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Song H, Shin U, Nam U, Lee Y. Exploring hematopoiesis in zebrafish using forward genetic screening. Exp Mol Med 2024; 56:51-58. [PMID: 38172599 PMCID: PMC10834449 DOI: 10.1038/s12276-023-01138-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 01/05/2024] Open
Abstract
Zebrafish have emerged as a powerful animal model for investigating the genetic basis of hematopoiesis. Owing to its close genetic and developmental similarities to humans, combined with its rapid reproduction and extensive genomic resources, zebrafish have become a versatile and efficient platform for genetic studies. In particular, the forward genetic screening approach has enabled the unbiased identification of novel genes and pathways related to blood development, from hematopoietic stem cell formation to terminal differentiation. Recent advances in mutant gene mapping have further expanded the scope of forward genetic screening, facilitating the identification of previously unknown genes and pathways relevant to hematopoiesis. In this review, we provide an overview of the zebrafish forward screening approach for hematopoietic gene discovery and highlight the key genes and pathways identified using this method. This review emphasizes the importance of zebrafish as a model system for understanding the genetic basis of hematopoiesis and its associated disorders.
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Affiliation(s)
- Hyemin Song
- Department of Biomedical Sciences, UC San Diego School of Medicine, La Jolla, CA, 92093, USA
- Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Unbeom Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Uijeong Nam
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul, 05278, Republic of Korea
| | - Yoonsung Lee
- Clinical Research Institute, Kyung Hee University Hospital at Gangdong, School of Medicine, Kyung Hee University, Seoul, 05278, Republic of Korea.
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2
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Henke K, Farmer DT, Niu X, Kraus JM, Galloway JL, Youngstrom DW. Genetically engineered zebrafish as models of skeletal development and regeneration. Bone 2023; 167:116611. [PMID: 36395960 PMCID: PMC11080330 DOI: 10.1016/j.bone.2022.116611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Zebrafish (Danio rerio) are aquatic vertebrates with significant homology to their terrestrial counterparts. While zebrafish have a centuries-long track record in developmental and regenerative biology, their utility has grown exponentially with the onset of modern genetics. This is exemplified in studies focused on skeletal development and repair. Herein, the numerous contributions of zebrafish to our understanding of the basic science of cartilage, bone, tendon/ligament, and other skeletal tissues are described, with a particular focus on applications to development and regeneration. We summarize the genetic strengths that have made the zebrafish a powerful model to understand skeletal biology. We also highlight the large body of existing tools and techniques available to understand skeletal development and repair in the zebrafish and introduce emerging methods that will aid in novel discoveries in skeletal biology. Finally, we review the unique contributions of zebrafish to our understanding of regeneration and highlight diverse routes of repair in different contexts of injury. We conclude that zebrafish will continue to fill a niche of increasing breadth and depth in the study of basic cellular mechanisms of skeletal biology.
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Affiliation(s)
- Katrin Henke
- Department of Orthopaedics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - D'Juan T Farmer
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA.
| | - Xubo Niu
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Jessica M Kraus
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel W Youngstrom
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
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3
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Gray RS, Gonzalez R, Ackerman SD, Minowa R, Griest JF, Bayrak MN, Troutwine B, Canter S, Monk KR, Sepich DS, Solnica-Krezel L. Postembryonic screen for mutations affecting spine development in zebrafish. Dev Biol 2021; 471:18-33. [PMID: 33290818 PMCID: PMC10785604 DOI: 10.1016/j.ydbio.2020.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
The spine gives structural support for the adult body, protects the spinal cord, and provides muscle attachment for moving through the environment. The development and maturation of the spine and its physiology involve the integration of multiple musculoskeletal tissues including bone, cartilage, and fibrocartilaginous joints, as well as innervation and control by the nervous system. One of the most common disorders of the spine in human is adolescent idiopathic scoliosis (AIS), which is characterized by the onset of an abnormal lateral curvature of the spine of <10° around adolescence, in otherwise healthy children. The genetic basis of AIS is largely unknown. Systematic genome-wide mutagenesis screens for embryonic phenotypes in zebrafish have been instrumental in the understanding of early patterning of embryonic tissues necessary to build and pattern the embryonic spine. However, the mechanisms required for postembryonic maturation and homeostasis of the spine remain poorly understood. Here we report the results from a small-scale forward genetic screen for adult-viable recessive and dominant zebrafish mutations, leading to overt morphological abnormalities of the adult spine. Germline mutations induced with N-ethyl N-nitrosourea (ENU) were transmitted and screened for dominant phenotypes in 1229 F1 animals, and subsequently bred to homozygosity in F3 families; from these, 314 haploid genomes were screened for adult-viable recessive phenotypes affecting general body shape. We cumulatively found 40 adult-viable (3 dominant and 37 recessive) mutations each leading to a defect in the morphogenesis of the spine. The largest phenotypic group displayed larval onset axial curvatures, leading to whole-body scoliosis without vertebral dysplasia in adult fish. Pairwise complementation testing of 16 mutant lines within this phenotypic group revealed at least 9 independent mutant loci. Using massively-parallel whole genome or whole exome sequencing and meiotic mapping we defined the molecular identity of several loci for larval onset whole-body scoliosis in zebrafish. We identified a new mutation in the skolios/kinesin family member 6 (kif6) gene, causing neurodevelopmental and ependymal cilia defects in mouse and zebrafish. We also report multiple recessive alleles of the scospondin and a disintegrin and metalloproteinase with thrombospondin motifs 9 (adamts9) genes, which all display defects in spine morphogenesis. Our results provide evidence of monogenic traits that are essential for normal spine development in zebrafish, that may help to establish new candidate risk loci for spine disorders in humans.
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Affiliation(s)
- Ryan S Gray
- Department of Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Roberto Gonzalez
- Department of Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA
| | - Sarah D Ackerman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryoko Minowa
- Department of Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA
| | - Johanna F Griest
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Melisa N Bayrak
- Department of Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA
| | - Benjamin Troutwine
- Department of Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA
| | - Stephen Canter
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kelly R Monk
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA; Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
| | - Diane S Sepich
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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4
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Preclinical methodological approaches investigating of the effects of alcohol on perinatal and adolescent neurodevelopment. Neurosci Biobehav Rev 2020; 116:436-451. [PMID: 32681938 DOI: 10.1016/j.neubiorev.2020.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 02/08/2023]
Abstract
Despite much evidence of its economic and social costs, alcohol use continues to increase. Much remains to be known as to the effects of alcohol on neurodevelopment across the lifespan and in both sexes. We provide a comprehensive overview of the methodological approaches to ethanol administration when using animal models (primarily rodent models) and their translational relevance, as well as some of the advantages and disadvantages of each approach. Special consideration is given to early developmental periods (prenatal through adolescence), as well as to the types of research questions that are best addressed by specific methodologies. The zebrafish is used increasingly in alcohol research, and how to use this model effectively as a preclinical model is reviewed as well.
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Lorincz R, Emfinger CH, Walcher A, Giolai M, Krautgasser C, Remedi MS, Nichols CG, Meyer D. In vivo monitoring of intracellular Ca 2+ dynamics in the pancreatic β-cells of zebrafish embryos. Islets 2018; 10:221-238. [PMID: 30521410 PMCID: PMC6300091 DOI: 10.1080/19382014.2018.1540234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Assessing the response of pancreatic islet cells to glucose stimulation is important for understanding β-cell function. Zebrafish are a promising model for studies of metabolism in general, including stimulus-secretion coupling in the pancreas. We used transgenic zebrafish embryos expressing a genetically-encoded Ca2+ sensor in pancreatic β-cells to monitor a key step in glucose induced insulin secretion; the elevations of intracellular [Ca2+]i. In vivo and ex vivo analyses of [Ca2+]i demonstrate that β-cell responsiveness to glucose is well established in late embryogenesis and that embryonic β-cells also respond to free fatty acid and amino acid challenges. In vivo imaging of whole embryos further shows that indirect glucose administration, for example by yolk injection, results in a slow and asynchronous induction of β-cell [Ca2+]i responses, while intravenous glucose injections cause immediate and islet-wide synchronized [Ca2+]i fluctuations. Finally, we demonstrate that embryos with disrupted mutation of the CaV1.2 channel gene cacna1c are hyperglycemic and that this phenotype is associated with glucose-independent [Ca2+]i fluctuation in β-cells. The data reveal a novel central role of cacna1c in β-cell specific stimulus-secretion coupling in zebrafish and demonstrate that the novel approach we propose - to monitor the [Ca2+]i dynamics in embryonic β-cells in vivo - will help to expand the understanding of β-cell physiological functions in healthy and diseased states.
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Affiliation(s)
- Reka Lorincz
- Institute of Molecular Biology/CMBI, University of Innsbruck, Innsbruck, Austria
| | - Christopher H. Emfinger
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases (CIMED), Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Walcher
- Institute of Molecular Biology/CMBI, University of Innsbruck, Innsbruck, Austria
| | - Michael Giolai
- Institute of Molecular Biology/CMBI, University of Innsbruck, Innsbruck, Austria
| | - Claudia Krautgasser
- Institute of Molecular Biology/CMBI, University of Innsbruck, Innsbruck, Austria
| | - Maria S. Remedi
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Colin G. Nichols
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases (CIMED), Washington University School of Medicine, St. Louis, MO, USA
| | - Dirk Meyer
- Institute of Molecular Biology/CMBI, University of Innsbruck, Innsbruck, Austria
- CONTACT Dirk Meyer Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, Innsbruck 6020, Austria
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Whole Genome Sequencing-Based Mapping and Candidate Identification of Mutations from Fixed Zebrafish Tissue. G3-GENES GENOMES GENETICS 2017; 7:3415-3425. [PMID: 28855284 PMCID: PMC5633390 DOI: 10.1534/g3.117.300212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As forward genetic screens in zebrafish become more common, the number of mutants that cannot be identified by gross morphology or through transgenic approaches, such as many nervous system defects, has also increased. Screening for these difficult-to-visualize phenotypes demands techniques such as whole-mount in situ hybridization (WISH) or antibody staining, which require tissue fixation. To date, fixed tissue has not been amenable for generating libraries for whole genome sequencing (WGS). Here, we describe a method for using genomic DNA from fixed tissue and a bioinformatics suite for WGS-based mapping of zebrafish mutants. We tested our protocol using two known zebrafish mutant alleles, gpr126st49 and egr2bfh227, both of which cause myelin defects. As further proof of concept we mapped a novel mutation, stl64, identified in a zebrafish WISH screen for myelination defects. We linked stl64 to chromosome 1 and identified a candidate nonsense mutation in the F-box and WD repeat domain containing 7 (fbxw7) gene. Importantly, stl64 mutants phenocopy previously described fbxw7vu56 mutants, and knockdown of fbxw7 in wild-type animals produced similar defects, demonstrating that stl64 disrupts fbxw7. Together, these data show that our mapping protocol can map and identify causative lesions in mutant screens that require tissue fixation for phenotypic analysis.
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Genetic Screen for Postembryonic Development in the Zebrafish ( Danio rerio): Dominant Mutations Affecting Adult Form. Genetics 2017; 207:609-623. [PMID: 28835471 DOI: 10.1534/genetics.117.300187] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
Large-scale forward genetic screens have been instrumental for identifying genes that regulate development, homeostasis, and regeneration, as well as the mechanisms of disease. The zebrafish, Danio rerio, is an established genetic and developmental model used in genetic screens to uncover genes necessary for early development. However, the regulation of postembryonic development has received less attention as these screens are more labor intensive and require extensive resources. The lack of systematic interrogation of late development leaves large aspects of the genetic regulation of adult form and physiology unresolved. To understand the genetic control of postembryonic development, we performed a dominant screen for phenotypes affecting the adult zebrafish. In our screen, we identified 72 adult viable mutants showing changes in the shape of the skeleton as well as defects in pigmentation. For efficient mapping of these mutants and mutation identification, we devised a new mapping strategy based on identification of mutant-specific haplotypes. Using this method in combination with a candidate gene approach, we were able to identify linked mutations for 22 out of 25 mutants analyzed. Broadly, our mutational analysis suggests that there are key genes and pathways associated with late development. Many of these pathways are shared with humans and are affected in various disease conditions, suggesting constraint in the genetic pathways that can lead to change in adult form. Taken together, these results show that dominant screens are a feasible and productive means to identify mutations that can further our understanding of gene function during postembryonic development and in disease.
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8
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He Y, Bao B, Li H. Using zebrafish as a model to study the role of epigenetics in hearing loss. Expert Opin Drug Discov 2017; 12:967-975. [PMID: 28682135 DOI: 10.1080/17460441.2017.1340270] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The rapid progress of bioinformatics and high-throughput screening techniques in recent years has led to the identification of many candidate genes and small-molecule drugs that have the potential to make significant contributions to our understanding of the developmental and pathological processes of hearing, but it remains unclear how these genes and regulatory factors are coordinated. Increasing evidence suggests that epigenetic mechanisms are essential for establishing gene expression profiles and likely play an important role in the development of inner ear and in the pathology of hearing-associated diseases. Zebrafish are a valuable and tractable in vivo model organism for monitoring changes in the epigenome and for identifying new epigenetic processes and drug molecules that can influence vertebrate development. Areas covered: In this review, the authors focus on zebrafish as a model to summarize recent findings concerning the roles of epigenetics in the development, regeneration, and protection of hair cells. Expert opinion: Using the zebrafish model in combination with high-throughput screening and genome-editing technologies to investigate the function of epigenetics in hearing is crucial to help us better understand the molecular and genetic mechanisms of auditory development and function. It will also contribute to the development of new strategies to restore hearing loss.
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Affiliation(s)
- Yingzi He
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China.,c Key Laboratory of Hearing Medicine of NHFPC , Shanghai , China
| | - Beier Bao
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China
| | - Huawei Li
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China.,b Institutes of Biomedical Sciences , Fudan University , Shanghai , China.,c Key Laboratory of Hearing Medicine of NHFPC , Shanghai , China.,d Shanghai Engineering Research Centre of Cochlear Implant , Shanghai , China.,e The Institutes of Brain Science and the Collaborative Innovation Center for Brain Science , Fudan University , Shanghai , China
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9
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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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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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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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12
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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: 41] [Impact Index Per Article: 5.1] [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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Shi X, He BL, Ma ACH, Leung AYH. Fishing the targets of myeloid malignancies in the era of next generation sequencing. Blood Rev 2015; 30:119-30. [PMID: 26443083 DOI: 10.1016/j.blre.2015.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/15/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
Abstract
Recent advent in next generation sequencing (NGS) and bioinformatics has generated an unprecedented amount of genetic information in myeloidmalignancies. This information may shed lights to the pathogenesis, diagnosis and prognostication of these diseases and provide potential targets for therapeutic intervention. However, the rapid emergence of genetic information will quickly outpace their functional validation by conventional laboratory platforms. Foundational knowledge about zebrafish hematopoiesis accumulated over the past two decades and novel genomeediting technologies and research strategies in thismodel organismhavemade it a unique and timely research tool for the study of human blood diseases. Recent studies modeling human myeloid malignancies in zebrafish have also highlighted the technical feasibility and clinical relevance of thesemodels. Careful validation of experimental protocols and standardization among laboratorieswill further enhance the application of zebrafish in the scientific communities and provide important insights to the personalized treatment ofmyeloid malignancies.
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Affiliation(s)
- Xiangguo Shi
- Division of Haematology, Medical Oncology and Bone Marrow Transplantation, Department of Medicine, LKS Faculty Medicine, The University of Hong Kong.
| | - Bai-Liang He
- Division of Haematology, Medical Oncology and Bone Marrow Transplantation, Department of Medicine, LKS Faculty Medicine, The University of Hong Kong.
| | - Alvin C H Ma
- Division of Haematology, Medical Oncology and Bone Marrow Transplantation, Department of Medicine, LKS Faculty Medicine, The University of Hong Kong.
| | - Anskar Y H Leung
- Division of Haematology, Medical Oncology and Bone Marrow Transplantation, Department of Medicine, LKS Faculty Medicine, The University of Hong Kong.
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14
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Czopka T. Insights into mechanisms of central nervous system myelination using zebrafish. Glia 2015; 64:333-49. [PMID: 26250418 DOI: 10.1002/glia.22897] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 12/12/2022]
Abstract
Myelin is the multi-layered membrane that surrounds most axons and is produced by oligodendrocytes in the central nervous system (CNS). In addition to its important role in enabling rapid nerve conduction, it has become clear in recent years that myelin plays additional vital roles in CNS function. Myelinating oligodendrocytes provide metabolic support to axons and active myelination is even involved in regulating forms of learning and memory formation. However, there are still large gaps in our understanding of how myelination by oligodendrocytes is regulated. The small tropical zebrafish has become an increasingly popular model organism to investigate many aspects of nervous system formation, function, and regeneration. This is mainly due to two approaches for which the zebrafish is an ideally suited vertebrate model--(1) in vivo live cell imaging using vital dyes and genetically encoded reporters, and (2) gene and target discovery using unbiased screens. This review summarizes how the use of zebrafish has helped understand mechanisms of oligodendrocyte behavior and myelination in vivo and discusses the potential use of zebrafish to shed light on important future questions relating to myelination in the context of CNS development, function and repair.
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Affiliation(s)
- Tim Czopka
- Institute of Neuronal Cell Biology, Technische Universität München, Munich, Germany
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Gerlai R. Embryonic alcohol exposure: Towards the development of a zebrafish model of fetal alcohol spectrum disorders. Dev Psychobiol 2015; 57:787-98. [DOI: 10.1002/dev.21318] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/08/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Robert Gerlai
- Department of Psychology; University of Toronto Mississsauga; 3359 Mississauga Road North Mississauga Ontario L5L 1C6 Canada
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16
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Haelterman NA, Jiang L, Li Y, Bayat V, Sandoval H, Ugur B, Tan KL, Zhang K, Bei D, Xiong B, Charng WL, Busby T, Jawaid A, David G, Jaiswal M, Venken KJT, Yamamoto S, Chen R, Bellen HJ. Large-scale identification of chemically induced mutations in Drosophila melanogaster. Genome Res 2015; 24:1707-18. [PMID: 25258387 PMCID: PMC4199363 DOI: 10.1101/gr.174615.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Forward genetic screens using chemical mutagens have been successful in defining the function of thousands of genes in eukaryotic model organisms. The main drawback of this strategy is the time-consuming identification of the molecular lesions causative of the phenotypes of interest. With whole-genome sequencing (WGS), it is now possible to sequence hundreds of strains, but determining which mutations are causative among thousands of polymorphisms remains challenging. We have sequenced 394 mutant strains, generated in a chemical mutagenesis screen, for essential genes on the Drosophila X chromosome and describe strategies to reduce the number of candidate mutations from an average of ∼3500 to 35 single-nucleotide variants per chromosome. By combining WGS with a rough mapping method based on large duplications, we were able to map 274 (∼70%) mutations. We show that these mutations are causative, using small 80-kb duplications that rescue lethality. Hence, our findings demonstrate that combining rough mapping with WGS dramatically expands the toolkit necessary for assigning function to genes.
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Affiliation(s)
- Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lichun Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Berrak Ugur
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kai Li Tan
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Theodore Busby
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adeel Jawaid
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gabriela David
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Koen J T Venken
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Verna and Mars Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
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Schierenbeck L, Ries D, Rogge K, Grewe S, Weisshaar B, Kruse O. Fast forward genetics to identify mutations causing a high light tolerant phenotype in Chlamydomonas reinhardtii by whole-genome-sequencing. BMC Genomics 2015; 16:57. [PMID: 25730202 PMCID: PMC4336690 DOI: 10.1186/s12864-015-1232-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High light tolerance of microalgae is a desired phenotype for efficient cultivation in large scale production systems under fluctuating outdoor conditions. Outdoor cultivation requires the use of either wild-type or non-GMO derived mutant strains due to safety concerns. The identification and molecular characterization of such mutants derived from untagged forward genetics approaches was limited previously by the tedious and time-consuming methods involving techniques such as classical meiotic mapping. The combination of mapping with next generation sequencing technologies offers alternative strategies to identify genes involved in high light adaptation in untagged mutants. RESULTS We used the model alga Chlamydomonas reinhardtii in a non-GMO mutation strategy without any preceding crossing step or pooled progeny to identify genes involved in the regulatory processes of high light adaptation. To generate high light tolerant mutants, wildtype cells were mutagenized only to a low extent, followed by a stringent selection. We performed whole-genome sequencing of two independent mutants hit1 and hit2 and the parental wildtype. The availability of a reference genome sequence and the removal of shared bakground variants between the wildtype strain and each mutant, enabled us to identify two single nucleotide polymorphisms within the same gene Cre02.g085050, hereafter called LRS1 (putative Light Response Signaling protein 1). These two independent single amino acid exchanges are both located in the putative WD40 propeller domain of the corresponding protein LRS1. Both mutants exhibited an increased rate of non-photochemical-quenching (NPQ) and an improved resistance against chemically induced reactive oxygen species. In silico analyses revealed homology of LRS1 to the photoregulatory protein COP1 in plants. CONCLUSIONS In this work we identified the nuclear encoded gene LRS1 as an essential factor for high light adaptation in C. reinhardtii. The causative random mutation within this gene was identified by a rapid and efficient method, avoiding any preceding crossing step, meiotic mapping, or pooled progeny. Our results open up new insights into mechanisms of high light adaptation in microalgae and at the same time provide a simplified strategy for non-GMO forward genetics, a crucial precondition that could result in the identification of key factors for economically relevant biological processes within algae.
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Affiliation(s)
- Lisa Schierenbeck
- />Department of Biology/Center for Biotechnology, Algae Biotechnology and Bioenergy, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - David Ries
- />Department of Biology/Center for Biotechnology, Genome Research, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Kristin Rogge
- />Department of Biology/Center for Biotechnology, Algae Biotechnology and Bioenergy, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Sabrina Grewe
- />Department of Biology/Center for Biotechnology, Algae Biotechnology and Bioenergy, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Bernd Weisshaar
- />Department of Biology/Center for Biotechnology, Genome Research, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Olaf Kruse
- />Department of Biology/Center for Biotechnology, Algae Biotechnology and Bioenergy, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
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18
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Dosch R. Next generation mothers: Maternal control of germline development in zebrafish. Crit Rev Biochem Mol Biol 2014; 50:54-68. [DOI: 10.3109/10409238.2014.985816] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Sander V, Patke S, Sahu S, Teoh CL, Peng Z, Chang YT, Davidson AJ. The small molecule probe PT-Yellow labels the renal proximal tubules in zebrafish. Chem Commun (Camb) 2014; 51:395-8. [PMID: 25407666 DOI: 10.1039/c4cc08075k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We report the development of a small fluorescent molecule, BDNCA3-D2, herein referred to as PT-Yellow. Soaking zebrafish embryos in PT-Yellow or intraperitoneal injection into adults results in non-toxic in vivo fluorescent labeling of the renal proximal tubules, the major site of blood filtrate reabsorption and a common target of injury in acute kidney injury. We demonstrate the applicability of this new compound as a rapid and simple readout for zebrafish kidney filtration and proximal tubule reabsorption function.
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Affiliation(s)
- Veronika Sander
- Department of Molecular Medicine & Pathology, The University of Auckland, Auckland 1142, New Zealand.
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20
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Preston MA, Macklin WB. Zebrafish as a model to investigate CNS myelination. Glia 2014; 63:177-93. [PMID: 25263121 DOI: 10.1002/glia.22755] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/12/2014] [Indexed: 12/18/2022]
Abstract
Myelin plays a critical role in proper neuronal function by providing trophic and metabolic support to axons and facilitating energy-efficient saltatory conduction. Myelination is influenced by numerous molecules including growth factors, hormones, transmembrane receptors and extracellular molecules, which activate signaling cascades that drive cellular maturation. Key signaling molecules and downstream signaling cascades controlling myelination have been identified in cell culture systems. However, in vitro systems are not able to faithfully replicate the complex in vivo signaling environment that occurs during development or following injury. Currently, it remains time-consuming and expensive to investigate myelination in vivo in rodents, the most widely used model for studying mammalian myelination. As such, there is a need for alternative in vivo myelination models, particularly ones that can test molecular mechanisms without removing oligodendrocyte lineage cells from their native signaling environment or disrupting intercellular interactions with other cell types present during myelination. Here, we review the ever-increasing role of zebrafish in studies uncovering novel mechanisms controlling vertebrate myelination. These innovative studies range from observations of the behavior of single cells during in vivo myelination as well as mutagenesis- and pharmacology-based screens in whole animals. Additionally, we discuss recent efforts to develop novel models of demyelination and oligodendrocyte cell death in adult zebrafish for the study of cellular behavior in real time during repair and regeneration of damaged nervous systems.
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Affiliation(s)
- Marnie A Preston
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado
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21
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Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 2014; 15:662-76. [PMID: 25139187 DOI: 10.1038/nrg3745] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.
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Affiliation(s)
- Korbinian Schneeberger
- Genome Plasticity and Computational Genetics, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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22
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Chakravarthy S, Sadagopan S, Nair A, Sukumaran SK. Zebrafish as anIn VivoHigh-Throughput Model for Genotoxicity. Zebrafish 2014; 11:154-66. [DOI: 10.1089/zeb.2013.0924] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Sathish Sadagopan
- Discovery Biology, Anthem Biosciences Private Limited, Bangalore, India
| | - Ayyappan Nair
- Discovery Biology, Anthem Biosciences Private Limited, Bangalore, India
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Abstract
In this review, we present an overview of the recent advances of genomic technologies applied to studies of fish species belonging to the superclass of Osteichthyes (bony fish) with a major emphasis on the infraclass of Teleostei, also called teleosts. This superclass that represents more than 50% of all known vertebrate species has gained considerable attention from genome researchers in the last decade. We discuss many examples that demonstrate that this highly deserved attention is currently leading to new opportunities for answering important biological questions on gene function and evolutionary processes. In addition to giving an overview of the technologies that have been applied for studying various fish species we put the recent advances in genome research on the model species zebrafish and medaka in the context of its impact for studies of all fish of the superclass of Osteichthyes. We thereby want to illustrate how the combined value of research on model species together with a broad angle perspective on all bony fish species will have a huge impact on research in all fields of fundamental science and will speed up applications in many societally important areas such as the development of new medicines, toxicology test systems, environmental sensing systems and sustainable aquaculture strategies.
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