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Gillespie W, Zhang Y, Ruiz OE, Cerda J, Ortiz-Guzman J, Turner WD, Largoza G, Sherman M, Mosser LE, Fujimoto E, Chien CB, Kwan KM, Arenkiel BR, Devine WP, Wythe JD. Multisite Assembly of Gateway Induced Clones (MAGIC): a flexible cloning toolbox with diverse applications in vertebrate model systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603267. [PMID: 39026881 PMCID: PMC11257631 DOI: 10.1101/2024.07.13.603267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Here we present the Multisite Assembly of Gateway Induced Clones (MAGIC) system, which harnesses site-specific recombination-based cloning via Gateway technology for rapid, modular assembly of between 1 and 3 "Entry" vector components, all into a fourth, standard high copy "Destination" plasmid backbone. The MAGIC toolkit spans a range of in vitro and in vivo uses, from directing tunable gene expression, to driving simultaneous expression of microRNAs and fluorescent reporters, to enabling site-specific recombinase-dependent gene expression. All MAGIC system components are directly compatible with existing multisite gateway Tol2 systems currently used in zebrafish, as well as existing eukaryotic cell culture expression Destination plasmids, and available mammalian lentiviral and adenoviral Destination vectors, allowing rapid cross-species experimentation. Moreover, herein we describe novel vectors with flanking piggyBac transposon elements for stable genomic integration in vitro or in vivo when used with piggyBac transposase. Collectively, the MAGIC system facilitates transgenesis in cultured mammalian cells, electroporated mouse and chick embryos, as well as in injected zebrafish embryos, enabling the rapid generation of innovative DNA constructs for biological research due to a shared, common plasmid platform.
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Metanat Y, Viktor P, Amajd A, Kaur I, Hamed AM, Abed Al-Abadi NK, Alwan NH, Chaitanya MVNL, Lakshmaiya N, Ghildiyal P, Khalaf OM, Ciongradi CI, Sârbu I. The paths toward non-viral CAR-T cell manufacturing: A comprehensive review of state-of-the-art methods. Life Sci 2024; 348:122683. [PMID: 38702027 DOI: 10.1016/j.lfs.2024.122683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/11/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Although CAR-T cell therapy has emerged as a game-changer in cancer immunotherapy several bottlenecks limit its widespread use as a front-line therapy. Current protocols for the production of CAR-T cells rely mainly on the use of lentiviral/retroviral vectors. Nevertheless, according to the safety concerns around the use of viral vectors, there are several regulatory hurdles to their clinical use. Large-scale production of viral vectors under "Current Good Manufacturing Practice" (cGMP) involves rigorous quality control assessments and regulatory requirements that impose exorbitant costs on suppliers and as a result, lead to a significant increase in the cost of treatment. Pursuing an efficient non-viral method for genetic modification of immune cells is a hot topic in cell-based gene therapy. This study aims to investigate the current state-of-the-art in non-viral methods of CAR-T cell manufacturing. In the first part of this study, after reviewing the advantages and disadvantages of the clinical use of viral vectors, different non-viral vectors and the path of their clinical translation are discussed. These vectors include transposons (sleeping beauty, piggyBac, Tol2, and Tc Buster), programmable nucleases (ZFNs, TALENs, and CRISPR/Cas9), mRNA, plasmids, minicircles, and nanoplasmids. Afterward, various methods for efficient delivery of non-viral vectors into the cells are reviewed.
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Affiliation(s)
- Yekta Metanat
- Faculty of Medicine, Zahedan University of Medical Sciences, Sistan and Baluchestan Province, Iran
| | - Patrik Viktor
- Óbuda University, Karoly Keleti faculty, Tavaszmező u. 15-17, H-1084 Budapest, Hungary
| | - Ayesha Amajd
- Faculty of Transport and Aviation Engineering, Silesian University of Technology, Krasińskiego 8 Street, 40-019 Katowice, Poland
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bangalore, Karnataka, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan-303012, India
| | | | | | | | - M V N L Chaitanya
- School of pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab - 144411, India
| | | | - Pallavi Ghildiyal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | | | - Carmen Iulia Ciongradi
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iași, Romania.
| | - Ioan Sârbu
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iași, Romania.
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Kalvaitytė M, Gabrilavičiūtė S, Balciunas D. Rapid generation of single-insertion transgenics by Tol2 transposition in zebrafish. Dev Dyn 2024. [PMID: 38946125 DOI: 10.1002/dvdy.719] [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: 10/12/2023] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 07/02/2024] Open
Abstract
BACKGROUND The Tol2 transposable element is the most widely used transgenesis tool in zebrafish. However, its high activity almost always leads to multiple unlinked integrations of the transgenic cassette in F1 fish. Each of these transgenes is susceptible to positional effects from the surrounding regulatory landscape, which can lead to altered expression and, consequently, activity. Scientists therefore must strike a balance between the need to maximize reproducibility by establishing single-insertion transgenic lines and the need to complete experiments within a reasonable timeframe. RESULTS In this article, we introduce a simple competitive dilution strategy for rapid generation of single-insertion transgenics. By using cry:BFP reporter plasmid as a competitor, we achieved a nearly fourfold reduction in the number of the transgene of interest integrations while simultaneously increasing the proportion of single-insertion F1 generation transgenics to over 50%. We also observed variations in transgene of interest expression among independent single-insertion transgenics, highlighting that the commonly used ubiquitous ubb promoter is susceptible to position effects. CONCLUSIONS Wide application of our competitive dilution strategy will save time, reduce animal usage, and improve reproducibility of zebrafish research.
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Affiliation(s)
- Miglė Kalvaitytė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Sofija Gabrilavičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Balciunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
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4
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Meenakshi Sundaram DN, Bahadur K C R, Fu W, Uludağ H. An optimized polymeric delivery system for piggyBac transposition. Biotechnol Bioeng 2024; 121:1503-1517. [PMID: 38372658 DOI: 10.1002/bit.28665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/14/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
The piggyBac transposon/transposase system has been explored for long-term, stable gene expression to execute genomic integration of therapeutic genes, thus emerging as a strong alternative to viral transduction. Most studies with piggyBac transposition have employed physical methods for successful delivery of the necessary components of the piggyBac system into the cells. Very few studies have explored polymeric gene delivery systems. In this short communication, we report an effective delivery system based on low molecular polyethylenimine polymer with lipid substitution (PEI-L) capable of delivering three components, (i) a piggyBac transposon plasmid DNA carrying a gene encoding green fluorescence protein (PB-GFP), (ii) a piggyBac transposase plasmid DNA or mRNA, and (iii) a 2 kDa polyacrylic acid as additive for transfection enhancement, all in a single complex. We demonstrate an optimized formulation for stable GFP expression in two model cell lines, MDA-MB-231 and SUM149 recorded till day 108 (3.5 months) and day 43 (1.4 months), respectively, following a single treatment with very low cell number as starting material. Moreover, the stability of the transgene (GFP) expression mediated by piggyBac/PEI-L transposition was retained following three consecutive cryopreservation cycles. The success of this study highlights the feasibility and potential of employing a polymeric delivery system to obtain piggyBac-based stable expression of therapeutic genes.
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Affiliation(s)
| | - Remant Bahadur K C
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Wei Fu
- Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University, Shanghai, China
| | - Hasan Uludağ
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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5
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Tian J, Tong D, Li Z, Wang E, Yu Y, Lv H, Hu Z, Sun F, Wang G, He M, Xia T. Mage transposon: a novel gene delivery system for mammalian cells. Nucleic Acids Res 2024; 52:2724-2739. [PMID: 38300794 PMCID: PMC10954464 DOI: 10.1093/nar/gkae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Transposons, as non-viral integration vectors, provide a secure and efficient method for stable gene delivery. In this study, we have discovered Mage (MG), a novel member of the piggyBac(PB) family, which exhibits strong transposability in a variety of mammalian cells and primary T cells. The wild-type MG showed a weaker insertion preference for near genes, transcription start sites (TSS), CpG islands, and DNaseI hypersensitive sites in comparison to PB, approaching the random insertion pattern. Utilizing in silico virtual screening and feasible combinatorial mutagenesis in vitro, we effectively produced the hyperactive MG transposase (hyMagease). This variant boasts a transposition rate 60% greater than its native counterpart without significantly altering its insertion pattern. Furthermore, we applied the hyMagease to efficiently deliver chimeric antigen receptor (CAR) into T cells, leading to stable high-level expression and inducing significant anti-tumor effects both in vitro and in xenograft mice models. These findings provide a compelling tool for gene transfer research, emphasizing its potential and prospects in the domains of genetic engineering and gene therapy.
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Affiliation(s)
- Jinghan Tian
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Doudou Tong
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | | | - Erqiang Wang
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yifei Yu
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Hangya Lv
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Zhendan Hu
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Fang Sun
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Guoping Wang
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Min He
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Tian Xia
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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6
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Bexte T, Reindl LM, Ullrich E. Nonviral technologies can pave the way for CAR-NK cell therapy. J Leukoc Biol 2023; 114:475-486. [PMID: 37403203 DOI: 10.1093/jleuko/qiad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
Natural killer cells are a promising platform for cancer immunotherapy. Natural killer cells have high intrinsic killing capability, and the insertion of a chimeric antigen receptor can further enhance their antitumor potential. In first-in-human trials, chimeric antigen receptor-natural killer cells demonstrated strong clinical activity without therapy-induced side effects. The applicability of natural killer cells as an "off-the-shelf" product makes them highly attractive for gene-engineered cell therapies. Traditionally, viral transduction has been used for gene editing; however, the use of viral vectors remains a safety concern and is associated with high costs and regulatory requirements. Here, we review the current landscape of nonviral approaches for chimeric antigen receptor-natural killer cell generation. This includes transfection of vector particles and electroporation of mRNA and DNA vectors, resulting in transient modification and chimeric antigen receptor expression. In addition, using nonviral transposon technologies, natural killer cells can be stably modified ensuring long-lasting chimeric antigen receptor expression. Finally, we discuss CRISPR/Cas9 tools to edit key genes for natural killer cell functionality.
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Affiliation(s)
- Tobias Bexte
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
- University Cancer Center (UCT), Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Lisa Marie Reindl
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
| | - Evelyn Ullrich
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
- University Cancer Center (UCT), Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Frankfurt/Mainz; Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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7
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Yamaguchi K, Ogawa R, Tsukahara M, Kawakami K. Efficient production of recombinant proteins in suspension CHO cells culture using the Tol2 transposon system coupled with cycloheximide resistance selection. Sci Rep 2023; 13:7628. [PMID: 37165015 PMCID: PMC10172305 DOI: 10.1038/s41598-023-34636-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
DNA recombination techniques in mammalian cells has been applied to the production of therapeutic proteins for several decades. To be used for commercial production, established cell lines should stably express target proteins with high productivity and acceptable quality for human use. In the conventional transfection method, the screening process is laborious and time-consuming since superior cell lines had to be selected from an enormous number of transfected cell pools and clonal cell lines with a wide variety of transgene insertion locations. In this study, we demonstrated that the combination of a Tol2 transposon system and cell selection by cycloheximide resistance is an efficient method to express therapeutic proteins, such as human antibody in suspension culture of Chinese hamster ovary cells. The resulting stable cell lines showed constant productivity and cell growth over a long enough cultivation periods for recombinant protein production. We anticipate that this approach will prove widely applicable to protein production in research and development of pharmaceutical products.
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Affiliation(s)
- Keina Yamaguchi
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Bio Process Research and Development Laboratories, Kyowa Kirin Co., Ltd., 100-1 Hagiwara-machi, Takasaki, Gunma, 370-0013, Japan.
| | - Risa Ogawa
- Bio Process Research and Development Laboratories, Kyowa Kirin Co., Ltd., 100-1 Hagiwara-machi, Takasaki, Gunma, 370-0013, Japan
| | - Masayoshi Tsukahara
- Bio Process Research and Development Laboratories, Kyowa Kirin Co., Ltd., 100-1 Hagiwara-machi, Takasaki, Gunma, 370-0013, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.
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8
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Inoue Y, Takeda H. Teratorn and its relatives - a cross-point of distinct mobile elements, transposons and viruses. Front Vet Sci 2023; 10:1158023. [PMID: 37187934 PMCID: PMC10175614 DOI: 10.3389/fvets.2023.1158023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Mobile genetic elements (e.g., transposable elements and plasmids) and viruses display significant diversity with various life cycles, but how this diversity emerges remains obscure. We previously reported a novel and giant (180 kb long) mobile element, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn is a composite DNA transposon created by a fusion of a piggyBac-like DNA transposon (piggyBac) and a novel herpesvirus of the Alloherpesviridae family. Genomic survey revealed that Teratorn-like herpesviruses are widely distributed among teleost genomes, the majority of which are also fused with piggyBac, suggesting that fusion with piggyBac is a trigger for the life-cycle shift of authentic herpesviruses to an intragenomic parasite. Thus, Teratorn-like herpesvirus provides a clear example of how novel mobile elements emerge, that is to say, the creation of diversity. In this review, we discuss the unique sequence and life-cycle characteristics of Teratorn, followed by the evolutionary process of piggyBac-herpesvirus fusion based on the distribution of Teratorn-like herpesviruses (relatives) among teleosts. Finally, we provide other examples of evolutionary associations between different classes of elements and propose that recombination could be a driving force generating novel mobile elements.
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Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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9
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Kemmler CL, Moran HR, Murray BF, Scoresby A, Klem JR, Eckert RL, Lepovsky E, Bertho S, Nieuwenhuize S, Burger S, D'Agati G, Betz C, Puller AC, Felker A, Ditrychova K, Bötschi S, Affolter M, Rohner N, Lovely CB, Kwan KM, Burger A, Mosimann C. Next-generation plasmids for transgenesis in zebrafish and beyond. Development 2023; 150:dev201531. [PMID: 36975217 PMCID: PMC10263156 DOI: 10.1242/dev.201531] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Transgenesis is an essential technique for any genetic model. Tol2-based transgenesis paired with Gateway-compatible vector collections has transformed zebrafish transgenesis with an accessible modular system. Here, we establish several next-generation transgenesis tools for zebrafish and other species to expand and enhance transgenic applications. To facilitate gene regulatory element testing, we generated Gateway middle entry vectors harboring the small mouse beta-globin minimal promoter coupled to several fluorophores, CreERT2 and Gal4. To extend the color spectrum for transgenic applications, we established middle entry vectors encoding the bright, blue-fluorescent protein mCerulean and mApple as an alternative red fluorophore. We present a series of p2A peptide-based 3' vectors with different fluorophores and subcellular localizations to co-label cells expressing proteins of interest. Finally, we established Tol2 destination vectors carrying the zebrafish exorh promoter driving different fluorophores as a pineal gland-specific transgenesis marker that is active before hatching and through adulthood. exorh-based reporters and transgenesis markers also drive specific pineal gland expression in the eye-less cavefish (Astyanax). Together, our vectors provide versatile reagents for transgenesis applications in zebrafish, cavefish and other models.
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Affiliation(s)
- Cassie L. Kemmler
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Hannah R. Moran
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Brooke F. Murray
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Aaron Scoresby
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - John R. Klem
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Rachel L. Eckert
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Elizabeth Lepovsky
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Sylvain Bertho
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Susan Nieuwenhuize
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Sibylle Burger
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Gianluca D'Agati
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Charles Betz
- Growth & Development, Biozentrum, Spitalstrasse 41, University of Basel, 4056 Basel, Switzerland
| | - Ann-Christin Puller
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Anastasia Felker
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Karolina Ditrychova
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Seraina Bötschi
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Markus Affolter
- Growth & Development, Biozentrum, Spitalstrasse 41, University of Basel, 4056 Basel, Switzerland
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - C. Ben Lovely
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Kristen M. Kwan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexa Burger
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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10
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Inotsume M, Chiba T, Matsushima T, Kurimoto R, Nakajima M, Kato T, Shishido K, Liu L, Kawakami K, Asahara H. One-step generation of mice with gene editing by Tol2 transposon-dependent gRNA delivery. FEBS Lett 2023; 597:975-984. [PMID: 36876986 DOI: 10.1002/1873-3468.14605] [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: 11/17/2022] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
Abstract
Conditional knockout mice are valuable tools for examining the functions of targeted genes in a time- and space-specific manner. Here, we generated gene-edited mice by using the Tol2 transposon to introduce guide RNA (gRNA) into fertilized eggs obtained by crossing LSL (loxP-stop-loxP)-CRISPR-associated 9 (Cas9) mice, which express Cas9 in a Cre-dependent manner, with CAG-CreER mice. Transposase mRNA and plasmid DNA, which contained a gRNA sequence for the gene encoding tyrosinase flanked by the transposase recognition sequence, were injected together into fertilized eggs. As a result, the transcribed gRNA cleaved the target genome in a Cas9-dependent manner. Using this method, it is possible to generate conditional genome-edited mice more easily in a shorter period of time.
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Affiliation(s)
- Maiko Inotsume
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Takahide Matsushima
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Ryota Kurimoto
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Mitsuyo Nakajima
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Tomomi Kato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Kana Shishido
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Lin Liu
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Bunkyo-ku, Japan
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
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11
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Espinosa-Medina I, Feliciano D, Belmonte-Mateos C, Linda Miyares R, Garcia-Marques J, Foster B, Lindo S, Pujades C, Koyama M, Lee T. TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages. Neuron 2023; 111:345-361.e10. [PMID: 36417906 DOI: 10.1016/j.neuron.2022.10.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/15/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022]
Abstract
During development, regulatory factors appear in a precise order to determine cell fates over time. Consequently, to investigate complex tissue development, it is necessary to visualize and manipulate cell lineages with temporal control. Current strategies for tracing vertebrate cell lineages lack genetic access to sequentially produced cells. Here, we present TEMPO (Temporal Encoding and Manipulation in a Predefined Order), an imaging-readable genetic tool allowing differential labeling and manipulation of consecutive cell generations in vertebrates. TEMPO is based on CRISPR and powered by a cascade of gRNAs that drive orderly activation and inactivation of reporters and/or effectors. Using TEMPO to visualize zebrafish and mouse neurogenesis, we recapitulated birth-order-dependent neuronal fates. Temporally manipulating cell-cycle regulators in mouse cortex progenitors altered the proportion and distribution of neurons and glia, revealing the effects of temporal gene perturbation on serial cell fates. Thus, TEMPO enables sequential manipulation of molecular factors, crucial to study cell-type specification.
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Affiliation(s)
| | - Daniel Feliciano
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Carla Belmonte-Mateos
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, PRBB, Barcelona 08003, Spain
| | - Rosa Linda Miyares
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jorge Garcia-Marques
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid 28049, Spain
| | - Benjamin Foster
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sarah Lindo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Cristina Pujades
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, PRBB, Barcelona 08003, Spain
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Tzumin Lee
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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12
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Wu M, Xu J, Zhang Y, Wen Z. Learning from Zebrafish Hematopoiesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:137-157. [PMID: 38228963 DOI: 10.1007/978-981-99-7471-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Hematopoiesis is a complex process that tightly regulates the generation, proliferation, differentiation, and maintenance of hematopoietic cells. Disruptions in hematopoiesis can lead to various diseases affecting both hematopoietic and non-hematopoietic systems, such as leukemia, anemia, thrombocytopenia, rheumatoid arthritis, and chronic granuloma. The zebrafish serves as a powerful vertebrate model for studying hematopoiesis, offering valuable insights into both hematopoietic regulation and hematopoietic diseases. In this chapter, we present a comprehensive overview of zebrafish hematopoiesis, highlighting its distinctive characteristics in hematopoietic processes. We discuss the ontogeny and modulation of both primitive and definitive hematopoiesis, as well as the microenvironment that supports hematopoietic stem/progenitor cells. Additionally, we explore the utility of zebrafish as a disease model and its potential in drug discovery, which not only advances our understanding of the regulatory mechanisms underlying hematopoiesis but also facilitates the exploration of novel therapeutic strategies for hematopoietic diseases.
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Affiliation(s)
- Mei Wu
- Affiliated Hospital of Guangdong Medical University and Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jin Xu
- South China University of Technology, School of Medicine, Guangzhou, Guangdong, China.
| | - Yiyue Zhang
- South China University of Technology, School of Medicine, Guangzhou, Guangdong, China.
| | - Zilong Wen
- Southern University of Science and Technology, School of Life Sciences, Shenzhen, Guangdong, China.
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13
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Abstract
Heart disease is the leading cause of death worldwide. Despite decades of research, most heart pathologies have limited treatments, and often the only curative approach is heart transplantation. Thus, there is an urgent need to develop new therapeutic approaches for treating cardiac diseases. Animal models that reproduce the human pathophysiology are essential to uncovering the biology of diseases and discovering therapies. Traditionally, mammals have been used as models of cardiac disease, but the cost of generating and maintaining new models is exorbitant, and the studies have very low throughput. In the last decade, the zebrafish has emerged as a tractable model for cardiac diseases, owing to several characteristics that made this animal popular among developmental biologists. Zebrafish fertilization and development are external; embryos can be obtained in high numbers, are cheap and easy to maintain, and can be manipulated to create new genetic models. Moreover, zebrafish exhibit an exceptional ability to regenerate their heart after injury. This review summarizes 25 years of research using the zebrafish to study the heart, from the classical forward screenings to the contemporary methods to model mutations found in patients with cardiac disease. We discuss the advantages and limitations of this model organism and introduce the experimental approaches exploited in zebrafish, including forward and reverse genetics and chemical screenings. Last, we review the models used to induce cardiac injury and essential ideas derived from studying natural regeneration. Studies using zebrafish have the potential to accelerate the discovery of new strategies to treat cardiac diseases.
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Affiliation(s)
- Juan Manuel González-Rosa
- Cardiovascular Research Center, Massachusetts General Hospital Research Institute, Harvard Medical School, Charlestown, MA
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14
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Weissbourd B, Momose T, Nair A, Kennedy A, Hunt B, Anderson DJ. A genetically tractable jellyfish model for systems and evolutionary neuroscience. Cell 2021; 184:5854-5868.e20. [PMID: 34822783 PMCID: PMC8629132 DOI: 10.1016/j.cell.2021.10.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/30/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022]
Abstract
Jellyfish are radially symmetric organisms without a brain that arose more than 500 million years ago. They achieve organismal behaviors through coordinated interactions between autonomously functioning body parts. Jellyfish neurons have been studied electrophysiologically, but not at the systems level. We introduce Clytia hemisphaerica as a transparent, genetically tractable jellyfish model for systems and evolutionary neuroscience. We generate stable F1 transgenic lines for cell-type-specific conditional ablation and whole-organism GCaMP imaging. Using these tools and computational analyses, we find that an apparently diffuse network of RFamide-expressing umbrellar neurons is functionally subdivided into a series of spatially localized subassemblies whose synchronous activation controls directional food transfer from the tentacles to the mouth. These data reveal an unanticipated degree of structured neural organization in this species. Clytia affords a platform for systems-level studies of neural function, behavior, and evolution within a clade of marine organisms with growing ecological and economic importance.
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Affiliation(s)
- Brandon Weissbourd
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA; Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Tsuyoshi Momose
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Aditya Nair
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA; Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ann Kennedy
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA; Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bridgett Hunt
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA; Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, CA 91125, USA
| | - David J Anderson
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA; Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, CA 91125, USA.
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15
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Hayashi S, Tsukiyama T, Iida A, Kinoshita M, Koga A. The medaka fish Tol2 transposable element is in an early stage of decay: identification of a nonautonomous copy. Genome 2021; 65:183-187. [PMID: 34529924 DOI: 10.1139/gen-2021-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The majority of DNA-based transposable elements comprise autonomous and nonautonomous copies, or only nonautonomous copies, where the autonomous copy contains an intact gene for a transposase protein and the nonautonomous copy does not. Even if autonomous copies coexist, they are generally less frequent. The Tol2 element of medaka fish is one of the few elements for which a nonautonomous copy has not yet been found. Here we report the presence of a nonautonomous Tol2 copy that was identified by surveying the medaka genome sequence database. This copy contained 3 local sequence alterations that affected the deduced amino acid sequence of the transposase: a deletion of 15 nucleotides resulting in a deletion of 5 amino acids, a base substitution causing a single amino acid change, and another base substitution giving rise to a stop codon. Transposition assays using cultured human cells revealed that the transposase activity was reduced by the 15-nucleotide deletion and abolished by the nonsense mutation. This is the first example of a nonautonomous Tol2 copy. Thus, Tol2 is in an early stage of decay in the medaka genome, and is therefore a unique element to observe an almost whole decay process that progresses in natural populations.
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Affiliation(s)
- Sakura Hayashi
- Kyoto University, 12918, Primate Research Institute, Inuyama, Japan;
| | | | - Atsuo Iida
- Nagoya University, 12965, Graduate School of Bioagricultural Sciences, Nagoya, Japan;
| | - Masato Kinoshita
- Kyoto University, 12918, Graduate School of Agriculture, Kyoto, Japan;
| | - Akihiko Koga
- Kyoto University, 12918, Primate Research Institute, Inuyama, Japan;
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16
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Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
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Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
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17
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Shen D, Song C, Miskey C, Chan S, Guan Z, Sang Y, Wang Y, Chen C, Wang X, Müller F, Ivics Z, Gao B. A native, highly active Tc1/mariner transposon from zebrafish (ZB) offers an efficient genetic manipulation tool for vertebrates. Nucleic Acids Res 2021; 49:2126-2140. [PMID: 33638993 PMCID: PMC7913693 DOI: 10.1093/nar/gkab045] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
New genetic tools and strategies are currently under development to facilitate functional genomics analyses. Here, we describe an active member of the Tc1/mariner transposon superfamily, named ZB, which invaded the zebrafish genome very recently. ZB exhibits high activity in vertebrate cells, in the range of those of the widely used transposons piggyBac (PB), Sleeping Beauty (SB) and Tol2. ZB has a similar structural organization and target site sequence preference to SB, but a different integration profile with respect to genome-wide preference among mammalian functional annotation features. Namely, ZB displays a preference for integration into transcriptional regulatory regions of genes. Accordingly, we demonstrate the utility of ZB for enhancer trapping in zebrafish embryos and in the mouse germline. These results indicate that ZB may be a powerful tool for genetic manipulation in vertebrate model species.
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Affiliation(s)
- Dan Shen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Shuheng Chan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhongxia Guan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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18
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Abstract
Cephalochordates (amphioxus) are invertebrate chordates closely related to vertebrates. As they are evolving very slowly, they are proving to be very appropriate for developmental genetics studies aimed at understanding how vertebrates evolved from their invertebrate ancestors. To date, techniques for gene knockdown and overexpression have been developed, but methods for continuous breeding cultures and generating germline mutants have been developed only recently. Here we describe methods for continuous laboratory breeding cultures of the cephalochordate Branchiostoma floridae and the TALEN and Tol2 methods for mutagenesis. Included are strategies for analyzing the mutants and raising successive generations to obtain homozygotes. These methods should be applicable to any warm water species of cephalochordates with a relatively short generation time of 3-4 months and a life span of 3 years or more.
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19
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Chu D, Nguyen A, Smith SS, Vavrušová Z, Schneider RA. Stable integration of an optimized inducible promoter system enables spatiotemporal control of gene expression throughout avian development. Biol Open 2020; 9:bio055343. [PMID: 32917762 PMCID: PMC7561481 DOI: 10.1242/bio.055343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/27/2020] [Indexed: 01/18/2023] Open
Abstract
Precisely altering gene expression is critical for understanding molecular processes of embryogenesis. Although some tools exist for transgene misexpression in developing chick embryos, we have refined and advanced them by simplifying and optimizing constructs for spatiotemporal control. To maintain expression over the entire course of embryonic development we use an enhanced piggyBac transposon system that efficiently integrates sequences into the host genome. We also incorporate a DNA targeting sequence to direct plasmid translocation into the nucleus and a D4Z4 insulator sequence to prevent epigenetic silencing. We designed these constructs to minimize their size and maximize cellular uptake, and to simplify usage by placing all of the integrating sequences on a single plasmid. Following electroporation of stage HH8.5 embryos, our tetracycline-inducible promoter construct produces robust transgene expression in the presence of doxycycline at any point during embryonic development in ovo or in culture. Moreover, expression levels can be modulated by titrating doxycycline concentrations and spatial control can be achieved using beads or gels. Thus, we have generated a novel, sensitive, tunable, and stable inducible-promoter system for high-resolution gene manipulation in vivo.
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Affiliation(s)
- Daniel Chu
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
| | - An Nguyen
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
| | - Spenser S Smith
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
| | - Zuzana Vavrušová
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
| | - Richard A Schneider
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA 94143-0514, USA
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20
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Bai J, Kondo R, Mayasari NI, Shigeoka T, Isotani A, Ikawa M, Sashida G, Kawaichi M, Ishida Y. Diphtheria toxin-mediated transposon-driven poly (A)-trapping efficiently disrupts transcriptionally silent genes in embryonic stem cells. Genesis 2020; 58:e23386. [PMID: 32645254 DOI: 10.1002/dvg.23386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 11/10/2022]
Abstract
Random gene trapping is the application of insertional mutagenesis techniques that are conventionally used to inactivate protein-coding genes in mouse embryonic stem (ES) cells. Transcriptionally silent genes are not effectively targeted by conventional random gene trapping techniques, thus we herein developed an unbiased poly (A) trap (UPATrap) method using a Tol2 transposon, which preferentially integrated into active genes rather than silent genes in ES cells. To achieve efficient trapping at transcriptionally silent genes using random insertional mutagenesis in ES cells, we generated a new diphtheria toxin (DT)-mediated trapping vector, DTrap that removed cells, through the expression of DT that was induced by the promoter activity of the trapped genes, and selected trapped clones using the neomycin-resistance gene of the vector. We found that a double-DT, the dDT vector, dominantly induced the disruption of silent genes, but not active genes, and showed more stable integration in ES cells than the UPATrap vector. The dDT vector disrupted differentiated cell lineage genes, which were silent in ES cells, and labeled trapped clone cells by the expression of EGFP upon differentiation. Thus, the dDT vector provides a systematic approach to disrupt silent genes and examine the cellular functions of trapped genes in the differentiation of target cells and development.
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Affiliation(s)
- Jie Bai
- Laboratory of Functional Genomics and Medicine, Division of Biological Science, Nara Institute of Science and Technology, Nara, Japan.,Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Ryohei Kondo
- Laboratory of Functional Genomics and Medicine, Division of Biological Science, Nara Institute of Science and Technology, Nara, Japan.,Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - N Ika Mayasari
- Laboratory of Functional Genomics and Medicine, Division of Biological Science, Nara Institute of Science and Technology, Nara, Japan.,Faculty of Veterinary Medicine, Bogor Agricultural University (IPB), Jalan Agatis Kampus IPB Darmaga, Bogor, West Java, Indonesia
| | - Toshiaki Shigeoka
- Laboratory of Functional Genomics and Medicine, Division of Biological Science, Nara Institute of Science and Technology, Nara, Japan.,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ayako Isotani
- Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Organ Developmental Engineering, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Masashi Kawaichi
- Division of Educational Development, Nara Institute of Science and Technology, Nara, Japan
| | - Yasumasa Ishida
- Laboratory of Functional Genomics and Medicine, Division of Biological Science, Nara Institute of Science and Technology, Nara, Japan
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21
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Mackey AS, Redd PS, DeLaurier A, Hancock CN. Codon optimized Tol2 transposase results in increased transient expression of a crystallin-GFP transgene in zebrafish. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000268. [PMID: 32626847 PMCID: PMC7326334 DOI: 10.17912/micropub.biology.000268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Allison S. Mackey
- University of South Carolina Aiken, Department of Biology and Geology, Aiken, SC
- University of Utah Bioscience Program, Salt Lake City, UT
| | - Priscilla S. Redd
- University of South Carolina Aiken, Department of Biology and Geology, Aiken, SC
| | - April DeLaurier
- University of South Carolina Aiken, Department of Biology and Geology, Aiken, SC
| | - C. Nathan Hancock
- University of South Carolina Aiken, Department of Biology and Geology, Aiken, SC
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22
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Li C, Lieber A. Adenovirus vectors in hematopoietic stem cell genome editing. FEBS Lett 2019; 593:3623-3648. [PMID: 31705806 PMCID: PMC10473235 DOI: 10.1002/1873-3468.13668] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/23/2019] [Accepted: 10/27/2019] [Indexed: 12/13/2022]
Abstract
Genome editing of hematopoietic stem cells (HSCs) represents a therapeutic option for a number of hematological genetic diseases, as HSCs have the potential for self-renewal and differentiation into all blood cell lineages. This review presents advances of genome editing in HSCs utilizing adenovirus vectors as delivery vehicles. We focus on capsid-modified, helper-dependent adenovirus vectors that are devoid of all viral genes and therefore exhibit an improved safety profile. We discuss HSC genome engineering for several inherited disorders and infectious diseases including hemoglobinopathies, Fanconi anemia, hemophilia, and HIV-1 infection by ex vivo and in vivo editing in transgenic mice, nonhuman primates, as well as in human CD34+ cells. Mechanisms of therapeutic gene transfer including episomal expression of designer nucleases and base editors, transposase-mediated random integration, and targeted homology-directed repair triggered integration into selected genomic safe harbor loci are also reviewed.
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Affiliation(s)
- Chang Li
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - André Lieber
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
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23
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Pourghadamyari H, Rezaei M, Basiri M, Tahamtani Y, Asgari B, Hassani SN, Meshkani R, Golmohammadi T, Baharvand H. Generation of a Transgenic Zebrafish Model for Pancreatic Beta Cell Regeneration. Galen Med J 2019; 8:e1056. [PMID: 34466457 PMCID: PMC8344119 DOI: 10.31661/gmj.v8i0.1056] [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: 11/06/2017] [Revised: 11/12/2017] [Accepted: 11/17/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Diabetes is a major worldwide health problem. It is widely accepted that the beta cell mass decreases in type I diabetes (T1D). Accordingly, beta cell regeneration is a promising approach to increase the beta cell mass in T1D patients. However, the underlying mechanisms of beta cell regeneration have yet to be elucidated. One promising avenue is to create a relevant animal model to explore the underlying molecular and cellular mechanisms of beta cell regeneration. The zebrafish can be considered a model in beta cell regeneration studies because the pancreas structure and gene expression pattern are highly conserved between human and zebrafish. MATERIALS AND METHODS In this study, the Tol2 transposase was exploited to generate a Tg(Ins:egfp-nfsB) zebrafish model that expressed a fusion protein composed of enhanced green fluorescent protein (EGFP) and nitroreductase (NTR) under control of the Ins promoter. RESULTS Metronidazole (MTZ) treatment of Tg(ins:egfp-nfsB) zebrafish larvae led to selective ablation of beta cells. Proof-of-concept evidence for beta cell regeneration in the transgenic larvae was observed two days after withdrawal of MTZ. CONCLUSION This study suggests that the Tg(ins:egfp-nfsB) zebrafish can be used as a disease model to study beta cell regeneration and elucidate underlying mechanisms during the regeneration process.
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Affiliation(s)
- Hossein Pourghadamyari
- Department of Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Rezaei
- Fishery Faculty, Gorgan University of Agriculture Science and Natural Resources, Gorgan, Iran
| | - Mohsen Basiri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Yaser Tahamtani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Behrouz Asgari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyedeh-Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Reza Meshkani
- Department of Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Taghi Golmohammadi
- Department of Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
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24
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D'Agati G, Cabello EM, Frontzek K, Rushing EJ, Klemm R, Robinson MD, White RM, Mosimann C, Burger A. Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish. Dis Model Mech 2019; 12:dmm.039545. [PMID: 31221659 PMCID: PMC6679381 DOI: 10.1242/dmm.039545] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 06/13/2019] [Indexed: 01/09/2023] Open
Abstract
The aberrant activation of developmental processes triggers diverse cancer types. Chordoma is a rare, aggressive tumor arising from transformed notochord remnants. Several potentially oncogenic factors have been found to be deregulated in chordoma, yet causation remains uncertain. In particular, sustained expression of TBXT – encoding the notochord regulator protein brachyury – is hypothesized as a key driver of chordoma, yet experimental evidence is absent. Here, we employ a zebrafish chordoma model to identify the notochord-transforming potential of implicated genes in vivo. We find that Brachyury, including a form with augmented transcriptional activity, is insufficient to initiate notochord hyperplasia. In contrast, the chordoma-implicated receptor tyrosine kinases (RTKs) EGFR and Kdr/VEGFR2 are sufficient to transform notochord cells. Aberrant activation of RTK/Ras signaling attenuates processes required for notochord differentiation, including the unfolded protein response and endoplasmic reticulum stress pathways. Our results provide the first in vivo evidence against a tumor-initiating potential of Brachyury in the notochord, and imply activated RTK signaling as a possible initiating event in chordoma. Furthermore, our work points at modulating endoplasmic reticulum and protein stress pathways as possible therapeutic avenues against chordoma. Summary: An injection-based chordoma model in zebrafish shows that the hypothesized chordoma oncogene brachyury is insufficient, whereas EGFR and VEGFR2 are sufficient, to trigger notochord hyperplasia in our model.
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Affiliation(s)
- Gianluca D'Agati
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Elena María Cabello
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Karl Frontzek
- Institute of Neuropathology, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Elisabeth J Rushing
- Institute of Neuropathology, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Robin Klemm
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland.,SIB Swiss Institute of Bioinformatics, University of Zürich, 8057 Zürich, Switzerland
| | - Richard M White
- Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
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25
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Rezaei M, Basiri M, Hasani SN, Asgari B, Kashiri H, Shabani A, Baharvand H. Establishment of a Transgenic Zebrafish Expressing GFP in the Skeletal Muscle as an Ornamental Fish. Galen Med J 2019; 8:e1068. [PMID: 34466458 PMCID: PMC8344052 DOI: 10.31661/gmj.v8i0.1068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/18/2018] [Accepted: 02/17/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Transgenic animals have a critical role in the advancement of our knowledge in different fields of life sciences. Along with recent advances in genome engineering technologies, a wide spectrum of techniques have been applied to produce transgenic animals. Tol2 transposase method is one of the most popular approaches that were used to generate transgenic animals. The current study was set out to produce an ornamental fish, which express enhanced green fluorescent protein (EGFP) under control of mylpfa promoter by using Tol2 transposase method. Materials and Methods: Polymerase chain reaction (PCR) cloning method was performed to insert zebrafish myosin promoter (mylpfa) into Tol2-EGFP plasmid at the upstream of EGFP. In vitro transcription method was used to prepare the transposase mRNA. The Tol2-EGFP plasmid and transposase mRNA were then co-injected into the one-cell stage of zebrafish zygotes. After two days, the fluorescent microscopic analysis was used to select transgenic zebrafishes. Results: Our data showed that the optimum concentration for recombinant Tol2 vector and transposase mRNA were 50 ng/ul and 100 ng/ul, respectively. The results also revealed that the quality of embryos and quantity of injected construct had the important effects on Tol2 transposase method efficiency. Conclusion: Data showed that Tol2 transposase is an appropriate method to generate zebrafish transgene. Our finding also showed that mylpfa promoter is a strong promoter that can be used as a selected promoter in the ornamental fish industry.
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Affiliation(s)
- Mohammad Rezaei
- Fishery Faculty, Gorgan University of agriculture science and natural resources, Gorgan, Iran
| | - Mohsen Basiri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyedeh-Nafiseh Hasani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Behrouz Asgari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hadis Kashiri
- Fishery Faculty, Gorgan University of agriculture science and natural resources, Gorgan, Iran
| | - Ali Shabani
- Fishery Faculty, Gorgan University of agriculture science and natural resources, Gorgan, Iran
- Correspondence to: Ali Shabani, Fishery faculty, Gorgan University of agriculture science and natural resources, Gorgan, Iran. Telephone Number: +981732427040 Email Address :
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
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26
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Fang J, Chen T, Pan Q, Wang Q. Generation of albino medaka (
Oryzias latipes
) by CRISPR/Cas9. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:242-246. [DOI: 10.1002/jez.b.22808] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/16/2018] [Accepted: 05/03/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Jian Fang
- College of FisheriesKey Laboratory of Freshwater Animal BreedingMinistry of AgricultureHuazhong Agricultural University Wuhan Hubei China
| | - Tiansheng Chen
- College of FisheriesKey Laboratory of Freshwater Animal BreedingMinistry of AgricultureHuazhong Agricultural University Wuhan Hubei China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province Changde China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province Wuhan China
| | - Qihua Pan
- College of FisheriesKey Laboratory of Freshwater Animal BreedingMinistry of AgricultureHuazhong Agricultural University Wuhan Hubei China
| | - Qian Wang
- College of FisheriesKey Laboratory of Freshwater Animal BreedingMinistry of AgricultureHuazhong Agricultural University Wuhan Hubei China
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27
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Ishikawa K, Kobayashi Y, Wakabayashi Y, Watanabe S, Semba K. A highly sensitive trap vector system for isolating reporter cells and identification of responsive genes. Biol Methods Protoc 2018; 3:bpy003. [PMID: 32161797 PMCID: PMC6994077 DOI: 10.1093/biomethods/bpy003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/22/2018] [Accepted: 04/18/2018] [Indexed: 01/03/2023] Open
Abstract
We devised a versatile vector system for efficient isolation of reporter cells responding to a certain condition of interest. This system combines nontoxic GAL4-UAS and piggyBac transposon systems, allowing application to mammalian cells and improved expression of a fluorescent reporter protein for cell sorting. Case studies under conditions of c-MYC gene induction or endoplasmic reticulum (ER) stress with thapsigargin on mouse or human cell lines confirmed easy and efficient isolation of responsive reporter cells. Sequence analyses of the integrated loci of the thapsigargin-responsive clones identified responsive genes including BiP and OSBPL9. OSBPL9 is a novel ER stress-responsive gene and we confirmed that endogenous mRNA expression of OSBPL9 is upregulated by thapsigargin, and is repressed by IRE1α inhibitors, 4μ8C and toyocamycin, but not significantly by a PERK inhibitor, GSK2656157. These results demonstrate that this approach can be used to discover novel genes regulated by any stimuli without the need for microarray analysis, and that it can concomitantly produce reporter cells without identification of stimuli-responsive promoter/enhancer elements. Therefore, this system has a variety of benefits for basic and clinical research.
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Affiliation(s)
- Kosuke Ishikawa
- Japan Biological Informatics Consortium (JBiC), 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan
| | - Yuta Kobayashi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yutaro Wakabayashi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Shinya Watanabe
- Translational Research Center, Fukushima Medical University, 1 Hikarigaoka, Fukushima 960-1295, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Translational Research Center, Fukushima Medical University, 1 Hikarigaoka, Fukushima 960-1295, Japan
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28
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Preclinical and clinical advances in transposon-based gene therapy. Biosci Rep 2017; 37:BSR20160614. [PMID: 29089466 PMCID: PMC5715130 DOI: 10.1042/bsr20160614] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 02/08/2023] Open
Abstract
Transposons derived from Sleeping Beauty (SB), piggyBac (PB), or Tol2 typically require cotransfection of transposon DNA with a transposase either as an expression plasmid or mRNA. Consequently, this results in genomic integration of the potentially therapeutic gene into chromosomes of the desired target cells, and thus conferring stable expression. Non-viral transfection methods are typically preferred to deliver the transposon components into the target cells. However, these methods do not match the efficacy typically attained with viral vectors and are sometimes associated with cellular toxicity evoked by the DNA itself. In recent years, the overall transposition efficacy has gradually increased by codon optimization of the transposase, generation of hyperactive transposases, and/or introduction of specific mutations in the transposon terminal repeats. Their versatility enabled the stable genetic engineering in many different primary cell types, including stem/progenitor cells and differentiated cell types. This prompted numerous preclinical proof-of-concept studies in disease models that demonstrated the potential of DNA transposons for ex vivo and in vivo gene therapy. One of the merits of transposon systems relates to their ability to deliver relatively large therapeutic transgenes that cannot readily be accommodated in viral vectors such as full-length dystrophin cDNA. These emerging insights paved the way toward the first transposon-based phase I/II clinical trials to treat hematologic cancer and other diseases. Though encouraging results were obtained, controlled pivotal clinical trials are needed to corroborate the efficacy and safety of transposon-based therapies.
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29
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Ishiyama S, Yamazaki K, Kurihara F, Yamashita D, Sao K, Hattori A, Koga A. DNA-based transposable elements with nucleotide sequence similar to Tol2 from medaka fish are prevalent in cyprinid fishes. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, Morishita S. Centromere evolution and CpG methylation during vertebrate speciation. Nat Commun 2017. [PMID: 29184138 DOI: 10.1038/s41467-017-01982-7.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.
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Affiliation(s)
- Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Shingo Tomioka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yui Uchida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Shinich Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan.
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31
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Centromere evolution and CpG methylation during vertebrate speciation. Nat Commun 2017; 8:1833. [PMID: 29184138 PMCID: PMC5705604 DOI: 10.1038/s41467-017-01982-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022] Open
Abstract
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20–345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320–350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation. Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here Ichikawa et al perform de novo long-read genome assembly of three inbred medaka strains, and report long-range structure of centromeres and their methylation as well as correlation of structural variants with differential gene expression.
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32
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Tipanee J, VandenDriessche T, Chuah MK. Transposons: Moving Forward from Preclinical Studies to Clinical Trials. Hum Gene Ther 2017; 28:1087-1104. [DOI: 10.1089/hum.2017.128] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Jaitip Tipanee
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
| | - Thierry VandenDriessche
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Marinee K. Chuah
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
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33
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Lee HJ, Kim YM, Ono T, Han JY. Genome Modification Technologies and Their Applications in Avian Species. Int J Mol Sci 2017; 18:ijms18112245. [PMID: 29072628 PMCID: PMC5713215 DOI: 10.3390/ijms18112245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 12/01/2022] Open
Abstract
The rapid development of genome modification technology has provided many great benefits in diverse areas of research and industry. Genome modification technologies have also been actively used in a variety of research areas and fields of industry in avian species. Transgenic technologies such as lentiviral systems and piggyBac transposition have been used to produce transgenic birds for diverse purposes. In recent years, newly developed programmable genome editing tools such as transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) have also been successfully adopted in avian systems with primordial germ cell (PGC)-mediated genome modification. These genome modification technologies are expected to be applied to practical uses beyond system development itself. The technologies could be used to enhance economic traits in poultry such as acquiring a disease resistance or producing functional proteins in eggs. Furthermore, novel avian models of human diseases or embryonic development could also be established for research purposes. In this review, we discuss diverse genome modification technologies used in avian species, and future applications of avian biotechnology.
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Affiliation(s)
- Hong Jo Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
| | - Young Min Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
| | - Tamao Ono
- Faculty of Agriculture, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan.
| | - Jae Yong Han
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Institute for Biomedical Sciences, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan.
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34
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Kawakami K, Largaespada DA, Ivics Z. Transposons As Tools for Functional Genomics in Vertebrate Models. Trends Genet 2017; 33:784-801. [PMID: 28888423 DOI: 10.1016/j.tig.2017.07.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023]
Abstract
Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes. For example, the Sleeping Beauty transposon has become highly instrumental to induce tumors in experimental animals in a tissue-specific manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models, including zebrafish, mice, and rats.
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Affiliation(s)
- Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan; These authors contributed equally to this work
| | - David A Largaespada
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN, USA; These authors contributed equally to this work
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany; These authors contributed equally to this work..
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35
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Morita H, Taimatsu K, Yanagi K, Kawahara A. Exogenous gene integration mediated by genome editing technologies in zebrafish. Bioengineered 2017; 8:287-295. [PMID: 28272984 DOI: 10.1080/21655979.2017.1300727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies, such as transcription activator-like effector nuclease (TALEN) and the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, can induce DNA double-strand breaks (DSBs) at the targeted genomic locus, leading to frameshift-mediated gene disruption in the process of DSB repair. Recently, the technology-induced DSBs followed by DSB repairs are applied to integrate exogenous genes into the targeted genomic locus in various model organisms. In addition to a conventional knock-in technology mediated by homology-directed repair (HDR), novel knock-in technologies using refined donor vectors have also been developed with the genome editing technologies based on other DSB repair mechanisms, including non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ). Therefore, the improved knock-in technologies would contribute to freely modify the genome of model organisms.
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Affiliation(s)
- Hitoshi Morita
- a Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science , University of Yamanashi , Chuo , Yamanashi , Japan
| | - Kiyohito Taimatsu
- a Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science , University of Yamanashi , Chuo , Yamanashi , Japan
| | - Kanoko Yanagi
- a Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science , University of Yamanashi , Chuo , Yamanashi , Japan
| | - Atsuo Kawahara
- a Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science , University of Yamanashi , Chuo , Yamanashi , Japan
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36
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Abstract
DNA transposons are defined segments of DNA that are able to move from one genomic location to another. Movement is facilitated by one or more proteins, called the transposase, typically encoded by the mobile element itself. Here, we first provide an overview of the classification of such mobile elements in a variety of organisms. From a mechanistic perspective, we have focused on one particular group of DNA transposons that encode a transposase with a DD(E/D) catalytic domain that is topologically similar to RNase H. For these, a number of three-dimensional structures of transpososomes (transposase-nucleic acid complexes) are available, and we use these to describe the basics of their mechanisms. The DD(E/D) group, in addition to being the largest and most common among all DNA transposases, is the one whose members have been used for a wide variety of genomic applications. Therefore, a second focus of the article is to provide a nonexhaustive overview of transposon applications. Although several non-transposon-based approaches to site-directed genome modifications have emerged in the past decade, transposon-based applications are highly relevant when integration specificity is not sought. In fact, for many applications, the almost-perfect randomness and high frequency of integration make transposon-based approaches indispensable.
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Affiliation(s)
- Alison B. Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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37
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Chugunova AA, Dontsova OA, Sergiev PV. Methods of genome engineering: a new era of molecular biology. BIOCHEMISTRY (MOSCOW) 2016; 81:662-77. [DOI: 10.1134/s0006297916070038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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38
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Jiang XY, Hou F, Shen XD, Du XD, Xu HL, Zou SM. The N-terminal zinc finger domain of Tgf2 transposase contributes to DNA binding and to transposition activity. Sci Rep 2016; 6:27101. [PMID: 27251101 PMCID: PMC4890040 DOI: 10.1038/srep27101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/13/2016] [Indexed: 01/14/2023] Open
Abstract
Active Hobo/Activator/Tam3 (hAT) transposable elements are rarely found in vertebrates. Previously, goldfish Tgf2 was found to be an autonomously active vertebrate transposon that is efficient at gene-transfer in teleost fish. However, little is known about Tgf2 functional domains required for transposition. To explore this, we first predicted in silico a zinc finger domain in the N-terminus of full length Tgf2 transposase (L-Tgf2TPase). Two truncated recombinant Tgf2 transposases with deletions in the N-terminal zinc finger domain, S1- and S2-Tgf2TPase, were expressed in bacteria from goldfish cDNAs. Both truncated Tgf2TPases lost their DNA-binding ability in vitro, specifically at the ends of Tgf2 transposon than native L-Tgf2TPase. Consequently, S1- and S2-Tgf2TPases mediated gene transfer in the zebrafish genome in vivo at a significantly (p < 0.01) lower efficiency (21%–25%), in comparison with L-Tgf2TPase (56% efficiency). Compared to L-Tgf2TPase, truncated Tgf2TPases catalyzed imprecise excisions with partial deletion of TE ends and/or plasmid backbone insertion/deletion. The gene integration into the zebrafish genome mediated by truncated Tgf2TPases was imperfect, creating incomplete 8-bp target site duplications at the insertion sites. These results indicate that the zinc finger domain in Tgf2 transposase is involved in binding to Tgf2 terminal sequences, and loss of those domains has effects on TE transposition.
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Affiliation(s)
- Xia-Yun Jiang
- College of Food Science and Technology, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
| | - Fei Hou
- College of Food Science and Technology, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
| | - Xiao-Dan Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
| | - Xue-Di Du
- College of animal science and technology, Yangzhou University, Wenhui Road 48, Yangzhou 225009, China
| | - Hai-Li Xu
- College of Food Science and Technology, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
| | - Shu-Ming Zou
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
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39
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Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. G3-GENES GENOMES GENETICS 2016; 6:805-17. [PMID: 26818075 PMCID: PMC4825651 DOI: 10.1534/g3.115.026849] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germ-line transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift, and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence the integration of heterologous DNA in genomes, and have implications for targeted genome engineering.
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Active recombinant Tol2 transposase for gene transfer and gene discovery applications. Mob DNA 2016; 7:6. [PMID: 27042235 PMCID: PMC4818426 DOI: 10.1186/s13100-016-0062-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/15/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The revolutionary concept of "jumping genes" was conceived by McClintock in the late 1940s while studying the Activator/Dissociation (Ac/Ds) system in maize. Transposable elements (TEs) represent the most abundant component of many eukaryotic genomes. Mobile elements are a driving force of eukaryotic genome evolution. McClintock's Ac, the autonomous element of the Ac/Ds system, together with hobo from Drosophila and Tam3 from snapdragon define an ancient and diverse DNA transposon superfamily named hAT. Other members of the hAT superfamily include the insect element Hermes and Tol2 from medaka. In recent years, genetic tools derived from the 'cut' and 'paste' Tol2 DNA transposon have been widely used for genomic manipulation in zebrafish, mammals and in cells in vitro. RESULTS We report the purification of a functional recombinant Tol2 protein from E.coli. We demonstrate here that following microinjection using a zebrafish embryo test system, purified Tol2 transposase protein readily catalyzes gene transfer in both somatic and germline tissues in vivo. We show that purified Tol2 transposase can promote both in vitro cutting and pasting in a defined system lacking other cellular factors. Notably, our analysis of Tol2 transposition in vitro reveals that the target site preference observed for Tol2 in complex host genomes is maintained using a simpler target plasmid test system, indicating that the primary sequence might encode intrinsic cues for transposon integration. CONCLUSIONS This active Tol2 protein is an important new tool for diverse applications including gene discovery and molecular medicine, as well as for the biochemical analysis of transposition and regulation of hAT transposon/genome interactions. The measurable but comparatively modest insertion site selection bias noted for Tol2 is largely determined by the primary sequence encoded in the target sequence as assessed through studying Tol2 protein-mediated transposition in a cell-free system.
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Abstract
The Tol2 element is an active transposon that was found from the genome of the Japanese medaka fish. Since the Tol2 transposition system is active in all vertebrate cells tested so far, it has been applied to germ line transgenesis in various model animals including fish, frog, chicken, and mouse, and to gene transfer in culture cells. In zebrafish, the Tol2 system consists of the transposase mRNA and a Tol2 transposon-donor plasmid, and is introduced into fertilized eggs by microinjection. Thus genomic integrations of the Tol2 construct are generated in the germ lineage and transmitted to the offspring very efficiently. By using the Tol2 transposition system, we have developed important genetic methods, such as transgenesis, gene trapping, enhancer trapping, and the Gal4-UAS system in zebrafish and applied to many aspects of biological studies. In this chapter, we describe how these methods are performed.
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Kawakami K, Asakawa K, Hibi M, Itoh M, Muto A, Wada H. Gal4 Driver Transgenic Zebrafish. GENETICS, GENOMICS AND FISH PHENOMICS 2016; 95:65-87. [DOI: 10.1016/bs.adgen.2016.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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43
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Comparison of three transposons for the generation of highly productive recombinant CHO cell pools and cell lines. Biotechnol Bioeng 2015; 113:1234-43. [DOI: 10.1002/bit.25888] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/30/2015] [Accepted: 11/16/2015] [Indexed: 01/01/2023]
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44
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Kozmikova I, Kozmik Z. Gene regulation in amphioxus: An insight from transgenic studies in amphioxus and vertebrates. Mar Genomics 2015; 24 Pt 2:159-66. [PMID: 26094865 DOI: 10.1016/j.margen.2015.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/10/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023]
Abstract
Cephalochordates, commonly known as amphioxus or lancelets, are the most basal subphylum of chordates. Cephalochordates are thus key to understanding the origin of vertebrates and molecular mechanisms underlying vertebrate evolution. The evolution of developmental control mechanisms during invertebrate-to-vertebrate transition involved not only gene duplication events, but also specific changes in spatial and temporal expression of many genes. To get insight into the spatiotemporal regulation of gene expression during invertebrate-to-vertebrate transition, functional studies of amphioxus gene regulatory elements are highly warranted. Here, we review transgenic studies performed in amphioxus and vertebrates using promoters and enhancers derived from the genome of Branchiostoma floridae. We describe the current methods of transgenesis in amphioxus, provide evidence of Tol2 transposon-generated transgenic embryos of Branchiostoma lanceolatum and discuss possible future directions. We envision that comparative transgenic analysis of gene regulatory sequences in the context of amphioxus and vertebrate embryos will likely provide an important mechanistic insight into the evolution of vertebrate body plan.
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Affiliation(s)
- Iryna Kozmikova
- Institute of Molecular Genetics of the Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic.
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45
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A Multifunctional Mutagenesis System for Analysis of Gene Function in Zebrafish. G3-GENES GENOMES GENETICS 2015; 5:1283-99. [PMID: 25840430 PMCID: PMC4478556 DOI: 10.1534/g3.114.015842] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Since the sequencing of the human reference genome, many human disease-related genes have been discovered. However, understanding the functions of all the genes in the genome remains a challenge. The biological activities of these genes are usually investigated in model organisms such as mice and zebrafish. Large-scale mutagenesis screens to generate disruptive mutations are useful for identifying and understanding the activities of genes. Here, we report a multifunctional mutagenesis system in zebrafish using the maize Ds transposon. Integration of the Ds transposable element containing an mCherry reporter for protein trap events and an EGFP reporter for enhancer trap events produced a collection of transgenic lines marking distinct cell and tissue types, and mutagenized genes in the zebrafish genome by trapping and prematurely terminating endogenous protein coding sequences. We obtained 642 zebrafish lines with dynamic reporter gene expression. The characterized fish lines with specific expression patterns will be made available through the European Zebrafish Resource Center (EZRC), and a database of reporter expression is available online (http://fishtrap.warwick.ac.uk/). Our approach complements other efforts using zebrafish to facilitate functional genomic studies in this model of human development and disease.
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Hosseinkhani H, Abedini F, Ou KL, Domb AJ. Polymers in gene therapy technology. POLYM ADVAN TECHNOL 2014. [DOI: 10.1002/pat.3432] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hossein Hosseinkhani
- Graduate Institute of Biomedical Engineering; National Taiwan University of Science and Technology (Taiwan Tech); Taipei 10607 Taiwan
- Center of Excellence in Nanomedicine; National Taiwan University of Science and Technology (Taiwan Tech); Taipei 10607 Taiwan
- Research Center for Biomedical Devices and Prototyping Production, Research Center for Biomedical Implants and Microsurgery Devices, Graduate Institute of Biomedical Materials and Tissue Engineering, College of Oral Medicine, Taipei Medical University, Department of Dentistry; Taipei Medical University-Shuang Ho Hospital; Taipei 235 Taiwan
| | - Fatemeh Abedini
- Razi Vaccine and Serum Research Institute; Karaj Alborz IRAN
| | - Keng-Liang Ou
- Research Center for Biomedical Devices and Prototyping Production, Research Center for Biomedical Implants and Microsurgery Devices, Graduate Institute of Biomedical Materials and Tissue Engineering, College of Oral Medicine, Taipei Medical University, Department of Dentistry; Taipei Medical University-Shuang Ho Hospital; Taipei 235 Taiwan
| | - Abraham J. Domb
- Institute of Drug Research, The Center for Nanoscience and Nanotechnology, School of Pharmacy-Faculty of Medicine; The Hebrew University of Jerusalem; Jerusalem 91120 Israel
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Mazur AJ, Morosan-Puopolo G, Makowiecka A, Malicka-Błaszkiewicz M, Nowak D, Brand-Saberi B. Analysis of gelsolin expression pattern in developing chicken embryo reveals high GSN expression level in tissues of neural crest origin. Brain Struct Funct 2014; 221:515-34. [PMID: 25352156 PMCID: PMC4720725 DOI: 10.1007/s00429-014-0923-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 10/16/2014] [Indexed: 12/20/2022]
Abstract
Gelsolin is one of the most intensively studied actin-binding proteins. However, in the literature comprehensive studies of GSN expression during development have not been performed yet in all model organisms. In zebrafish, gelsolin is a dorsalizing factor that modulates bone morphogenetic proteins signaling pathways, whereas knockout of the gelsolin coding gene, GSN is not lethal in murine model. To study the role of gelsolin in development of higher vertebrates, it is crucial to estimate GSN expression pattern during development. Here, we examined GSN expression in the developing chicken embryo. We applied numerous methods to track GSN expression in developing embryos at mRNA and protein level. We noted a characteristic GSN expression pattern. Although GSN transcripts were present in several cell types starting from early developmental stages, a relatively high GSN expression was observed in eye, brain vesicles, midbrain, neural tube, heart tube, and splanchnic mesoderm. In older embryos, we observed a high GSN expression in the cranial ganglia and dorsal root ganglia. A detailed analysis of 10-day-old chicken embryos revealed high amounts of gelsolin especially within the head region: in the olfactory and optic systems, meninges, nerves, muscles, presumptive pituitary gland, and pericytes, but not oligodendrocytes in the brain. Obtained results suggest that GSN is expressed at high levels in some tissues of ectodermal origin including all neural crest derivatives. Additionally, we describe that silencing of GSN expression in brain vesicles leads to altered morphology of the mesencephalon. This implies gelsolin is crucial for chicken brain development.
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Affiliation(s)
- Antonina Joanna Mazur
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wrocław, Poland.
| | | | - Aleksandra Makowiecka
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Maria Malicka-Błaszkiewicz
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Dorota Nowak
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Beate Brand-Saberi
- Department of Anatomy and Molecular Embryology, Ruhr University of Bochum, Bochum, Germany
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Retrograde migration of pectoral girdle muscle precursors depends on CXCR4/SDF-1 signaling. Histochem Cell Biol 2014; 142:473-88. [PMID: 24972797 DOI: 10.1007/s00418-014-1237-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2014] [Indexed: 01/26/2023]
Abstract
In vertebrates, muscles of the pectoral girdle connect the forelimbs with the thorax. During development, the myogenic precursor cells migrate from the somites into the limb buds. Whereas most of the myogenic precursors remain in the limb bud to form the forelimb muscles, several cells migrate back toward the trunk to give rise to the superficial pectoral girdle muscles, such as the large pectoral muscle, the latissimus dorsi and the deltoid. Recently, this developing mode has been referred to as the "In-Out" mechanism. The present study focuses on the mechanisms of the "In-Out" migration during formation of the pectoral girdle muscles. Combining in ovo electroporation, tissue slice-cultures and confocal laser scanning microscopy, we visualize live in detail the retrograde migration of myogenic precursors from the forelimb bud into the trunk region by live imaging. Furthermore, we present for the first time evidence for the involvement of the chemokine receptor CXCR4 and its ligand SDF-1 during these processes. After microsurgical implantations of CXCR4 inhibitor beads in the proximal forelimb region of chicken embryos, we demonstrate with the aid of in situ hybridization and live-cell imaging that CXCR4/SDF-1 signaling is crucial for the retrograde migration of pectoral girdle muscle precursors. Moreover, we analyzed the MyoD expression in CXCR4-mutant mouse embryos and observed a considerable decrease in pectoral girdle musculature. We thus demonstrate the importance of the CXCR4/SDF-1 axis for the pectoral girdle muscle formation in avians and mammals.
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Watanabe K, Koga H, Nakamura K, Fujita A, Hattori A, Matsuda M, Koga A. Spontaneous germline excision of Tol1, a DNA-based transposable element naturally occurring in the medaka fish genome. Genome 2014; 57:193-9. [PMID: 24905071 DOI: 10.1139/gen-2014-0011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA-based transposable elements are ubiquitous constituents of eukaryotic genomes. Vertebrates are, however, exceptional in that most of their DNA-based elements appear to be inactivated. The Tol1 element of the medaka fish, Oryzias latipes, is one of the few elements for which copies containing an undamaged gene have been found. Spontaneous transposition of this element in somatic cells has previously been demonstrated, but there is only indirect evidence for its germline transposition. Here, we show direct evidence of spontaneous excision in the germline. Tyrosinase is the key enzyme in melanin biosynthesis. In an albino laboratory strain of medaka fish, which is homozygous for a mutant tyrosinase gene in which a Tol1 copy is inserted, we identified de novo reversion mutations related to melanin pigmentation. The gamete-based reversion rate was as high as 0.4%. The revertant fish carried the tyrosinase gene from which the Tol1 copy had been excised. We previously reported the germline transposition of Tol2, another DNA-based element that is thought to be a recent invader of the medaka fish genome. Tol1 is an ancient resident of the genome. Our results indicate that even an old element can contribute to genetic variation in the host genome as a natural mutator.
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Affiliation(s)
- Kohei Watanabe
- a Matsuyama High School, Higashimatsuyama 355-0018, Japan
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