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Deis R, Lerer-Goldshtein T, Baiko O, Eyal Z, Brenman-Begin D, Goldsmith M, Kaufmann S, Heinig U, Dong Y, Lushchekina S, Varsano N, Olender T, Kupervaser M, Porat Z, Levin-Zaidman S, Pinkas I, Mateus R, Gur D. Genetic control over biogenic crystal morphogenesis in zebrafish. Nat Chem Biol 2024:10.1038/s41589-024-01722-1. [PMID: 39215102 DOI: 10.1038/s41589-024-01722-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Organisms evolve mechanisms that regulate the properties of biogenic crystals to support a wide range of functions, from vision and camouflage to communication and thermal regulation. Yet, the mechanism underlying the formation of diverse intracellular crystals remains enigmatic. Here we unravel the biochemical control over crystal morphogenesis in zebrafish iridophores. We show that the chemical composition of the crystals determines their shape, particularly through the ratio between the nucleobases guanine and hypoxanthine. We reveal that these variations in composition are genetically controlled through tissue-specific expression of specialized paralogs, which exhibit remarkable substrate selectivity. This orchestrated combination grants the organism with the capacity to generate a broad spectrum of crystal morphologies. Overall, our findings suggest a mechanism for the morphological and functional diversity of biogenic crystals and may, thus, inspire the development of genetically designed biomaterials and medical therapeutics.
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Affiliation(s)
- Rachael Deis
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Olha Baiko
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Zohar Eyal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dolev Brenman-Begin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Moshe Goldsmith
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sylvia Kaufmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Uwe Heinig
- Department of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yonghui Dong
- Department of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sofya Lushchekina
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Neta Varsano
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Meital Kupervaser
- The De Botton Protein Profiling institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Department of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Smadar Levin-Zaidman
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Iddo Pinkas
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Rita Mateus
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Dvir Gur
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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2
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Salisbury SJ, Daniels RR, Monaghan SJ, Bron JE, Villamayor PR, Gervais O, Fast MD, Sveen L, Houston RD, Robinson N, Robledo D. Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon. BMC Biol 2024; 22:160. [PMID: 39075472 PMCID: PMC11287951 DOI: 10.1186/s12915-024-01952-8] [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: 11/15/2023] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. RESULTS We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. CONCLUSIONS Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.
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Affiliation(s)
- S J Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - R Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - S J Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - J E Bron
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - P R Villamayor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - O Gervais
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - M D Fast
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | | | - R D Houston
- Benchmark Genetics, 1 Pioneer BuildingMilton Bridge, Edinburgh TechnopolePenicuik, UK
| | - N Robinson
- Nofima AS, Tromsø, Norway.
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), Deakin University, Melbourne, VIC, 3225, Australia.
| | - D Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain.
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3
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Miyadai M, Takada H, Shiraishi A, Kimura T, Watakabe I, Kobayashi H, Nagao Y, Naruse K, Higashijima SI, Shimizu T, Kelsh RN, Hibi M, Hashimoto H. A gene regulatory network combining Pax3/7, Sox10 and Mitf generates diverse pigment cell types in medaka and zebrafish. Development 2023; 150:dev202114. [PMID: 37823232 PMCID: PMC10617610 DOI: 10.1242/dev.202114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023]
Abstract
Neural crest cells generate numerous derivatives, including pigment cells, and are a model for studying how fate specification from multipotent progenitors is controlled. In mammals, the core gene regulatory network for melanocytes (their only pigment cell type) contains three transcription factors, Sox10, Pax3 and Mitf, with the latter considered a master regulator of melanocyte development. In teleosts, which have three to four pigment cell types (melanophores, iridophores and xanthophores, plus leucophores e.g. in medaka), gene regulatory networks governing fate specification are poorly understood, although Mitf function is considered conserved. Here, we show that the regulatory relationships between Sox10, Pax3 and Mitf are conserved in zebrafish, but the role for Mitf is more complex than previously emphasized, affecting xanthophore development too. Similarly, medaka Mitf is necessary for melanophore, xanthophore and leucophore formation. Furthermore, expression patterns and mutant phenotypes of pax3 and pax7 suggest that Pax3 and Pax7 act sequentially, activating mitf expression. Pax7 modulates Mitf function, driving co-expressing cells to differentiate as xanthophores and leucophores rather than melanophores. We propose that pigment cell fate specification should be considered to result from the combinatorial activity of Mitf with other transcription factors.
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Affiliation(s)
- Motohiro Miyadai
- Laboratory of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Hiroyuki Takada
- Laboratory of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Akiko Shiraishi
- Laboratory of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tetsuaki Kimura
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Ikuko Watakabe
- National Institutes of Natural Sciences, Exploratory Research Center on Life and Living Systems, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - Hikaru Kobayashi
- Laboratory of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yusuke Nagao
- Laboratory of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Shin-ichi Higashijima
- National Institutes of Natural Sciences, Exploratory Research Center on Life and Living Systems, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - Takashi Shimizu
- Laboratory of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Robert N. Kelsh
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Masahiko Hibi
- Laboratory of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Hisashi Hashimoto
- Laboratory of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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4
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Fitzgerald T, Brettell I, Leger A, Wolf N, Kusminski N, Monahan J, Barton C, Herder C, Aadepu N, Gierten J, Becker C, Hammouda OT, Hasel E, Lischik C, Lust K, Sokolova N, Suzuki R, Tsingos E, Tavhelidse T, Thumberger T, Watson P, Welz B, Khouja N, Naruse K, Birney E, Wittbrodt J, Loosli F. The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. Genome Biol 2022; 23:59. [PMID: 35189950 PMCID: PMC8862526 DOI: 10.1186/s13059-022-02623-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmental factors is often problematic. To address this, we establish a vertebrate genetic resource specifically to allow for robust genotype-to-phenotype investigations. The teleost medaka (Oryzias latipes) is an established genetic model system with a long history of genetic research and a high tolerance to inbreeding from the wild. RESULTS Here we present the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel: the first near-isogenic panel of 80 inbred lines in a vertebrate model derived from a wild founder population. Inbred lines provide fixed genomes that are a prerequisite for the replication of studies, studies which vary both the genetics and environment in a controlled manner, and functional testing. The MIKK panel will therefore enable phenotype-to-genotype association studies of complex genetic traits while allowing for careful control of interacting factors, with numerous applications in genetic research, human health, drug development, and fundamental biology. CONCLUSIONS Here we present a detailed characterization of the genetic variation across the MIKK panel, which provides a rich and unique genetic resource to the community by enabling large-scale experiments for mapping complex traits.
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Affiliation(s)
- Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian Brettell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadeshda Wolf
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Natalja Kusminski
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Jack Monahan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carl Barton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cathrin Herder
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Narendar Aadepu
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Clara Becker
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Omar T Hammouda
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Eva Hasel
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Colin Lischik
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Risa Suzuki
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Erika Tsingos
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Philip Watson
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Nadia Khouja
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Kiyoshi Naruse
- National Institute for Basic Biology, Laboratory of Bioresources, Okazaki, Japan
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Felix Loosli
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.
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5
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Jang HS, Chen Y, Ge J, Wilkening AN, Hou Y, Lee HJ, Choi YR, Lowdon RF, Xing X, Li D, Kaufman CK, Johnson SL, Wang T. Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish. Genome Biol 2021; 22:282. [PMID: 34607603 PMCID: PMC8489059 DOI: 10.1186/s13059-021-02493-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/09/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Zebrafish pigment cell differentiation provides an attractive model for studying cell fate progression as a neural crest progenitor engenders diverse cell types, including two morphologically distinct pigment cells: black melanophores and reflective iridophores. Nontrivial classical genetic and transcriptomic approaches have revealed essential molecular mechanisms and gene regulatory circuits that drive neural crest-derived cell fate decisions. However, how the epigenetic landscape contributes to pigment cell differentiation, especially in the context of iridophore cell fate, is poorly understood. RESULTS We chart the global changes in the epigenetic landscape, including DNA methylation and chromatin accessibility, during neural crest differentiation into melanophores and iridophores to identify epigenetic determinants shaping cell type-specific gene expression. Motif enrichment in the epigenetically dynamic regions reveals putative transcription factors that might be responsible for driving pigment cell identity. Through this effort, in the relatively uncharacterized iridophores, we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway. CONCLUSIONS Pigment cell fate is marked by substantial DNA demethylation events coupled with dynamic chromatin accessibility to potentiate gene regulation through cis-regulatory control. Here, we provide a multi-omic resource for neural crest differentiation into melanophores and iridophores. This work led to the discovery and validation of iridophore-specific alx4a transcription factor.
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Affiliation(s)
- Hyo Sik Jang
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
- Present address: Department of Epigenetics, Van Andel Institute, Grand Rapids, MI USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Jiaxin Ge
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Alicia N. Wilkening
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - You Rim Choi
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Rebecca F. Lowdon
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Charles K. Kaufman
- Department of Medicine, Division of Medical Oncology, and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO USA
| | - Stephen L. Johnson
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St Louis, MO USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA
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6
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Wang C, Lu B, Li T, Liang G, Xu M, Liu X, Tao W, Zhou L, Kocher TD, Wang D. Nile Tilapia: A Model for Studying Teleost Color Patterns. J Hered 2021; 112:469-484. [PMID: 34027978 DOI: 10.1093/jhered/esab018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/08/2021] [Indexed: 11/12/2022] Open
Abstract
The diverse color patterns of cichlid fishes play an important role in mate choice and speciation. Here we develop the Nile tilapia (Oreochromis niloticus) as a model system for studying the developmental genetics of cichlid color patterns. We identified 4 types of pigment cells: melanophores, xanthophores, iridophores and erythrophores, and characterized their first appearance in wild-type fish. We mutated 25 genes involved in melanogenesis, pteridine metabolism, and the carotenoid absorption and cleavage pathways. Among the 25 mutated genes, 13 genes had a phenotype in both the F0 and F2 generations. None of F1 heterozygotes had phenotype. By comparing the color pattern of our mutants with that of red tilapia (Oreochromis spp), a natural mutant produced during hybridization of tilapia species, we found that the pigmentation of the body and eye is controlled by different genes. Previously studied genes like mitf, kita/kitlga, pmel, tyrb, hps4, gch2, csf1ra, pax7b, and bco2b were proved to be of great significance for color patterning in tilapia. Our results suggested that tilapia, a fish with 4 types of pigment cells and a vertically barred wild-type color pattern, together with various natural and artificially induced color gene mutants, can serve as an excellent model system for study color patterning in vertebrates.
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Affiliation(s)
- Chenxu Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Baoyue Lu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Tao Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Guangyuan Liang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Mengmeng Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- the Department of Biology, University of Maryland, College Park, MD
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
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7
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Andrade P, Gazda MA, Araújo PM, Afonso S, Rasmussen JA, Marques CI, Lopes RJ, Gilbert. MTP, Carneiro M. Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates. PLoS Genet 2021; 17:e1009404. [PMID: 33621224 PMCID: PMC7935293 DOI: 10.1371/journal.pgen.1009404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/05/2021] [Accepted: 02/08/2021] [Indexed: 01/04/2023] Open
Abstract
Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Małgorzata A. Gazda
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Pedro M. Araújo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- MARE–Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Jacob. A. Rasmussen
- Center for Evolutionary Genomics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Cristiana I. Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Ricardo J. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - M. Thomas P. Gilbert.
- Center for Evolutionary Genomics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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8
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Zhou L, Liang H, Zhou X, Jia J, Ye C, Hu Q, Xu S, Yu Y, Zou G, Hu G. Genetic Characteristic and RNA-Seq Analysis in Transparent Mutant of Carp-Goldfish Nucleocytoplasmic Hybrid. Genes (Basel) 2019; 10:genes10090704. [PMID: 31547242 PMCID: PMC6771007 DOI: 10.3390/genes10090704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/27/2019] [Accepted: 09/07/2019] [Indexed: 01/24/2023] Open
Abstract
In teleost, pigment in the skin and scales played important roles in various biological processes. Iridophores, one of the main pigment cells in teleost, could produce silver pigments to reflect light. However, the specific mechanism of the formation of silver pigments is still unclear. In our previous study, some transparent mutant individuals were found in the carp-goldfish nucleocytoplasmic hybrid (CyCa hybrid) population. In the present study, using transparent mutants (TM) and wild type (WT) of the CyCa hybrid as a model, firstly, microscopic observations showed that the silver pigments and melanin were both lost in the scales of transparent mutants compared to that in wild types. Secondly, genetic study demonstrated that the transparent trait in the CyCa hybrid was recessively inherent, and controlled by an allele in line with Mendelism. Thirdly, RNA-Seq analysis showed that differential expression genes (DEGs) between wild type and transparent mutants were mainly enriched in the metabolism of guanine, such as hydrolase, guanyl nucleotide binding, guanyl ribonucleotide binding, and GTPase activity. Among the DEGs, purine nucleoside phosphorylase 4a (pnp4a) and endothelin receptor B (ednrb) were more highly expressed in the wild type compared to the transparent mutant (p < 0.05). Finally, miRNA-Seq analysis showed that miRNA-146a and miR-153b were both more highly expressed in the transparent mutant compared to that in wild type (p < 0.05). Interaction analysis between miRNAs and mRNAs indicated that miRNA-146a was associated with six DEGs (MGAT5B, MFAP4, GP2, htt, Sema6b, Obscn) that might be involved in silver pigmentation.
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Affiliation(s)
- Lingling Zhou
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hongwei Liang
- Key Lab of Freshwater Biodiversity Conservation Ministry of Agriculture, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan 430223, China.
| | - Xiaoyun Zhou
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jingyi Jia
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Cheng Ye
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qiongyao Hu
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shaohua Xu
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yongning Yu
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guiwei Zou
- Key Lab of Freshwater Biodiversity Conservation Ministry of Agriculture, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan 430223, China.
| | - Guangfu Hu
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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9
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Bian F, Yang X, Ou Z, Luo J, Tan B, Yuan M, Chen T, Yang R. Morphological Characteristics and Comparative Transcriptome Analysis of Three Different Phenotypes of Pristella maxillaris. Front Genet 2019; 10:698. [PMID: 31428133 PMCID: PMC6687772 DOI: 10.3389/fgene.2019.00698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/03/2019] [Indexed: 01/09/2023] Open
Abstract
Pristella maxillaris is known as the X-ray fish based on its translucent body. However, the morphological characteristics and the molecular regulatory mechanisms of these translucent bodies are still unknown. In this study, the following three phenotypes, a black-and-gray body color or wild-type (WT), a silvery-white body color defined as mutant I (MU1), and a fully transparent body with a visible visceral mass named as mutant II (MU2), were investigated to analyze their chromatophores and molecular mechanisms. The variety and distribution of pigment cells in the three phenotypes of P. maxillaris significantly differed by histological assessment. Three types of chromatophores (melanophores, iridophores, and xanthophores) were observed in the WT, whereas MU1 fish were deficient in melanophores, and MU2 fish lacked melanophores and iridophores. Transcriptome sequencing of the skin and peritoneal tissues of P. maxillaris identified a total of 166,089 unigenes. After comparing intergroup gene expression levels, more than 3,000 unigenes with significantly differential expression levels were identified among three strains. Functional annotation and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the differentially expressed genes (DEGs) identified a number of candidates melanophores and iridophores genes that influence body color. Some DEGs that were identified using transcriptome analysis were confirmed by quantitative real-time PCR. This study serves as a global survey of the morphological characteristics and molecular mechanism of different body colors observed in P. maxillaris and thus provides a valuable theoretical foundation for the molecular regulation of the transparent phenotype.
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Affiliation(s)
- Fangfang Bian
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xuefen Yang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhijie Ou
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Department of Fisheries, Guangdong Maoming Agriculture & Forestry Technical College, Maoming, China
| | - Junzhi Luo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Bozhen Tan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Mingrui Yuan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Tiansheng Chen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, China
| | - Ruibin Yang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China
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10
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Lischik CQ, Adelmann L, Wittbrodt J. Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation. PLoS One 2019; 14:e0212956. [PMID: 30845151 PMCID: PMC6405165 DOI: 10.1371/journal.pone.0212956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
Fish are ideally suited for in vivo-imaging due to their transparency at early stages combined with a large genetic toolbox. Key challenges to further advance imaging are fluorophore selection, immobilization of the specimen and approaches to eliminate pigmentation. We addressed all three and identified the fluorophores and anaesthesia of choice by high throughput time-lapse imaging. Our results indicate that eGFP and mCherry are the best conservative choices for in vivo-fluorescence experiments, when availability of well-established antibodies and nanobodies matters. Still, mVenusNB and mGFPmut2 delivered highest absolute fluorescence intensities in vivo. Immobilization is of key importance during extended in vivo imaging. Here, traditional approaches are outperformed by mRNA injection of α-Bungarotoxin which allows a complete and reversible, transient immobilization. In combination with fully transparent juvenile and adult fish established by the targeted inactivation of both, oca2 and pnp4a via CRISPR/Cas9-mediated gene editing in medaka we could dramatically improve the state-of-the art imaging conditions in post-embryonic fish, now enabling light-sheet microscopy of the growing retina, brain, gills and inner organs in the absence of side effects caused by anaesthetic drugs or pigmentation.
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Affiliation(s)
- Colin Q Lischik
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany
| | - Leonie Adelmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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11
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Luc H, Sears C, Raczka A, Gross JB. Wholemount In Situ Hybridization for Astyanax Embryos. J Vis Exp 2019. [PMID: 30882790 DOI: 10.3791/59114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In recent years, a draft genome for the blind Mexican cavefish (Astyanax mexicanus) has been released, revealing the sequence identities for thousands of genes. Prior research into this emerging model system capitalized on comprehensive genome-wide investigations that have identified numerous quantitative trait loci (QTL) associated with various cave-associated phenotypes. However, the ability to connect genes of interest to the heritable basis for phenotypic change remains a significant challenge. One technique that can facilitate deeper understanding of the role of development in troglomorphic evolution is whole-mount in situ hybridization. This technique can be implemented to directly compare gene expression between cave- and surface-dwelling forms, nominate candidate genes underlying established QTL, identify genes of interest from next-generation sequencing studies, or develop other discovery-based approaches. In this report, we present a simple protocol, supported by a flexible checklist, that can be widely adapted for use well beyond the presented study system. It is hoped that this protocol can serve as a broad resource for the Astyanax community and beyond.
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Affiliation(s)
- Heidi Luc
- Department of Biological Sciences, University of Cincinnati
| | - Connor Sears
- Department of Biological Sciences, University of Cincinnati
| | - Andrew Raczka
- Department of Biological Sciences, University of Cincinnati
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati;
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12
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Salis P, Lorin T, Lewis V, Rey C, Marcionetti A, Escande ML, Roux N, Besseau L, Salamin N, Sémon M, Parichy D, Volff JN, Laudet V. Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish. Pigment Cell Melanoma Res 2019; 32:391-402. [PMID: 30633441 DOI: 10.1111/pcmr.12766] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/11/2018] [Accepted: 12/26/2018] [Indexed: 12/18/2022]
Abstract
Actinopterygian fishes harbor at least eight distinct pigment cell types, leading to a fascinating diversity of colors. Among this diversity, the cellular origin of the white color appears to be linked to several pigment cell types such as iridophores or leucophores. We used the clownfish Amphiprion ocellaris, which has a color pattern consisting of white bars over a darker body, to characterize the pigment cells that underlie the white hue. We observe by electron microscopy that cells in white bars are similar to iridophores. In addition, the transcriptomic signature of clownfish white bars exhibits similarities with that of zebrafish iridophores. We further show by pharmacological treatments that these cells are necessary for the white color. Among the top differentially expressed genes in white skin, we identified several genes (fhl2a, fhl2b, saiyan, gpnmb, and apoD1a) and show that three of them are expressed in iridophores. Finally, we show by CRISPR/Cas9 mutagenesis that these genes are critical for iridophore development in zebrafish. Our analyses provide clues to the genomic underpinning of color diversity and allow identification of new iridophore genes in fish.
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Affiliation(s)
- Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Thibault Lorin
- IGFL, ENS de Lyon, UMR 5242 CNRS, Université Claude Bernard Lyon I, Lyon Cedex 07, France
| | - Victor Lewis
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Carine Rey
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Université Claude Bernard, Lyon, France.,LBBE, CNRS, Université Lyon 1, Villeurbanne, France
| | - Anna Marcionetti
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marie-Line Escande
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Laurence Besseau
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Nicolas Salamin
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marie Sémon
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Université Claude Bernard, Lyon, France
| | - David Parichy
- Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Jean-Nicolas Volff
- IGFL, ENS de Lyon, UMR 5242 CNRS, Université Claude Bernard Lyon I, Lyon Cedex 07, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
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13
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Petratou K, Subkhankulova T, Lister JA, Rocco A, Schwetlick H, Kelsh RN. A systems biology approach uncovers the core gene regulatory network governing iridophore fate choice from the neural crest. PLoS Genet 2018; 14:e1007402. [PMID: 30286071 PMCID: PMC6191144 DOI: 10.1371/journal.pgen.1007402] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/16/2018] [Accepted: 08/22/2018] [Indexed: 12/29/2022] Open
Abstract
Multipotent neural crest (NC) progenitors generate an astonishing array of derivatives, including neuronal, skeletal components and pigment cells (chromatophores), but the molecular mechanisms allowing balanced selection of each fate remain unknown. In zebrafish, melanocytes, iridophores and xanthophores, the three chromatophore lineages, are thought to share progenitors and so lend themselves to investigating the complex gene regulatory networks (GRNs) underlying fate segregation of NC progenitors. Although the core GRN governing melanocyte specification has been previously established, those guiding iridophore and xanthophore development remain elusive. Here we focus on the iridophore GRN, where mutant phenotypes identify the transcription factors Sox10, Tfec and Mitfa and the receptor tyrosine kinase, Ltk, as key players. Here we present expression data, as well as loss and gain of function results, guiding the derivation of an initial iridophore specification GRN. Moreover, we use an iterative process of mathematical modelling, supplemented with a Monte Carlo screening algorithm suited to the qualitative nature of the experimental data, to allow for rigorous predictive exploration of the GRN dynamics. Predictions were experimentally evaluated and testable hypotheses were derived to construct an improved version of the GRN, which we showed produced outputs consistent with experimentally observed gene expression dynamics. Our study reveals multiple important regulatory features, notably a sox10-dependent positive feedback loop between tfec and ltk driving iridophore specification; the molecular basis of sox10 maintenance throughout iridophore development; and the cooperation between sox10 and tfec in driving expression of pnp4a, a key differentiation gene. We also assess a candidate repressor of mitfa, a melanocyte-specific target of sox10. Surprisingly, our data challenge the reported role of Foxd3, an established mitfa repressor, in iridophore regulation. Our study builds upon our previous systems biology approach, by incorporating physiologically-relevant parameter values and rigorous evaluation of parameter values within a qualitative data framework, to establish for the first time the core GRN guiding specification of the iridophore lineage.
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Affiliation(s)
- Kleio Petratou
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, Faculty of Science, University of Bath, Bath, United Kingdom
| | - Tatiana Subkhankulova
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, Faculty of Science, University of Bath, Bath, United Kingdom
| | - James A. Lister
- Department of Human and Molecular Genetics and Massey Cancer Center, VCU School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Andrea Rocco
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Hartmut Schwetlick
- Department of Mathematical Sciences, Faculty of Science, University of Bath, Bath, United Kingdom
| | - Robert N. Kelsh
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, Faculty of Science, University of Bath, Bath, United Kingdom
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14
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Watakabe I, Hashimoto H, Kimura Y, Yokoi S, Naruse K, Higashijima SI. Highly efficient generation of knock-in transgenic medaka by CRISPR/Cas9-mediated genome engineering. ZOOLOGICAL LETTERS 2018; 4:3. [PMID: 29445519 PMCID: PMC5798193 DOI: 10.1186/s40851-017-0086-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/29/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND Medaka (Oryzias latipes) is a popular animal model used in vertebrate genetic analysis. Recently, an efficient (~ 30%) knock-in system via non-homologous end joining (NHEJ) was established in zebrafish using the CRISPR/Cas9 system. If the same technique were applicable in medaka, it would greatly expand the usefulness of this model organism. The question of the applicability of CRISPR/Cas9 in medaka, however, has yet to be addressed. RESULTS We report the highly efficient generation of knock-in transgenic medaka via non-homologous end joining (NHEJ). Donor plasmid containing a heat-shock promoter and a reporter gene was co-injected with a short guide RNA (sgRNA) targeted for genome digestion, an sgRNA targeted for donor plasmid digestion, and Cas9 mRNA. Broad transgene expression in the expression domain of a target gene was observed in approximately 25% of injected embryos. By raising these animals, we established stable knock-in transgenic fish with several different constructs for five genetic loci, obtaining transgenic founders at efficiencies of > 50% for all five loci. Further, we show that the method is useful for obtaining mutant alleles. In the experiments where transgene integrations were targeted between the transcription start site and the initiation methionine, the resultant transgenic fish became mutant alleles. CONCLUSION With its simplicity, design flexibility, and high efficiency, we propose that CRISPR/Cas9-mediated knock-in via NHEJ will become a standard method for the generation of transgenic and mutant medaka.
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Affiliation(s)
- Ikuko Watakabe
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, Aichi 444-8787 Japan
| | - Hisashi Hashimoto
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601 Japan
| | - Yukiko Kimura
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, Aichi 444-8787 Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787 Japan
| | - Saori Yokoi
- National Institutes of Natural Sciences, National Institute for Basic Biology, Okazaki, Aichi 444-8585 Japan
- Present address: Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812 Japan
| | - Kiyoshi Naruse
- National Institutes of Natural Sciences, National Institute for Basic Biology, Okazaki, Aichi 444-8585 Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787 Japan
| | - Shin-ichi Higashijima
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, Aichi 444-8787 Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787 Japan
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