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Torres-Dowdall J, Karagic N, Prabhukumar F, Meyer A. Differential Regulation of Opsin Gene Expression in Response to Internal and External Stimuli. Genome Biol Evol 2024; 16:evae125. [PMID: 38860496 DOI: 10.1093/gbe/evae125] [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: 07/23/2023] [Revised: 05/24/2024] [Accepted: 06/01/2024] [Indexed: 06/12/2024] Open
Abstract
Determining how internal and external stimuli interact to determine developmental trajectories of traits is a challenge that requires the integration of different subfields of biology. Internal stimuli, such as hormones, control developmental patterns of phenotypic changes, which might be modified by external environmental cues (e.g. plasticity). Thyroid hormone (TH) modulates the timing of opsin gene expression in developing Midas cichlid fish (Amphilophus citrinellus). Moreover, fish reared in red light accelerate this developmental timing compared to fish reared in white light. Hence, we hypothesized that plasticity caused by variation in light conditions has coopted the TH signaling pathway to induce changes in opsin gene expression. We treated Midas cichlids with TH and crossed this treatment with two light conditions, white and red. We observed that not only opsin expression responded similarly to TH and red light but also that, at high TH levels, there is limited capacity for light-induced plasticity. Transcriptomic analysis of the eye showed that genes in the TH pathway were affected by TH, but not by light treatments. Coexpression network analyses further suggested that response to light was independent of the response to TH manipulations. Taken together, our results suggest independent mechanisms mediating development and plasticity during development of opsin gene expression, and that responses to environmental stimuli may vary depending on internal stimuli. This conditional developmental response to external factors depending on internal ones (e.g. hormones) might play a fundamental role in the patterns of phenotypic divergence observed in Midas cichlids and potentially other organisms.
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Affiliation(s)
- Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Nidal Karagic
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Femina Prabhukumar
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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2
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Wang YY, Liang XF, Lu K. Knockout of SWS2 in zebrafish (Danio rerio) reveals its roles in feeding and phototactic behaviors. Gene 2024; 897:148059. [PMID: 38043833 DOI: 10.1016/j.gene.2023.148059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 10/30/2023] [Accepted: 11/30/2023] [Indexed: 12/05/2023]
Abstract
Common ancestor of vertebrates had four cone opsin subfamilies to obtain color vision: ultraviolet-sensitive (SWS1), blue-sensitive (SWS2), middle wavelength sensitive (RH2) and long wavelength sensitive (LWS). Nevertheless, eutherian mammals had lost the SWS2 and RH2 opsins during their nocturnal lifestyle. Many studies had demonstrated the role of SWS1 and LWS cones in feeding, mate choice and skin pigment cell formation. However, the role of SWS2 and RH2 cones remain elusive. In the present study, we used an ideal model visual system, zebrafish, which still have the four cone opsins, to generate a SWS2 knockout zebrafish line. Through various behavioral test, we found that sws2-/- zebrafish larvae exhibited increased food intake compared with WT. Additionally, there were significantly increased the gene expression of phototransduction pathways in sws2-/- zebrafish larvae. Compared to WT, mutant zebrafish showed weaker phototaxis of red light and changed sensitivity of yellow, red and blue lights. But both mutant and WT zebrafish preferred the red light than other wavelengths of light. Taken together, we proposed that SWS2 cone is not necessary for feeding and phototaxis in zebrafish.
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Affiliation(s)
- Yu-Ye Wang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China.
| | - Ke Lu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
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3
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Lu K, Liang XF, Tang SL, Wu J, Zhang L, Wang Y, Chai F. Role of short-wave-sensitive 1 (sws1) in cone development and first feeding in larval zebrafish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:801-813. [PMID: 37495865 DOI: 10.1007/s10695-023-01213-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
Color vision is mediated by the expression of different major visual pigment proteins (opsins) on retinal photoreceptors. Vertebrates have four classes of cone opsins that are most sensitive to different wavelengths of light: short wavelength sensitive 1 (SWS1), short wavelength sensitive 2 (SWS2), medium wavelength sensitive (RH2), and long wavelength sensitive (LWS). UV wavelengths play important roles in foraging and communication. However, direct evidence provide links between sws1 and first feeding is lacking. Here, CRISPR/Cas9 technology was performed to generate mutant zebrafish lines with sws1 deletion. sws1 mutant zebrafish larvae exhibited decreased sws1, rh2-2, and lws1 expression, and increased rod gene (rho and gnat1) expression. Furthermore, the sws1-deficient larvae exhibited significantly reduced food intake, and the orexigenic genes npy and agrp signaling were upregulated at 6 days postfertilization (dpf). The transcription expression of sws1 and rh2-3 genes decreased in sws1-/- adults compared to wild type. Surprisingly, the results of feeding at the adult stage were not the same with larvae. sws1 deficiency did not affect food intake and appetite gene expression at adult stages. These results reveal a role for sws1 in normal cone development and first feeding in larval zebrafish.
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Affiliation(s)
- Ke Lu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
| | - Shu-Lin Tang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Jiaqi Wu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Lixin Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Yuye Wang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Farui Chai
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
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4
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Angueyra JM, Kunze VP, Patak LK, Kim H, Kindt K, Li W. Transcription factors underlying photoreceptor diversity. eLife 2023; 12:e81579. [PMID: 36745553 PMCID: PMC9901936 DOI: 10.7554/elife.81579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/22/2023] [Indexed: 02/07/2023] Open
Abstract
During development, retinal progenitors navigate a complex landscape of fate decisions to generate the major cell classes necessary for proper vision. Transcriptional regulation is critical to generate diversity within these major cell classes. Here, we aim to provide the resources and techniques required to identify transcription factors necessary to generate and maintain diversity in photoreceptor subtypes, which are critical for vision. First, we generate a key resource: a high-quality and deep transcriptomic profile of each photoreceptor subtype in adult zebrafish. We make this resource openly accessible, easy to explore, and have integrated it with other currently available photoreceptor transcriptomic datasets. Second, using our transcriptomic profiles, we derive an in-depth map of expression of transcription factors in photoreceptors. Third, we use efficient CRISPR-Cas9 based mutagenesis to screen for null phenotypes in F0 larvae (F0 screening) as a fast, efficient, and versatile technique to assess the involvement of candidate transcription factors in the generation of photoreceptor subtypes. We first show that known phenotypes can be easily replicated using this method: loss of S cones in foxq2 mutants and loss of rods in nr2e3 mutants. We then identify novel functions for the transcription factor Tbx2, demonstrating that it plays distinct roles in controlling the generation of all photoreceptor subtypes within the retina. Our study provides a roadmap to discover additional factors involved in this process. Additionally, we explore four transcription factors of unknown function (Skor1a, Sall1a, Lrrfip1a, and Xbp1), and find no evidence for their involvement in the generation of photoreceptor subtypes. This dataset and screening method will be a valuable way to explore the genes involved in many other essential aspects of photoreceptor biology.
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Affiliation(s)
- Juan M Angueyra
- Unit of Retinal Neurophysiology, National Eye Institute, National Institutes of HealthBethesdaUnited States
| | - Vincent P Kunze
- Unit of Retinal Neurophysiology, National Eye Institute, National Institutes of HealthBethesdaUnited States
| | - Laura K Patak
- Unit of Retinal Neurophysiology, National Eye Institute, National Institutes of HealthBethesdaUnited States
| | - Hailey Kim
- Unit of Retinal Neurophysiology, National Eye Institute, National Institutes of HealthBethesdaUnited States
| | - Katie Kindt
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaUnited States
| | - Wei Li
- Unit of Retinal Neurophysiology, National Eye Institute, National Institutes of HealthBethesdaUnited States
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5
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The Developmental Progression of Eight Opsin Spectral Signals Recorded from the Zebrafish Retinal Cone Layer Is Altered by the Timing and Cell Type Expression of Thyroxin Receptor β2 (trβ2) Gain-Of-Function Transgenes. eNeuro 2022; 9:ENEURO.0326-22.2022. [PMID: 36351817 PMCID: PMC9718360 DOI: 10.1523/eneuro.0326-22.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/10/2022] Open
Abstract
Zebrafish retinal cone signals shift in spectral shape through larval, juvenile, and adult development as expression patterns of eight cone-opsin genes change. An algorithm extracting signal amplitudes for the component cone spectral types is developed and tested on two thyroxin receptor β2 (trβ2) gain-of-function lines crx:mYFP-2A-trβ2 and gnat2:mYFP-2A-trβ2, allowing correlation between opsin signaling and opsin immunoreactivity in lines with different developmental timing and cell-type expression of this red-opsin-promoting transgene. Both adult transgenics became complete, or nearly complete, "red-cone dichromats," with disproportionately large long-wavelength-sensitive (LWS)1 opsin amplitudes as compared with controls, where LWS1 and LWS2 amplitudes were about equal, and significant signals from SWS1, SWS2, and Rh2 opsins were detected. But in transgenic larvae and juveniles of both lines it was LWS2 amplitudes that increased, with LWS1 cone signals rarely encountered. In gnat2:mYFP-2A-trβ2 embryos at 5 d postfertilization (dpf), red-opsin immunoreactive cone density doubled, but red-opsin amplitudes (LWS2) increased <10%, and green-opsin, blue-opsin, and UV-opsin signals were unchanged, despite co-expressed red opsins, and the finding that an sws1 UV-opsin reporter gene was shut down by the gnat2:mYFP-2A-trβ2 transgene. By contrast both LWS2 red-cone amplitudes and the density of red-cone immunoreactivity more than doubled in 5-dpf crx:mYFP-2A-trβ2 embryos, while UV-cone amplitudes were reduced 90%. Embryonic cones with trβ2 gain-of-function transgenes were morphologically distinct from control red, blue or UV cones, with wider inner segments and shorter axons than red cones, suggesting cone spectral specification, opsin immunoreactivity and shape are influenced by the abundance and developmental timing of trβ2 expression.
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6
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Krueger LA, Morris AC. Eyes on CHARGE syndrome: Roles of CHD7 in ocular development. Front Cell Dev Biol 2022; 10:994412. [PMID: 36172288 PMCID: PMC9512043 DOI: 10.3389/fcell.2022.994412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
The development of the vertebrate visual system involves complex morphogenetic interactions of cells derived from multiple embryonic lineages. Disruptions in this process are associated with structural birth defects such as microphthalmia, anophthalmia, and coloboma (collectively referred to as MAC), and inherited retinal degenerative diseases such as retinitis pigmentosa and allied dystrophies. MAC and retinal degeneration are also observed in systemic congenital malformation syndromes. One important example is CHARGE syndrome, a genetic disorder characterized by coloboma, heart defects, choanal atresia, growth retardation, genital abnormalities, and ear abnormalities. Mutations in the gene encoding Chromodomain helicase DNA binding protein 7 (CHD7) cause the majority of CHARGE syndrome cases. However, the pathogenetic mechanisms that connect loss of CHD7 to the ocular complications observed in CHARGE syndrome have not been identified. In this review, we provide a general overview of ocular development and congenital disorders affecting the eye. This is followed by a comprehensive description of CHARGE syndrome, including discussion of the spectrum of ocular defects that have been described in this disorder. In addition, we discuss the current knowledge of CHD7 function and focus on its contributions to the development of ocular structures. Finally, we discuss outstanding gaps in our knowledge of the role of CHD7 in eye formation, and propose avenues of investigation to further our understanding of how CHD7 activity regulates ocular and retinal development.
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Affiliation(s)
| | - Ann C. Morris
- Department of Biology, University of Kentucky, Lexington, KY, United States
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7
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Fogg LG, Cortesi F, Lecchini D, Gache C, Marshall NJ, de Busserolles F. Development of dim-light vision in the nocturnal reef fish family Holocentridae I: retinal gene expression. J Exp Biol 2022; 225:276222. [PMID: 35929500 PMCID: PMC9482368 DOI: 10.1242/jeb.244513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/24/2022] [Indexed: 11/20/2022]
Abstract
Developmental changes to the visual systems of animals are often associated with ecological shifts. Reef fishes experience a change in habitat between larval life in the shallow open ocean to juvenile and adult life on the reef. Some species also change their lifestyle over this period and become nocturnal. While these ecological transitions are well documented, little is known about the ontogeny of nocturnal reef fish vision. Here, we used transcriptomics to investigate visual development in 12 representative species from both subfamilies, Holocentrinae (squirrelfishes) and Myripristinae (soldierfishes), in the nocturnal coral reef fish family, Holocentridae. Results revealed that the visual systems of holocentrids are initially well adapted to photopic conditions with pre-settlement larvae having high levels of cone opsin gene expression and a broad cone opsin gene repertoire (8 genes). At reef settlement, holocentrids started to invest more in their scotopic visual system, and compared with adults, showed upregulation of genes involved in cell differentiation/proliferation. By adulthood, holocentrids had well developed scotopic vision with high levels of rod opsin gene expression, reduced cone opsin gene expression and repertoire (1–4 genes) and upregulated phototransduction genes. Finally, although the two subfamilies shared similar ecologies across development, their visual systems diverged after settlement, with Myripristinae investing more in scotopic vision than Holocentrinae. Hence, both ecology and phylogeny are likely to determine the development of the holocentrid visual system. Summary: Coral reef fishes in the family Holocentridae remodel their retina at the molecular level to adapt to a nocturnal lifestyle during development.
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Affiliation(s)
- Lily G Fogg
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David Lecchini
- PSL Research University, EPHE-UPVD-CNRS, UAR3278 CRIOBE, 98729 Papetoai, Moorea, French Polynesia, France.,Laboratoire d'Excellence "CORAIL", Paris, France
| | - Camille Gache
- PSL Research University, EPHE-UPVD-CNRS, UAR3278 CRIOBE, 98729 Papetoai, Moorea, French Polynesia, France.,Laboratoire d'Excellence "CORAIL", Paris, France
| | - N Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Fanny de Busserolles
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, 4072, Australia
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8
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Wei S, Chen F, Xu T, Cao M, Yang X, Zhang B, Guo X, Yin D. BDE-99 Disrupts the Photoreceptor Patterning of Zebrafish Larvae via Transcription Factor six7. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5673-5683. [PMID: 35413178 DOI: 10.1021/acs.est.1c08914] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Proper visual function is essential for collecting environmental information and supporting the decision-making in the central nervous system and is therefore tightly associated with wildlife survival and human health. Polybrominated diphenyl ethers (PBDEs) were reported to impair zebrafish vision development, and thyroid hormone (TH) signaling was suspected as the main contributor. In this study, a pentabrominated PBDE, BDE-99, was chosen to further explore the action mechanism of PBDEs on the disruption of zebrafish color vision. The results showed that BDE-99 could impair multiple photoreceptors in the retina and disturb the behavior guided by the color vision of zebrafish larvae at 120 h post-fertilization. Although the resulting alteration in photoreceptor patterning highly resembled the effects of 3,3',5-triiodo-l-thyroine, introducing the antagonist for TH receptors was unable to fully recover the alteration, which suggested the involvement of other potential regulatory factors. By modulating the expression of six7, a key inducer of middle-wavelength opsins, we demonstrated that six7, not THs, dominated the photoreceptor patterning in the disruption of BDE-99. Our work promoted the understanding of the regulatory role of six7 in the process of photoreceptor patterning and proposed a novel mechanism for the visual toxicity of PBDEs.
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Affiliation(s)
- Sheng Wei
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Fu Chen
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Department of Environmental Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai 200234, China
| | - Ting Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Miao Cao
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xinyue Yang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Bin Zhang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, China
| | - Xueping Guo
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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9
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Valencia JE, Feuda R, Mellott DO, Burke RD, Peter IS. Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation. BMC Biol 2021; 19:257. [PMID: 34863182 PMCID: PMC8642985 DOI: 10.1186/s12915-021-01194-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolutionary history of cell types provides insights into how morphological and functional complexity arose during animal evolution. Photoreceptor cell types are particularly broadly distributed throughout Bilateria; however, their evolutionary relationship is so far unresolved. Previous studies indicate that ciliary photoreceptors are homologous at least within chordates, and here, we present evidence that a related form of this cell type is also present in echinoderm larvae. RESULTS Larvae of the purple sea urchin Strongylocentrotus purpuratus have photoreceptors that are positioned bilaterally in the oral/anterior apical neurogenic ectoderm. Here, we show that these photoreceptors express the transcription factor Rx, which is commonly expressed in ciliary photoreceptors, together with an atypical opsin of the GO family, opsin3.2, which localizes in particular to the cilia on the cell surface of photoreceptors. We show that these ciliary photoreceptors express the neuronal marker synaptotagmin and are located in proximity to pigment cells. Furthermore, we systematically identified additional transcription factors expressed in these larval photoreceptors and found that a majority are orthologous to transcription factors expressed in vertebrate ciliary photoreceptors, including Otx, Six3, Tbx2/3, and Rx. Based on the developmental expression of rx, these photoreceptors derive from the anterior apical neurogenic ectoderm. However, genes typically involved in eye development in bilateria, including pax6, six1/2, eya, and dac, are not expressed in sea urchin larval photoreceptors but are instead co-expressed in the hydropore canal. CONCLUSIONS Based on transcription factor expression, location, and developmental origin, we conclude that the sea urchin larval photoreceptors constitute a cell type that is likely homologous to the ciliary photoreceptors present in chordates.
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Affiliation(s)
- Jonathan E Valencia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Roberto Feuda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.,Present address: Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Dan O Mellott
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
| | - Isabelle S Peter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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10
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Ogawa Y, Shiraki T, Fukada Y, Kojima D. Foxq2 determines blue cone identity in zebrafish. SCIENCE ADVANCES 2021; 7:eabi9784. [PMID: 34613771 PMCID: PMC8494292 DOI: 10.1126/sciadv.abi9784] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/13/2021] [Indexed: 05/26/2023]
Abstract
Most vertebrate lineages retain a tetrachromatic visual system, which is supported by a functional combination of spectrally distinct multiple cone photoreceptors, ultraviolet (UV), blue, green, and red cones. The blue cone identity is ensured by selective expression of blue (sws2) opsin, and the mechanism is poorly understood because sws2 gene has been lost in mammalian species such as mouse, whose visual system has been extensively studied. Here, we pursued loss-of-function studies on transcription factors expressed predominantly in zebrafish cone photoreceptors and identified Foxq2 as a blue cone–specific factor driving sws2 gene expression. Foxq2 has dual functions acting as an activator of sws2 transcription and as a suppressor of UV (sws1) opsin transcription in blue cones. A wide range of vertebrate species retain both foxq2 and sws2 genes. We propose that Foxq2-dependent sws2 expression is a prevalent regulatory mechanism that was acquired at the early stage of vertebrate evolution.
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11
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Ogawa Y, Corbo JC. Partitioning of gene expression among zebrafish photoreceptor subtypes. Sci Rep 2021; 11:17340. [PMID: 34462505 PMCID: PMC8405809 DOI: 10.1038/s41598-021-96837-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Vertebrate photoreceptors are categorized into two broad classes, rods and cones, responsible for dim- and bright-light vision, respectively. While many molecular features that distinguish rods and cones are known, gene expression differences among cone subtypes remain poorly understood. Teleost fishes are renowned for the diversity of their photoreceptor systems. Here, we used single-cell RNA-seq to profile adult photoreceptors in zebrafish, a teleost. We found that in addition to the four canonical zebrafish cone types, there exist subpopulations of green and red cones (previously shown to be located in the ventral retina) that express red-shifted opsin paralogs (opn1mw4 or opn1lw1) as well as a unique combination of cone phototransduction genes. Furthermore, the expression of many paralogous phototransduction genes is partitioned among cone subtypes, analogous to the partitioning of the phototransduction paralogs between rods and cones seen across vertebrates. The partitioned cone-gene pairs arose via the teleost-specific whole-genome duplication or later clade-specific gene duplications. We also discovered that cone subtypes express distinct transcriptional regulators, including many factors not previously implicated in photoreceptor development or differentiation. Overall, our work suggests that partitioning of paralogous gene expression via the action of differentially expressed transcriptional regulators enables diversification of cone subtypes in teleosts.
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Affiliation(s)
- Yohey Ogawa
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA.
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12
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Yu P, Wang Y, Yang WT, Li Z, Zhang XJ, Zhou L, Gui JF. Upregulation of the PPAR signaling pathway and accumulation of lipids are related to the morphological and structural transformation of the dragon-eye goldfish eye. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1031-1049. [PMID: 33428077 DOI: 10.1007/s11427-020-1814-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
Goldfish comprise around 300 different strains with drastically altered and aesthetical morphologies making them suitable models for evolutionary developmental biology. The dragon-eye strain is characterized by protruding eyes (analogous to those of Chinese dragons). Although the strain has been selected for about 400 years, the mechanism of its eye development remains unclear. In this study, a stable dragon-eye goldfish strain with a clear genetic background was rapidly established and studied. We found that upregulation of the PPAR signaling pathway accompanied by an increase in lipid accumulation might trigger the morphological and structural transformation of the eye in dragon-eye goldfish. At the developmental stage of proptosis (eye protrusion), downregulation of the phototransduction pathway was consistent with the structural defects and myopia of the dragon-eye strain. With the impairment of retinal development, cytokine-induced inflammation was activated, especially after proptosis, similar to the pathologic symptoms of many human ocular diseases. In addition, differentially expressed transcription factors were significantly enriched in the PAX and homeobox families, two well-known transcription factor families involved in eye development. Therefore, our findings reveal the dynamic changes in key pathways during eye development in dragon-eye goldfish, and provide insights into the molecular mechanisms underlying drastically altered eyes in goldfish and human ocular disease.
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Tao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Raj B, Farrell JA, Liu J, El Kholtei J, Carte AN, Navajas Acedo J, Du LY, McKenna A, Relić Đ, Leslie JM, Schier AF. Emergence of Neuronal Diversity during Vertebrate Brain Development. Neuron 2020; 108:1058-1074.e6. [PMID: 33068532 PMCID: PMC8286448 DOI: 10.1016/j.neuron.2020.09.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/05/2020] [Accepted: 09/17/2020] [Indexed: 01/03/2023]
Abstract
Neurogenesis comprises many highly regulated processes including proliferation, differentiation, and maturation. However, the transcriptional landscapes underlying brain development are poorly characterized. We describe a developmental single-cell catalog of ∼220,000 zebrafish brain cells encompassing 12 stages from embryo to larva. We characterize known and novel gene markers for ∼800 clusters and provide an overview of the diversification of neurons and progenitors across these time points. We also introduce an optimized GESTALT lineage recorder that enables higher expression and recovery of Cas9-edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post-embryonic stages. Reconstruction of cell specification trajectories reveals that late-stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis.
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Affiliation(s)
- Bushra Raj
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
| | - Jeffrey A Farrell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Unit on Cell Specification and Differentiation, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Jialin Liu
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Jakob El Kholtei
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Adam N Carte
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland; Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA
| | - Joaquin Navajas Acedo
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Lucia Y Du
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH 03756, USA
| | - Đorđe Relić
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), 4056 Basel, Switzerland
| | - Jessica M Leslie
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
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Tsujimura T. Mechanistic insights into the evolution of the differential expression of tandemly arrayed cone opsin genes in zebrafish. Dev Growth Differ 2020; 62:465-475. [PMID: 32712957 DOI: 10.1111/dgd.12690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/10/2020] [Accepted: 07/18/2020] [Indexed: 12/21/2022]
Abstract
The genome of many organisms contains several loci consisting of duplicated genes that are arrayed in tandem. The daughter genes produced by duplication typically exhibit differential expression patterns with each other or otherwise experience pseudogenization. Remarkably, opsin genes in fish are preserved after many duplications in different lineages. This fact indicates that fish opsin genes are characterized by a regulatory mechanism that could intrinsically facilitate the differentiation of the expression patterns. However, little is known about the mechanisms that underlie the differential expression patterns or how they were established during evolution. The loci of green (RH2)- and red (LWS)-sensitive cone opsin genes in zebrafish have been used as model systems to study the differential regulation of tandemly arrayed opsin genes. Over a decade of studies have uncovered several mechanistic features that might have assisted the differentiation and preservation of duplicated genes. Furthermore, recent progress in the understanding of the transcriptional process in general has added essential insights. In this article, the current understanding of the transcriptional regulation of differentially expressed tandemly arrayed cone opsin genes in zebrafish is summarized and a possible evolutionary scenario that could achieve this differentiation is discussed.
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Affiliation(s)
- Taro Tsujimura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
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15
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Abstract
Vertebrate color vision requires spectrally selective opsin-based pigments, expressed in distinct cone photoreceptor populations. In primates and in fish, spectrally divergent opsin genes may reside in head-to-tail tandem arrays. Mechanisms underlying differential expression from such arrays have not been fully elucidated. Regulation of human red (LWS) vs. green (MWS) opsins is considered a stochastic event, whereby upstream enhancers associate randomly with promoters of the proximal or distal gene, and one of these associations becomes permanent. We demonstrate that, distinct from this stochastic model, the endocrine signal thyroid hormone (TH) regulates differential expression of the orthologous zebrafish lws1/lws2 array, and of the tandemly quadruplicated rh2-1/rh2-2/rh2-3/rh2-4 array. TH treatment caused dramatic, dose-dependent increases in abundance of lws1, the proximal member of the lws array, and reduced lws2 Fluorescent lws reporters permitted direct visualization of individual cones switching expression from lws2 to lws1 Athyroidism increased lws2 and reduced lws1, except within a small ventral domain of lws1 that was likely sustained by retinoic acid signaling. Changes in lws abundance and distribution in athyroid zebrafish were rescued by TH, demonstrating plasticity of cone phenotype in response to this signal. TH manipulations also regulated the rh2 array, with athyroidism reducing abundance of distal members. Interestingly, the opsins encoded by the proximal lws gene and distal rh2 genes are sensitive to longer wavelengths than other members of their respective arrays; therefore, endogenous TH acts upon each opsin array to shift overall spectral sensitivity toward longer wavelengths, underlying coordinated changes in visual system function during development and growth.
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16
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DuVal MG, Allison WT. Photoreceptor Progenitors Depend Upon Coordination of gdf6a, thrβ, and tbx2b to Generate Precise Populations of Cone Photoreceptor Subtypes. Invest Ophthalmol Vis Sci 2019; 59:6089-6101. [PMID: 30592497 DOI: 10.1167/iovs.18-24461] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Replacing cone photoreceptors, the units of the retina necessary for daytime vision, depends upon the successful production of a full variety of new cones from, for example, stem cells. Using genetic experiments in a model organism with high cone diversity, zebrafish, we map the intersecting effects of cone development factors gdf6a, tbx2b, and thrβ. Methods We investigated these genes of interest by using genetic combinations of mutants, gene knockdown, and dominant negative gene expression, and then quantified cone subtype outcomes (which normally develop in tightly regulated ratios). Results Gdf6a mutants have reduced blue cones and, discovered here, reduced red cones. In combined gdf6a/tbx2b disruption, the loss of gdf6a in heterozygous tbx2b mutants reduced UV cones. Intriguingly, when we disrupted thrβ in gdf6a mutants by using a thrβ morpholino, their combined early disruption revealed a lamination phenotype. Disrupting thrβ activity via expression of a dominant negative thrβ (dnthrβ) at either early or late retinal development had differential outcomes on red cones (reduced abundance), versus UV and blue cones (increased abundance). By using dnthrβ in gdf6a mutants, we revealed that disrupting thrβ activity did not change gdf6a mutant cone phenotypes. Conclusions Gdf6a loss directly affects blue and red cones and indirectly affects UV cones by increasing sensitivity to additional disruption, such as reduced tbx2b, resulting in fewer UV cones. The effects of thrβ change through photoreceptor development, first promoting red cones and restricting UV cones, and later restricting UV and blue cones. The effects of gdf6a on UV, blue, and red cone development overlap with, but likely supersede, those of thrβ.
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Affiliation(s)
- Michèle G DuVal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - W Ted Allison
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada.,Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
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17
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Six6 and Six7 coordinately regulate expression of middle-wavelength opsins in zebrafish. Proc Natl Acad Sci U S A 2019; 116:4651-4660. [PMID: 30765521 PMCID: PMC6410792 DOI: 10.1073/pnas.1812884116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Color discrimination in the vertebrate retina is mediated by a combination of cone cell types expressing UV (SWS1), blue (SWS2), green (RH2), and red (LWS) opsins. Although the tetrachromatic cone system is retained in most nonmammalian vertebrate lineages, the transcriptional mechanism underlying gene expression of cone opsins remains elusive. Here, we found that the retinal transcription factors, sine oculis homeobox 6 (Six6b) and Six7, synergistically and positively regulate gene expression of zebrafish SWS2 and RH2 opsins. Larvae deficient for both of these transcription factors showed heavily impaired visually driven foraging behavior and were unable to compete for food when reared in a group with normal siblings. The results suggest that six6b and six7 play a pivotal role in blue- and green-light sensitivity and daylight vision. Color discrimination in the vertebrate retina is mediated by a combination of spectrally distinct cone photoreceptors, each expressing one of multiple cone opsins. The opsin genes diverged early in vertebrate evolution into four classes maximally sensitive to varying wavelengths of light: UV (SWS1), blue (SWS2), green (RH2), and red (LWS) opsins. Although the tetrachromatic cone system is retained in most nonmammalian vertebrate lineages, the transcriptional mechanism underlying gene expression of the cone opsins remains elusive, particularly for SWS2 and RH2 opsins, both of which have been lost in the mammalian lineage. In zebrafish, which have all four cone subtypes, rh2 opsin gene expression depends on a homeobox transcription factor, sine oculis homeobox 7 (Six7). However, the six7 gene is found only in the ray-finned fish lineage, suggesting the existence of another evolutionarily conserved transcriptional factor(s) controlling rh2 opsin expression in vertebrates. Here, we found that the reduced rh2 expression caused by six7 deficiency was rescued by forced expression of six6b, which is a six7-related transcription factor conserved widely among vertebrates. The compensatory role of six6b was reinforced by ChIP-sequencing analysis, which revealed a similar pattern of Six6b- and Six7-binding sites within and near the cone opsin genes. TAL effector nuclease-induced genetic ablation of six6b and six7 revealed that they coordinately regulate SWS2 opsin gene expression. Mutant larvae deficient for these transcription factors showed severely impaired visually driven foraging behavior. These results demonstrate that in zebrafish, six6b and six7 govern expression of the SWS2 and RH2 opsins responsible for middle-wavelength sensitivity, which would be physiologically important for daylight vision.
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18
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Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF, Durbin R. Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nat Ecol Evol 2018; 2:1940-1955. [PMID: 30455444 PMCID: PMC6443041 DOI: 10.1038/s41559-018-0717-x] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/10/2018] [Indexed: 12/30/2022]
Abstract
The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. The average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep-water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.
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Affiliation(s)
- Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK.
- Zoological Institute, University of Basel, Basel, Switzerland.
| | - Hannes Svardal
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Alexandra M Tyers
- School of Natural Sciences, Bangor University, Bangor, UK
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Eric A Miska
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
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19
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Toxicity Evaluation and Biomarker Selection with Validated Reference Gene in Embryonic Zebrafish Exposed to Mitoxantrone. Int J Mol Sci 2018; 19:ijms19113516. [PMID: 30413070 PMCID: PMC6274943 DOI: 10.3390/ijms19113516] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/03/2018] [Accepted: 11/06/2018] [Indexed: 12/20/2022] Open
Abstract
Notwithstanding the widespread use and promising clinical value of chemotherapy, the pharmacokinetics, toxicology, and mechanism of mitoxantrone remains unclear. To promote the clinical value in the treatment of human diseases and the exploration of potential subtle effects of mitoxantrone, zebrafish embryos were employed to evaluate toxicity with validated reference genes based on independent stability evaluation programs. The most stable and recommended reference gene was gapdh, followed by tubα1b, for the 48 h post fertilization (hpf) zebrafish embryo mitoxantrone test, while both eef1a1l1 and rpl13α were recommended as reference genes for the 96 hpf zebrafish embryo mitoxantrone test. With gapdh as an internal control, we analyzed the mRNA levels of representative hepatotoxicity biomarkers, including fabp10a, gclc, gsr, nqo1, cardiotoxicity biomarker erg, and neurotoxicity biomarker gfap in the 48 hpf embryo mitoxantrone test. The mRNA levels of gclc, gsr, and gfap increased significantly in 10 and 50 μg/L mitoxantrone-treated 48 hpf embryos, while the transcript levels of fabp10a decreased in a dose-dependent manner, indicating that mitoxantrone induced hepatotoxicity and neurotoxicity. Liver hematoxylin–eosin staining and the spontaneous movement of embryos confirmed the results. Thus, the present research suggests that mitoxantrone induces toxicity during the development of the liver and nervous system in zebrafish embryos and that fabp10a is recommended as a potential biomarker for hepatotoxicity in zebrafish embryos. Additionally, gapdh is proposed as a reference gene for the 48 hpf zebrafish embryo mitoxantrone toxicity test, while eef1a1l1 and rpl13α are proposed as that for the 96 hpf test.
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20
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Meier A, Nelson R, Connaughton VP. Color Processing in Zebrafish Retina. Front Cell Neurosci 2018; 12:327. [PMID: 30337857 PMCID: PMC6178926 DOI: 10.3389/fncel.2018.00327] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Zebrafish (Danio rerio) is a model organism for vertebrate developmental processes and, through a variety of mutant and transgenic lines, various diseases and their complications. Some of these diseases relate to proper function of the visual system. In the US, the National Eye Institute indicates >140 million people over the age of 40 have some form of visual impairment. The causes of the impairments range from refractive error to cataract, diabetic retinopathy and glaucoma, plus heritable diseases such as retinitis pigmentosa and color vision deficits. Most impairments directly affect the retina, the nervous tissue at the back of the eye. Zebrafish with long or short-wavelength color blindness, altered retinal anatomy due to hyperglycemia, high intraocular pressure, and reduced pigment epithelium are all used, and directly applicable, to study how these symptoms affect visual function. However, many published reports describe only molecular/anatomical/structural changes or behavioral deficits. Recent work in zebrafish has documented physiological responses of the different cell types to colored (spectral) light stimuli, indicating a complex level of information processing and color vision in this species. The purpose of this review article is to consolidate published morphological and physiological data from different cells to describe how zebrafish retina is capable of complex visual processing. This information is compared to findings in other vertebrates and relevance to disorders affecting color processing is discussed.
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Affiliation(s)
- April Meier
- Zebrafish Ecotoxicology, Neuropharmacology, and Vision Lab, Department of Biology, and Center for Behavioral Neuroscience, American University, Washington, DC, United States
| | - Ralph Nelson
- Neural Circuits Unit, National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, MD, United States
| | - Victoria P Connaughton
- Zebrafish Ecotoxicology, Neuropharmacology, and Vision Lab, Department of Biology, and Center for Behavioral Neuroscience, American University, Washington, DC, United States
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21
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Crespo C, Soroldoni D, Knust E. A novel transgenic zebrafish line for red opsin expression in outer segments of photoreceptor cells. Dev Dyn 2018; 247:951-959. [PMID: 29603474 PMCID: PMC6099204 DOI: 10.1002/dvdy.24631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/16/2018] [Accepted: 03/17/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Opsins are a group of light-sensitive proteins present in photoreceptor cells, which convert the energy of photons into electrochemical signals, thus allowing vision. Given their relevance, we aimed to visualize the two red opsins at subcellular scale in photoreceptor cells. RESULTS We generated a novel Zebrafish BAC transgenic line, which express fluorescently tagged, full-length Opsin 1 long-wave-sensitive 1 (Opn1lw1) and full-length Opsin 1 long-wave-sensitive 2 (Opn1lw2) under the control of their endogenous promoters. Both fusion proteins are localized in the outer segments of photoreceptor cells. During development, Opn1lw2-mKate2 is detected from the initial formation of outer segments onward. In contrast, Opn1lw1-mNeonGreen is first detected in juvenile Zebrafish at about 2 weeks postfertilization, and both opsins continue to be expressed throughout adulthood. It is important to note that the presence of the transgene did not significantly alter the size of outer segments. CONCLUSIONS We have generated a transgenic line that mimics the endogenous expression pattern of Opn1lw1 and Opn1lw2 in the developing and adult retina. In contrast to existing lines, our transgene design allows to follow protein localization. Hence, we expect that these lines could act as useful real-time reporters to directly measure phenomena in retinal development and disease models. Developmental Dynamics 247:951-959, 2018. © 2018 The Authors Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.
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Affiliation(s)
- Cátia Crespo
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Elisabeth Knust
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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22
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Sun C, Galicia C, Stenkamp DL. Transcripts within rod photoreceptors of the Zebrafish retina. BMC Genomics 2018; 19:127. [PMID: 29422031 PMCID: PMC5806438 DOI: 10.1186/s12864-018-4499-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/28/2018] [Indexed: 12/03/2022] Open
Abstract
Background The purpose of this study was to identify transcripts of retinal rod photoreceptors of the zebrafish. The zebrafish is an important animal model for vision science due to rapid and tractable development, persistent neurogenesis of rods throughout the lifespan, and capacity for functional retinal regeneration. Results Zebrafish rods, and non-rod retinal cells of the xops:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. At a false discovery rate of < 0.01, 597 transcripts were upregulated (“enriched”) in rods vs. other retinal cells, and 1032 were downregulated (“depleted”). Thirteen thousand three hundred twenty four total transcripts were detected in rods, including many not previously known to be expressed by rods. Forty five transcripts were validated by qPCR in FACS-sorted rods vs. other retinal cells. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in rods sorted from retinas subjected to a neurotoxic lesion and allowed to regenerate. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions We report the generation and validation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Electronic supplementary material The online version of this article (10.1186/s12864-018-4499-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chi Sun
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
| | - Carlos Galicia
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
| | - Deborah L Stenkamp
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA.
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Mechanisms of Photoreceptor Patterning in Vertebrates and Invertebrates. Trends Genet 2017; 32:638-659. [PMID: 27615122 DOI: 10.1016/j.tig.2016.07.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 11/22/2022]
Abstract
Across the animal kingdom, visual systems have evolved to be uniquely suited to the environments and behavioral patterns of different species. Visual acuity and color perception depend on the distribution of photoreceptor (PR) subtypes within the retina. Retinal mosaics can be organized into three broad categories: stochastic/regionalized, regionalized, and ordered. We describe here the retinal mosaics of flies, zebrafish, chickens, mice, and humans, and the gene regulatory networks controlling proper PR specification in each. By drawing parallels in eye development between these divergent species, we identify a set of conserved organizing principles and transcriptional networks that govern PR subtype differentiation.
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Musser JM, Arendt D. Loss and gain of cone types in vertebrate ciliary photoreceptor evolution. Dev Biol 2017; 431:26-35. [DOI: 10.1016/j.ydbio.2017.08.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 01/09/2023]
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25
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Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors. Sci Rep 2017; 7:43184. [PMID: 28256534 PMCID: PMC5335693 DOI: 10.1038/srep43184] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/19/2017] [Indexed: 12/24/2022] Open
Abstract
Rod photoreceptors are specialized neurons that mediate vision in dim light and are the predominant photoreceptor type in nocturnal mammals. The rods of nocturnal mammals are unique among vertebrate cell types in having an ‘inverted’ nuclear architecture, with a dense mass of heterochromatin in the center of the nucleus rather than dispersed clumps at the periphery. To test if this unique nuclear architecture is correlated with a unique epigenomic landscape, we performed ATAC-seq on mouse rods and their most closely related cell type, cone photoreceptors. We find that thousands of loci are selectively closed in rods relative to cones as well as >60 additional cell types. Furthermore, we find that the open chromatin profile of photoreceptors lacking the rod master regulator Nrl is nearly indistinguishable from that of native cones, indicating that Nrl is required for selective chromatin closure in rods. Finally, we identified distinct enrichments of transcription factor binding sites in rods and cones, revealing key differences in the cis-regulatory grammar of these cell types. Taken together, these data provide insight into the development and maintenance of photoreceptor identity, and highlight rods as an attractive system for studying the relationship between nuclear organization and local changes in gene regulation.
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26
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Hagerman GF, Noel NCL, Cao SY, DuVal MG, Oel AP, Allison WT. Rapid Recovery of Visual Function Associated with Blue Cone Ablation in Zebrafish. PLoS One 2016; 11:e0166932. [PMID: 27893779 PMCID: PMC5125653 DOI: 10.1371/journal.pone.0166932] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Hurdles in the treatment of retinal degeneration include managing the functional rewiring of surviving photoreceptors and integration of any newly added cells into the remaining second-order retinal neurons. Zebrafish are the premier genetic model for such questions, and we present two new transgenic lines allowing us to contrast vision loss and recovery following conditional ablation of specific cone types: UV or blue cones. The ablation of each cone type proved to be thorough (killing 80% of cells in each intended cone class), specific, and cell-autonomous. We assessed the loss and recovery of vision in larvae via the optomotor behavioural response (OMR). This visually mediated behaviour decreased to about 5% or 20% of control levels following ablation of UV or blue cones, respectively (P<0.05). We further assessed ocular photoreception by measuring the effects of UV light on body pigmentation, and observed that photoreceptor deficits and recovery occurred (p<0.01) with a timeline coincident to the OMR results. This corroborated and extended previous conclusions that UV cones are required photoreceptors for modulating body pigmentation, addressing assumptions that were unavoidable in previous experiments. Functional vision recovery following UV cone ablation was robust, as measured by both assays, returning to control levels within four days. In contrast, robust functional recovery following blue cone ablation was unexpectedly rapid, returning to normal levels within 24 hours after ablation. Ablation of cones led to increased proliferation in the retina, though the rapid recovery of vision following blue cone ablation was demonstrated to not be mediated by blue cone regeneration. Thus rapid visual recovery occurs following ablation of some, but not all, cone subtypes, suggesting an opportunity to contrast and dissect the sources and mechanisms of outer retinal recovery during cone photoreceptor death and regeneration.
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Affiliation(s)
- Gordon F. Hagerman
- Department of Biological Sciences, University of Alberta, Edmonton Alberta, Canada
| | - Nicole C. L. Noel
- Department of Biological Sciences, University of Alberta, Edmonton Alberta, Canada
| | - Sylvia Y. Cao
- Department of Biological Sciences, University of Alberta, Edmonton Alberta, Canada
| | - Michèle G. DuVal
- Department of Biological Sciences, University of Alberta, Edmonton Alberta, Canada
| | - A. Phillip Oel
- Department of Biological Sciences, University of Alberta, Edmonton Alberta, Canada
| | - W. Ted Allison
- Department of Biological Sciences, University of Alberta, Edmonton Alberta, Canada
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton Alberta, Canada
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Valen R, Eilertsen M, Edvardsen RB, Furmanek T, Rønnestad I, van der Meeren T, Karlsen Ø, Nilsen TO, Helvik JV. The two-step development of a duplex retina involves distinct events of cone and rod neurogenesis and differentiation. Dev Biol 2016; 416:389-401. [PMID: 27374844 DOI: 10.1016/j.ydbio.2016.06.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 11/15/2022]
Abstract
Unlike in mammals, persistent postembryonic retinal growth is a characteristic feature of fish, which includes major remodeling events that affect all cell types including photoreceptors. Consequently, visual capabilities change during development, where retinal sensitivity to different wavelengths of light (photopic vision), -and to limited photons (scotopic vision) are central capabilities for survival. Differently from well-established model fish, Atlantic cod has a prolonged larval stage where only cone photoreceptors are present. Rods do not appear until juvenile transition (metamorphosis), a hallmark of indirect developing species. Previously we showed that whole gene families of lws (red-sensitive) and sws1 (UV-sensitive) opsins have been lost in cod, while rh2a (green-sensitive) and sws2 (blue-sensitive) genes have tandem duplicated. Here, we provide a comprehensive characterization of a two-step developing duplex retina in Atlantic cod. The study focuses on cone subtype dynamics and delayed rod neurogenesis and differentiation in all cod life stages. Using transcriptomic and histological approaches we show that different opsins disappear in a topographic manner during development where central to peripheral retina is a key axis of expressional change. Early cone differentiation was initiated in dorso-temporal retina different from previously described in fish. Rods first appeared during initiation of metamorphosis and expression of the nuclear receptor transcription factor nr2e3-1, suggest involvement in rod specification. The indirect developmental strategy thus allows for separate studies of cones and rods development, which in nature correlates with visual changes linked to habitat shifts. The clustering of key retinal genes according to life stage, suggests that Atlantic cod with its sequenced genome may be an important resource for identification of underlying factors required for development and function of photopic and scotopic vision.
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Affiliation(s)
- Ragnhild Valen
- Department of Biology, University of Bergen, NO-5020 Bergen, Norway
| | | | | | - Tomasz Furmanek
- Institute of Marine Research, Nordnes, NO-5005 Bergen, Norway
| | - Ivar Rønnestad
- Department of Biology, University of Bergen, NO-5020 Bergen, Norway
| | - Terje van der Meeren
- Institute of Marine Research, Austevoll Research station and Hjort Centre for Marine Ecosystem Dynamics, NO-5392 Storebø, Norway
| | - Ørjan Karlsen
- Institute of Marine Research, Austevoll Research station and Hjort Centre for Marine Ecosystem Dynamics, NO-5392 Storebø, Norway
| | | | - Jon Vidar Helvik
- Department of Biology, University of Bergen, NO-5020 Bergen, Norway
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Deming JD, Pak JS, Shin JA, Brown BM, Kim MK, Aung MH, Lee EJ, Pardue MT, Craft CM. Arrestin 1 and Cone Arrestin 4 Have Unique Roles in Visual Function in an All-Cone Mouse Retina. Invest Ophthalmol Vis Sci 2016; 56:7618-28. [PMID: 26624493 DOI: 10.1167/iovs.15-17832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Previous studies discovered cone phototransduction shutoff occurs normally for Arr1-/- and Arr4-/-; however, it is defective when both visual arrestins are simultaneously not expressed (Arr1-/-Arr4-/-). We investigated the roles of visual arrestins in an all-cone retina (Nrl-/-) since each arrestin has differential effects on visual function, including ARR1 for normal light adaptation, and ARR4 for normal contrast sensitivity and visual acuity. METHODS We examined Nrl-/-, Nrl-/-Arr1-/-, Nrl-/-Arr4-/-, and Nrl-/-Arr1-/-Arr4-/- mice with photopic electroretinography (ERG) to assess light adaptation and retinal responses, immunoblot and immunohistochemical localization analysis to measure retinal expression levels of M- and S-opsin, and optokinetic tracking (OKT) to measure the visual acuity and contrast sensitivity. RESULTS Study results indicated that Nrl-/- and Nrl-/-Arr4-/- mice light adapted normally, while Nrl-/-Arr1-/- and Nrl-/-Arr1-/-Arr4-/- mice did not. Photopic ERG a-wave, b-wave, and flicker amplitudes followed a general pattern in which Nrl-/-Arr4-/- amplitudes were higher than the amplitudes of Nrl-/-, while the amplitudes of Nrl-/-Arr1-/- and Nrl-/-Arr1-/-Arr4-/- were lower. All three visual arrestin knockouts had faster implicit times than Nrl-/- mice. M-opsin expression is lower when ARR1 is not expressed, while S-opsin expression is lower when ARR4 is not expressed. Although M-opsin expression is mislocalized throughout the photoreceptor cells, S-opsin is confined to the outer segments in all genotypes. Contrast sensitivity is decreased when ARR4 is not expressed, while visual acuity was normal except in Nrl-/-Arr1-/-Arr4-/-. CONCLUSIONS Based on the opposite visual phenotypes in an all-cone retina in the Nrl-/-Arr1-/- and Nrl-/-Arr4-/- mice, we conclude that ARR1 and ARR4 perform unique modulatory roles in cone photoreceptors.
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Affiliation(s)
- Janise D Deming
- Mary D. Allen Laboratory for Vision Research, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, USC Eye Institute, Los Angeles, California, United States
| | - Joseph S Pak
- Mary D. Allen Laboratory for Vision Research, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, USC Eye Institute, Los Angeles, California, United States
| | - Jung-A Shin
- Mary D. Allen Laboratory for Vision Research, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, USC Eye Institute, Los Angeles, California, United States 2Department of Anatomy, School of Medicine, Ewha Womans
| | - Bruce M Brown
- Mary D. Allen Laboratory for Vision Research, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, USC Eye Institute, Los Angeles, California, United States
| | - Moon K Kim
- Rehabilitation Research & Development Center of Excellence, Atlanta VA Medical Center, Decatur, Georgia, United States
| | - Moe H Aung
- Neuroscience/Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Eun-Jin Lee
- Mary D. Allen Laboratory for Vision Research, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, USC Eye Institute, Los Angeles, California, United States 5Department of Biomedical Engineering, University of Sou
| | - Machelle T Pardue
- Rehabilitation Research & Development Center of Excellence, Atlanta VA Medical Center, Decatur, Georgia, United States 4Neuroscience/Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Cheryl Mae Craft
- Mary D. Allen Laboratory for Vision Research, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, USC Eye Institute, Los Angeles, California, United States 6Department of Cell & Neurobiology, Keck School of Medic
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Sotolongo-Lopez M, Alvarez-Delfin K, Saade CJ, Vera DL, Fadool JM. Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish. PLoS Genet 2016; 12:e1005968. [PMID: 27058886 PMCID: PMC4825938 DOI: 10.1371/journal.pgen.1005968] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/09/2016] [Indexed: 11/30/2022] Open
Abstract
The visual system of a particular species is highly adapted to convey detailed ecological and behavioral information essential for survival. The consequences of structural mutations of opsins upon spectral sensitivity and environmental adaptation have been studied in great detail, but lacking is knowledge of the potential influence of alterations in gene regulatory networks upon the diversity of cone subtypes and the variation in the ratio of rods and cones observed in numerous diurnal and nocturnal species. Exploiting photoreceptor patterning in cone-dominated zebrafish, we uncovered two independent mechanisms by which the sine oculis homeobox homolog 7 (six7) regulates photoreceptor development. In a genetic screen, we isolated the lots-of-rods-junior (ljrp23ahub) mutation that resulted in an increased number and uniform distribution of rods in otherwise normal appearing larvae. Sequence analysis, genome editing using TALENs and knockdown strategies confirm ljrp23ahub as a hypomorphic allele of six7, a teleost orthologue of six3, with known roles in forebrain patterning and expression of opsins. Based on the lack of predicted protein-coding changes and a deletion of a conserved element upstream of the transcription start site, a cis-regulatory mutation is proposed as the basis of the reduced expression of six7 in ljrp23ahub. Comparison of the phenotypes of the hypomorphic and knock-out alleles provides evidence of two independent roles in photoreceptor development. EdU and PH3 labeling show that the increase in rod number is associated with extended mitosis of photoreceptor progenitors, and TUNEL suggests that the lack of green-sensitive cones is the result of cell death of the cone precursor. These data add six7 to the small but growing list of essential genes for specification and patterning of photoreceptors in non-mammalian vertebrates, and highlight alterations in transcriptional regulation as a potential source of photoreceptor variation across species.
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Affiliation(s)
- Mailin Sotolongo-Lopez
- Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
| | - Karen Alvarez-Delfin
- Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
| | - Carole J. Saade
- Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
- Program in Neuroscience, The Florida State University, Tallahassee, Florida, United States of America
| | - Daniel L. Vera
- Center for Genomics and Personalized Medicine, The Florida State University, Tallahassee, Florida, United States of America
| | - James M. Fadool
- Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
- Program in Neuroscience, The Florida State University, Tallahassee, Florida, United States of America
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31
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Tsujimura T, Masuda R, Ashino R, Kawamura S. Spatially differentiated expression of quadruplicated green-sensitive RH2 opsin genes in zebrafish is determined by proximal regulatory regions and gene order to the locus control region. BMC Genet 2015; 16:130. [PMID: 26537431 PMCID: PMC4634787 DOI: 10.1186/s12863-015-0288-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/27/2015] [Indexed: 11/22/2022] Open
Abstract
Background Fish are remarkably diverse in repertoires of visual opsins by gene duplications. Differentiation of their spatiotemporal expression patterns and absorption spectra enables fine-tuning of feature detection in spectrally distinct regions of the visual field during ontogeny. Zebrafish have quadruplicated green-sensitive (RH2) opsin genes in tandem (RH2-1, −2, −3, −4), which are expressed in the short member of the double cones (SDC). The shortest wavelength RH2 subtype (RH2-1) is expressed in the central to dorsal area of the adult retina. The second shortest wave subtype (RH2-2) is expressed overlapping with RH2-1 but extending outside of it. The second longest wave subtype (RH2-3) is expressed surrounding the RH2–2 area, and the longest wave subtype (RH2-4) is expressed outside of the RH2-3 area broadly occupying the ventral area. Expression of the four RH2 genes in SDC requires a single enhancer (RH2-LCR), but the mechanism of their spatial differentiation remains elusive. Results Functional comparison of the RH2-LCR with its counterpart in medaka revealed that the regulatory role of the RH2-LCR in SDC-specific expression is evolutionarily conserved. By combining the RH2-LCR and the proximal upstream region of each RH2 gene with fluorescent protein reporters, we show that the RH2-LCR and the RH2-3 proximal regulatory region confer no spatial selectivity of expression in the retina. But those of RH2-1, −2 and −4 are capable of inducing spatial differentiation of expression. Furthermore, by analyzing transgenic fish with a series of arrays consisting of the RH2-LCR and multiple upstream regions of the RH2 genes in different orders, we show that a gene expression pattern related to an upstream region is greatly influenced by another flanking upstream region in a relative position-dependent manner. Conclusions The zebrafish RH2 genes except RH2-3 acquired differential cis-elements in the proximal upstream regions to specify the differential expression patterns. The input from these proximal elements collectively dictates the actual gene expression pattern of the locus, context-dependently. Importantly, competition for the RH2-LCR activity among the replicates is critical in this collective regulation, facilitating differentiation of expression among them. This combination of specificity and generality enables seemingly complicated spatial differentiation of duplicated opsin genes characteristic in fish. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0288-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taro Tsujimura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, 277-8562, Chiba, Japan. .,Department of Advanced Nephrology and Regenerative Medicine, Division of Tissue Engineering, the University of Tokyo Hospital, Hongo 7-3-1, Bunkyo-ku, 113-8655, Tokyo, Japan.
| | - Ryoko Masuda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, 277-8562, Chiba, Japan.
| | - Ryuichi Ashino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, 277-8562, Chiba, Japan.
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, 277-8562, Chiba, Japan.
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