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Chapman B, Han JH, Lee HJ, Ruud I, Kim TH. Targeted Modulation of Chicken Genes In Vitro Using CRISPRa and CRISPRi Toolkit. Genes (Basel) 2023; 14:genes14040906. [PMID: 37107664 PMCID: PMC10137795 DOI: 10.3390/genes14040906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Engineering of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) system has enabled versatile applications of CRISPR beyond targeted DNA cleavage. Combination of nuclease-deactivated Cas9 (dCas9) and transcriptional effector domains allows activation (CRISPRa) or repression (CRISPRi) of target loci. To demonstrate the effectiveness of the CRISPR-mediated transcriptional regulation in chickens, three CRISPRa (VP64, VPR, and p300) and three CRISPRi (dCas9, dCas9-KRAB, and dCas9-KRAB-MeCP2) systems were tested in chicken DF-1 cells. By introducing guide RNAs (gRNAs) targeting near the transcription start site (TSS) of each gene in CRISPRa and CRISPRi effector domain-expressing chicken DF-1 cell lines, significant gene upregulation was induced in dCas9-VPR and dCas9-VP64 cells, while significant downregulation was observed with dCas9 and dCas9-KRAB. We further investigated the effect of gRNA positions across TSS and discovered that the location of gRNA is an important factor for targeted gene regulation. RNA sequencing analysis of IRF7 CRISPRa and CRISPRi- DF-1 cells revealed the specificity of CRISPRa and CRISPRi-based targeted transcriptional regulation with minimal off-target effects. These findings suggest that the CRISPRa and CRISPRi toolkits are an effective and adaptable platform for studying the chicken genome by targeted transcriptional modulation.
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Affiliation(s)
- Brittany Chapman
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jeong Hoon Han
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hong Jo Lee
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Isabella Ruud
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tae Hyun Kim
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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Espino-Saldaña AE, Rodríguez-Ortiz R, Pereida-Jaramillo E, Martínez-Torres A. Modeling Neuronal Diseases in Zebrafish in the Era of CRISPR. Curr Neuropharmacol 2020; 18:136-152. [PMID: 31573887 PMCID: PMC7324878 DOI: 10.2174/1570159x17666191001145550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/04/2019] [Accepted: 09/29/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Danio rerio is a powerful experimental model for studies in genetics and development. Recently, CRISPR technology has been applied in this species to mimic various human diseases, including those affecting the nervous system. Zebrafish offer multiple experimental advantages: external embryogenesis, rapid development, transparent embryos, short life cycle, and basic neurobiological processes shared with humans. This animal model, together with the CRISPR system, emerging imaging technologies, and novel behavioral approaches, lay the basis for a prominent future in neuropathology and will undoubtedly accelerate our understanding of brain function and its disorders. OBJECTIVE Gather relevant findings from studies that have used CRISPR technologies in zebrafish to explore basic neuronal function and model human diseases. METHODS We systematically reviewed the most recent literature about CRISPR technology applications for understanding brain function and neurological disorders in D. rerio. We highlighted the key role of CRISPR in driving forward our understanding of particular topics in neuroscience. RESULTS We show specific advances in neurobiology when the CRISPR system has been applied in zebrafish and describe how CRISPR is accelerating our understanding of brain organization. CONCLUSION Today, CRISPR is the preferred method to modify genomes of practically any living organism. Despite the rapid development of CRISPR technologies to generate disease models in zebrafish, more efforts are needed to efficiently combine different disciplines to find the etiology and treatments for many brain diseases.
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Affiliation(s)
- Angeles Edith Espino-Saldaña
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Campus UNAM Juriquilla, Querétaro, Qro CP76230, México
- Universidad Autónoma de Querétaro, Facultad de Ciencias Naturales, Av. de las Ciencias S/N, Querétaro, Mexico
| | - Roberto Rodríguez-Ortiz
- CONACYT - Instituto de Neurobiología, Universidad Nacional Autónoma de México. Querétaro, Qro., México
| | - Elizabeth Pereida-Jaramillo
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Campus UNAM Juriquilla, Querétaro, Qro CP76230, México
| | - Ataúlfo Martínez-Torres
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Campus UNAM Juriquilla, Querétaro, Qro CP76230, México
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Li W, Zhang Y, Han B, Li L, Li M, Lu X, Chen C, Lu M, Zhang Y, Jia X, Zhu Z, Tong X, Zhang B. One-step efficient generation of dual-function conditional knockout and geno-tagging alleles in zebrafish. eLife 2019; 8:48081. [PMID: 31663848 PMCID: PMC6845224 DOI: 10.7554/elife.48081] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/30/2019] [Indexed: 12/14/2022] Open
Abstract
CRISPR/Cas systems are widely used to knock out genes by inducing indel mutations, which are prone to genetic compensation. Complex genome modifications such as knockin (KI) might bypass compensation, though difficult to practice due to low efficiency. Moreover, no ‘two-in-one’ KI strategy combining conditional knockout (CKO) with fluorescent gene-labeling or further allele-labeling has been reported. Here, we developed a dual-cassette-donor strategy and achieved one-step and efficient generation of dual-function KI alleles at tbx5a and kctd10 loci in zebrafish via targeted insertion. These alleles display fluorescent gene-tagging and CKO effects before and after Cre induction, respectively. By introducing a second fluorescent reporter, geno-tagging effects were achieved at tbx5a and sox10 loci, exhibiting CKO coupled with fluorescent reporter switch upon Cre induction, enabling tracing of three distinct genotypes. We found that LiCl purification of gRNA is critical for highly efficient KI, and preselection of founders allows the efficient germline recovery of KI events.
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Affiliation(s)
- Wenyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Yage Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Bingzhou Han
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Lianyan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Muhang Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Xiaochan Lu
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Cheng Chen
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Mengjia Lu
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yujie Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Xuefeng Jia
- Gcrispr (Tianjin) Genetic Technology, Tianjin, China
| | - Zuoyan Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Xiangjun Tong
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
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Mao CZ, Zheng L, Zhou YM, Wu HY, Xia JB, Liang CQ, Guo XF, Peng WT, Zhao H, Cai WB, Kim SK, Park KS, Cai DQ, Qi XF. CRISPR/Cas9-mediated efficient and precise targeted integration of donor DNA harboring double cleavage sites in Xenopus tropicalis. FASEB J 2018; 32:fj201800093. [PMID: 29897811 DOI: 10.1096/fj.201800093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 system has emerged as a powerful tool for knock-in of DNA fragments via donor plasmid and homology-independent DNA repair mechanism; however, conventional integration includes unnecessary plasmid backbone and may result in the unfaithful expression of the modified endogenous genes. Here, we report an efficient and precise CRISPR/Cas9-mediated integration strategy using a donor plasmid that harbors 2 of the same cleavage sites that flank the cassette at both sides. After the delivery of donor plasmid, together with Cas9 mRNA and guide RNA, into cells or fertilized eggs, concurrent cleavages at both sides of the exogenous cassette and the desired chromosomal site result in precise targeted integration without plasmid backbone. We successfully used this approach to precisely integrate the EGFP reporter gene into the myh6 locus or the GAPDH locus in Xenopus tropicalis or human cells, respectively. Furthermore, we demonstrate that replacing conventional terminators with the endogenous 3UTR of target genes in the cassette greatly improves the expression of reporter gene after integration. Our efficient and precise method will be useful for a variety of targeted genome modifications, not only in X. tropicalis, but also in mammalian cells, and can be readily adapted to many other organisms.-Mao, C.-Z., Zheng, L., Zhou, Y.-M., Wu, H.-Y., Xia, J.-B., Liang, C.-Q., Guo, X.-F., Peng, W.-T., Zhao, H., Cai, W.-B., Kim, S.-K., Park, K.-S., Cai, D.-Q., Qi, X.-F. CRISPR/Cas9-mediated efficient and precise targeted integration of donor DNA harboring double cleavage sites in Xenopus tropicalis.
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Affiliation(s)
- Cheng-Zhou Mao
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
- Guangdong Engineering and Technology Research Center for Disease-Model Animals, Sun Yat-sen University, Guangzhou, China
| | - Li Zheng
- College of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, China
| | - Yi-Min Zhou
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Hai-Yan Wu
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Jing-Bo Xia
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Chi-Qian Liang
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Xiao-Fang Guo
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Wen-Tao Peng
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Hui Zhao
- Stem Cell and Regeneration Transient Receptor Potential (TRP), School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei-Bin Cai
- Guangdong Engineering and Technology Research Center for Disease-Model Animals, Sun Yat-sen University, Guangzhou, China
| | - Soo-Ki Kim
- Department of Microbiology, Wonju College of Medicine, Yonsei University, Wonju, South Korea
| | - Kyu-Sang Park
- Department of Physiology, Wonju College of Medicine, Yonsei University, Wonju, South Korea
| | - Dong-Qing Cai
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Xu-Feng Qi
- Key Laboratory of Regenerative Medicine, Ministry of Education, Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
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Yanik M, Ponnam SPG, Wimmer T, Trimborn L, Müller C, Gambert I, Ginsberg J, Janise A, Domicke J, Wende W, Lorenz B, Stieger K. Development of a Reporter System to Explore MMEJ in the Context of Replacing Large Genomic Fragments. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 11:407-415. [PMID: 29858075 PMCID: PMC5992787 DOI: 10.1016/j.omtn.2018.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/13/2018] [Accepted: 03/20/2018] [Indexed: 01/21/2023]
Abstract
Common genome-editing strategies are either based on non-homologous end joining (NHEJ) or, in the presence of a template DNA, based on homologous recombination with long (homology-directed repair [HDR]) or short (microhomology-mediated end joining [MMEJ]) homologous sequences. In the current study, we aim to develop a model system to test the activity of MMEJ after CRISPR/Cas9-mediated cleavage in cell culture. Following successful proof of concept in an episomally based reporter system, we tested template plasmids containing a promoter-less luciferase gene flanked by microhomologous sequences (mhs) of different length (5, 10, 15, 20, 30, and 50 bp) that are complementary to the mouse retinitis pigmentosa GTPase regulator (RPGR)-ORF15, which is under the control of a CMV promoter stably integrated into a HEK293 cell line. Luciferase signal appearance represented successful recombination events and was highest when the mhs were 5 bp long, while longer mhs revealed lower luciferase signal. In addition, presence of Csy4 RNase was shown to increase luciferase signaling. The luciferase reporter system is a valuable tool to study the input of the different DNA repair mechanisms in the replacement of large DNA sequences by mhs.
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Affiliation(s)
- Mert Yanik
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Surya Prakash Goud Ponnam
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany; Department of Molecular Biology & Biotechnology, Tezpur University, Napaam, Assam 784028, India
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Lennart Trimborn
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Carina Müller
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Isabel Gambert
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Johanna Ginsberg
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Annabella Janise
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Janina Domicke
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Wolfgang Wende
- Institute for Biochemistry, Justus-Liebig-University, Giessen 35392, Germany
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany.
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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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Albadri S, Del Bene F, Revenu C. Genome editing using CRISPR/Cas9-based knock-in approaches in zebrafish. Methods 2017; 121-122:77-85. [PMID: 28300641 DOI: 10.1016/j.ymeth.2017.03.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/13/2017] [Accepted: 03/03/2017] [Indexed: 12/19/2022] Open
Abstract
With its variety of applications, the CRISPR/Cas9 genome editing technology has been rapidly evolving in the last few years. In the zebrafish community, knock-out reports are constantly increasing but insertion studies have been so far more challenging. With this review, we aim at giving an overview of the homologous directed repair (HDR)-based knock-in generation in zebrafish. We address the critical points and limitations of the procedure such as cutting efficiency of the chosen single guide RNA, use of cas9 mRNA or Cas9 protein, homology arm size etc. but also ways to circumvent encountered issues with HDR insertions by the development of non-homologous dependent strategies. While imprecise, these homology-independent mechanisms based on non-homologous-end-joining (NHEJ) repair have been employed in zebrafish to generate reporter lines or to accurately edit an open reading frame by the use of intron-targeting modifications. Therefore, with higher efficiency and insertion rate, NHEJ-based knock-in seems to be a promising approach to target endogenous loci and to circumvent the limitations of HDR whenever it is possible and appropriate. In this perspective, we propose new strategies to generate cDNA edited or tagged insertions, which once established will constitute a new and versatile toolbox for CRISPR/Cas9-based knock-ins in zebrafish.
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Affiliation(s)
- Shahad Albadri
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France.
| | - Céline Revenu
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France
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Abstract
In recent years, genome engineering technology has provided unprecedented opportunities for site-specific modification of biological genomes. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 is one such means that can target a specific genome locus. It has been applied in human cells and many other organisms. Meanwhile, to efficiently enrich targeted cells, several surrogate systems have also been developed. However, very limited information exists on the application of CRISPR/Cas9 in chickens. In this study, we employed the CRISPR/Cas9 system to induce mutations in the peroxisome proliferator-activated receptor-γ (PPAR-γ), ATP synthase epsilon subunit (ATP5E), and ovalbumin (OVA) genes in chicken DF-1 cells. The results of T7E1 assays showed that the mutation rate at the three different loci was 0.75%, 0.5%, and 3.0%, respectively. In order to improve the mutation efficiency, we used the PuroR gene for efficient enrichment of genetically modified cells with the surrogate reporter system. The mutation rate, as assessed via the T7E1 assay, increased to 60.7%, 61.3%, and 47.3%, and subsequent sequence analysis showed that the mutation efficiency increased to 94.7%, 95%, and 95%, respectively. In addition, there were no detectable off-target mutations in three potential off-target sites using the T7E1 assay. As noted above, the CRISPR/Cas9 system is a robust tool for chicken genome editing.
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Abstract
Programmable nucleases enable engineering of the genome by utilizing endogenous DNA double-strand break (DSB) repair pathways. Although homologous recombination (HR)-mediated gene knock-in is well established, it cannot necessarily be applied in every cell type and organism because of variable HR frequencies. We recently reported an alternative method of gene knock-in, named the PITCh (Precise Integration into Target Chromosome) system, assisted by microhomology-mediated end-joining (MMEJ). MMEJ harnesses independent machinery from HR, and it requires an extremely short homologous sequence (5-25 bp) for DSB repair, resulting in precise gene knock-in with a more easily constructed donor vector. Here we describe a streamlined protocol for PITCh knock-in, including the design and construction of the PITCh vectors, and their delivery to either human cell lines by transfection or to frog embryos by microinjection. The construction of the PITCh vectors requires only a few days, and the entire process takes ∼ 1.5 months to establish knocked-in cells or ∼ 1 week from injection to early genotyping in frog embryos.
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