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Bardhan A, Deiters A, Ettensohn CA. Conditional gene knockdowns in sea urchins using caged morpholinos. Dev Biol 2021; 475:21-29. [PMID: 33684434 DOI: 10.1016/j.ydbio.2021.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 02/28/2021] [Indexed: 12/01/2022]
Abstract
Echinoderms are important experimental models for analyzing embryonic development, but a lack of spatial and temporal control over gene perturbations has hindered developmental studies using these animals. Morpholino antisense oligonucleotides (MOs) have been used successfully by the echinoderm research community for almost two decades, and MOs remain the most widely used tool for acute gene knockdowns in these organisms. Echinoderm embryos develop externally and are optically transparent, making them ideally-suited to many light-based approaches for analyzing and manipulating development. Studies using zebrafish embryos have demonstrated the effectiveness of photoactivatable (caged) MOs for conditional gene knockdowns. Here we show that caged MOs, synthesized using nucleobase-caged monomers, provide light-regulated control over gene expression in sea urchin embryos. Our work provides the first robust approach for conditional gene silencing in this prominent model system.
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Affiliation(s)
- Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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2
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Schmitt C, Peterson E, Willis A, Kumar N, McManus M, Subbiah S, Crago J. Transgenerational effects of developmental exposure to chlorpyrifos-oxon in zebrafish (DANIO RERIO). Toxicol Appl Pharmacol 2020; 408:115275. [DOI: 10.1016/j.taap.2020.115275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 02/08/2023]
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3
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Comparative analyses of the neurobehavioral, molecular, and enzymatic effects of organophosphates on embryo-larval zebrafish (Danio rerio). Neurotoxicol Teratol 2019; 73:67-75. [DOI: 10.1016/j.ntt.2019.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 12/15/2022]
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4
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Pattanayak S, Vázquez-Maldonado LA, Deiters A, Chen JK. Combinatorial control of gene function with wavelength-selective caged morpholinos. Methods Enzymol 2019; 624:69-88. [PMID: 31370936 DOI: 10.1016/bs.mie.2019.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Caged morpholino oligonucleotides (cMOs) are useful research tools in developmental biology because they allow spatiotemporal control of gene expression in whole organisms. While cMOs are usually triggered by light of a single wavelength, the introduction of spectrally distinct chromophores can enable combinatorial regulation of multiple genes. This chapter describes the general principles and methods of wavelength-selective cMO design and synthesis from commercially available reagents. Synthetic protocols for the linkers and the two-step cMO assembly are described in detail, as well as the microinjection and photoactivation techniques. Following these protocols, spectrally separated cyclic cMOs for multiple genes of interest can be prepared, enabling their inhibition in zebrafish embryos and other animal models.
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Affiliation(s)
- Sankha Pattanayak
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, United States
| | | | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States.
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, United States; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States.
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5
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Skugor A, Tveiten H, Krasnov A, Andersen O. Knockdown of the germ cell factor Dead end induces multiple transcriptional changes in Atlantic cod (Gadus morhua) hatchlings. Anim Reprod Sci 2013; 144:129-37. [PMID: 24439024 DOI: 10.1016/j.anireprosci.2013.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 11/05/2013] [Accepted: 12/18/2013] [Indexed: 11/30/2022]
Abstract
The RNA binding protein Dead end (DnD) is essential for maintaining viable germ cells in vertebrates and silencing of the gene has been demonstrated to cause sterility in several mammalian and fish species. Here we investigated transcriptome changes in hatched larvae of Atlantic cod induced by DnD knockdown using morpholino oligonucleotides (MO) injected in two-cell embryos. Whereas no fluorescently labeled germ cells were shown in embryos coinjected with dnd MO and nanos3 3'UTR coupled to green fluorescent protein, DnD knockdown had no visible effect on the number and location of Vasa protein positive cells in larvae. However, quantitative real-time RT-PCR (qPCR) revealed decreased vasa, nanos3 and tudor domain containing protein 7 mRNA expression and genome-wide oligonucleotide microarray analyses indicated profound suppression of genes involved in development and regulation of the reproductive system. DnD morphants showed lowered expression of genes encoding proteins involved in lipid, retinoid, cholesterol and steroid metabolism, including those with roles in sex hormone metabolism. Biotransformation of lipophilic compounds appeared suppressed too, as evidenced by down-regulation of several key genes from the phases 1 and 2 detoxification pathways. Effects of DnD silencing were highly pleiotropic and consisted of endocrine and metabolic changes, massive induction of histones and suppression of diverse developmental processes, including erythropoiesis and formation of extracellular matrix. While transient inhibition of dnd mRNA translation did not block development of primordial germ cells until hatch, results suggested that ablation of DnD might have major indirect consequences, including suppression of reproductive functions.
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Affiliation(s)
- Adrijana Skugor
- Nofima, Osloveien 1, N-1432 Ås, Norway; Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, N-1432 Ås, Norway.
| | | | | | - Oivind Andersen
- Nofima, Osloveien 1, N-1432 Ås, Norway; Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, N-1432 Ås, Norway.
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6
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Yin W, Hu B. Knockdown of Lingo1b protein promotes myelination and oligodendrocyte differentiation in zebrafish. Exp Neurol 2013; 251:72-83. [PMID: 24262204 DOI: 10.1016/j.expneurol.2013.11.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 10/29/2013] [Accepted: 11/08/2013] [Indexed: 12/23/2022]
Abstract
Demyelinating diseases include multiple sclerosis, which is a neurodegenerative disease characterized by immune attacks on the central nervous system (CNS), resulting in myelin sheath damage and axonal loss. Leucine-rich repeat and immunoglobulin domain-containing neurite outgrowth inhibitory protein (Nogo) receptor-interacting protein-1 (LINGO-1) have been identified as a negative regulator of oligodendrocytes differentiation. Targeted LINGO-1 inhibition promotes neuron survival, axon regeneration, oligodendrocyte differentiation, and remyelination in diverse animal models. Although studies in rodent models have extended our understanding of LINGO-1, its roles in neural development and myelination in zebrafish (Danio rerio) are not yet clear. In this study, we cloned the zebrafish homolog of the human LINGO-1 and found that lingo1b regulated myelination and oligodendrocyte differentiation. The expression of lingo1b started 1 (mRNA) and 2 (protein) days post-fertilization (dpf) in the CNS. Morpholino oligonucleotide knockdown of lingo1b resulted in developmental abnormalities, including less dark pigment, small eyes, and a curly spinal cord. The lack of lingo1b enhanced myelination and oligodendrocyte differentiation during embryogenesis. Furthermore, immunohistochemistry and movement analysis showed that lingo1b was involved in the axon development of primary motor neurons. These results suggested that Lingo1b protein functions as a negative regulator of myelination and oligodendrocyte differentiation during zebrafish development.
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Affiliation(s)
- Wu Yin
- CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Bing Hu
- CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
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7
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Vergara MN, Canto-Soler MV. Rediscovering the chick embryo as a model to study retinal development. Neural Dev 2012; 7:22. [PMID: 22738172 PMCID: PMC3541172 DOI: 10.1186/1749-8104-7-22] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/22/2012] [Indexed: 01/20/2023] Open
Abstract
The embryonic chick occupies a privileged place among animal models used in developmental studies. Its rapid development and accessibility for visualization and experimental manipulation are just some of the characteristics that have made it a vertebrate model of choice for more than two millennia. Until a few years ago, the inability to perform genetic manipulations constituted a major drawback of this system. However, the completion of the chicken genome project and the development of techniques to manipulate gene expression have allowed this classic animal model to enter the molecular age. Such techniques, combined with the embryological manipulations that this system is well known for, provide a unique toolkit to study the genetic basis of neural development. A major advantage of these approaches is that they permit targeted gene misexpression with extremely high spatiotemporal resolution and over a large range of developmental stages, allowing functional analysis at a level, speed and ease that is difficult to achieve in other systems. This article provides a general overview of the chick as a developmental model focusing more specifically on its application to the study of eye development. Special emphasis is given to the state of the art of the techniques that have made gene gain- and loss-of-function studies in this model a reality. In addition, we discuss some methodological considerations derived from our own experience that we believe will be beneficial to researchers working with this system.
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Affiliation(s)
- M Natalia Vergara
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Smith Building 3023, 400 N Broadway, Baltimore, MD 21287-9257, USA
| | - M Valeria Canto-Soler
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Smith Building 3023, 400 N Broadway, Baltimore, MD 21287-9257, USA
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Timme-Laragy AR, Karchner SI, Hahn ME. Gene knockdown by morpholino-modified oligonucleotides in the zebrafish (Danio rerio) model: applications for developmental toxicology. Methods Mol Biol 2012; 889:51-71. [PMID: 22669659 PMCID: PMC4218736 DOI: 10.1007/978-1-61779-867-2_5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The zebrafish (Danio rerio) has long been used as a model for developmental biology, making it an excellent model to use also in developmental toxicology. The many advantages of zebrafish include their small size, prolific spawning, rapid development, and transparent embryos. They can be easily manipulated genetically through the use of transgenic technology and gene knockdown via morpholino-modified antisense oligonucleotides (MOs). Knocking down specific genes to assess their role in the response to toxicant exposure provides a way to further our knowledge of how developmental toxicants work on a molecular and mechanistic level while establishing a relationship between these molecular events and morphological, behavioral, and/or physiological effects (i.e., phenotypic anchoring). In this chapter, we address important considerations for using MOs to study developmental toxicology in zebrafish embryos and provide a protocol for their use.
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Bedell VM, Westcot SE, Ekker SC. Lessons from morpholino-based screening in zebrafish. Brief Funct Genomics 2011; 10:181-8. [PMID: 21746693 PMCID: PMC3144740 DOI: 10.1093/bfgp/elr021] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Morpholino oligonucleotides (MOs) are an effective, gene-specific antisense knockdown technology used in many model systems. Here we describe the application of MOs in zebrafish (Danio rerio) for in vivo functional characterization of gene activity. We summarize our screening experience beginning with gene target selection. We then discuss screening parameter considerations and data and database management. Finally, we emphasize the importance of off-target effect management and thorough downstream phenotypic validation. We discuss current morpholino limitations, including reduced stability when stored in aqueous solution. Advances in MO technology now provide a measure of spatiotemporal control over MO activity, presenting the opportunity for incorporating more finely tuned analyses into MO-based screening. Therefore, with careful management, MOs remain a valuable tool for discovery screening as well as individual gene knockdown analysis.
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Shestopalov IA, Chen JK. Spatiotemporal control of embryonic gene expression using caged morpholinos. Methods Cell Biol 2011; 104:151-72. [PMID: 21924162 DOI: 10.1016/b978-0-12-374814-0.00009-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Embryonic development depends on spatial and temporal control of gene function, and deciphering the molecular mechanisms that underlie pattern formation requires methods for perturbing gene expression with similar precision. Emerging chemical technologies can enable such perturbations, as exemplified by the use of caged morpholino (cMO) oligonucleotides to photo-inactivate genes in zebrafish embryos with spatiotemporal control. This chapter describes general principles for cMO design and methods for cMO assembly in three steps from commercially available reagents. Experimental techniques for the microinjection and photoactivation of these reagents are described in detail, as well as the preparation and application of caged fluorescein dextran (cFD) for labeling irradiated cells. Using these protocols, cMOs can be effective tools for functional genomic studies in zebrafish and other model organisms.
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Affiliation(s)
- Ilya A Shestopalov
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford,California, USA
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11
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Feng Y, Xu Q. Pivotal role of hmx2 and hmx3 in zebrafish inner ear and lateral line development. Dev Biol 2010; 339:507-18. [DOI: 10.1016/j.ydbio.2009.12.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 10/20/2022]
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12
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Bill BR, Petzold AM, Clark KJ, Schimmenti LA, Ekker SC. A primer for morpholino use in zebrafish. Zebrafish 2009; 6:69-77. [PMID: 19374550 DOI: 10.1089/zeb.2008.0555] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Morpholino oligonucleotides are the most common anti-sense "knockdown" technique used in zebrafish (Danio rerio). This review discusses common practices for the design, preparation, and deployment of morpholinos in this vertebrate model system. Off-targeting effects of morpholinos are discussed as well as method to minimize this potentially confounding variable via co-injection of a tP53-targeting morpholino. Finally, new uses of morpholinos are summarized and contextualized with respect to the complementary, DNA-based knockout technologies recently developed for zebrafish.
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Affiliation(s)
- Brent R Bill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
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Jenny MJ, Karchner SI, Franks DG, Woodin BR, Stegeman JJ, Hahn ME. Distinct roles of two zebrafish AHR repressors (AHRRa and AHRRb) in embryonic development and regulating the response to 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol Sci 2009; 110:426-41. [PMID: 19494032 DOI: 10.1093/toxsci/kfp116] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The aryl hydrocarbon receptor (AHR) repressor (AHRR), an AHR-related basic helix-loop-helix/Per-AHR nuclear translocator-Sim protein, is regulated by an AHR-dependent mechanism and acts as a transcriptional repressor of AHR function. Resulting from a teleost-specific genome duplication, zebrafish have two AHRR genes (AHRRa and AHRRb), but their functions in vivo are not well understood. We used antisense morpholino oligonucleotides (MOs) in zebrafish embryos and a zebrafish liver cell line (ZF-L) to characterize the interaction of AHRRs and AHRs in normal embryonic development, AHR signaling, and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity. Zebrafish embryos exposed to TCDD (2 and 8nM) during early development showed strong induction of CYP1A, AHRRa, and AHRRb at 48 and 72 hours post-fertilization (hpf). An MO targeting AHR2 inhibited TCDD-induced expression of CYP1A, AHRRa, and AHRRb by 84-95% in 48 hpf embryos, demonstrating a primary role for AHR2 in mediating AHRR induction. Dual MO knockdown of both AHRRs in ZF-L cells enhanced TCDD induction of CYP1A, but not other CYP1 genes. In embryos, dual knockdown of AHRRs, or knockdown of AHRRb alone, enhanced the induction of CYP1A, CYP1B1, and CYP1C1 by TCDD and decreased the constitutive expression of Sox9b. In contrast, knockdown of AHRRa did not affect Sox9b expression or CYP1 inducibility. Embryos microinjected with each of two different MOs targeting AHRRa and exposed to dimethyl sulfoxide (DMSO) displayed developmental phenotypes resembling those typical of TCDD-exposed embryos (pericardial edema and lower jaw malformations). In contrast, no developmental phenotypes were observed in DMSO-exposed AHRRb morphants. These data demonstrate distinct roles of AHRRa and AHRRb in regulating AHR signaling in vivo and suggest that they have undergone subfunction partitioning since the teleost-specific genome duplication.
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Affiliation(s)
- Matthew J Jenny
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA
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Young DD, Lusic H, Lively MO, Yoder JA, Deiters A. Gene silencing in mammalian cells with light-activated antisense agents. Chembiochem 2009; 9:2937-40. [PMID: 19021142 DOI: 10.1002/cbic.200800627] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Douglas D Young
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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Alcaraz-Pérez F, Mulero V, Cayuela ML. Application of the dual-luciferase reporter assay to the analysis of promoter activity in Zebrafish embryos. BMC Biotechnol 2008; 8:81. [PMID: 18954456 PMCID: PMC2596795 DOI: 10.1186/1472-6750-8-81] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 10/27/2008] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The dual-luciferase assay has been widely used in cell lines to determine rapidly but accurately the activity of a given promoter. Although this strategy has proved very useful, it does not allow the promoter and gene function to be analyzed in the context of the whole organism. RESULTS Here, we present a rapid and sensitive assay based on the classical dual-luciferase reporter technique which can be used as a new tool to characterize the minimum promoter region of a gene as well as the in vivo response of inducible promoters to different stimuli. We illustrate the usefulness of this system for studying both constitutive (telomerase) and inducible (NF-kappaB-dependent) promoters. The flexibility of this assay is demonstrated by induction of the NF-kappaB-dependent promoters using simultaneous microinjection of different pathogen-associated molecular patterns as well as with the use of morpholino-gene mediated knockdown. CONCLUSION This assay has several advantages compared with the classical in vitro (cell lines) and in vivo (transgenic mice) approaches. Among others, the assay allows a rapid and quantitative measurement of the effects of particular genes or drugs in a given promoter in the context of a whole organism and it can also be used in high throughput screening experiments.
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Affiliation(s)
- Francisca Alcaraz-Pérez
- Research Unit, Department of Surgery, University Hospital Virgen de la Arrixaca, 30120 Murcia, Spain.
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Kamachi Y, Okuda Y, Kondoh H. Quantitative assessment of the knockdown efficiency of morpholino antisense oligonucleotides in zebrafish embryos using a luciferase assay. Genesis 2008; 46:1-7. [PMID: 18196596 DOI: 10.1002/dvg.20361] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Despite the broad use of morpholino antisense oligonucleotides (MO) to knockdown gene function in zebrafish embryos, the efficiency of this method has not been successfully assessed, particularly in the cases of translation-blocking MOs. In our current study, we describe a luciferase assay-based system that can monitor the MO knockdown levels in zebrafish by the use of a fusion reporter construct containing the 5'-mRNA sequence of the gene of interest and the luciferase coding sequence. The decrease in luciferase activity in zebrafish embryos that have been coinjected with this reporter RNA construct and a MO that targets the gene of interest correlated well with the level of inhibition of the corresponding endogenous protein synthesis, and also with the appearance of a knockdown phenotype. This indicates the usefulness of our method. We have also found that MOs can exert considerable knockdown effects upon unintended gene targets if 15 bases or longer of contiguous homology exists between these genes and the 25-base MO in question. Our quantitative assessment method also reveals, however, that an effective and specific knockdown can be achieved when employing a strategy that takes advantage of the synergistic effect of double MOs used at low levels.
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Affiliation(s)
- Yusuke Kamachi
- Graduate School of Frontier Biosciences, Developmental Biology Group, Osaka University, Suita, Japan.
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Deiters A, Yoder JA. Conditional transgene and gene targeting methodologies in zebrafish. Zebrafish 2008; 3:415-29. [PMID: 18377222 DOI: 10.1089/zeb.2006.3.415] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The zebrafish has become a powerful tool for dissecting vertebrate gene function during embryogenesis. Numerous molecular systems have been developed to examine gene function in zebrafish, including transgenics for creating lineage-tracer lines of zebrafish that express a fluorescent protein as a marker for specific populations of cells, and antisense strategies, primarily morpholinos, for knocking down gene function. The focus of this review is to summarize the pros and cons of the currently available systems for functional genomics in zebrafish, and to discuss the need for future methodologies.
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Affiliation(s)
- Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
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Stock DW. Zebrafish dentition in comparative context. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2007; 308:523-49. [PMID: 17607704 DOI: 10.1002/jez.b.21187] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Studies of the zebrafish (Danio rerio) promise to contribute much to an understanding of the developmental genetic mechanisms underlying diversification of the vertebrate dentition. Tooth development, structure, and replacement in the zebrafish largely reflect the primitive condition of jawed vertebrates, providing a basis for comparison with features of the more extensively studied mammalian dentition. A distinctive derived feature of the zebrafish dentition is restriction of teeth to a single pair of pharyngeal bones. Such reduction of the dentition, characteristic of the order Cypriniformes, has never been reversed, despite subsequent and extensive diversification of the group in numbers of species and variety of feeding modes. Studies of the developmental genetic mechanism of dentition reduction in the zebrafish suggest a potential explanation for irreversibility in that tooth loss seems to be associated with loss of developmental activators rather than gain of repressors. The zebrafish and other members of the family Cyprinidae exhibit species-specific numbers and arrangements of pharyngeal teeth, and extensive variation in tooth shape also occurs within the family. Mutant screens and experimental alteration of gene expression in the zebrafish are likely to yield variant tooth number and shape phenotypes that can be compared with those occurring naturally within the Cyprinidae. Such studies may reveal the relative contribution to trends in dental evolution of biases in the generation of variation and sorting of this variation by selection or drift.
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Affiliation(s)
- David W Stock
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309-0334, USA.
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Abstract
Molecular biologists have long dreamed of switching genes on and off at will in any part of the body during embryonic development. Their dream is now coming true thanks to the transparency of the embryonic body of the zebrafish ( Danio rerio), which has made gene manipulation by photoillumination possible.
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Affiliation(s)
- Hitoshi Okamoto
- Laboratory for Developmental Gene Regulation, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Pickart MA, Klee EW, Nielsen AL, Sivasubbu S, Mendenhall EM, Bill BR, Chen E, Eckfeldt CE, Knowlton M, Robu ME, Larson JD, Deng Y, Schimmenti LA, Ellis LB, Verfaillie CM, Hammerschmidt M, Farber SA, Ekker SC. Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome. PLoS One 2006; 1:e104. [PMID: 17218990 PMCID: PMC1766371 DOI: 10.1371/journal.pone.0000104] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Accepted: 11/12/2006] [Indexed: 11/18/2022] Open
Abstract
Background Understanding the functional role(s) of the more than 20,000 proteins of the vertebrate genome is a major next step in the post-genome era. The approximately 4,000 co-translationally translocated (CTT) proteins – representing the vertebrate secretome – are important for such vertebrate-critical processes as organogenesis. However, the role(s) for most of these genes is currently unknown. Results We identified 585 putative full-length zebrafish CTT proteins using cross-species genomic and EST-based comparative sequence analyses. We further investigated 150 of these genes (Figure 1) for unique function using morpholino-based analysis in zebrafish embryos. 12% of the CTT protein-deficient embryos resulted in specific developmental defects, a notably higher rate of gene function annotation than the 2%–3% estimate from random gene mutagenesis studies. Conclusion(s) This initial collection includes novel genes required for the development of vascular, hematopoietic, pigmentation, and craniofacial tissues, as well as lipid metabolism, and organogenesis. This study provides a framework utilizing zebrafish for the systematic assignment of biological function in a vertebrate genome.
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Affiliation(s)
- Michael A. Pickart
- Department of Oral Sciences and Minnesota Craniofacial Research Training Program MinnCResT, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eric W. Klee
- Laboratory Medicine and Pathology and Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Aubrey L. Nielsen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Sridhar Sivasubbu
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eric M. Mendenhall
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, and Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brent R. Bill
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Pediatrics, Genetics and Metabolism and Department of Ophthalmology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eleanor Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Craig E. Eckfeldt
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, and Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michelle Knowlton
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Mara E. Robu
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Oral Sciences and Minnesota Craniofacial Research Training Program MinnCResT, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jon D. Larson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Yun Deng
- Carnegie Institute of Washington, Baltimore, Maryland, United States of America
| | - Lisa A. Schimmenti
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Pediatrics, Genetics and Metabolism and Department of Ophthalmology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lynda B.M. Ellis
- Laboratory Medicine and Pathology and Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Catherine M. Verfaillie
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, and Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Steven A. Farber
- Carnegie Institute of Washington, Baltimore, Maryland, United States of America
| | - Stephen C. Ekker
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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21
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Takahashi N, Dawid IB. Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis. Nucleic Acids Res 2005; 33:e120. [PMID: 16061934 PMCID: PMC1182173 DOI: 10.1093/nar/gni122] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Zebrafish has become a favorite model organism not only in genetics and developmental biology, but also for the study of cancer, neuroscience and metabolism. However, strategies for reverse genetics in zebrafish are mostly limited to the use of antisense oligonucleotides, and therefore the development of other targeting methods is highly desirable. Here, we report an approach to gene targeting in this system in which single-stranded oligonucleotides and zebrafish Rad52 protein are employed. It has been proposed that a single-stranded oligonucleotide containing a mutation can be incorporated into the genome by annealing to the single-stranded region of the lagging strand of the replication fork. Rad52 is expected to accelerate the annealing step. In vitro experiments using purified truncated Rad52 proteins and replication protein A (RPA) showed that annealing of oligonucleotides is accelerated by Rad52 in the presence of RPA. We developed a simple and sensitive PCR-based method to detect point mutations in the genome. In exploratory experiments, we found that microinjection of single-stranded oligonucleotide targeted to a specific gene together with truncated Rad52 into zebrafish embryos resulted in a low level of recombinant copies in 3 of the 80 embryos tested under these conditions.
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Affiliation(s)
| | - Igor B. Dawid
- To whom correspondence should be addressed. Tel: +1 301 496 4448; Fax: +1 301 496 0243;
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