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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. SCIENCE ADVANCES 2024; 10:eadn6603. [PMID: 38838146 PMCID: PMC11152119 DOI: 10.1126/sciadv.adn6603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Standard zebrafish transgenesis involves random transgene integration with resource-intensive screening. While phiC31 integrase-based attP/attB recombination has streamlined transgenesis in mice and Drosophila, validated attP-based landing sites for universal applications are lacking in zebrafish. Here, we developed phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET) as transgenesis approach, with two attP landing sites pIGLET14a and pIGLET24b from well-validated Tol2 transgenes. Both sites facilitate diverse transgenesis applications including reporters and Cre/loxP transgenes. The pIGLET14a and pIGLET24b landing sites consistently yield 25 to 50% germline transmission, substantially reducing the resources needed for transgenic line generation. Transgenesis into these sites enables reproducible expression patterns in F0 zebrafish embryos for enhancer discovery and testing of gene regulatory variants. Together, our new landing sites streamline targeted, reproducible zebrafish transgenesis as a robust platform for various applications while minimizing the workload for generating transgenic lines.
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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
| | - 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
| | - Raymundo Lerma
- 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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2
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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570868. [PMID: 38106217 PMCID: PMC10723424 DOI: 10.1101/2023.12.08.570868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Standard methods for transgenesis in zebrafish depend on random transgene integration into the genome followed by resource-intensive screening and validation. Targeted vector integration into validated genomic loci using phiC31 integrase-based attP/attB recombination has transformed mouse and Drosophila transgenesis. However, while the phiC31 system functions in zebrafish, validated loci carrying attP-based landing or safe harbor sites suitable for universal transgenesis applications in zebrafish have not been established. Here, using CRISPR-Cas9, we converted two well-validated single insertion Tol2-based zebrafish transgenes with long-standing genetic stability into two attP landing sites, called phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET). Generating fluorescent reporters, loxP-based Switch lines, CreERT2 drivers, and gene-regulatory variant reporters in the pIGLET14a and pIGLET24b landing site alleles, we document their suitability for transgenesis applications across cell types and developmental stages. For both landing sites, we routinely achieve 25-50% germline transmission of targeted transgene integrations, drastically reducing the number of required animals and necessary resources to generate individual transgenic lines. We document that phiC31 integrase-based transgenesis into pIGLET14a and pIGLET24b reproducibly results in representative reporter expression patterns in injected F0 zebrafish embryos suitable for enhancer discovery and qualitative and quantitative comparison of gene-regulatory element variants. Taken together, our new phiC31 integrase-based transgene landing sites establish reproducible, targeted zebrafish transgenesis for numerous applications while greatly reducing the workload of generating new transgenic zebrafish lines.
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Affiliation(s)
- Robert L. Lalonde
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Harrison H. Wells
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - 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
| | - 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
| | - Raymundo Lerma
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, 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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3
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Chowdhury K, Lin S, Lai SL. Comparative Study in Zebrafish and Medaka Unravels the Mechanisms of Tissue Regeneration. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.783818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue regeneration has been in the spotlight of research for its fascinating nature and potential applications in human diseases. The trait of regenerative capacity occurs diversely across species and tissue contexts, while it seems to decline over evolution. Organisms with variable regenerative capacity are usually distinct in phylogeny, anatomy, and physiology. This phenomenon hinders the feasibility of studying tissue regeneration by directly comparing regenerative with non-regenerative animals, such as zebrafish (Danio rerio) and mice (Mus musculus). Medaka (Oryzias latipes) is a fish model with a complete reference genome and shares a common ancestor with zebrafish approximately 110–200 million years ago (compared to 650 million years with mice). Medaka shares similar features with zebrafish, including size, diet, organ system, gross anatomy, and living environment. However, while zebrafish regenerate almost every organ upon experimental injury, medaka shows uneven regenerative capacity. Their common and distinct biological features make them a unique platform for reciprocal analyses to understand the mechanisms of tissue regeneration. Here we summarize current knowledge about tissue regeneration in these fish models in terms of injured tissues, repairing mechanisms, available materials, and established technologies. We further highlight the concept of inter-species and inter-organ comparisons, which may reveal mechanistic insights and hint at therapeutic strategies for human diseases.
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Yang FJ, Chen CN, Chang T, Cheng TW, Chang NC, Kao CY, Lee CC, Huang YC, Hsu JC, Li J, Lu MJ, Chan SP, Wang J. phiC31 integrase for recombination mediated single copy insertion and genome manipulation in C. elegans. Genetics 2021; 220:6428549. [PMID: 34791215 DOI: 10.1093/genetics/iyab206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 11/02/2021] [Indexed: 11/14/2022] Open
Abstract
C. elegans benefits from a large set of tools for genome manipulation. Yet, the precise single-copy insertion of very large DNA constructs (>10 kb) and the generation of inversions are still challenging. Here, we adapted the phiC31 integrase system for C. elegans. We generated an integrated phiC31 integrase expressing strain flanked by attP sites that serves as a landing pad for integration of transgenes by recombination mediated cassette exchange (RCME). This strain is unc-119(-) so RMCE integrants can be produced simply by injection of a plasmid carrying attB sites flanking unc-119(+) and the gene(s) of interest. Additionally, phiC31 integrase is removed concomitantly with integration, eliminating the need to outcross away the integrase. Integrations were obtained for insert sizes up to ∼33.4 kb. Taking advantage of this integration method we establish a dual color fluorescent operon reporter system able to study post-transcriptional regulation of mRNA. Last, we show that large chromosomal segments can be inverted using phiC31 integrase. Thus, the phiC31 integrase system should be a useful addition to the C. elegans toolkit.
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Affiliation(s)
- Fang-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chiao-Nung Chen
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tiffany Chang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Ting-Wei Cheng
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ni-Chen Chang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Yi Kao
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Chi Lee
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ching Huang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jung-Chen Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jengyi Li
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Meiyeh J Lu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shih-Peng Chan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
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Matinyan N, Karkhanis MS, Gonzalez Y, Jain A, Saltzman A, Malovannaya A, Sarrion-Perdigones A, Dierick HA, Venken KJT. Multiplexed drug-based selection and counterselection genetic manipulations in Drosophila. Cell Rep 2021; 36:109700. [PMID: 34525356 PMCID: PMC8480232 DOI: 10.1016/j.celrep.2021.109700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/10/2021] [Accepted: 08/20/2021] [Indexed: 01/27/2023] Open
Abstract
The power of Drosophila melanogaster as a model system relies on tractable germline genetic manipulations. Despite Drosophila's expansive genetics toolbox, such manipulations are still accomplished one change at a time and depend predominantly on phenotypic screening. We describe a drug-based genetic platform consisting of four selection and two counterselection markers, eliminating the need to screen for modified progeny. These markers work reliably individually or in combination to produce specific genetic outcomes. We demonstrate three example applications of multiplexed drug-based genetics by generating (1) transgenic animals, expressing both components of binary overexpression systems in a single transgenesis step; (2) dual selectable and counterselectable balancer chromosomes; and (3) selectable, fluorescently tagged P[acman] bacterial artificial chromosome (BAC) strains. We perform immunoprecipitation followed by proteomic analysis on one tagged BAC line, demonstrating our platform's applicability to biological discovery. Lastly, we provide a plasmid library resource to facilitate custom transgene design and technology transfer to other model systems.
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Affiliation(s)
- Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mansi S Karkhanis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander Saltzman
- Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Herman A Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX 77030, USA.
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6
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Roca FJ, Whitworth LJ, Redmond S, Jones AA, Ramakrishnan L. TNF Induces Pathogenic Programmed Macrophage Necrosis in Tuberculosis through a Mitochondrial-Lysosomal-Endoplasmic Reticulum Circuit. Cell 2019; 178:1344-1361.e11. [PMID: 31474371 PMCID: PMC6736209 DOI: 10.1016/j.cell.2019.08.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/15/2019] [Accepted: 08/02/2019] [Indexed: 01/07/2023]
Abstract
Necrosis of infected macrophages constitutes a critical pathogenetic event in tuberculosis by releasing mycobacteria into the growth-permissive extracellular environment. In zebrafish infected with Mycobacterium marinum or Mycobacterium tuberculosis, excess tumor necrosis factor triggers programmed necrosis of infected macrophages through the production of mitochondrial reactive oxygen species (ROS) and the participation of cyclophilin D, a component of the mitochondrial permeability transition pore. Here, we show that this necrosis pathway is not mitochondrion-intrinsic but results from an inter-organellar circuit initiating and culminating in the mitochondrion. Mitochondrial ROS induce production of lysosomal ceramide that ultimately activates the cytosolic protein BAX. BAX promotes calcium flow from the endoplasmic reticulum into the mitochondrion through ryanodine receptors, and the resultant mitochondrial calcium overload triggers cyclophilin-D-mediated necrosis. We identify ryanodine receptors and plasma membrane L-type calcium channels as druggable targets to intercept mitochondrial calcium overload and necrosis of mycobacterium-infected zebrafish and human macrophages. TNF induces mitochondrial ROS to cause necrosis of mycobacterium-infected macrophages Mitochondrial ROS activate lysosomal enzymes that lead to BAX activation BAX activates ER ryanodine receptors to cause Ca2+ flow into the mitochondrion Drugs preventing mitochondrial Ca2+ overload prevent pathogenic macrophage necrosis in TB
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Affiliation(s)
- Francisco J Roca
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, UK.
| | - Laura J Whitworth
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, UK
| | - Sarah Redmond
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, UK; Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Ana A Jones
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, UK
| | - Lalita Ramakrishnan
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, UK; Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
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7
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Wagner N, Norlin N, Gierten J, de Medeiros G, Balázs B, Wittbrodt J, Hufnagel L, Prevedel R. Instantaneous isotropic volumetric imaging of fast biological processes. Nat Methods 2019; 16:497-500. [PMID: 31036959 DOI: 10.1038/s41592-019-0393-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/05/2019] [Indexed: 11/09/2022]
Abstract
To capture highly dynamic biological processes at cellular resolution is a recurring challenge in biology. Here we show that combining selective-volume illumination with simultaneous acquisition of orthogonal light fields yields three-dimensional images with high, isotropic spatial resolution and a significant reduction of reconstruction artefacts, thereby overcoming current limitations of light-field microscopy implementations. We demonstrate medaka heart and blood flow imaging at single-cell resolution and free of motion artefacts at volume rates of up to 200 Hz.
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Affiliation(s)
- Nils Wagner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nils Norlin
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Gustavo de Medeiros
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Bálint Balázs
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Lars Hufnagel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy.
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8
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Knickmeyer MD, Mateo JL, Eckert P, Roussa E, Rahhal B, Zuniga A, Krieglstein K, Wittbrodt J, Heermann S. TGFβ-facilitated optic fissure fusion and the role of bone morphogenetic protein antagonism. Open Biol 2019; 8:rsob.170134. [PMID: 29593116 PMCID: PMC5881030 DOI: 10.1098/rsob.170134] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 03/02/2018] [Indexed: 12/25/2022] Open
Abstract
The optic fissure is a transient gap in the developing vertebrate eye, which must be closed as development proceeds. A persisting optic fissure, coloboma, is a major cause for blindness in children. Although many genes have been linked to coloboma, the process of optic fissure fusion is still little appreciated, especially on a molecular level. We identified a coloboma in mice with a targeted inactivation of transforming growth factor β2 (TGFβ2). Notably, here the optic fissure margins must have touched, however failed to fuse. Transcriptomic analyses indicated an effect on remodelling of the extracellular matrix (ECM) as an underlying mechanism. TGFβ signalling is well known for its effect on ECM remodelling, but it is at the same time often inhibited by bone morphogenetic protein (BMP) signalling. Notably, we also identified two BMP antagonists among the downregulated genes. For further functional analyses we made use of zebrafish, in which we found TGFβ ligands expressed in the developing eye, and the ligand binding receptor in the optic fissure margins where we also found active TGFβ signalling and, notably, also gremlin 2b (grem2b) and follistatin a (fsta), homologues of the regulated BMP antagonists. We hypothesized that TGFβ is locally inducing expression of BMP antagonists within the margins to relieve the inhibition from its regulatory capacity regarding ECM remodelling. We tested our hypothesis and found that induced BMP expression is sufficient to inhibit optic fissure fusion, resulting in coloboma. Our findings can likely be applied also to other fusion processes, especially when TGFβ signalling or BMP antagonism is involved, as in fusion processes during orofacial development.
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Affiliation(s)
- Max D Knickmeyer
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, Freiburg D-79104, Germany
| | - Juan L Mateo
- Departamento de Informática, Universidad de Oviedo, Jesús Arias de Velasco, Oviedo 33005, Spain
| | - Priska Eckert
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, Freiburg D-79104, Germany
| | - Eleni Roussa
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
| | - Belal Rahhal
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
| | - Aimee Zuniga
- Developmental Genetics, University of Basel Medical School, Basel CH-4058, Switzerland
| | - Kerstin Krieglstein
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
| | | | - Stephan Heermann
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
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9
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A Collection of Transgenic Medaka Strains for Efficient Site-Directed Transgenesis Mediated by phiC31 Integrase. G3-GENES GENOMES GENETICS 2018; 8:2585-2593. [PMID: 29848622 PMCID: PMC6071608 DOI: 10.1534/g3.118.200130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genetic analysis is facilitated by the efficient production of transgenic strains expressing a DNA of interest as a single copy at a designated chromosomal location. However, technical progress toward this goal in medaka fish (Oryzias latipes), a vertebrate model organism, has been slow. It is well known that phiC31 integrase enables efficient site-directed transgenesis by catalyzing the recombination of an attP DNA motif in a host genome with an attB motif in a targeting vector. This system was pioneered in medaka using the Sleeping Beauty transposon system, and the attP site was established at three chromosomal locations. However, this number appeared insufficient with regard to genetic linkage between the attP-landing site and a genetically modified locus of interest. Here, to establish a collection of transgenic strains of medaka, we introduced an attP motif into the medaka genome using the Ac/Ds maize transposon system and established 12 independent transgenic strains harboring a single copy of the attP motif in at least 11 of the 24 medaka chromosomes. We designed an attB-targeting vector that was integrated efficiently and precisely into the attP-landing site, and with which the DNA of interest was efficiently transmitted to germline cells. Extraneous sequences in the integrants derived from the bacterial backbone of the attB-targeting vector as well as a transgenic fluorescence marker present in the attP-landing site were removable through flippase-mediated recombination. Further, an advanced targeting vector with a heart-specific recombination marker served as a useful tool for easily screening phiC31 integrase-mediated recombinant G0 embryos, leading to the efficient establishment of transgenic strains. Thus, our resources advance genetic research in medaka.
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10
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Sekhavati MH, Hosseini SM, Tahmoorespur M, Ghaedi K, Jafarpour F, Hajian M, Dormiani K, Nasr-Esfahani MH. PhiC31-based Site-Specific Transgenesis System for Production of Transgenic Bovine Embryos by Somatic Cell Nuclear Transfer and Intracytoplasmic Sperm Injection. CELL JOURNAL 2018; 20:98-107. [PMID: 29308625 PMCID: PMC5759686 DOI: 10.22074/cellj.2018.4385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 03/01/2017] [Indexed: 01/10/2023]
Abstract
OBJECTIVES The Streptomyces phage phiC31 integrase offers a sequence-specific method of transgenesis with a robust long-term gene expression. PhiC31 has been successfully developed in a variety of tissues and organs for purpose of in vivo gene therapy. The objective of the present experiment was to evaluate PhiC31-based site-specific transgenesis system for production of transgenic bovine embryos by somatic cell nuclear transfer and intracytoplasmic sperm injection. MATERIALS AND METHODS In this experimental study, the application of phiC31 integrase system was evaluated for generating transgenic bovine embryos by somatic cell nuclear transfer (SCNT) and sperm mediated gene transfer (SMGT) approaches. RESULTS PhiC31 integrase mRNA and protein was produced in vitro and their functionality was confirmed. Seven phiC31 recognizable bovine pseudo attachment sites of phage (attP) sites were considered for evaluation of site specific recombination. The accuracy of these sites was validated in phic31 targeted bovine fibroblasts using polymerase chain reaction (PCR) and sequencing. The efficiency and site-specificity of phiC31 integrase system was also confirmed in generated transgenic bovine embryo which successfully obtained using SCNT and SMGT technique. CONCLUSIONS The results showed that both SMGT and SCNT-derived embryos were enhanced green fluorescent protein (EGFP) positive and phiC31 integrase could recombine the reporter gene in a site specific manner. These results demonstrate that attP site can be used as a proper location to conduct site directed transgenesis in both mammalian cells and embryos in phiC31 integrase system when even combinaed to SCNT and intracytoplasmic sperm injection (ICSI) method.
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Affiliation(s)
| | - Sayed Morteza Hosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | | | - Kamran Ghaedi
- Department of Biology, Facualty of Sciences, Uneversity of Isfahan, Isfahan, Iran
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Farnoosh Jafarpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mehdi Hajian
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kyanoosh Dormiani
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossain Nasr-Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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11
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Cheung NKM, Nakamura R, Uno A, Kumagai M, Fukushima HS, Morishita S, Takeda H. Unlinking the methylome pattern from nucleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish. PLoS Genet 2017; 13:e1007123. [PMID: 29267279 PMCID: PMC5755920 DOI: 10.1371/journal.pgen.1007123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/05/2018] [Accepted: 11/23/2017] [Indexed: 11/17/2022] Open
Abstract
The heavily methylated vertebrate genomes are punctuated by stretches of poorly methylated DNA sequences that usually mark gene regulatory regions. It is known that the methylation state of these regions confers transcriptional control over their associated genes. Given its governance on the transcriptome, cellular functions and identity, genome-wide DNA methylation pattern is tightly regulated and evidently predefined. However, how is the methylation pattern determined in vivo remains enigmatic. Based on in silico and in vitro evidence, recent studies proposed that the regional hypomethylated state is primarily determined by local DNA sequence, e.g., high CpG density and presence of specific transcription factor binding sites. Nonetheless, the dependency of DNA methylation on nucleotide sequence has not been carefully validated in vertebrates in vivo. Herein, with the use of medaka (Oryzias latipes) as a model, the sequence dependency of DNA methylation was intensively tested in vivo. Our statistical modeling confirmed the strong statistical association between nucleotide sequence pattern and methylation state in the medaka genome. However, by manipulating the methylation state of a number of genomic sequences and reintegrating them into medaka embryos, we demonstrated that artificially conferred DNA methylation states were predominantly and robustly maintained in vivo, regardless of their sequences and endogenous states. This feature was also observed in the medaka transgene that had passed across generations. Thus, despite the observed statistical association, nucleotide sequence was unable to autonomously determine its own methylation state in medaka in vivo. Our results apparently argue against the notion of the governance on the DNA methylation by nucleotide sequence, but instead suggest the involvement of other epigenetic factors in defining and maintaining the DNA methylation landscape. Further investigation in other vertebrate models in vivo will be needed for the generalization of our observations made in medaka. The genomes of vertebrate animals are naturally and extensively modified by methylation. The DNA methylation is essential to normal functions of cells, hence the whole animal, since it governs gene expression. Defects in the establishment and maintenance of proper methylation pattern are commonly associated with various developmental abnormalities and diseases. How exactly is the normal pattern defined in vertebrate animals is not fully understood, but recent researches with computational analyses and cultured cells suggested that DNA sequence is a primary determinant of the methylation pattern. This study encompasses the first experiments that rigorously test this notion in whole animal (medaka fish). In statistical sense, we observed the very strong correlation between DNA sequence and methylation state. However, by introducing unmethylated and artificially methylated native genomic DNA sequences into the genome, we demonstrated that the artificially conferred methylation states were robustly maintained in the animal, independent of the sequence and native state. Our results thus demonstrate that genome-wide DNA methylation pattern is not autonomously determined by the DNA sequence, which underpins the vital role of DNA methylation pattern as a core epigenetic element.
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Affiliation(s)
- Napo K M Cheung
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Uno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Japan
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12
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Tonelli FMP, Lacerda SMSN, Tonelli FCP, Costa GMJ, de França LR, Resende RR. Progress and biotechnological prospects in fish transgenesis. Biotechnol Adv 2017; 35:832-844. [PMID: 28602961 DOI: 10.1016/j.biotechadv.2017.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/04/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022]
Abstract
The history of transgenesis is marked by milestones such as the development of cellular transdifferentiation, recombinant DNA, genetic modification of target cells, and finally, the generation of simpler genetically modified organisms (e.g. bacteria and mice). The first transgenic fish was developed in 1984, and since then, continuing technological advancements to improve gene transfer have led to more rapid, accurate, and efficient generation of transgenic animals. Among the established methods are microinjection, electroporation, lipofection, viral vectors, and gene targeting. Here, we review the history of animal transgenesis, with an emphasis on fish, in conjunction with major developments in genetic engineering over the past few decades. Importantly, spermatogonial stem cell modification and transplantation are two common techniques capable of revolutionizing the generation of transgenic fish. Furthermore, we discuss recent progress and future biotechnological prospects of fish transgenesis, which has strong applications for the aquaculture industry. Indeed, some transgenic fish are already available in the current market, validating continued efforts to improve economically important species with biotechnological advancements.
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Affiliation(s)
- Fernanda M P Tonelli
- Laboratório de Sinalização Celular e Nanobiotecnologia, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Instituto Nanocell, Divinópolis, MG, Brazil
| | - Samyra M S N Lacerda
- Laboratório de Biologia Celular, Departamento de Morfologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávia C P Tonelli
- Laboratório de Sinalização Celular e Nanobiotecnologia, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme M J Costa
- Laboratório de Biologia Celular, Departamento de Morfologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiz Renato de França
- Laboratório de Biologia Celular, Departamento de Morfologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil.
| | - Rodrigo R Resende
- Laboratório de Sinalização Celular e Nanobiotecnologia, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Instituto Nanocell, Divinópolis, MG, Brazil.
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13
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Yu T, Winkler C. Drug Treatment and In Vivo Imaging of Osteoblast-Osteoclast Interactions in a Medaka Fish Osteoporosis Model. J Vis Exp 2017. [PMID: 28117826 DOI: 10.3791/55025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bone-forming osteoblasts interact with bone-resorbing osteoclasts to coordinate the turnover of bone matrix and to control skeletal homeostasis. Medaka and zebrafish larvae are widely used to analyze the behavior of bone cells during bone formation, degeneration, and repair. Their optical clarity allows the visualization of fluorescently labeled bone cells and fluorescent dyes bound to the mineralized skeletal matrix. Our lab has generated transgenic medaka fish that express the osteoclast-inducing factor Receptor Activator of Nuclear-factor κB Ligand (RANKL) under the control of a heat shock-inducible promoter. Ectopic expression of RANKL results in the excess formation of activated osteoclasts, which can be visualized in reporter lines with nlGFP expression under the control of the cathepsin K (ctsk) promoter. RANKL induction and ectopic osteoclast formation leads to severe osteoporosis-like phenotypes. Compound transgenic medaka lines that express ctsk:nlGFP in osteoclasts, as well as mCherry under the control of the osterix (osx) promoter in premature osteoblasts, can be used to study the interaction of both cell types. This facilitates the in vivo observation of cellular behavior under conditions of bone degeneration and repair. Here, we describe the use of this system to test a drug commonly used in human osteoporosis therapy and describe a protocol for live imaging. The medaka model complements studies in cell culture and mice, and offers a novel system for the in vivo analysis of drug action in the skeletal system.
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Affiliation(s)
- Tingsheng Yu
- Department of Biological Sciences, National University of Singapore; NUS Centre for Bioimaging Sciences (CBIS), National University of Singapore
| | - Christoph Winkler
- Department of Biological Sciences, National University of Singapore; NUS Centre for Bioimaging Sciences (CBIS), National University of Singapore;
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14
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Felker A, Mosimann C. Contemporary zebrafish transgenesis with Tol2 and application for Cre/lox recombination experiments. Methods Cell Biol 2016; 135:219-44. [PMID: 27443928 DOI: 10.1016/bs.mcb.2016.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Spatiotemporal transgene regulation by transgenic DNA recombinases is a central tool for reverse genetics in multicellular organisms, with excellent applications for misexpression and lineage tracing experiments. One of the most widespread technologies for this purpose is Cre recombinase-controlled lox site recombination that is attracting increasing interest in the zebrafish field. Tol2-mediated zebrafish transgenesis provides a stable platform to integrate lox cassette transgenes, while the amenability of the zebrafish embryo to drug treatments makes the model an ideal candidate for tamoxifen-inducible CreERT2 experiments. In addition, advanced transgenesis technologies such as phiC31 or CRISPR-Cas9-based knock-ins are even further promoting zebrafish transgenesis for Cre/lox applications. In this chapter, we will first introduce the basics of Cre/lox methodology, CreERT2 regulation by tamoxifen, as well as the utility of Tol2 and other contemporary transgenesis techniques for Cre/lox experiments. We will then outline in detail practical experimental steps for efficient transgenesis toward the creation of single-insertion transgenes and will introduce protocols for 4-hydroxytamoxifen-mediated CreERT2 induction to perform spatiotemporal lox transgene regulation experiments in zebrafish embryos. Last, we will discuss advanced experimental applications of Cre/lox beyond traditional lineage tracing approaches.
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Affiliation(s)
- A Felker
- University of Zürich, Zürich, Switzerland
| | - C Mosimann
- University of Zürich, Zürich, Switzerland
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15
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Mayrhofer M, Mione M. The Toolbox for Conditional Zebrafish Cancer Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:21-59. [PMID: 27165348 DOI: 10.1007/978-3-319-30654-4_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here we describe the conditional zebrafish cancer toolbox, which allows for fine control of the expression of oncogenes or downregulation of tumor suppressors at the spatial and temporal level. Methods such as the Gal4/UAS or the Cre/lox systems paved the way to the development of elegant tumor models, which are now being used to study cancer cell biology, clonal evolution, identification of cancer stem cells and anti-cancer drug screening. Combination of these tools, as well as novel developments such as the promising genome editing system through CRISPR/Cas9 and clever application of light reactive proteins will enable the development of even more sophisticated zebrafish cancer models. Here, we introduce this growing toolbox of conditional transgenic approaches, discuss its current application in zebrafish cancer models and provide an outlook on future perspectives.
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Affiliation(s)
- Marie Mayrhofer
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
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16
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Abstract
The Japanese medaka, Oryzias latipes, is a vertebrate teleost model with a long history of genetic research. A number of unique features and established resources distinguish medaka from other vertebrate model systems. A large number of laboratory strains from different locations are available. Due to a high tolerance to inbreeding, many highly inbred strains have been established, thus providing a rich resource for genetic studies. Furthermore, closely related species native to different habitats in Southeast Asia permit comparative evolutionary studies. The transparency of embryos, larvae, and juveniles allows a detailed in vivo analysis of development. New tools to study diverse aspects of medaka biology are constantly being generated. Thus, medaka has become an important vertebrate model organism to study development, behavior, and physiology. In this review, we provide a comprehensive overview of established genetic and molecular-genetic tools that render medaka fish a full-fledged vertebrate system.
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17
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Alonso-Barba JI, Rahman RU, Wittbrodt J, Mateo JL. MEPD: medaka expression pattern database, genes and more. Nucleic Acids Res 2015; 44:D819-21. [PMID: 26450962 PMCID: PMC4702773 DOI: 10.1093/nar/gkv1029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
The Medaka Expression Pattern Database (MEPD; http://mepd.cos.uni-heidelberg.de/) is designed as a repository of medaka expression data for the scientific community. In this update we present two main improvements. First, we have changed the previous clone-centric view for in situ data to a gene-centric view. This is possible because now we have linked all the data present in MEPD to the medaka gene annotation in ENSEMBL. In addition, we have also connected the medaka genes in MEPD to their corresponding orthologous gene in zebrafish, again using the ENSEMBL database. Based on this, we provide a link to the Zebrafish Model Organism Database (ZFIN) to allow researches to compare expression data between these two fish model organisms. As a second major improvement, we have modified the design of the database to enable it to host regulatory elements, promoters or enhancers, expression patterns in addition to gene expression. The combination of gene expression, by traditional in situ, and regulatory element expression, typically by fluorescence reporter gene, within the same platform assures consistency in terms of annotation. In our opinion, this will allow researchers to uncover new insights between the expression domain of genes and their regulatory landscape.
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Affiliation(s)
- Juan I Alonso-Barba
- Department of Computing Systems, University of Castilla-La Mancha, Albacete, 02071, Spain
| | - Raza-Ur Rahman
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Juan L Mateo
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
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18
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The integration characteristics of the exogenous growth hormone gene in a transgenic common carp (Cyprinus carpio L.) with fast-growth performance. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-015-0893-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Bhatia S, Gordon CT, Foster RG, Melin L, Abadie V, Baujat G, Vazquez MP, Amiel J, Lyonnet S, van Heyningen V, Kleinjan DA. Functional assessment of disease-associated regulatory variants in vivo using a versatile dual colour transgenesis strategy in zebrafish. PLoS Genet 2015; 11:e1005193. [PMID: 26030420 PMCID: PMC4452300 DOI: 10.1371/journal.pgen.1005193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/02/2015] [Indexed: 11/26/2022] Open
Abstract
Disruption of gene regulation by sequence variation in non-coding regions of the genome is now recognised as a significant cause of human disease and disease susceptibility. Sequence variants in cis-regulatory elements (CREs), the primary determinants of spatio-temporal gene regulation, can alter transcription factor binding sites. While technological advances have led to easy identification of disease-associated CRE variants, robust methods for discerning functional CRE variants from background variation are lacking. Here we describe an efficient dual-colour reporter transgenesis approach in zebrafish, simultaneously allowing detailed in vivo comparison of spatio-temporal differences in regulatory activity between putative CRE variants and assessment of altered transcription factor binding potential of the variant. We validate the method on known disease-associated elements regulating SHH, PAX6 and IRF6 and subsequently characterise novel, ultra-long-range SOX9 enhancers implicated in the craniofacial abnormality Pierre Robin Sequence. The method provides a highly cost-effective, fast and robust approach for simultaneously unravelling in a single assay whether, where and when in embryonic development a disease-associated CRE-variant is affecting its regulatory function. Cis-regulatory elements (CREs) play a vital role in gene regulation by providing spatial and temporal specificity to the expression of their target genes. Understanding how these regions of the genome work is of vital importance for human health as it has been demonstrated that genetic changes in these regions can result in incorrect gene expression, leading to a variety of human diseases. Functional characterization of putative CREs and the effects of mutations on their activity is currently a major bottleneck in many studies towards understanding the causes and mechanisms of disease and disease susceptibility. We describe a robust in-vivo approach using dual-colour reporter transgenesis in zebrafish for unambiguous assessment of the effects of disease-associated CRE mutations on CRE activity during the entire time-course of embryonic development. The highly efficient, cost-effective and modular design of the assay allows rapid analysis of several CRE-variants in parallel. We illustrate the robustness of our approach using examples of CRE-variants associated with a broad spectrum of genetic diseases including brain, limb, eye and jaw disorders. In a single assay the method can address where and when in development the CRE variant affects its activity, what potential target genes are misregulated by the change and what upstream trans-acting factors are likely to mediate this effect.
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Affiliation(s)
- Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (SB); (VvH); (DAK)
| | - Christopher T. Gordon
- INSERM U781, Hôpital Necker-Enfants Malades and Université Paris Descartes-Sorbonne Paris Cité, Institute Imagine, Paris, France
| | - Robert G. Foster
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Lucie Melin
- INSERM U781, Hôpital Necker-Enfants Malades and Université Paris Descartes-Sorbonne Paris Cité, Institute Imagine, Paris, France
| | - Véronique Abadie
- Service de Pédiatrie Générale, Université Paris Descartes, Hôpital Necker-Enfants Malades, Paris, France
| | - Geneviève Baujat
- Departement de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris France
| | - Marie-Paule Vazquez
- Service de Chirurgie Maxillo-Faciale et Plastique, CRMR des Malformations de la Face et de la Cavité Buccale, Hôpital Necker-Enfants Malades, Paris, France
| | - Jeanne Amiel
- INSERM U781, Hôpital Necker-Enfants Malades and Université Paris Descartes-Sorbonne Paris Cité, Institute Imagine, Paris, France
- Departement de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris France
| | - Stanislas Lyonnet
- INSERM U781, Hôpital Necker-Enfants Malades and Université Paris Descartes-Sorbonne Paris Cité, Institute Imagine, Paris, France
- Departement de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris France
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (SB); (VvH); (DAK)
| | - Dirk A. Kleinjan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (SB); (VvH); (DAK)
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20
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Abstract
The use of transgenics in fish is a relatively recent development for advancing understanding of genetic mechanisms and developmental processes, improving aquaculture, and for pharmaceutical discovery. Transgenic fish have also been applied in ecotoxicology where they have the potential to provide more advanced and integrated systems for assessing health impacts of chemicals. The zebrafish (Daniorerio) is the most popular fish for transgenic models, for reasons including their high fecundity, transparency of their embryos, rapid organogenesis and availability of extensive genetic resources. The most commonly used technique for producing transgenic zebrafish is via microinjection of transgenes into fertilized eggs. Transposon and meganuclease have become the most reliable methods for insertion of the genetic construct in the production of stable transgenic fish lines. The GAL4-UAS system, where GAL4 is placed under the control of a desired promoter and UAS is fused with a fluorescent marker, has greatly enhanced model development for studies in ecotoxicology. Transgenic fish have been developed to study for the effects of heavy metal toxicity (via heat-shock protein genes), oxidative stress (via an electrophile-responsive element), for various organic chemicals acting through the aryl hydrocarbon receptor, thyroid and glucocorticoid response pathways, and estrogenicity. These models vary in their sensitivity with only very few able to detect responses for environmentally relevant exposures. Nevertheless, the potential of these systems for analyses of chemical effects in real time and across multiple targets in intact organisms is considerable. Here we illustrate the techniques used for generating transgenic zebrafish and assess progress in the development and application of transgenic fish (principally zebrafish) for studies in environmental toxicology. We further provide a viewpoint on future development opportunities.
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Affiliation(s)
- Okhyun Lee
- Biosciences, College of Life & Environmental Sciences, University of Exeter , Exeter, Devon , UK
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21
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Auer TO, Del Bene F. CRISPR/Cas9 and TALEN-mediated knock-in approaches in zebrafish. Methods 2014; 69:142-50. [DOI: 10.1016/j.ymeth.2014.03.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/07/2014] [Accepted: 03/24/2014] [Indexed: 12/26/2022] Open
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22
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Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
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23
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Shakes LA, Wolf HM, Norford DC, Grant DJ, Chatterjee PK. Harnessing mobile genetic elements to explore gene regulation. Mob Genet Elements 2014; 4:e29759. [PMID: 25054085 PMCID: PMC4092005 DOI: 10.4161/mge.29759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/20/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
Sequences that regulate expression of a gene in cis but are located at large distances along the DNA from the gene, as found with most developmentally regulated genes in higher vertebrates, are difficult to identify if those sequences are not conserved across species. Mutating suspected gene-regulatory sequences to alter expression then becomes a hit-or-miss affair. The relaxed specificity of transposon insertions offers an opportunity to develop alternate strategies, to scan in an unbiased manner, pieces of chromosomal DNA cloned in BACs for transcription enhancing elements. This article illustrates how insertions of Tn10 with enhancer-traps into BAC DNA containing the gene, and its germ-line expression in zebrafish, have identified distal regulatory elements functionally. Transposition of Tn10 first introduces the enhancer-trap with a loxP site randomly into BAC DNA. Cre-recombination between the inserted loxP and the loxP endogenous to a BAC-end positions the enhancer-trap to the newly created truncated end of BAC DNA. The procedure generates a library of integration-ready enhancer-trap BACs with progressive truncations from an end in a single experiment. Individual enhancer-trap BACs from the library can be evaluated functionally in zebrafish or mice. Furthermore, the ability to readily alter sequences in a small transposon plasmid containing a regulatory domain of the gene allows re-introduction of altered parts of a BAC back into itself. It serves as a useful strategy to functionally dissect multiple discontinuous regulatory domains of a gene quickly. These methodologies have been successfully used in identifying novel regulatory domains of the Amyloid Precursor Protein (appb) gene in zebrafish, and provided important clues for regulation of the gene in humans.
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Affiliation(s)
- Leighcraft A Shakes
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Hope M Wolf
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Derek C Norford
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Delores J Grant
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Pradeep K Chatterjee
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
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24
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Roberts JA, Miguel-Escalada I, Slovik KJ, Walsh KT, Hadzhiev Y, Sanges R, Stupka E, Marsh EK, Balciuniene J, Balciunas D, Müller F. Targeted transgene integration overcomes variability of position effects in zebrafish. Development 2014; 141:715-24. [PMID: 24449846 DOI: 10.1242/dev.100347] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Zebrafish transgenesis is increasingly popular owing to the optical transparency and external development of embryos, which provide a scalable vertebrate model for in vivo experimentation. The ability to express transgenes in a tightly controlled spatio-temporal pattern is an important prerequisite for exploitation of zebrafish in a wide range of biomedical applications. However, conventional transgenesis methods are plagued by position effects: the regulatory environment of genomic integration sites leads to variation of expression patterns of transgenes driven by engineered cis-regulatory modules. This limitation represents a bottleneck when studying the precise function of cis-regulatory modules and their subtle variants or when various effector proteins are to be expressed for labelling and manipulation of defined sets of cells. Here, we provide evidence for the efficient elimination of variability of position effects by developing a PhiC31 integrase-based targeting method. To detect targeted integration events, a simple phenotype scoring of colour change in the lens of larvae is used. We compared PhiC31-based integration and Tol2 transgenesis in the analysis of the activity of a novel conserved enhancer from the developmentally regulated neural-specific esrrga gene. Reporter expression was highly variable among independent lines generated with Tol2, whereas all lines generated with PhiC31 into a single integration site displayed nearly identical, enhancer-specific reporter expression in brain nuclei. Moreover, we demonstrate that a modified integrase system can also be used for the detection of enhancer activity in transient transgenesis. These results demonstrate the power of the PhiC31-based transgene integration for the annotation and fine analysis of transcriptional regulatory elements and it promises to be a generally desirable tool for a range of applications, which rely on highly reproducible patterns of transgene activity in zebrafish.
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Affiliation(s)
- Jennifer Anne Roberts
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
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