201
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CRISPR/Cas9-Mediated Knockin and Knockout in Zebrafish. RESEARCH AND PERSPECTIVES IN NEUROSCIENCES 2017. [DOI: 10.1007/978-3-319-60192-2_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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202
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Brockerhoff SE. Genome Editing to Study Ca 2+ Homeostasis in Zebrafish Cone Photoreceptors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1016:91-100. [PMID: 29130155 DOI: 10.1007/978-3-319-63904-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Photoreceptors are specialized sensory neurons with unique biological features. Phototransduction is well understood due in part to the exclusive expression and function of the molecular components of this cascade. Many other processes are less well understood, but also extremely important for understanding photoreceptor function and for treating disease. One example is the role of Ca2+ in the cell body and overall compartmentalization and regulation of Ca2+ within the cell. The recent development of CRISPR/Cas9 genome editing techniques has made it possible to rapidly and cheaply alter specific genes. This will help to define the biological function of elusive processes that have been more challenging to study. CRISPR/Cas9 has been optimized in many systems including zebrafish, which already has some distinct advantages for studying photoreceptor biology and function. These new genome editing technologies and the continued use of the zebrafish model system will help advance our understanding of important understudied aspects of photoreceptor biology.
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Affiliation(s)
- Susan E Brockerhoff
- Departments of Biochemistry and Ophthalmology, University of Washington, UW Medicine, 750 Republican St, Box 358058, Seattle, WA, 98109, USA.
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203
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204
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Avagyan S, Zon LI. Fish to Learn: Insights into Blood Development and Blood Disorders from Zebrafish Hematopoiesis. Hum Gene Ther 2016; 27:287-94. [PMID: 27018965 DOI: 10.1089/hum.2016.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Since its introduction in early 1980s, the zebrafish (Danio rerio) has become an invaluable vertebrate animal model system to study many human disorders in almost all systems, from hepatic and brain pathology, to autoimmune and psychiatric disorders. Hematopoiesis between zebrafish and mammals is highly conserved, making the zebrafish an attractive model to study hematopoietic development and blood disorders. Unique attributes of the zebrafish include the ability to perform large-scale genetic and chemical screens in vivo, study development at the cellular level, and use transgenic fish to dissect mechanisms of disease or drug effects. This review summarizes major discoveries that helped define molecular control of hematopoiesis in vertebrates and specific contributions from studies in zebrafish.
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Affiliation(s)
- Serine Avagyan
- 1 Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute , Boston, Massachusetts
| | - Leonard I Zon
- 1 Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute , Boston, Massachusetts.,2 Howard Hughes Medical Institute, Harvard Stem Cell Institute , Harvard Medical School, Boston, Massachusetts.,3 Chemical Biology Program, Harvard University , Cambridge, Massachusetts
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205
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Noyes PD, Garcia GR, Tanguay RL. ZEBRAFISH AS AN IN VIVO MODEL FOR SUSTAINABLE CHEMICAL DESIGN. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2016; 18:6410-6430. [PMID: 28461781 PMCID: PMC5408959 DOI: 10.1039/c6gc02061e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Heightened public awareness about the many thousands of chemicals in use and present as persistent contaminants in the environment has increased the demand for safer chemicals and more rigorous toxicity testing. There is a growing recognition that the use of traditional test models and empirical approaches is impractical for screening for toxicity the many thousands of chemicals in the environment and the hundreds of new chemistries introduced each year. These realities coupled with the green chemistry movement have prompted efforts to implement more predictive-based approaches to evaluate chemical toxicity early in product development. While used for many years in environmental toxicology and biomedicine, zebrafish use has accelerated more recently in genetic toxicology, high throughput screening (HTS), and behavioral testing. This review describes major advances in these testing methods that have positioned the zebrafish as a highly applicable model in chemical safety evaluations and sustainable chemistry efforts. Many toxic responses have been shown to be shared among fish and mammals owing to their generally well-conserved development, cellular networks, and organ systems. These shared responses have been observed for chemicals that impair endocrine functioning, development, and reproduction, as well as those that elicit cardiotoxicity and carcinogenicity, among other diseases. HTS technologies with zebrafish enable screening large chemical libraries for bioactivity that provide opportunities for testing early in product development. A compelling attribute of the zebrafish centers on being able to characterize toxicity mechanisms across multiple levels of biological organization from the genome to receptor interactions and cellular processes leading to phenotypic changes such as developmental malformations. Finally, there is a growing recognition of the links between human and wildlife health and the need for approaches that allow for assessment of real world multi-chemical exposures. The zebrafish is poised to be an important model in bridging these two conventionally separate areas of toxicology and characterizing the biological effects of chemical mixtures that could augment its role in sustainable chemistry.
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Affiliation(s)
- Pamela D. Noyes
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Gloria R. Garcia
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
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206
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Reade A, Motta-Mena LB, Gardner KH, Stainier DY, Weiner OD, Woo S. TAEL: a zebrafish-optimized optogenetic gene expression system with fine spatial and temporal control. Development 2016; 144:345-355. [PMID: 27993986 DOI: 10.1242/dev.139238] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 11/28/2016] [Indexed: 01/27/2023]
Abstract
Here, we describe an optogenetic gene expression system optimized for use in zebrafish. This system overcomes the limitations of current inducible expression systems by enabling robust spatial and temporal regulation of gene expression in living organisms. Because existing optogenetic systems show toxicity in zebrafish, we re-engineered the blue-light-activated EL222 system for minimal toxicity while exhibiting a large range of induction, fine spatial precision and rapid kinetics. We validate several strategies to spatially restrict illumination and thus gene induction with our new TAEL (TA4-EL222) system. As a functional example, we show that TAEL is able to induce ectopic endodermal cells in the presumptive ectoderm via targeted sox32 induction. We also demonstrate that TAEL can be used to resolve multiple roles of Nodal signaling at different stages of embryonic development. Finally, we show how inducible gene editing can be achieved by combining the TAEL and CRISPR/Cas9 systems. This toolkit should be a broadly useful resource for the fish community.
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Affiliation(s)
- Anna Reade
- CVRI & Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Laura B Motta-Mena
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY 10031, USA.,Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA.,Biochemistry, Chemistry and Biology PhD Programs, Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Didier Y Stainier
- CVRI & Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.,Max Planck Institute for Heart and Lung Research, Dept. of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Orion D Weiner
- CVRI & Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stephanie Woo
- CVRI & Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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207
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Chen L, Groenewoud A, Tulotta C, Zoni E, Kruithof-de Julio M, van der Horst G, van der Pluijm G, Ewa Snaar-Jagalska B. A zebrafish xenograft model for studying human cancer stem cells in distant metastasis and therapy response. Methods Cell Biol 2016; 138:471-496. [PMID: 28129855 DOI: 10.1016/bs.mcb.2016.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lethal and incurable bone metastasis is one of the main causes of death in multiple types of cancer. A small subpopulation of cancer stem/progenitor-like cells (CSCs), also known as tumor-initiating cells from heterogenetic cancer is considered to mediate bone metastasis. Although over the past decades numerous studies have been performed in different types of cancer, it is still difficult to track small numbers of CSCs during the onset of metastasis. With use of noninvasive high-resolution imaging, transparent zebrafish embryos can be employed to dynamically visualize cancer progression and reciprocal interaction with stroma in a living organism. Recently we established a zebrafish CSC-xenograft model to visually and functionally analyze the role of CSCs and their interactions with the microenvironment at the onset of metastasis. Given the highly conserved human and zebrafish genome, transplanted human cancer cells are able to respond to zebrafish cytokines, modulate the zebrafish microenvironment, and take advantage of the zebrafish stroma during cancer progression. This chapter delineates the zebrafish CSC-xenograft model as a useful tool for both CSC biological study and anticancer drug screening.
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Affiliation(s)
- L Chen
- Leiden University, Leiden, The Netherlands
| | | | - C Tulotta
- Leiden University, Leiden, The Netherlands
| | - E Zoni
- University of Bern, Bern, Switzerland; Leiden University Medical Centre, Leiden, The Netherlands
| | - M Kruithof-de Julio
- University of Bern, Bern, Switzerland; Leiden University Medical Centre, Leiden, The Netherlands
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208
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Abstract
Iron is a crucial component of heme- and iron-sulfur clusters, involved in vital cellular functions such as oxygen transport, DNA synthesis, and respiration. Both excess and insufficient levels of iron and heme-precursors cause human disease, such as iron-deficiency anemia, hemochromatosis, and porphyrias. Hence, their levels must be tightly regulated, requiring a complex network of transporters and feedback mechanisms. The use of zebrafish to study these pathways and the underlying genetics offers many advantages, among others their optical transparency, ex-vivo development and high genetic and physiological conservations. This chapter first reviews well-established methods, such as large-scale mutagenesis screens that have led to the initial identification of a series of iron and heme transporters and the generation of a variety of mutant lines. Other widely used techniques are based on injection of RNA, including complementary morpholino knockdown and gene overexpression. In addition, we highlight several recently developed approaches, most notably endonuclease-based gene knockouts such as TALENs or the CRISPR/Cas9 system that have been used to study how loss of function can induce human disease phenocopies in zebrafish. Rescue by chemical complementation with iron-based compounds or small molecules can subsequently be used to confirm causality of the genetic defect for the observed phenotype. All together, zebrafish have proven to be - and will continue to serve as an ideal model to advance our understanding of the pathogenesis of human iron and heme-related diseases and to develop novel therapies to treat these conditions.
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Affiliation(s)
| | - Barry H. Paw
- Brigham & Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Dana-Farber Cancer Institute, Boston, MA, United States
- Boston Children’s Hospital, Boston, MA, United States
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209
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Henninger J, Santoso B, Hans S, Durand E, Moore J, Mosimann C, Brand M, Traver D, Zon L. Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development. Nat Cell Biol 2016; 19:17-27. [PMID: 27870830 DOI: 10.1038/ncb3444] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 10/27/2016] [Indexed: 12/15/2022]
Abstract
Haematopoietic stem cells (HSCs) arise in the developing aorta during embryogenesis. The number of HSC clones born has been estimated through transplantation, but experimental approaches to assess the absolute number of forming HSCs in a native setting have remained challenging. Here, we applied single-cell and clonal analysis of HSCs in zebrafish to quantify developing HSCs. Targeting creERT2 in developing cd41:eGFP+ HSCs enabled long-term assessment of their blood contribution. We also applied the Brainbow-based multicolour Zebrabow system with drl:creERT2 that is active in early haematopoiesis to induce heritable colour barcoding unique to each HSC and its progeny. Our findings reveal that approximately 21 HSC clones exist prior to HSC emergence and 30 clones are present during peak production from aortic endothelium. Our methods further reveal that stress haematopoiesis, including sublethal irradiation and transplantation, reduces clonal diversity. Our findings provide quantitative insights into the early clonal events that regulate haematopoietic development.
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Affiliation(s)
- Jonathan Henninger
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.,Biological and Biomedical Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Buyung Santoso
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Stefan Hans
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Tatzberg 47-49, 01307 Dresden, Germany
| | - Ellen Durand
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.,Biological and Biomedical Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jessica Moore
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Michael Brand
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Tatzberg 47-49, 01307 Dresden, Germany
| | - David Traver
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093-0380, USA
| | - Leonard Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.,Biological and Biomedical Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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210
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Khan AH, Bayat H, Rajabibazl M, Sabri S, Rahimpour A. Humanizing glycosylation pathways in eukaryotic expression systems. World J Microbiol Biotechnol 2016; 33:4. [DOI: 10.1007/s11274-016-2172-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 11/04/2016] [Indexed: 01/27/2023]
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211
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Lee RTH, Ng ASM, Ingham PW. Ribozyme Mediated gRNA Generation for In Vitro and In Vivo CRISPR/Cas9 Mutagenesis. PLoS One 2016; 11:e0166020. [PMID: 27832146 PMCID: PMC5104441 DOI: 10.1371/journal.pone.0166020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/21/2016] [Indexed: 12/27/2022] Open
Abstract
CRISPR/Cas9 is now regularly used for targeted mutagenesis in a wide variety of systems. Here we report the use of ribozymes for the generation of gRNAs both in vitro and in zebrafish embryos. We show that incorporation of ribozymes increases the types of promoters and number of target sites available for mutagenesis without compromising mutagenesis efficiency. We have tested this by comparing the efficiency of mutagenesis of gRNA constructs with and without ribozymes and also generated a transgenic zebrafish expressing gRNA using a heat shock promoter (RNA polymerase II-dependent promoter) that was able to induce mutagenesis of its target. Our method provides a streamlined approach to test gRNA efficiency as well as increasing the versatility of conditional gene knock out in zebrafish.
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Affiliation(s)
- Raymond Teck Ho Lee
- Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell biology, Agency of Science, Technology and Research (A-STAR), Singapore
| | - Ashley Shu Mei Ng
- Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell biology, Agency of Science, Technology and Research (A-STAR), Singapore
| | - Philip W. Ingham
- Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell biology, Agency of Science, Technology and Research (A-STAR), Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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212
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Li M, Zhao L, Page-McCaw PS, Chen W. Zebrafish Genome Engineering Using the CRISPR-Cas9 System. Trends Genet 2016; 32:815-827. [PMID: 27836208 DOI: 10.1016/j.tig.2016.10.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 12/21/2022]
Abstract
Geneticists have long sought the ability to manipulate vertebrate genomes by directly altering the information encoded in specific genes. The recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 endonuclease has the ability to bind single loci within vertebrate genomes and generate double-strand breaks (DSBs) at those sites. These DSBs induce an endogenous DSB repair response that results in small insertions or deletions at the targeted site. Alternatively, a template can be supplied, in which case homology-directed repair results in the generation of engineered alleles at the break site. These changes alter the function of the targeted gene facilitating the analysis of gene function. This tool has been widely adopted in the zebrafish model; we discuss the development of this system in the zebrafish and how it can be manipulated to facilitate genome engineering.
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Affiliation(s)
- Mingyu Li
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Liyuan Zhao
- Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Patrick S Page-McCaw
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Division of Nephrology and Hypertension, Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN.
| | - Wenbiao Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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213
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Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DYR, Seydoux G, Mohr SE, Zuber J, Perrimon N. Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet 2016; 18:24-40. [PMID: 27795562 DOI: 10.1038/nrg.2016.118] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Our understanding of the genetic mechanisms that underlie biological processes has relied extensively on loss-of-function (LOF) analyses. LOF methods target DNA, RNA or protein to reduce or to ablate gene function. By analysing the phenotypes that are caused by these perturbations the wild-type function of genes can be elucidated. Although all LOF methods reduce gene activity, the choice of approach (for example, mutagenesis, CRISPR-based gene editing, RNA interference, morpholinos or pharmacological inhibition) can have a major effect on phenotypic outcomes. Interpretation of the LOF phenotype must take into account the biological process that is targeted by each method. The practicality and efficiency of LOF methods also vary considerably between model systems. We describe parameters for choosing the optimal combination of method and system, and for interpreting phenotypes within the constraints of each method.
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Affiliation(s)
- Benjamin E Housden
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Matthew Gemberling
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 43 Ludwigstrasse, Bad Nauheim 61231, Germany
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21218, USA.,Howard Hughes Medical Institute, 725 North Wolfe Street, Baltimore, Maryland 21218, USA
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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214
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Wang X, Cai B, Zhou J, Zhu H, Niu Y, Ma B, Yu H, Lei A, Yan H, Shen Q, Shi L, Zhao X, Hua J, Huang X, Qu L, Chen Y. Disruption of FGF5 in Cashmere Goats Using CRISPR/Cas9 Results in More Secondary Hair Follicles and Longer Fibers. PLoS One 2016; 11:e0164640. [PMID: 27755602 PMCID: PMC5068700 DOI: 10.1371/journal.pone.0164640] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/28/2016] [Indexed: 11/19/2022] Open
Abstract
Precision genetic engineering accelerates the genetic improvement of livestock for agriculture and biomedicine. We have recently reported our success in producing gene-modified goats using the CRISPR/Cas9 system through microinjection of Cas9 mRNA and sgRNAs targeting the MSTN and FGF5 genes in goat embryos. By investigating the influence of gene modification on the phenotypes of Cas9-mediated goats, we herein demonstrate that the utility of this approach involving the disruption of FGF5 results in increased number of second hair follicles and enhanced fiber length in Cas9-mediated goats, suggesting more cashmere will be produced. The effects of genome modifications were characterized using H&E and immunohistochemistry staining, quantitative PCR, and western blotting techniques. These results indicated that the gene modifications induced by the disruption of FGF5 had occurred at the morphological and genetic levels. We further show that the knockout alleles were likely capable of germline transmission, which is essential for goat population expansion. These results provide sufficient evidences of the merit of using the CRISPR/Cas9 approach for the generation of gene-modified goats displaying the corresponding mutant phenotypes.
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Affiliation(s)
- Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Bei Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jiankui Zhou
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin 719000, China
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Yiyuan Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Baohua Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Honghao Yu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin 719000, China
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Anmin Lei
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin 719000, China
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Qiaoyan Shen
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Lei Shi
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin 719000, China
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Xiaoe Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Jinlian Hua
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Xingxu Huang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- * E-mail: (YC); (LQ); (XH)
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin 719000, China
- Life Science Research Center, Yulin University, Yulin 719000, China
- * E-mail: (YC); (LQ); (XH)
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- * E-mail: (YC); (LQ); (XH)
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215
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Deveau AP, Bentley VL, Berman JN. Using zebrafish models of leukemia to streamline drug screening and discovery. Exp Hematol 2016; 45:1-9. [PMID: 27720937 DOI: 10.1016/j.exphem.2016.09.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/19/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
Current treatment strategies for acute leukemias largely rely on nonspecific cytotoxic drugs that result in high therapy-related morbidity and mortality. Cost-effective, pertinent animal models are needed to link in vitro studies with the development of new therapeutic agents in clinical trials on a high-throughput scale. However, targeted therapies have had limited success moving from bench to clinic, often due to unexpected off-target effects. The zebrafish has emerged as a reliable in vivo tool for modeling human leukemia. Zebrafish genetic and xenograft models of acute leukemia provide an unprecedented opportunity to conduct rapid, phenotype-based screens. This allows for the identification of relevant therapies while simultaneously evaluating drug toxicity, thus circumventing the limitations of target-centric approaches.
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Affiliation(s)
- Adam P Deveau
- Department of Pediatrics, IWK Health Centre, Halifax, Nova Scotia, Canada
| | - Victoria L Bentley
- Undergraduate Medical Program, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason N Berman
- Department of Pediatrics, IWK Health Centre, Halifax, Nova Scotia, Canada; Departments of Microbiology and Immunology and Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.
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216
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Abstract
The recent advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated protein 9 (Cas9) system for precise genome editing has revolutionized methodologies in haematology and oncology studies. CRISPR-Cas9 technology can be used to remove and correct genes or mutations, and to introduce site-specific therapeutic genes in human cells. Inherited haematological disorders represent ideal targets for CRISPR-Cas9-mediated gene therapy. Correcting disease-causing mutations could alleviate disease-related symptoms in the near future. The CRISPR-Cas9 system is also a useful tool for delineating molecular mechanisms involving haematological malignancies. Prior to the use of CRISPR-Cas9-mediated gene correction in humans, appropriate delivery systems with higher efficiency and specificity must be identified, and ethical guidelines for applying the technology with controllable safety must be established. Here, the latest applications of CRISPR-Cas9 technology in haematological disorders, current challenges and future directions are reviewed and discussed.
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Affiliation(s)
- Han Zhang
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Centre at Houston, Houston, TX, USA
| | - Nami McCarty
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Centre at Houston, Houston, TX, USA.
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217
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Sedykh I, TeSlaa JJ, Tatarsky RL, Keller AN, Toops KA, Lakkaraju A, Nyholm MK, Wolman MA, Grinblat Y. Novel roles for the radial spoke head protein 9 in neural and neurosensory cilia. Sci Rep 2016; 6:34437. [PMID: 27687975 PMCID: PMC5043386 DOI: 10.1038/srep34437] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 09/14/2016] [Indexed: 01/25/2023] Open
Abstract
Cilia are cell surface organelles with key roles in a range of cellular processes, including generation of fluid flow by motile cilia. The axonemes of motile cilia and immotile kinocilia contain 9 peripheral microtubule doublets, a central microtubule pair, and 9 connecting radial spokes. Aberrant radial spoke components RSPH1, 3, 4a and 9 have been linked with primary ciliary dyskinesia (PCD), a disorder characterized by ciliary dysmotility; yet, radial spoke functions remain unclear. Here we show that zebrafish Rsph9 is expressed in cells bearing motile cilia and kinocilia, and localizes to both 9 + 2 and 9 + 0 ciliary axonemes. Using CRISPR mutagenesis, we show that rsph9 is required for motility of presumptive 9 + 2 olfactory cilia and, unexpectedly, 9 + 0 neural cilia. rsph9 is also required for the structural integrity of 9 + 2 and 9 + 0 ciliary axonemes. rsph9 mutant larvae exhibit reduced initiation of the acoustic startle response consistent with hearing impairment, suggesting a novel role for Rsph9 in the kinocilia of the inner ear and/or lateral line neuromasts. These data identify novel roles for Rsph9 in 9 + 0 motile cilia and in sensory kinocilia, and establish a useful zebrafish PCD model.
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Affiliation(s)
- Irina Sedykh
- Department of Zoology, University of Wisconsin, Madison, WI, 53706, USA.,Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Jessica J TeSlaa
- Department of Zoology, University of Wisconsin, Madison, WI, 53706, USA.,Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA.,Cellular and Molecular Biology Training Program, University of Wisconsin, Madison, WI, 53706, USA
| | - Rose L Tatarsky
- Department of Zoology, University of Wisconsin, Madison, WI, 53706, USA.,Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Abigail N Keller
- Department of Zoology, University of Wisconsin, Madison, WI, 53706, USA.,Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Kimberly A Toops
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.,McPherson Eye Research Institute, University of Wisconsin, Madison, WI, 53706, USA
| | - Aparna Lakkaraju
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.,McPherson Eye Research Institute, University of Wisconsin, Madison, WI, 53706, USA
| | - Molly K Nyholm
- Department of Zoology, University of Wisconsin, Madison, WI, 53706, USA.,Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Marc A Wolman
- Department of Zoology, University of Wisconsin, Madison, WI, 53706, USA
| | - Yevgenya Grinblat
- Department of Zoology, University of Wisconsin, Madison, WI, 53706, USA.,Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA.,McPherson Eye Research Institute, University of Wisconsin, Madison, WI, 53706, USA
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218
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Abstract
Myelin is a lipid-rich sheath formed by the spiral wrapping of specialized glial cells around axon segments. Myelinating glia allow for rapid transmission of nerve impulses and metabolic support of axons, and the absence of or disruption to myelin results in debilitating motor, cognitive, and emotional deficits in humans. Because myelin is a jawed vertebrate innovation, zebrafish are one of the simplest vertebrate model systems to study the genetics and development of myelinating glia. The morphogenetic cellular movements and genetic program that drive myelination are conserved between zebrafish and mammals, and myelin develops rapidly in zebrafish larvae, within 3-5days postfertilization. Myelin ultrastructure can be visualized in the zebrafish from larval to adult stages via transmission electron microscopy, and the dynamic development of myelinating glial cells may be observed in vivo via transgenic reporter lines in zebrafish larvae. Zebrafish are amenable to genetic and pharmacological screens, and screens for myelinating glial phenotypes have revealed both genes and drugs that promote myelin development, many of which are conserved in mammalian glia. Recently, zebrafish have been employed as a model to understand the complex dynamics of myelinating glia during development and regeneration. In this chapter, we describe these key methodologies and recent insights into mechanisms that regulate myelination using the zebrafish model.
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Affiliation(s)
- M D'Rozario
- Washington University School of Medicine, St. Louis, MO, United States
| | - K R Monk
- Washington University School of Medicine, St. Louis, MO, United States; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
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219
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Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM, Chang HY, Young RA, Zon LI. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Mol Cell 2016; 62:34-46. [PMID: 27058786 DOI: 10.1016/j.molcel.2016.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/02/2016] [Accepted: 03/10/2016] [Indexed: 12/29/2022]
Abstract
Studying cancer metabolism gives insight into tumorigenic survival mechanisms and susceptibilities. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a melanoma tumor suppressor that responds to nucleotide stress. HEXIM1 expression is low in melanoma. Its overexpression in a zebrafish melanoma model suppresses cancer formation, while its inactivation accelerates tumor onset in vivo. Knockdown of HEXIM1 rescues zebrafish neural crest defects and human melanoma proliferation defects that arise from nucleotide depletion. Under nucleotide stress, HEXIM1 is induced to form an inhibitory complex with P-TEFb, the kinase that initiates transcription elongation, to inhibit elongation at tumorigenic genes. The resulting alteration in gene expression also causes anti-tumorigenic RNAs to bind to and be stabilized by HEXIM1. HEXIM1 plays an important role in inhibiting cancer cell-specific gene transcription while also facilitating anti-cancer gene expression. Our study reveals an important role for HEXIM1 in coupling nucleotide metabolism with transcriptional regulation in melanoma.
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Affiliation(s)
- Justin L Tan
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Rachel D Fogley
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julien Ablain
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Song Yang
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Violaine Saint-André
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Brian T Do
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alvaro C Laga
- Department of Pathology, Brigham & Women's Hospital, Boston, MA 02215, USA
| | - Koh Fujinaga
- Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cristina Santoriello
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Celeste B Greer
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Yoon Jung Kim
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - John G Clohessy
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Bothmer
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Pandell
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Serine Avagyan
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - John E Brogie
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Elliott J Hagedorn
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Ng Shyh-Chang
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Richard M White
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY 10065, USA
| | - David H Price
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - B Matija Peterlin
- Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yi Zhou
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Tae Hoon Kim
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - John M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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220
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Ceasar SA, Rajan V, Prykhozhij SV, Berman JN, Ignacimuthu S. Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:2333-44. [PMID: 27350235 DOI: 10.1016/j.bbamcr.2016.06.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 12/26/2022]
Abstract
The clustered, regularly interspaced, short palindromic repeat (CRISPR) and CRISPR associated protein 9 (Cas9) system discovered as an adaptive immunity mechanism in prokaryotes has emerged as the most popular tool for the precise alterations of the genomes of diverse species. CRISPR/Cas9 system has taken the world of genome editing by storm in recent years. Its popularity as a tool for altering genomes is due to the ability of Cas9 protein to cause double-stranded breaks in DNA after binding with short guide RNA molecules, which can be produced with dramatically less effort and expense than required for production of transcription-activator like effector nucleases (TALEN) and zinc-finger nucleases (ZFN). This system has been exploited in many species from prokaryotes to higher animals including human cells as evidenced by the literature showing increasing sophistication and ease of CRISPR/Cas9 as well as increasing species variety where it is applicable. This technology is poised to solve several complex molecular biology problems faced in life science research including cancer research. In this review, we highlight the recent advancements in CRISPR/Cas9 system in editing genomes of prokaryotes, fungi, plants and animals and provide details on software tools available for convenient design of CRISPR/Cas9 targeting plasmids. We also discuss the future prospects of this advanced molecular technology.
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Affiliation(s)
- S Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India; Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Vinothkumar Rajan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason N Berman
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - S Ignacimuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India; International Scientific Partnership Program, Deanship of Scientific Research, College of Science, King Saud University, Riyadh, Saudi Arabia.
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221
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222
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Dow LE. Modeling Disease In Vivo With CRISPR/Cas9. Trends Mol Med 2016; 21:609-621. [PMID: 26432018 DOI: 10.1016/j.molmed.2015.07.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/26/2015] [Accepted: 07/31/2015] [Indexed: 01/11/2023]
Abstract
The recent advent of CRISPR/Cas9-mediated genome editing has created a wave of excitement across the scientific research community, carrying the promise of simple and effective genomic manipulation of nearly any cell type. CRISPR has quickly become the preferred tool for genetic manipulation, and shows incredible promise as a platform for studying gene function in vivo. I discuss the current application of CRISPR technology to create new in vivo disease models, with a particular focus on how these tools, derived from an adaptive bacterial immune system, are helping us to better model the complexity of human cancer.
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Affiliation(s)
- Lukas E Dow
- Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medical College, New York, NY 10021, USA.
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223
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Pelegri F, Mullins MC. Genetic screens for mutations affecting adult traits and parental-effect genes. Methods Cell Biol 2016; 135:39-87. [PMID: 27443920 DOI: 10.1016/bs.mcb.2016.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Forward genetics remains an important approach for the unbiased identification of factors involved in biological pathways. Forward genetic analysis in the zebrafish has until now largely been restricted to the developmental period from zygotic genome activation through the end of embryogenesis. However, the use of the zebrafish as a model system for the analysis of late larval, juvenile and adult traits, including fertility and maternal and paternal effects, continues to gain momentum. Here, we describe two approaches, based on an F3-extended family and gynogenetic methods, that allow genetic screening for, and recovery of mutations affecting post-embryonic stages, including adult traits, fertility, and parental effects. For each approach, we also describe strategies to maintain, map, and molecularly clone the identified mutations.
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Affiliation(s)
- F Pelegri
- University of Wisconsin-Madison, Madison, WI, United States
| | - M C Mullins
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
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224
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Kowalko JE, Ma L, Jeffery WR. Genome Editing in Astyanax mexicanus Using Transcription Activator-like Effector Nucleases (TALENs). J Vis Exp 2016. [PMID: 27404092 DOI: 10.3791/54113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Identifying alleles of genes underlying evolutionary change is essential to understanding how and why evolution occurs. Towards this end, much recent work has focused on identifying candidate genes for the evolution of traits in a variety of species. However, until recently it has been challenging to functionally validate interesting candidate genes. Recently developed tools for genetic engineering make it possible to manipulate specific genes in a wide range of organisms. Application of this technology in evolutionarily relevant organisms will allow for unprecedented insight into the role of candidate genes in evolution. Astyanax mexicanus (A. mexicanus) is a species of fish with both surface-dwelling and cave-dwelling forms. Multiple independent lines of cave-dwelling forms have evolved from ancestral surface fish, which are interfertile with one another and with surface fish, allowing elucidation of the genetic basis of cave traits. A. mexicanus has been used for a number of evolutionary studies, including linkage analysis to identify candidate genes responsible for a number of traits. Thus, A. mexicanus is an ideal system for the application of genome editing to test the role of candidate genes. Here we report a method for using transcription activator-like effector nucleases (TALENs) to mutate genes in surface A. mexicanus. Genome editing using TALENs in A. mexicanus has been utilized to generate mutations in pigmentation genes. This technique can also be utilized to evaluate the role of candidate genes for a number of other traits that have evolved in cave forms of A. mexicanus.
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Affiliation(s)
| | - Li Ma
- Department of Biological Sciences, University of Cincinnati
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225
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Willis A, Mazon-Moya M, Mostowy S. Investigation of septin biology in vivo using zebrafish. Methods Cell Biol 2016; 136:221-41. [PMID: 27473912 DOI: 10.1016/bs.mcb.2016.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The zebrafish (Danio rerio) is an important animal model to study cell biology in vivo. Benefits of the zebrafish include a fully annotated reference genome, an easily manipulable genome (for example, by morpholino oligonucleotide or CRISPR-Cas9), and transparent embryos for noninvasive, real-time microscopy using fluorescent transgenic lines. Zebrafish have orthologues of most human septins, and studies using larvae were used to investigate the role of septins in vertebrate development. The zebrafish larva is also an established model to study the cell biology of infection and has recently been used to visualize septin assembly during bacterial infection in vivo. Here, we describe protocols for the study of septins in zebrafish, with emphasis on techniques used to investigate the role of septins in host defense against bacterial infection.
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Affiliation(s)
- A Willis
- Imperial College London, London, United Kingdom
| | | | - S Mostowy
- Imperial College London, London, United Kingdom
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226
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Fei JF, Knapp D, Schuez M, Murawala P, Zou Y, Pal Singh S, Drechsel D, Tanaka EM. Tissue- and time-directed electroporation of CAS9 protein-gRNA complexes in vivo yields efficient multigene knockout for studying gene function in regeneration. NPJ Regen Med 2016; 1:16002. [PMID: 29302334 PMCID: PMC5744710 DOI: 10.1038/npjregenmed.2016.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/05/2023] Open
Abstract
A rapid method for temporally and spatially controlled CRISPR-mediated gene knockout in vertebrates will be an important tool to screen for genes involved in complex biological phenomena like regeneration. Here we show that in vivo injection of CAS9 protein-guide RNA (gRNA) complexes into the spinal cord lumen of the axolotl and subsequent electroporation leads to comprehensive knockout of Sox2 gene expression in SOX2+ neural stem cells with corresponding functional phenotypes from the gene knockout. This is particularly surprising considering the known prevalence of RNase activity in cerebral spinal fluid, which apparently the CAS9 protein protects against. The penetrance/efficiency of gene knockout in the protein-based system is far higher than corresponding electroporation of plasmid-based CRISPR systems. We further show that simultaneous delivery of CAS9-gRNA complexes directed against Sox2 and GFP yields efficient knockout of both genes in GFP-reporter animals. Finally, we show that this method can also be applied to other tissues such as skin and limb mesenchyme. This efficient delivery method opens up the possibility for rapid in vivo genetic screens during axolotl regeneration and can in principle be applied to other vertebrate tissue systems.
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Affiliation(s)
- Ji-Feng Fei
- DFG Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Dunja Knapp
- DFG Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Maritta Schuez
- DFG Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Prayag Murawala
- DFG Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Yan Zou
- DFG Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Sumeet Pal Singh
- DFG Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - David Drechsel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elly M Tanaka
- DFG Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
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227
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Burger A, Lindsay H, Felker A, Hess C, Anders C, Chiavacci E, Zaugg J, Weber LM, Catena R, Jinek M, Robinson MD, Mosimann C. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development 2016; 143:2025-37. [PMID: 27130213 DOI: 10.1242/dev.134809] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/12/2016] [Indexed: 12/14/2022]
Abstract
CRISPR-Cas9 enables efficient sequence-specific mutagenesis for creating somatic or germline mutants of model organisms. Key constraints in vivo remain the expression and delivery of active Cas9-sgRNA ribonucleoprotein complexes (RNPs) with minimal toxicity, variable mutagenesis efficiencies depending on targeting sequence, and high mutation mosaicism. Here, we apply in vitro assembled, fluorescent Cas9-sgRNA RNPs in solubilizing salt solution to achieve maximal mutagenesis efficiency in zebrafish embryos. MiSeq-based sequence analysis of targeted loci in individual embryos using CrispRVariants, a customized software tool for mutagenesis quantification and visualization, reveals efficient bi-allelic mutagenesis that reaches saturation at several tested gene loci. Such virtually complete mutagenesis exposes loss-of-function phenotypes for candidate genes in somatic mutant embryos for subsequent generation of stable germline mutants. We further show that targeting of non-coding elements in gene regulatory regions using saturating mutagenesis uncovers functional control elements in transgenic reporters and endogenous genes in injected embryos. Our results establish that optimally solubilized, in vitro assembled fluorescent Cas9-sgRNA RNPs provide a reproducible reagent for direct and scalable loss-of-function studies and applications beyond zebrafish experiments that require maximal DNA cutting efficiency in vivo.
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Affiliation(s)
- Alexa Burger
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Helen Lindsay
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich 8057, Switzerland
| | - Anastasia Felker
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Christopher Hess
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Carolin Anders
- Institute of Biochemistry, University of Zürich, Zürich 8057, Switzerland
| | - Elena Chiavacci
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Jonas Zaugg
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Lukas M Weber
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich 8057, Switzerland
| | - Raul Catena
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Martin Jinek
- Institute of Biochemistry, University of Zürich, Zürich 8057, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich 8057, Switzerland
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
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228
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Abstract
Zebrafish (Danio rerio) is a unique model organism at the functional intersection between a high fecundity and conserved vertebrate physiology while being amenable to a multitude of genome editing techniques. The genome engineering field has experienced an unprecedented rate of growth in the recent years since the introduction of designer endonucleases, such as zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats-Cas9 systems. With the ever-evolving toolset available to the scientific community, the important question one should ask is not simply how to make a mutant line, but rather how best to do so. For this purpose, understanding the toolset is just one end of the equation; understanding how DNA is repaired once double-strand breaks are induced by designer endonucleases, as well as understanding proper fish handling and line maintenance techniques, are also essential to rapidly edit the zebrafish genome. This chapter is outlined to provide a bird's-eye view on each of these three components. The goal of this chapter is to facilitate the adoption of the zebrafish as a model to study human genetic disease and to rapidly analyze the function of the vertebrate genome.
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Affiliation(s)
- H Ata
- Mayo Clinic, Rochester, MN, United States
| | - K J Clark
- Mayo Clinic, Rochester, MN, United States
| | - S C Ekker
- Mayo Clinic, Rochester, MN, United States
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229
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McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 2016; 353:aaf7907. [PMID: 27229144 DOI: 10.1126/science.aaf7907] [Citation(s) in RCA: 465] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/20/2016] [Indexed: 12/27/2022]
Abstract
Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable and that thousands of lineage-informative barcode alleles can be generated. By sampling hundreds of thousands of cells from individual zebrafish, we find that most cells in adult organs derive from relatively few embryonic progenitors. In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease.
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Affiliation(s)
- Aaron McKenna
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gregory M Findlay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - James A Gagnon
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Marshall S Horwitz
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. Department of Pathology, University of Washington, Seattle, WA, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. Center for Brain Science, Harvard University, Cambridge, MA, USA. The Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. Howard Hughes Medical Institute, Seattle, WA, USA.
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230
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Bolukbasi MF, Gupta A, Wolfe SA. Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery. Nat Methods 2016; 13:41-50. [PMID: 26716561 DOI: 10.1038/nmeth.3684] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/05/2015] [Indexed: 12/12/2022]
Abstract
The simplicity of site-specific genome targeting by type II clustered, regularly interspaced, short palindromic repeat (CRISPR)-Cas9 nucleases, along with their robust activity profile, has changed the landscape of genome editing. These favorable properties have made the CRISPR-Cas9 system the technology of choice for sequence-specific modifications in vertebrate systems. For many applications, whether the focus is on basic science investigations or therapeutic efficacy, activity and precision are important considerations when one is choosing a nuclease platform, target site and delivery method. Here we review recent methods for increasing the activity and accuracy of Cas9 and assessing the extent of off-target cleavage events.
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Affiliation(s)
- Mehmet Fatih Bolukbasi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ankit Gupta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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231
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Marshall RA, Osborn DPS. Zebrafish: a vertebrate tool for studying basal body biogenesis, structure, and function. Cilia 2016; 5:16. [PMID: 27168933 PMCID: PMC4862167 DOI: 10.1186/s13630-016-0036-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/01/2016] [Indexed: 02/27/2023] Open
Abstract
Understanding the role of basal bodies (BBs) during development and disease has been largely overshadowed by research into the function of the cilium. Although these two organelles are closely associated, they have specific roles to complete for successful cellular development. Appropriate development and function of the BB are fundamental for cilia function. Indeed, there are a growing number of human genetic diseases affecting ciliary development, known collectively as the ciliopathies. Accumulating evidence suggests that BBs establish cell polarity, direct ciliogenesis, and provide docking sites for proteins required within the ciliary axoneme. Major contributions to our knowledge of BB structure and function have been provided by studies in flagellated or ciliated unicellular eukaryotic organisms, specifically Tetrahymena and Chlamydomonas. Reproducing these and other findings in vertebrates has required animal in vivo models. Zebrafish have fast become one of the primary organisms of choice for modeling vertebrate functional genetics. Rapid ex-utero development, proficient egg laying, ease of genetic manipulation, and affordability make zebrafish an attractive vertebrate research tool. Furthermore, zebrafish share over 80 % of disease causing genes with humans. In this article, we discuss the merits of using zebrafish to study BB functional genetics, review current knowledge of zebrafish BB ultrastructure and mechanisms of function, and consider the outlook for future zebrafish-based BB studies.
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Affiliation(s)
- Ryan A Marshall
- Cell Sciences and Genetics Research Centre, St George's University of London, London, SW17 0RE UK
| | - Daniel P S Osborn
- Cell Sciences and Genetics Research Centre, St George's University of London, London, SW17 0RE UK
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232
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Williams MR, Fricano-Kugler CJ, Getz SA, Skelton PD, Lee J, Rizzuto CP, Geller JS, Li M, Luikart BW. A Retroviral CRISPR-Cas9 System for Cellular Autism-Associated Phenotype Discovery in Developing Neurons. Sci Rep 2016; 6:25611. [PMID: 27161796 PMCID: PMC4861960 DOI: 10.1038/srep25611] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/20/2016] [Indexed: 12/20/2022] Open
Abstract
Retroviruses expressing a fluorescent protein, Cas9, and a small guide RNA are used to mimic nonsense PTEN mutations from autism patients in developing mouse neurons. We compare the cellular phenotype elicited by CRISPR-Cas9 to those elicited using shRNA or Cre/Lox technologies and find that knockdown or knockout (KO) produced a corresponding moderate or severe neuronal hypertrophy in all cells. In contrast, the Cas9 approach produced missense and nonsense Pten mutations, resulting in a mix of KO-equivalent hypertrophic and wild type-like phenotypes. Importantly, despite this mixed phenotype, the neuronal hypertrophy resulting from Pten loss was evident on average in the population of manipulated cells. Having reproduced the known Pten KO phenotype using the CRISPR-Cas9 system we design viruses to target a gene that has recently been associated with autism, KATNAL2. Katnal2 deletion in the mouse results in decreased dendritic arborization of developing neurons. We conclude that retroviral implementation of the CRISPR-Cas9 system is an efficient system for cellular phenotype discovery in wild-type animals.
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Affiliation(s)
- Michael R Williams
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, USA
| | | | - Stephanie A Getz
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, USA
| | - Patrick D Skelton
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, USA
| | - Jeonghoon Lee
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, USA
| | - Christian P Rizzuto
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, USA
| | - Joseph S Geller
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, USA
| | - Meijie Li
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, USA
| | - Bryan W Luikart
- Department of Physiology and Neurobiology, Geisel School of Medicine at Dartmouth College, USA
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233
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Eisenhoffer GT, Slattum G, Ruiz OE, Otsuna H, Bryan CD, Lopez J, Wagner DS, Bonkowsky JL, Chien CB, Dorsky RI, Rosenblatt J. A toolbox to study epidermal cell types in zebrafish. J Cell Sci 2016; 130:269-277. [PMID: 27149923 DOI: 10.1242/jcs.184341] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/20/2016] [Indexed: 12/19/2022] Open
Abstract
Epithelia provide a crucial protective barrier for our organs and are also the sites where the majority of carcinomas form. Most studies on epithelia and carcinomas use cell culture or organisms where high-resolution live imaging is inaccessible without invasive techniques. Here, we introduce the developing zebrafish epidermis as an excellent in vivo model system for studying a living epithelium. We developed tools to fluorescently tag specific epithelial cell types and express genes in a mosaic fashion using five Gal4 lines identified from an enhancer trap screen. When crossed to a variety of UAS effector lines, we can now track, ablate or monitor single cells at sub-cellular resolution. Using photo-cleavable morpholino oligonucleotides that target gal4, we can also express genes in a mosaic fashion at specific times during development. Together, this system provides an excellent in vivo alternative to tissue culture cells, without the intrinsic concerns of culture conditions or transformation, and enables the investigation of distinct cell types within living epithelial tissues.
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Affiliation(s)
- George T Eisenhoffer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Unit 1010, 1515 Holcombe Blvd., Houston, TX 77030-4009, USA
| | - Gloria Slattum
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Oscar E Ruiz
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Unit 1010, 1515 Holcombe Blvd., Houston, TX 77030-4009, USA
| | - Hideo Otsuna
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, 320 BPRB, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Chase D Bryan
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Justin Lopez
- Department of BioSciences, Rice University, W100 George R. Brown Hall, Houston, TX 77251-1892, USA
| | - Daniel S Wagner
- Department of BioSciences, Rice University, W100 George R. Brown Hall, Houston, TX 77251-1892, USA
| | - Joshua L Bonkowsky
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, 320 BPRB, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Chi-Bin Chien
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, 320 BPRB, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Richard I Dorsky
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, 320 BPRB, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Jody Rosenblatt
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
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234
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Zhou W, Deiters A. Conditional Control of CRISPR/Cas9 Function. Angew Chem Int Ed Engl 2016; 55:5394-9. [PMID: 26996256 DOI: 10.1002/anie.201511441] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/21/2016] [Indexed: 12/26/2022]
Abstract
The recently discovered CRISPR/Cas9 endonuclease system, comprised of a guide RNA for the recognition of a DNA target and the Cas9 nuclease protein for binding and processing the target, has been extensively studied and has been widely applied in genome editing, synthetic biology, and transcriptional modulation in cells and animals. Toward more precise genomic modification and further expansion of the CRISPR/Cas9 system as a spatiotemporally controlled gene regulatory system, several approaches of conditional activation of Cas9 function using small molecules and light have recently been developed. These methods have led to improvements in the genome editing specificity of the CRISPR/Cas9 system and enabled its activation with temporal and spatial precision.
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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235
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Abstract
The zebrafish has been a powerful model in forward genetic screens to identify genes essential for organogenesis and embryonic development. Conversely, using reverse genetics to investigate specific gene function requires phenotypic analysis of complete gene inactivation. Despite the availability and efficacy of morpholinos, the lack of tractable and efficient knockout technologies has impeded reverse genetic studies in the zebrafish, particularly in adult animals. The recent development of genome-editing technologies such as CRISPR/Cas9 greatly widened the scope of loss-of-function studies in the zebrafish, allowing for the rapid phenotypic assessment of gene silencing in embryos, the generation of knockout lines, and large-scale reverse genetic screens. Tissue-specific gene inactivation would be ideal for these studies given the caveats of whole-embryo gene silencing, yet spatial control of gene targeting remains a challenge. In this chapter, we focus on tissue-specific gene inactivation using the CRISPR/Cas9 technology. We first explain the rationale for this technique, including some of its potential applications to tackle important biological issues and the inability of current technologies to address these issues. We then present a method to target genes in a tissue-specific manner in the zebrafish. Finally, we discuss technical difficulties and limitations of this method as well as possible future developments.
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Affiliation(s)
- J Ablain
- Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
| | - L I Zon
- Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
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236
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Pan C, Ye L, Qin L, Liu X, He Y, Wang J, Chen L, Lu G. CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Sci Rep 2016; 6:24765. [PMID: 27097775 PMCID: PMC4838866 DOI: 10.1038/srep24765] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/04/2016] [Indexed: 12/18/2022] Open
Abstract
The CRISPR/Cas9 system has successfully been used in various organisms for precise targeted gene editing. Although it has been demonstrated that CRISPR/Cas9 system can induce mutation in tomato plants, the stability of heredity in later generations and mutant specificity induced by the CRISPR/Cas9 system in tomato plants have not yet been elucidated in detail. In this study, two genes, SlPDS and SlPIF4, were used for testing targeted mutagenesis in tomato plants through an Agrobacterium tumefaciens-mediated transformation method. A high mutation frequency was observed in all tested targets in the T0 transgenic tomato plants, with an average frequency of 83.56%. Clear albino phenotypes were observed for the psd mutants. High frequencies of homozygous and biallelic mutants were detected even in T0 plants. The majority of the detected mutations were 1- to 3-nucleotide deletions, followed by 1-bp insertions. The target mutations in the T0 lines were stably transmitted to the T1 and T2 generations, without new modifications or revision. Off-target activities associated with SlPDS and SlPIF4 were also evaluated by sequencing the putative off-target sites, and no clear off-target events were detected. Our results demonstrate that the CRISPR/Cas9 system is an efficient tool for generating stable and heritable modifications in tomato plants.
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Affiliation(s)
- Changtian Pan
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Lei Ye
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Li Qin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Xue Liu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Yanjun He
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Jie Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Lifei Chen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Gang Lu
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
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237
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Brown DR, Samsa LA, Qian L, Liu J. Advances in the Study of Heart Development and Disease Using Zebrafish. J Cardiovasc Dev Dis 2016; 3. [PMID: 27335817 PMCID: PMC4913704 DOI: 10.3390/jcdd3020013] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Animal models of cardiovascular disease are key players in the translational medicine pipeline used to define the conserved genetic and molecular basis of disease. Congenital heart diseases (CHDs) are the most common type of human birth defect and feature structural abnormalities that arise during cardiac development and maturation. The zebrafish, Danio rerio, is a valuable vertebrate model organism, offering advantages over traditional mammalian models. These advantages include the rapid, stereotyped and external development of transparent embryos produced in large numbers from inexpensively housed adults, vast capacity for genetic manipulation, and amenability to high-throughput screening. With the help of modern genetics and a sequenced genome, zebrafish have led to insights in cardiovascular diseases ranging from CHDs to arrhythmia and cardiomyopathy. Here, we discuss the utility of zebrafish as a model system and summarize zebrafish cardiac morphogenesis with emphasis on parallels to human heart diseases. Additionally, we discuss the specific tools and experimental platforms utilized in the zebrafish model including forward screens, functional characterization of candidate genes, and high throughput applications.
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Affiliation(s)
- Daniel R. Brown
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.R.B.); (L.Q.)
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leigh Ann Samsa
- Department of Cell Biology and Physiology; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.R.B.); (L.Q.)
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.R.B.); (L.Q.)
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: ; Tel.: +1-919-962-0326; Fax: +1-919- 843-2063
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238
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Affiliation(s)
- Jorge Barriuso
- Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK
| | | | - Adam Hurlstone
- Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK
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239
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A genome editing primer for the hematologist. Blood 2016; 127:2525-35. [PMID: 27053532 DOI: 10.1182/blood-2016-01-678151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
Abstract
Gene editing enables the site-specific modification of the genome. These technologies have rapidly advanced such that they have entered common use in experimental hematology to investigate genetic function. In addition, genome editing is becoming increasingly plausible as a treatment modality to rectify genetic blood disorders and improve cellular therapies. Genome modification typically ensues from site-specific double-strand breaks and may result in a myriad of outcomes. Even single-strand nicks and targeted biochemical modifications that do not permanently alter the DNA sequence (epigenome editing) may be powerful instruments. In this review, we examine the various technologies, describe their advantages and shortcomings for engendering useful genetic alterations, and consider future prospects for genome editing to impact hematology.
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240
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Liu D, Hu R, Palla KJ, Tuskan GA, Yang X. Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:70-7. [PMID: 26896588 DOI: 10.1016/j.pbi.2016.01.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 05/18/2023]
Abstract
Genome editing with site-specific nucleases has become a powerful tool for functional characterization of plant genes and genetic improvement of agricultural crops. Among the various site-specific nuclease-based technologies available for genome editing, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems have shown the greatest potential for rapid and efficient editing of genomes in plant species. This article reviews the current status of application of CRISPR/Cas9 to plant genomics research, with a focus on loss-of-function and gain-of-function analysis of individual genes in the context of perennial plants and the potential application of CRISPR/Cas9 to perturbation of gene expression, and identification and analysis of gene modules as part of an accelerated domestication and synthetic biology effort.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA.
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241
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Biallelic editing of a lamprey genome using the CRISPR/Cas9 system. Sci Rep 2016; 6:23496. [PMID: 27005311 PMCID: PMC4804306 DOI: 10.1038/srep23496] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/07/2016] [Indexed: 12/31/2022] Open
Abstract
Lampreys are extant representatives of agnathans. Descriptions of lamprey development, physiology and genome have provided critical insights into early evolution of vertebrate traits. However, efficient means for genetic manipulation in agnathan species have not been developed, hindering functional studies of genes in these important Evo-Devo models. Here, we report a CRISPR/Cas system optimized for lamprey genomes and use it to disrupt genomic loci in the Northeast Chinese lamprey (Lethenteron morii) with efficiencies ranging between 84~99%. The frequencies of indels observed in the target loci of golden (gol), kctd10, wee1, soxe2, and wnt7b, estimated from direct sequencing of genomic DNA samples of injected lamprey larvae, were 68/69, 47/56, 38/39, 36/37 and 36/42, respectively. These indels often occurred in both alleles. In the CRISPR/Cas9 treatment for gol or kctd10, 38.6% or 85.3% of the targeted larvae had the respective recessive null-like phenotypes, further confirming the disruption of both loci. The kctd10 gRNA, designed against an essential functional region of Kctd10, resulted in null-like phenotypes and in-frame mutations in alleles. We suggest that the CRISPR/Cas-based approach has the potential for efficient genetic perturbation in organisms less amenable to germ line transmission based approaches.
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242
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Abstract
The zebrafish model is the only available high-throughput vertebrate assessment system, and it is uniquely suited for studies of in vivo cell biology. A sequenced and annotated genome has revealed a large degree of evolutionary conservation in comparison to the human genome. Due to our shared evolutionary history, the anatomical and physiological features of fish are highly homologous to humans, which facilitates studies relevant to human health. In addition, zebrafish provide a very unique vertebrate data stream that allows researchers to anchor hypotheses at the biochemical, genetic, and cellular levels to observations at the structural, functional, and behavioral level in a high-throughput format. In this review, we will draw heavily from toxicological studies to highlight advances in zebrafish high-throughput systems. Breakthroughs in transgenic/reporter lines and methods for genetic manipulation, such as the CRISPR-Cas9 system, will be comprised of reports across diverse disciplines.
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Affiliation(s)
- Gloria R Garcia
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA
| | - Pamela D Noyes
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA
| | - Robert L Tanguay
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA.
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243
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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244
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Di Donato V, De Santis F, Auer TO, Testa N, Sánchez-Iranzo H, Mercader N, Concordet JP, Del Bene F. 2C-Cas9: a versatile tool for clonal analysis of gene function. Genome Res 2016; 26:681-92. [PMID: 26957310 PMCID: PMC4864464 DOI: 10.1101/gr.196170.115] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 02/24/2016] [Indexed: 11/24/2022]
Abstract
CRISPR/Cas9-mediated targeted mutagenesis allows efficient generation of loss-of-function alleles in zebrafish. To date, this technology has been primarily used to generate genetic knockout animals. Nevertheless, the study of the function of certain loci might require tight spatiotemporal control of gene inactivation. Here, we show that tissue-specific gene disruption can be achieved by driving Cas9 expression with the Gal4/UAS system. Furthermore, by combining the Gal4/UAS and Cre/loxP systems, we establish a versatile tool to genetically label mutant cell clones, enabling their phenotypic analysis. Our technique has the potential to be applied to diverse model organisms, enabling tissue-specific loss-of-function and phenotypic characterization of live and fixed tissues.
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Affiliation(s)
- Vincenzo Di Donato
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
| | - Flavia De Santis
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
| | - Thomas O Auer
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
| | - Noé Testa
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
| | - Héctor Sánchez-Iranzo
- Department of Cardiovascular Development and Repair, Atherothrombosis and Imaging, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28028 Madrid, Spain
| | - Nadia Mercader
- Department of Cardiovascular Development and Repair, Atherothrombosis and Imaging, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28028 Madrid, Spain
| | - Jean-Paul Concordet
- Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Paris F-75231, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
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245
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Abstract
In the nervous system, axons transmit information in the form of electrical impulses over long distances. The speed of impulse conduction is enhanced by myelin, a lipid-rich membrane that wraps around axons. Myelin also is required for the long-term health of axons by providing metabolic support. Accordingly, myelin deficiencies are implicated in a wide range of neurodevelopmental and neuropsychiatric disorders, intellectual disabilities, and neurodegenerative conditions. Central nervous system myelin is formed by glial cells called oligodendrocytes. During development, oligodendrocyte precursor cells migrate from their origins to their target axons, extend long membrane processes that wrap axons, and produce the proteins and lipids that provide myelin membrane with its unique characteristics. Myelination is a dynamic process that involves intricate interactions between multiple cell types. Therefore, an in vivo myelination model, such as the zebrafish, which allows for live observation of cell dynamics and cell-to-cell interactions, is well suited for investigating oligodendrocyte development. Zebrafish offer several advantages to investigating myelination, including the use of transgenic reporter lines, live imaging, forward genetic screens, chemical screens, and reverse genetic approaches. This chapter will describe how these tools and approaches have provided new insights into the regulatory mechanisms that guide myelination.
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Affiliation(s)
- E S Mathews
- University of Colorado School of Medicine, Aurora, CO, United States
| | - B Appel
- University of Colorado School of Medicine, Aurora, CO, United States
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246
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Spermatogenic Cell-Specific Gene Mutation in Mice via CRISPR-Cas9. J Genet Genomics 2016; 43:289-96. [PMID: 27210043 DOI: 10.1016/j.jgg.2016.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/02/2016] [Accepted: 02/15/2016] [Indexed: 12/30/2022]
Abstract
Tissue-specific knockout technology enables the analysis of the gene function in specific tissues in adult mammals. However, conventional strategy for producing tissue-specific knockout mice is a time- and labor-consuming process, restricting rapid study of the gene function in vivo. CRISPR-Cas9 system from bacteria is a simple and efficient gene-editing technique, which has enabled rapid generation of gene knockout lines in mouse by direct injection of CRISPR-Cas9 into zygotes. Here, we demonstrate CRISPR-Cas9-mediated spermatogenic cell-specific disruption of Scp3 gene in testes in one step. We first generated transgenic mice by pronuclear injection of a plasmid containing Hspa2 promoter driving Cas9 expression and showed Cas9 specific expression in spermatogenic cells. We then produced transgenic mice carrying Hspa2 promoter driven Cas9 and constitutive expressed sgRNA targeting Scp3 gene. Male founders were infertile due to developmental arrest of spermatogenic cells while female founders could produce progeny normally. Consistently, male progeny from female founders were infertile and females could transmit the transgenes to the next generation. Our study establishes a CRISPR-Cas9-based one-step strategy to analyze the gene function in adult tissues by a temporal-spatial pattern.
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247
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Schick UM, Jain D, Hodonsky CJ, Morrison JV, Davis JP, Brown L, Sofer T, Conomos MP, Schurmann C, McHugh CP, Nelson SC, Vadlamudi S, Stilp A, Plantinga A, Baier L, Bien SA, Gogarten SM, Laurie CA, Taylor KD, Liu Y, Auer PL, Franceschini N, Szpiro A, Rice K, Kerr KF, Rotter JI, Hanson RL, Papanicolaou G, Rich SS, Loos RJF, Browning BL, Browning SR, Weir BS, Laurie CC, Mohlke KL, North KE, Thornton TA, Reiner AP. Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans. Am J Hum Genet 2016; 98:229-42. [PMID: 26805783 PMCID: PMC4746331 DOI: 10.1016/j.ajhg.2015.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/07/2015] [Indexed: 12/23/2022] Open
Abstract
Platelets play an essential role in hemostasis and thrombosis. We performed a genome-wide association study of platelet count in 12,491 participants of the Hispanic Community Health Study/Study of Latinos by using a mixed-model method that accounts for admixture and family relationships. We discovered and replicated associations with five genes (ACTN1, ETV7, GABBR1-MOG, MEF2C, and ZBTB9-BAK1). Our strongest association was with Amerindian-specific variant rs117672662 (p value = 1.16 × 10(-28)) in ACTN1, a gene implicated in congenital macrothrombocytopenia. rs117672662 exhibited allelic differences in transcriptional activity and protein binding in hematopoietic cells. Our results underscore the value of diverse populations to extend insights into the allelic architecture of complex traits.
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Affiliation(s)
- Ursula M Schick
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Jean V Morrison
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - James P Davis
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lisa Brown
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Claudia Schurmann
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | | | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Anna Plantinga
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Leslie Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, NIH, 445 North 5(th) Street, Phoenix, AZ 85004, USA
| | - Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | | | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yongmei Liu
- School of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53201, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Adam Szpiro
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kathleen F Kerr
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, NIH, 445 North 5(th) Street, Phoenix, AZ 85004, USA
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Division of Endocrinology, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian L Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA.
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248
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Reid W, O'Brochta DA. Applications of genome editing in insects. CURRENT OPINION IN INSECT SCIENCE 2016; 13:43-54. [PMID: 27436552 DOI: 10.1016/j.cois.2015.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/14/2023]
Abstract
Insect genome editing was first reported 1991 in Drosophila melanogaster but the technology used was not portable to other species. Not until the recent development of facile, engineered DNA endonuclease systems has gene editing become widely available to insect scientists. Most applications in insects to date have been technical in nature but this is rapidly changing. Functional genomics and genetics-based insect control efforts will be major beneficiaries of the application of contemporary gene editing technologies. Engineered endonucleases like Cas9 make it possible to create powerful and effective gene drive systems that could be used to reduce or even eradicate specific insect populations. 'Best practices' for using Cas9-based editing are beginning to emerge making it easier and more effective to design and use but gene editing technologies still require traditional means of delivery in order to introduce them into somatic and germ cells of insects-microinjection of developing embryos. This constrains the use of these technologies by insect scientists. Insects created using editing technologies challenge existing governmental regulatory structures designed to manage genetically modified organisms.
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Affiliation(s)
- William Reid
- Institute for Bioscience and Biotechnology Research, Department of Entomology, University of Maryland, College Park, 9600 Gudelsky Drive, Rockville, MD 20850, United States
| | - David A O'Brochta
- Institute for Bioscience and Biotechnology Research, Department of Entomology, University of Maryland, College Park, 9600 Gudelsky Drive, Rockville, MD 20850, United States.
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249
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Kaufman CK, Mosimann C, Fan ZP, Yang S, Thomas AJ, Ablain J, Tan JL, Fogley RD, van Rooijen E, Hagedorn EJ, Ciarlo C, White RM, Matos DA, Puller AC, Santoriello C, Liao EC, Young RA, Zon LI. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science 2016; 351:aad2197. [PMID: 26823433 PMCID: PMC4868069 DOI: 10.1126/science.aad2197] [Citation(s) in RCA: 277] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/22/2015] [Indexed: 12/12/2022]
Abstract
The "cancerized field" concept posits that cancer-prone cells in a given tissue share an oncogenic mutation, but only discreet clones within the field initiate tumors. Most benign nevi carry oncogenic BRAF(V600E) mutations but rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and specifically reexpressed in melanoma. Live imaging of transgenic zebrafish crestin reporters shows that within a cancerized field (BRAF(V600E)-mutant; p53-deficient), a single melanocyte reactivates the NCP state, revealing a fate change at melanoma initiation in this model. NCP transcription factors, including sox10, regulate crestin expression. Forced sox10 overexpression in melanocytes accelerated melanoma formation, which is consistent with activation of NCP genes and super-enhancers leading to melanoma. Our work highlights NCP state reemergence as a key event in melanoma initiation.
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Affiliation(s)
- Charles K Kaufman
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA. Harvard Stem Cell Institute, Boston, MA 02115, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Harvard Medical School, Boston, MA 02115, USA
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA. Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Andrew J Thomas
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Julien Ablain
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA. Harvard Stem Cell Institute, Boston, MA 02115, USA. Harvard Medical School, Boston, MA 02115, USA
| | - Justin L Tan
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Rachel D Fogley
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Ellen van Rooijen
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA. Harvard Stem Cell Institute, Boston, MA 02115, USA. Harvard Medical School, Boston, MA 02115, USA
| | - Elliott J Hagedorn
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA. Harvard Stem Cell Institute, Boston, MA 02115, USA. Harvard Medical School, Boston, MA 02115, USA
| | - Christie Ciarlo
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA. Harvard Medical School, Boston, MA 02115, USA
| | - Richard M White
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY 10075, USA
| | - Dominick A Matos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ann-Christin Puller
- Research Institute Children's Cancer Center Hamburg and Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Cristina Santoriello
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Eric C Liao
- Harvard Stem Cell Institute, Boston, MA 02115, USA. Harvard Medical School, Boston, MA 02115, USA. Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute, Boston, MA 02115, USA. Harvard Stem Cell Institute, Boston, MA 02115, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Harvard Medical School, Boston, MA 02115, USA. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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250
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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