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Tan L, Hu Y, Li Y, Yang L, Cai X, Liu W, He J, Wu Y, Liu T, Wang N, Yang Y, Adelstein RS, Wang A. Investigation of the molecular biology underlying the pronounced high gene targeting frequency at the Myh9 gene locus in mouse embryonic stem cells. PLoS One 2020; 15:e0230126. [PMID: 32226034 PMCID: PMC7105122 DOI: 10.1371/journal.pone.0230126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 02/23/2020] [Indexed: 11/21/2022] Open
Abstract
The generation of genetically modified mouse models derived from gene targeting (GT) in mouse embryonic stem (ES) cells (mESCs) has greatly advanced both basic and clinical research. Our previous finding that gene targeting at the Myh9 exon2 site in mESCs has a pronounced high homologous recombination (HR) efficiency (>90%) has facilitated the generation of a series of nonmuscle myosin II (NM II) related mouse models. Furthermore, the Myh9 gene locus has been well demonstrated to be a new safe harbor for site-specific insertion of other exogenous genes. In the current study, we intend to investigate the molecular biology underlying for this high HR efficiency from other aspects. Our results confirmed some previously characterized properties and revealed some unreported observations: 1) The comparison and analysis of the targeting events occurring at the Myh9 and several widely used loci for targeting transgenesis, including ColA1, HPRT, ROSA26, and the sequences utilized for generating these targeting constructs, indicated that a total length about 6 kb with approximate 50% GC-content of the 5’ and 3’ homologous arms, may facilitate a better performance in terms of GT efficiency. 2) Despite increasing the length of the homologous arms, shifting the targeting site from the Myh9 exon2, to intron2, or exon3 led to a gradually reduced GT frequency (91.7, 71.8 and 50.0%, respectively). This finding provides the first evidence that the HR frequency may also be associated with the targeting site even in the same locus. Meanwhile, the decreased trend of the GT efficiency at these targeting sites was consistent with the reduced percentage of simple sequence repeat (SSR) and short interspersed nuclear elements (SINEs) in the sequences for generating the targeting constructs, suggesting the potential effects of these DNA elements on GT efficiency; 3) Our series of targeting experiments and analyses with truncated 5’ and 3’ arms at the Myh9 exon2 site demonstrated that GT efficiency positively correlates with the total length of the homologous arms (R = 0.7256, p<0.01), confirmed that a 2:1 ratio of the length, a 50% GC-content and the higher amount of SINEs for the 5’ and 3’ arms may benefit for appreciable GT frequency. Though more investigations are required, the Myh9 gene locus appears to be an ideal location for identifying HR-related cis and trans factors, which in turn provide mechanistic insights and also facilitate the practical application of gene editing.
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Affiliation(s)
- Lei Tan
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yi Hu
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yalan Li
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Lingchen Yang
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Xiong Cai
- Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Wei Liu
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Jiayi He
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yingxin Wu
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Tanbin Liu
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Naidong Wang
- Laboratory of Functional Proteomics (LFP), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, HUNAU, Changsha, Hunan, China
| | - Yi Yang
- Laboratory of Functional Proteomics (LFP), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, HUNAU, Changsha, Hunan, China
| | - Robert S. Adelstein
- Laboratory of Molecular Cardiology (LMC), NHLBI/NIH, Bethesda, MD, United States of America
| | - Aibing Wang
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
- Laboratory of Molecular Cardiology (LMC), NHLBI/NIH, Bethesda, MD, United States of America
- * E-mail:
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Jarazo J, Qing X, Schwamborn JC. Guidelines for Fluorescent Guided Biallelic HDR Targeting Selection With PiggyBac System Removal for Gene Editing. Front Genet 2019; 10:190. [PMID: 30930935 PMCID: PMC6425911 DOI: 10.3389/fgene.2019.00190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/22/2019] [Indexed: 12/22/2022] Open
Abstract
The development of new and easy-to-use nucleases, such as CRISPR/Cas9, made tools for gene editing widely accessible to the scientific community. Cas9-based gene editing protocols are robust for creating knock-out models, but the generation of single nucleotide transitions or transversions remains challenging. This is mainly due to the low frequency of homology directed repair, which leads to the screening of a high number of clones to identify positive events. Moreover, lack of simultaneous biallelic modifications, frequently results in second-allele indels. For example, while one allele might undergo homology directed repair, the second can undergo non-homologous end joining repair. Here we present a step-wise protocol for biallelic gene editing. It uses two donors carrying a combination of fluorescent reporters alongside homology arms directed to the same genomic region for biallelic targeting. These homology arms carry the desired composite of modifications to be introduced (homozygous or heterozygous changes). Plus, the backbone of the plasmid carries a third fluorescent reporter for negative selection (to discard random integration events). Fluorescent selection of non-random biallelic targeted clones can be performed by microscopy guided picking or cell sorting (FACS). The positive selection module (PSM), carrying the fluorescence reporter and an antibiotic resistance, is flanked by inverted terminal repeats (ITR) that are recognized by transposase. Upon purification of the clones correctly modified, transfection of the excision-only transposase allows the removal of the PSM resulting in the integration of only the desired modifications.
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Affiliation(s)
- Javier Jarazo
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Xiaobing Qing
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Jens C Schwamborn
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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Zhou D, Tan L, Li J, Liu T, Hu Y, Li Y, Kawamoto S, Liu C, Guo S, Wang A. Identification of Homologous Recombination Events in Mouse Embryonic Stem Cells Using Southern Blotting and Polymerase Chain Reaction. J Vis Exp 2018. [PMID: 30531726 DOI: 10.3791/58467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Relative to the issues of off-target effects and the difficulty of inserting a long DNA fragment in the application of designer nucleases for genome editing, embryonic stem (ES) cell-based gene-targeting technology does not have these shortcomings and is widely used to modify animal/mouse genome ranging from large deletions/insertions to single nucleotide substitutions. Notably, identifying the relatively few homologous recombination (HR) events necessary to obtain desired ES clones is a key step, which demands accurate and reliable methods. Southern blotting and/or conventional PCR are often utilized for this purpose. Here, we describe the detailed procedures of using those two methods to identify HR events that occurred in mouse ES cells in which the endogenous Myh9 gene is intended to be disrupted and replaced by cDNAs encoding other nonmuscle myosin heavy chain IIs (NMHC IIs). The whole procedure of Southern blotting includes the construction of targeting vector(s), electroporation, drug selection, the expansion and storage of ES cells/clones, the preparation, digestion, and blotting of genomic DNA (gDNA), the hybridization and washing of probe(s), and a final step of autoradiography on the X-ray films. PCR can be performed directly with prepared and diluted gDNA. To obtain ideal results, the probes and restriction enzyme (RE) cutting sites for Southern blotting and the primers for PCR should be carefully planned. Though the execution of Southern blotting is time-consuming and labor-intensive and PCR results have false positives, the correct identification by Southern blotting and the rapid screening by PCR allow the sole or combined application of these methods described in this paper to be widely used and consulted by most labs in the identification of genotypes of ES cells and genetically modified animals.
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Affiliation(s)
- Dan Zhou
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU); Department of Pathology, Georgetown University Medical School
| | - Lei Tan
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU)
| | - Jian Li
- College of Food Science and Technology, Hunan Agricultural University (HUNAU)
| | - Tanbin Liu
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU)
| | - Yi Hu
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU)
| | - Yalan Li
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU)
| | - Sachiyo Kawamoto
- Lab of Molecular Cardiology (LMC), National Heart, Lung, and Blood Institute (NHLBI)/National Institutes of Health (NIH)
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute (NHLBI)/National Institutes of Health (NIH)
| | - Shiyin Guo
- College of Food Science and Technology, Hunan Agricultural University (HUNAU);
| | - Aibing Wang
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU);
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Qing X, Walter J, Jarazo J, Arias-Fuenzalida J, Hillje AL, Schwamborn JC. CRISPR/Cas9 and piggyBac-mediated footprint-free LRRK2-G2019S knock-in reveals neuronal complexity phenotypes and α-Synuclein modulation in dopaminergic neurons. Stem Cell Res 2017; 24:44-50. [PMID: 28826027 DOI: 10.1016/j.scr.2017.08.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/25/2017] [Accepted: 08/15/2017] [Indexed: 01/01/2023] Open
Abstract
The p.G2019S mutation of the leucine-rich repeat kinase 2 (LRRK2) has been identified as the most prevalent genetic cause of familial and sporadic Parkinson's disease (PD). The Cre-LoxP recombination system has been used to correct the LRRK2-G2019S mutation in patient derived human induced pluripotent stem cells (hiPSCs) in order to generate isogenic controls. However, the remaining LoxP site can influence gene expression. In this study, we report the generation of a footprint-free LRRK2-G2019S isogenic hiPS cell line edited with the CRISPR/Cas9 and piggyBac technologies. We observed that the percentage of Tyrosine Hydroxylase (TH) positive neurons with a total neurite length of >2000μm was significantly reduced in LRRK2-G2019S dopaminergic (DA) neurons. The average branch number in LRRK2-G2019S DA neurons was also decreased. In addition, we have shown that in vitro TH positive neurons with a total neurite length of >2000μm were positive for Serine 129 phosphorylated (S129P) alpha-Synuclein (αS) and we hypothesize that S129P-αS plays a role in the maintenance or formation of long neurites. In summary, our footprint-free LRRK2-G2019S isogenic cell lines allow standardized, genetic background independent, in vitro PD modeling and provide new insights into the role of LRRK2-G2019S and S129P-αS in the pathogenesis of PD.
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Affiliation(s)
- Xiaobing Qing
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB), 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Jonas Walter
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB), 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Javier Jarazo
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB), 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Jonathan Arias-Fuenzalida
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB), 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Anna-Lena Hillje
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB), 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Jens C Schwamborn
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB), 6, avenue du Swing, L-4367 Belvaux, Luxembourg.
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Zelensky AN, Schimmel J, Kool H, Kanaar R, Tijsterman M. Inactivation of Pol θ and C-NHEJ eliminates off-target integration of exogenous DNA. Nat Commun 2017; 8:66. [PMID: 28687761 PMCID: PMC5501794 DOI: 10.1038/s41467-017-00124-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/01/2017] [Indexed: 11/09/2022] Open
Abstract
Off-target or random integration of exogenous DNA hampers precise genomic engineering and presents a safety risk in clinical gene therapy strategies. Genetic definition of random integration has been lacking for decades. Here, we show that the A-family DNA polymerase θ (Pol θ) promotes random integration, while canonical non-homologous DNA end joining plays a secondary role; cells double deficient for polymerase θ and canonical non-homologous DNA end joining are devoid of any integration events, demonstrating that these two mechanisms define random integration. In contrast, homologous recombination is not reduced in these cells and gene targeting is improved to 100% efficiency. Such complete reversal of integration outcome, from predominately random integration to exclusively gene targeting, provides a rational way forward to improve the efficacy and safety of DNA delivery and gene correction approaches.Random off-target integration events can impair precise gene targeting and poses a safety risk for gene therapy. Here the authors show that repression of polymerase θ and classical non-homologous recombination eliminates random integration.
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Affiliation(s)
- Alex N Zelensky
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Centre, Rotterdam,, 3000 CA, The Netherlands
| | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Centre, Rotterdam,, 3000 CA, The Netherlands.
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands.
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