR and its application in studies of human diseases. In addition, we also briefly discussed the therapeutic application of CRISPR in the near future.
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Affiliation(s)
- Puping Liang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiya Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuxi Chen
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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85
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Abstract
Knock-in mice are useful for evaluating endogenous gene expressions and functions in vivo. Instead of the conventional gene-targeting method using embryonic stem cells, an exogenous DNA sequence can be inserted into the target locus in the zygote using genome editing technology. In this chapter, I describe the generation of epitope-tagged mice using engineered endonuclease and single-stranded oligodeoxynucleotide through the mouse zygote as an example of how to generate a knock-in mouse by genome editing.
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Affiliation(s)
- Wataru Fujii
- Laboratory of Applied Genetics, Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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86
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Ohtsuka M, Sato M, Miura H, Takabayashi S, Matsuyama M, Koyano T, Arifin N, Nakamura S, Wada K, Gurumurthy CB. i-GONAD: a robust method for in situ germline genome engineering using CRISPR nucleases. Genome Biol 2018; 19:25. [PMID: 29482575 PMCID: PMC5828090 DOI: 10.1186/s13059-018-1400-x] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/30/2018] [Indexed: 11/10/2022] Open
Abstract
We present a robust method called improved-Genome editing via Oviductal Nucleic Acids Delivery (i-GONAD) that delivers CRISPR ribonucleoproteins to E0.7 embryos via in situ electroporation. The method generates mouse models containing single-base changes, kilobase-sized deletions, and knock-ins. The efficiency of i-GONAD is comparable to that of traditional microinjection methods, which rely on ex vivo handling of zygotes and require recipient animals for embryo transfer. In contrast, i-GONAD avoids these technically difficult steps, and it can be performed at any laboratory with simple equipment and technical expertise. Further, i-GONAD-treated females retain reproductive function, suggesting future use of the method for germline gene therapy.
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Affiliation(s)
- Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan.
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, Japan.
- The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan.
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima, Japan
| | - Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, Japan
| | - Shuji Takabayashi
- Laboratory Animal Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Makoto Matsuyama
- Division of Molecular Genetics, Shigei Medical Research Institute, Minami-ku, Okayama, Japan
| | - Takayuki Koyano
- Division of Molecular Genetics, Shigei Medical Research Institute, Minami-ku, Okayama, Japan
| | - Naomi Arifin
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan
- Department of Applied Biochemistry, School of Engineering, Tokai University, Hiratsuka, Kanagawa, Japan
| | - Shingo Nakamura
- Division of Biomedical Engineering, National Defense Medical College Research Institute, Tokorozawa, Saitama, Japan
| | - Kenta Wada
- Department of Bioproduction, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
- Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA
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87
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Optimized co-transfection of murine embryonic stem cells. Transgenic Res 2018; 27:131-133. [PMID: 29305772 DOI: 10.1007/s11248-017-0055-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/14/2017] [Indexed: 10/18/2022]
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88
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Miura H, Quadros RM, Gurumurthy CB, Ohtsuka M. Easi-CRISPR for creating knock-in and conditional knockout mouse models using long ssDNA donors. Nat Protoc 2018; 13:195-215. [PMID: 29266098 PMCID: PMC6058056 DOI: 10.1038/nprot.2017.153] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
CRISPR/Cas9-based genome editing can easily generate knockout mouse models by disrupting the gene sequence, but its efficiency for creating models that require either insertion of exogenous DNA (knock-in) or replacement of genomic segments is very poor. The majority of mouse models used in research involve knock-in (reporters or recombinases) or gene replacement (e.g., conditional knockout alleles containing exons flanked by LoxP sites). A few methods for creating such models have been reported that use double-stranded DNA as donors, but their efficiency is typically 1-10% and therefore not suitable for routine use. We recently demonstrated that long single-stranded DNAs (ssDNAs) serve as very efficient donors, both for insertion and for gene replacement. We call this method efficient additions with ssDNA inserts-CRISPR (Easi-CRISPR) because it is a highly efficient technology (efficiency is typically 30-60% and reaches as high as 100% in some cases). The protocol takes ∼2 months to generate the founder mice.
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Affiliation(s)
- Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of
Medicine, Tokai University, Kanagawa 259-1193, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa 259-1193,
Japan
| | - Rolen M. Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical
Center, Omaha, NE, USA
| | - Channabasavaiah B. Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical
Center, Omaha, NE, USA
- Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska
Medical Center, Omaha, NE, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of
Medicine, Tokai University, Kanagawa 259-1193, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa 259-1193,
Japan
- The Institute of Medical Sciences, Tokai University, Kanagawa 259-1193, Japan
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89
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Remy S, Chenouard V, Tesson L, Usal C, Ménoret S, Brusselle L, Heslan JM, Nguyen TH, Bellien J, Merot J, De Cian A, Giovannangeli C, Concordet JP, Anegon I. Generation of gene-edited rats by delivery of CRISPR/Cas9 protein and donor DNA into intact zygotes using electroporation. Sci Rep 2017; 7:16554. [PMID: 29185448 PMCID: PMC5707420 DOI: 10.1038/s41598-017-16328-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/06/2017] [Indexed: 02/05/2023] Open
Abstract
The generation of gene-edited animals using the CRISPRs/Cas9 system is based on microinjection into zygotes which is inefficient, time consuming and demands high technical skills. We report the optimization of an electroporation method for intact rat zygotes using sgRNAs and Cas9 protein in combination or not with ssODNs (~100 nt). This resulted in high frequency of knockouts, between 15 and 50% of analyzed animals. Importantly, using ssODNs as donor template resulted in precise knock-in mutations in 25–100% of analyzed animals, comparable to microinjection. Electroporation of long ssDNA or dsDNA donors successfully used in microinjection in the past did not allow generation of genome-edited animals despite dsDNA visualization within zygotes. Thus, simultaneous electroporation of a large number of intact rat zygotes is a rapid, simple, and efficient method for the generation of a variety of genome-edited rats.
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Affiliation(s)
- Séverine Remy
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France. .,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France. .,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France.
| | - Vanessa Chenouard
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Laurent Tesson
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Claire Usal
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Séverine Ménoret
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Lucas Brusselle
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Jean-Marie Heslan
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France.,Platform GenoCellEdit, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Tuan Huan Nguyen
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform GenoCellEdit, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | | | - Jean Merot
- Institut du thorax, INSERM UMR 1087, CNRS UMR 6291, F44007, Nantes, France
| | - Anne De Cian
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005, Paris, France
| | - Carine Giovannangeli
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005, Paris, France
| | - Jean-Paul Concordet
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005, Paris, France
| | - Ignacio Anegon
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France. .,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France. .,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France.
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90
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Application of genome editing technologies in rats for human disease models. J Hum Genet 2017; 63:115-123. [DOI: 10.1038/s10038-017-0346-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 02/02/2023]
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91
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Zhou W, Wan Y, Guo R, Deng M, Deng K, Wang Z, Zhang Y, Wang F. Generation of beta-lactoglobulin knock-out goats using CRISPR/Cas9. PLoS One 2017; 12:e0186056. [PMID: 29016691 PMCID: PMC5634636 DOI: 10.1371/journal.pone.0186056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 09/25/2017] [Indexed: 12/12/2022] Open
Abstract
Goat's milk, considered a substitute for cow's milk, has a high nutritional value. However, goat's milk contains various allergens, predominantly β-lactoglobulin (BLG). In this study, we employed the CRISPR/Cas9 system to target the BLG locus in goat fibroblasts for sgRNA optimization and generate BLG knock-out goats through co-injection of Cas9 mRNA and small guide RNAs (sgRNAs) into goat embryos at the one-cell stage. We firstly tested sgRNA editing efficiencies in goat fibroblast cells, and approximately 8.00%-9.09% of the cells were modified in single sgRNA-guided targeting experiment. Among the kids, the genome-targeting efficiencies of single sgRNA were 12.5% (10 ng/μL sg1) and 0% (10 ng/μL sg2) and efficiencies of dual sgRNAs were 25.0% (25 ng/μL sg2+sg3 group) and 28.6% (50 ng/μL sg2+sg3 group). Relative expression of BLG in BLG knock-out goat mammary glands significantly (p < 0.01) decreased as well as other milk protein coding genes, such as CSN1S1, CSN1S2, CSN2, CSN3 and LALBA (p < 0.05). As expected, BLG protein had been abolished in the milk of the BLG knock-out goat. In addition, most of the targeted kids were chimeric (3/4), and their various body tissues were edited simultaneously. Our study thus provides a basis for optimizing the quality of goat milk, which can be applied to biomedical and agricultural research.
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Affiliation(s)
- Wenjun Zhou
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, Jiangsu, PR, China
| | - Yongjie Wan
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, Jiangsu, PR, China
| | - Rihong Guo
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, Jiangsu, PR, China
| | - Mingtian Deng
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, Jiangsu, PR, China
| | - Kaiping Deng
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, Jiangsu, PR, China
| | - Zhen Wang
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, Jiangsu, PR, China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, Jiangsu, PR, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, Jiangsu, PR, China
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92
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Sakuma T, Yamamoto T. Magic wands of CRISPR—lots of choices for gene knock-in. Cell Biol Toxicol 2017; 33:501-505. [DOI: 10.1007/s10565-017-9409-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 12/18/2022]
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93
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Aslan Y, Tadjuidje E, Zorn AM, Cha SW. High-efficiency non-mosaic CRISPR-mediated knock-in and indel mutation in F0 Xenopus. Development 2017; 144:2852-2858. [PMID: 28694259 DOI: 10.1242/dev.152967] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/28/2017] [Indexed: 01/03/2023]
Abstract
The revolution in CRISPR-mediated genome editing has enabled the mutation and insertion of virtually any DNA sequence, particularly in cell culture where selection can be used to recover relatively rare homologous recombination events. The efficient use of this technology in animal models still presents a number of challenges, including the time to establish mutant lines, mosaic gene editing in founder animals, and low homologous recombination rates. Here we report a method for CRISPR-mediated genome editing in Xenopus oocytes with homology-directed repair (HDR) that provides efficient non-mosaic targeted insertion of small DNA fragments (40-50 nucleotides) in 4.4-25.7% of F0 tadpoles, with germline transmission. For both CRISPR/Cas9-mediated HDR gene editing and indel mutation, the gene-edited F0 embryos are uniformly heterozygous, consistent with a mutation in only the maternal genome. In addition to efficient tagging of proteins in vivo, this HDR methodology will allow researchers to create patient-specific mutations for human disease modeling in Xenopus.
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Affiliation(s)
- Yetki Aslan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Emmanuel Tadjuidje
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Sang-Wook Cha
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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94
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Quadros RM, Miura H, Harms DW, Akatsuka H, Sato T, Aida T, Redder R, Richardson GP, Inagaki Y, Sakai D, Buckley SM, Seshacharyulu P, Batra SK, Behlke MA, Zeiner SA, Jacobi AM, Izu Y, Thoreson WB, Urness LD, Mansour SL, Ohtsuka M, Gurumurthy CB. Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins. Genome Biol 2017; 18:92. [PMID: 28511701 PMCID: PMC5434640 DOI: 10.1186/s13059-017-1220-4] [Citation(s) in RCA: 309] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/24/2017] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Conditional knockout mice are generated using labor-intensive methods of homologous recombination in embryonic stem cells and are available for only ~25% of all mouse genes. Transgenic mice generated by random genomic insertion approaches pose problems of unreliable expression, and thus there is a need for targeted-insertion models. Although CRISPR-based strategies were reported to create conditional and targeted-insertion alleles via one-step delivery of targeting components directly to zygotes, these strategies are quite inefficient. RESULTS Here we describe Easi-CRISPR (Efficient additions with ssDNA inserts-CRISPR), a targeting strategy in which long single-stranded DNA donors are injected with pre-assembled crRNA + tracrRNA + Cas9 ribonucleoprotein (ctRNP) complexes into mouse zygotes. We show for over a dozen loci that Easi-CRISPR generates correctly targeted conditional and insertion alleles in 8.5-100% of the resulting live offspring. CONCLUSIONS Easi-CRISPR solves the major problem of animal genome engineering, namely the inefficiency of targeted DNA cassette insertion. The approach is robust, succeeding for all tested loci. It is versatile, generating both conditional and targeted insertion alleles. Finally, it is highly efficient, as treating an average of only 50 zygotes is sufficient to produce a correctly targeted allele in up to 100% of live offspring. Thus, Easi-CRISPR offers a comprehensive means of building large-scale Cre-LoxP animal resources.
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MESH Headings
- Animals
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Endonucleases/genetics
- Endonucleases/metabolism
- Founder Effect
- Gene Editing/methods
- Genes, Reporter
- Genetic Loci
- Integrases/genetics
- Integrases/metabolism
- Mice
- Mice, Transgenic/genetics
- Mice, Transgenic/growth & development
- Microinjections
- Mutagenesis, Insertional/methods
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Recombinational DNA Repair
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Zygote/growth & development
- Zygote/metabolism
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Affiliation(s)
- Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Hisako Akatsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Department of Host Defense Mechanism, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Takehito Sato
- Department of Host Defense Mechanism, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Tomomi Aida
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510, Japan
- Laboratory of Recombinant Animals, MRI, TMDU, 2-3-10, 2-3-10, Surugadai, Kanda, Chiyoda, Tokyo, 101-0062, Japan
- Present address: McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ronald Redder
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Guy P Richardson
- Sussex Neuroscience, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Yutaka Inagaki
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Department of Regenerative Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Daisuke Sakai
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Department of Orthopaedic Surgery, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Shannon M Buckley
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Disease, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Disease, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | - Sarah A Zeiner
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | - Ashley M Jacobi
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | - Yayoi Izu
- Department of Animal Risk Management, Chiba Institute of Science, 3 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Wallace B Thoreson
- Truhlsen Eye Institute and Department of Ophthalmology & Visual Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Lisa D Urness
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Suzanne L Mansour
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.
- Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA.
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95
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Nakagawa Y, Sakuma T, Nishimichi N, Yokosaki Y, Takeo T, Nakagata N, Yamamoto T. Culture time of vitrified/warmed zygotes before microinjection affects the production efficiency of CRISPR-Cas9-mediated knock-in mice. Biol Open 2017; 6:706-713. [PMID: 28396487 PMCID: PMC5450330 DOI: 10.1242/bio.025122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Robust reproductive engineering techniques are required for the efficient and rapid production of genetically modified mice. We have reported the efficient production of genome-edited mice using reproductive engineering techniques, such as ultra-superovulation, in vitro fertilization (IVF) and vitrification/warming of zygotes. We usually use vitrified/warmed fertilized oocytes created by IVF for microinjection because of work efficiency and flexible scheduling. Here, we investigated whether the culture time of zygotes before microinjection influences the efficiency of producing knock-in mice. Knock-in mice were generated using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system and single-stranded oligodeoxynucleotide (ssODN) or PITCh (Precise Integration into Target Chromosome) system, a method of integrating a donor vector assisted by microhomology-mediated end-joining. The cryopreserved fertilized oocytes were warmed, cultured for several hours and microinjected at different timings. Microinjection was performed with Cas9 protein, guide RNA(s), and an ssODN or PITCh donor plasmid for the ssODN knock-in and the PITCh knock-in, respectively. Different production efficiencies of knock-in mice were observed by changing the timing of microinjection. Our study provides useful information for the CRISPR-Cas9-based generation of knock-in mice. Summary: We report variable production efficiencies of CRISPR-Cas9-mediated knock-in mice depending on a series of microinjection timings using vitrified, warmed, and cultured zygotes created via ultra-superovulation and in vitro fertilization.
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Affiliation(s)
- Yoshiko Nakagawa
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Norihisa Nishimichi
- Cell-Matrix Frontier Laboratory, Health Administration Center, Hiroshima University, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan
| | - Yasuyuki Yokosaki
- Cell-Matrix Frontier Laboratory, Health Administration Center, Hiroshima University, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan.,Clinical Genetics, Hiroshima University Hospital, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan
| | - Toru Takeo
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Naomi Nakagata
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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96
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Jacobi AM, Rettig GR, Turk R, Collingwood MA, Zeiner SA, Quadros RM, Harms DW, Bonthuis PJ, Gregg C, Ohtsuka M, Gurumurthy CB, Behlke MA. Simplified CRISPR tools for efficient genome editing and streamlined protocols for their delivery into mammalian cells and mouse zygotes. Methods 2017; 121-122:16-28. [PMID: 28351759 PMCID: PMC5761324 DOI: 10.1016/j.ymeth.2017.03.021] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/09/2017] [Accepted: 03/23/2017] [Indexed: 01/14/2023] Open
Abstract
Genome editing using the CRISPR/Cas9 system requires the presence of guide RNAs bound to the Cas9 endonuclease as a ribonucleoprotein (RNP) complex in cells, which cleaves the host cell genome at sites specified by the guide RNAs. New genetic material may be introduced during repair of the double-stranded break via homology dependent repair (HDR) if suitable DNA templates are delivered with the CRISPR components. Early methods used plasmid or viral vectors to make these components in the host cell, however newer approaches using recombinant Cas9 protein with synthetic guide RNAs introduced directly as an RNP complex into cells shows faster onset of action with fewer off-target effects. This approach also enables use of chemically modified synthetic guide RNAs that have improved nuclease stability and reduces the risk of triggering an innate immune response in the host cell. This article provides detailed methods for genome editing using the RNP approach with synthetic guide RNAs using lipofection or electroporation in mammalian cells or using microinjection in murine zygotes, with or without addition of a single-stranded HDR template DNA.
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Affiliation(s)
- Ashley M Jacobi
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | | | - Rolf Turk
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | | | - Sarah A Zeiner
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Paul J Bonthuis
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Christopher Gregg
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa 259-1193, Japan; Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa 259-1193, Japan; The Institute of Medical Sciences, Tokai University, Kanagawa 259-1193, Japan
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA; Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA.
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97
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Suzuki T, Imada T, Komatsu Y, Kamiya H. Comparison of DNA fragments as donor DNAs upon sequence conversion of cleaved target DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:428-434. [PMID: 28486036 DOI: 10.1080/15257770.2017.1310385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pinpoint sequence alteration (genome editing) by the combination of the site-specific cleavage of a target DNA and a donor nucleic acid has attracted much attention and the sequence of the target DNA is expected to be changed to that of a donor nucleic acid. In most cases, oligodeoxyribonucleotides (ODNs) and plasmid DNAs have been used as donors. However, a several hundred-base single-stranded (ss) DNA fragment and a 5'-tailed duplex (TD) accomplished the desired sequence changes without DNA cleavage, and might serve as better donors for the cleaved target DNA than ODNs and plasmid DNAs. In this study, sequence conversion efficiencies were compared with various donor DNAs in model sequence alteration experiments, using episomal DNA. The efficiencies with the ss and TD fragments were higher than those with the ODN and plasmid DNA. The sequence change by the TD seemed somewhat less efficient but slightly more accurate than that by the ss DNA fragment. These results suggested that the ss and TD fragments are better donors for targeted sequence alteration.
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Affiliation(s)
- Tetsuya Suzuki
- a Graduate School of Biomedical and Health Sciences , Hiroshima University , Kasumi, Minami-ku , Hiroshima , Japan
| | - Takashi Imada
- a Graduate School of Biomedical and Health Sciences , Hiroshima University , Kasumi, Minami-ku , Hiroshima , Japan
| | - Yasuo Komatsu
- b Bioproduction Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukisamu-Higashi, Toyohira-ku, Sapporo , Japan
| | - Hiroyuki Kamiya
- a Graduate School of Biomedical and Health Sciences , Hiroshima University , Kasumi, Minami-ku , Hiroshima , Japan
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98
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Abstract
Genome integration is a powerful tool in both basic and applied biological research. However, traditional genome integration, which is typically mediated by homologous recombination, has been constrained by low efficiencies and limited host range. In recent years, the emergence of homing endonucleases and programmable nucleases has greatly enhanced integration efficiencies and allowed alternative integration mechanisms such as nonhomologous end joining and microhomology-mediated end joining, enabling integration in hosts deficient in homologous recombination. In this review, we will highlight recent advances and breakthroughs in genome integration methods made possible by programmable nucleases, and their new applications in synthetic biology and metabolic engineering.
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Affiliation(s)
- Zihe Liu
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Youyun Liang
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Ee Lui Ang
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Huimin Zhao
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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99
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Doetschman T, Georgieva T. Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease. Circ Res 2017; 120:876-894. [DOI: 10.1161/circresaha.116.309727] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 01/30/2017] [Accepted: 02/06/2017] [Indexed: 12/22/2022]
Abstract
Genetic engineering of model organisms and cultured cells has for decades provided important insights into the mechanisms underlying cardiovascular development and disease. In the past few years the development of several nuclease systems has broadened the range of model/cell systems that can be engineered. Of these, the CRISPR (clustered regularly interspersed short palindromic repeats)/Cas9 (CRISPR-associated protein 9) system has become the favorite for its ease of application. Here we will review this RNA-guided nuclease system for gene editing with respect to its usefulness for cardiovascular studies and with an eye toward potential therapy. Studies on its off-target activity, along with approaches to minimize this activity will be given. The advantages of gene editing versus gene targeting in embryonic stem cells, including the breadth of species and cell types to which it is applicable, will be discussed. We will also cover its use in iPSC for research and possible therapeutic purposes; and we will review its use in muscular dystrophy studies where considerable progress has been made toward dystrophin correction in mice. The CRISPR/Ca9s system is also being used for high-throughput screening of genes, gene regulatory regions, and long noncoding RNAs. In addition, the CRISPR system is being used for nongene-editing purposes such as activation and inhibition of gene expression, as well as for fluorescence tagging of chromosomal regions and individual mRNAs to track their cellular location. Finally, an approach to circumvent the inability of post-mitotic cells to support homologous recombination-based gene editing will be presented. In conclusion, applications of the CRISPR/Cas system are expanding at a breath-taking pace and are revolutionizing approaches to gain a better understanding of human diseases.
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Affiliation(s)
- Thomas Doetschman
- From the BIO5 Institute (T.D., T.G.) and Department of Cellular and Molecular Medicine (T.D.), University of Arizona, Tucson
| | - Teodora Georgieva
- From the BIO5 Institute (T.D., T.G.) and Department of Cellular and Molecular Medicine (T.D.), University of Arizona, Tucson
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100
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Raveux A, Vandormael-Pournin S, Cohen-Tannoudji M. Optimization of the production of knock-in alleles by CRISPR/Cas9 microinjection into the mouse zygote. Sci Rep 2017; 7:42661. [PMID: 28209967 PMCID: PMC5314402 DOI: 10.1038/srep42661] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/12/2017] [Indexed: 12/26/2022] Open
Abstract
Microinjection of the CRISPR/Cas9 system in zygotes is an efficient and comparatively fast method to generate genetically modified mice. So far, only few knock-in mice have been generated using this approach, and because no systematic study has been performed, parameters controlling the efficacy of CRISPR/Cas9-mediated targeted insertion are not fully established. Here, we evaluated the effect of several parameters on knock-in efficiency changing only one variable at a time. We found that knock-in efficiency was dependent on injected Cas9 mRNA and single-guide RNA concentrations and that cytoplasmic injection resulted in more genotypic complexity compared to pronuclear injection. Our results also indicated that injection into the pronucleus compared to the cytoplasm is preferable to generate knock-in alleles with an oligonucleotide or a circular plasmid. Finally, we showed that Cas9D10A nickase variant was less efficient than wild-type Cas9 for generating knock-in alleles and caused a higher rate of mosaicism. Thus, our study provides valuable information that will help to improve the future production of precise genetic modifications in mice.
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Affiliation(s)
- Aurélien Raveux
- Institut Pasteur, CNRS, Unité de Génétique Fonctionnelle de la Souris, UMR 3738, Department of Developmental & Stem Cell Biology, 25 rue du docteur Roux, F-75015 Paris
| | - Sandrine Vandormael-Pournin
- Institut Pasteur, CNRS, Unité de Génétique Fonctionnelle de la Souris, UMR 3738, Department of Developmental & Stem Cell Biology, 25 rue du docteur Roux, F-75015 Paris
| | - Michel Cohen-Tannoudji
- Institut Pasteur, CNRS, Unité de Génétique Fonctionnelle de la Souris, UMR 3738, Department of Developmental & Stem Cell Biology, 25 rue du docteur Roux, F-75015 Paris
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