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The spliceosome factor sart3 regulates hematopoietic stem/progenitor cell development in zebrafish through the p53 pathway. Cell Death Dis 2021; 12:906. [PMID: 34611130 PMCID: PMC8492694 DOI: 10.1038/s41419-021-04215-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/09/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Hematopoietic stem cells (HSCs) possess the potential for self-renew and the capacity, throughout life, to differentiate into all blood cell lineages. Yet, the mechanistic basis for HSC development remains largely unknown. In this study, we characterized a zebrafish smu471 mutant with hematopoietic stem/progenitor cell (HSPC) defects and found that sart3 was the causative gene. RNA expression profiling of the sart3smu471 mutant revealed spliceosome and p53 signaling pathway to be the most significantly enriched pathways in the sart3smu471 mutant. Knock down of p53 rescued HSPC development in the sart3smu471 mutant. Interestingly, the p53 inhibitor, mdm4, had undergone an alternative splicing event in the mutant. Restoration of mdm4 partially rescued HSPC deficiency. Thus, our data suggest that HSPC proliferation and maintenance require sart3 to ensure the correct splicing and expression of mdm4, so that the p53 pathway is properly inhibited to prevent definitive hematopoiesis failure. This study expands our knowledge of the regulatory mechanisms that impact HSPC development and sheds light on the mechanistic basis and potential therapeutic use of sart3 in spliceosome-mdm4-p53 related disorders.
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Chu L, Yin H, Gao L, Gao L, Xia Y, Zhang C, Chen Y, Liu T, Huang J, Boheler KR, Zhou Y, Yang HT. Cardiac Na +-Ca 2+ exchanger 1 (ncx1h) is critical for the ventricular cardiomyocyte formation via regulating the expression levels of gata4 and hand2 in zebrafish. SCIENCE CHINA-LIFE SCIENCES 2020; 64:255-268. [PMID: 32648190 DOI: 10.1007/s11427-019-1706-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/22/2020] [Indexed: 10/23/2022]
Abstract
Ca2+ signaling is critical for heart development; however, the precise roles and regulatory pathways of Ca2+ transport proteins in cardiogenesis remain largely unknown. Sodium-calcium exchanger 1 (Ncx1) is responsible for Ca2+ efflux in cardiomyocytes. It is involved in cardiogenesis, while the mechanism is unclear. Here, using the forward genetic screening in zebrafish, we identified a novel mutation at a highly-conserved leucine residue in ncx1 gene (mutantLDD353/ncx1hL154P) that led to smaller hearts with reduced heart rate and weak contraction. Mechanistically, the number of ventricular but not atrial cardiomyocytes was reduced in ncx1hL154P zebrafish. These defects were mimicked by knockdown or knockout of ncx1h. Moreover, ncx1hL154P had cytosolic and mitochondrial Ca2+ overloading and Ca2+ transient suppression in cardiomyocytes. Furthermore, ncx1hL154P and ncx1h morphants downregulated cardiac transcription factors hand2 and gata4 in the cardiac regions, while overexpression of hand2 and gata4 partially rescued cardiac defects including the number of ventricular myocytes. These findings demonstrate an essential role of the novel 154th leucine residue in the maintenance of Ncx1 function in zebrafish, and reveal previous unrecognized critical roles of the 154th leucine residue and Ncx1 in the formation of ventricular cardiomyocytes by at least partially regulating the expression levels of gata4 and hand2.
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Affiliation(s)
- Liming Chu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China.,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
| | - Huimin Yin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China.,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
| | - Lei Gao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China.,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
| | - Li Gao
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yu Xia
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China.,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
| | - Chiyuan Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China.,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
| | - Yi Chen
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tingxi Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China.,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
| | - Jijun Huang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China.,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
| | - Kenneth R Boheler
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Yong Zhou
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China. .,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China.
| | - Huang-Tian Yang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology and Laboratory of Development and Diseases, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences (CAS), CAS, Shanghai, 200031, China. .,Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China.
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3
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Yu T, Kuang H, Chen J, Lin X, Wu Y, Chen K, Zhang M, Zhang W, Wen Z. Tripartite-motif family protein 35-28 regulates microglia development by preventing necrotic death of microglial precursors in zebrafish. J Biol Chem 2020; 295:8846-8856. [PMID: 32398256 DOI: 10.1074/jbc.ra119.012043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 05/04/2020] [Indexed: 02/02/2023] Open
Abstract
Microglia are tissue-resident macrophages in the central nervous system (CNS) that play essential roles in the regulation of CNS development and homeostasis. Yet, the genetic networks governing microglia development remain incompletely defined. Here, we report the identification and characterization of a microglia-defective zebrafish mutant wulonghkz12 (wulhkz12 ) isolated from an ethylnitrosourea (ENU)-based genetic screen. We show that wulhkz12 mutants harbors a missense point mutation in the gene region encoding the PRY/SPRY domain of the tripartite-motif family protein 35-28 (trim35-28) gene. Time-lapse imaging revealed that the loss of Trim35-28 function causes lytic necrosis of microglial precursors/peripheral macrophages, as indicated by cytoplasmic swelling and membrane rupture of these precursors and accompanied by neutrophil infiltration and systemic inflammation. Intriguingly, the lytic necrosis of microglial precursors in trim35-28-deficient mutants appeared to depend neither on the canonical pyroptotic nor necroptotic pathways, as inhibition of the key component in each pathway could not rescue the microglia phenotype in trim35-28-deficient mutants. Finally, results from tissue-specific rescue experiments suggested that Trim35-28 acts cell-autonomously in the survival of microglial precursors. Taken together, the findings of our study reveal Trim35-28 as a regulatory protein essential for microglia development.
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Affiliation(s)
- Tao Yu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Haoyue Kuang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jiahao Chen
- Department of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangdong, Guangzhou, China
| | - Xi Lin
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yi Wu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Keyu Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, China
| | - Mingjie Zhang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, China; Division of Life Science, State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, China
| | - Wenqing Zhang
- Department of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangdong, Guangzhou, China.
| | - Zilong Wen
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, China; Division of Life Science, State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, China.
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Dstyk mutation leads to congenital scoliosis-like vertebral malformations in zebrafish via dysregulated mTORC1/TFEB pathway. Nat Commun 2020; 11:479. [PMID: 31980602 PMCID: PMC6981171 DOI: 10.1038/s41467-019-14169-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
Congenital scoliosis (CS) is a complex genetic disorder characterized by vertebral malformations. The precise etiology of CS is not fully defined. Here, we identify that mutation in dual serine/threonine and tyrosine protein kinase (dstyk) lead to CS-like vertebral malformations in zebrafish. We demonstrate that the scoliosis in dstyk mutants is related to the wavy and malformed notochord sheath formation and abnormal axial skeleton segmentation due to dysregulated biogenesis of notochord vacuoles and notochord function. Further studies show that DSTYK is located in late endosomal/lysosomal compartments and is involved in the lysosome biogenesis in mammalian cells. Dstyk knockdown inhibits notochord vacuole and lysosome biogenesis through mTORC1-dependent repression of TFEB nuclear translocation. Inhibition of mTORC1 activity can rescue the defect in notochord vacuole biogenesis and scoliosis in dstyk mutants. Together, our findings reveal a key role of DSTYK in notochord vacuole biogenesis, notochord morphogenesis and spine development through mTORC1/TFEB pathway. Congenital scoliosis is a complex genetic disorder characterized by vertebral malformation. Here, the authors demonstrate that loss of dstyk leads to scoliosis in zebrafish due to dysregulated biogenesis of notochord vacuoles and that DSTYK is required for lysosome biogenesis through mTORC1 regulation.
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Yan L, Chen J, Zhu X, Sun J, Wu X, Shen W, Zhang W, Tao Q, Meng A. Maternal Huluwa dictates the embryonic body axis through β-catenin in vertebrates. Science 2018; 362:362/6417/eaat1045. [DOI: 10.1126/science.aat1045] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/27/2018] [Indexed: 12/26/2022]
Abstract
The vertebrate body is formed by cell movements and shape change during embryogenesis. It remains undetermined which maternal signals govern the formation of the dorsal organizer and the body axis. We found that maternal depletion of huluwa, a previously unnamed gene, causes loss of the dorsal organizer, the head, and the body axis in zebrafish and Xenopus embryos. Huluwa protein is found on the plasma membrane of blastomeres in the future dorsal region in early zebrafish blastulas. Huluwa has strong dorsalizing and secondary axis–inducing activities, which require β-catenin but can function independent of Wnt ligand/receptor signaling. Mechanistically, Huluwa binds to and promotes the tankyrase-mediated degradation of Axin. Therefore, maternal Huluwa is an essential determinant of the dorsal organizer and body axis in vertebrate embryos.
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Yao L, Chen J, Wu X, Jia S, Meng A. Zebrafish cdc6 hypomorphic mutation causes Meier-Gorlin syndrome-like phenotype. Hum Mol Genet 2018; 26:4168-4180. [PMID: 28985365 PMCID: PMC5886151 DOI: 10.1093/hmg/ddx305] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/26/2017] [Indexed: 11/13/2022] Open
Abstract
Cell Division Cycle 6 (Cdc6) is a component of pre-replicative complex (preRC) forming on DNA replication origins in eukaryotes. Recessive mutations in ORC1, ORC4, ORC6, CDT1 or CDC6 of the preRC in human cause Meier-Gorlin syndrome (MGS) that is characterized by impaired post-natal growth, short stature and microcephaly. However, vertebrate models of MGS have not been reported. Through N-ethyl-N-nitrosourea mutagenesis and Cas9 knockout, we generate several cdc6 mutant lines in zebrafish. Loss-of-function mutations of cdc6, as manifested by cdc6tsu4305 and cdc6tsu7cd mutants, lead to embryonic lethality due to cell cycle arrest at the S phase and extensive apoptosis. Embryos homozygous for a cdc6 hypomorphic mutation, cdc6tsu21cd, develop normally during embryogenesis. Later on, compared with their wild-type (WT) siblings, cdc6tsu21cd mutant fish show growth retardation, and their body weight and length in adulthood are greatly reduced, which resemble human MGS. Surprisingly, cdc6tsu21cd mutant fish become males with a short life and fail to mate with WT females, suggesting defective reproduction. Overexpression of Cdc6 mutant forms, which mimic human CDC6(T323R) mutation found in a MGS patient, in zebrafish cdc6tsu4305 mutant embryos partially represses cell death phenotype, suggesting that the human CDC6(T323R) mutation is a hypomorph. cdc6tsu21cd mutant fish will be useful to detect more tissue defects and develop medical treatment strategies for MGS patients.
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Affiliation(s)
- Likun Yao
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaotong Wu
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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7
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Whole Genome Sequencing-Based Mapping and Candidate Identification of Mutations from Fixed Zebrafish Tissue. G3-GENES GENOMES GENETICS 2017; 7:3415-3425. [PMID: 28855284 PMCID: PMC5633390 DOI: 10.1534/g3.117.300212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As forward genetic screens in zebrafish become more common, the number of mutants that cannot be identified by gross morphology or through transgenic approaches, such as many nervous system defects, has also increased. Screening for these difficult-to-visualize phenotypes demands techniques such as whole-mount in situ hybridization (WISH) or antibody staining, which require tissue fixation. To date, fixed tissue has not been amenable for generating libraries for whole genome sequencing (WGS). Here, we describe a method for using genomic DNA from fixed tissue and a bioinformatics suite for WGS-based mapping of zebrafish mutants. We tested our protocol using two known zebrafish mutant alleles, gpr126st49 and egr2bfh227, both of which cause myelin defects. As further proof of concept we mapped a novel mutation, stl64, identified in a zebrafish WISH screen for myelination defects. We linked stl64 to chromosome 1 and identified a candidate nonsense mutation in the F-box and WD repeat domain containing 7 (fbxw7) gene. Importantly, stl64 mutants phenocopy previously described fbxw7vu56 mutants, and knockdown of fbxw7 in wild-type animals produced similar defects, demonstrating that stl64 disrupts fbxw7. Together, these data show that our mapping protocol can map and identify causative lesions in mutant screens that require tissue fixation for phenotypic analysis.
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8
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D'Agati G, Beltre R, Sessa A, Burger A, Zhou Y, Mosimann C, White RM. A defect in the mitochondrial protein Mpv17 underlies the transparent casper zebrafish. Dev Biol 2017; 430:11-17. [PMID: 28760346 DOI: 10.1016/j.ydbio.2017.07.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 10/19/2022]
Abstract
The casper strain of zebrafish is widely used in studies ranging from cancer to neuroscience. casper offers the advantage of relative transparency throughout adulthood, making it particularly useful for in vivo imaging by epifluorescence, confocal, and light sheet microscopy. casper was developed by selective breeding of two previously described recessive pigment mutants: 1) nacre, which harbors an inactivating mutation of the mitfa gene, rendering the fish devoid of pigmented melanocytes; and 2) roy orbison, a mutant with a so-far unidentified genetic cause that lacks reflective iridophores. To clarify the molecular nature of the roy orbison mutation, such that it can inform studies using casper, we undertook an effort to positionally clone the roy orbison mutation. We find that roy orbison is caused by an intronic defect in the gene mpv17, encoding an inner mitochondrial membrane protein that has been implicated in the human mitochondrial DNA depletion syndrome. The roy orbison mutation is phenotypically and molecularly remarkably similar to another zebrafish iridophore mutant called transparent. Using Cas9-induced crispants and germline mutants with a disrupted mpv17 open reading frame, we show in trans-heterozygote embryos that new frameshift alleles of mpv17, roy orbison, and transparent fail to complement each other. Our work provides genetic evidence that both roy orbison and transparent affect the mpv17 locus by a similar if not identical genetic lesion. Identification of mpv17 mutants will allow for further work probing the relationship between mitochondrial function and pigmentation, which has to date received little attention.
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Affiliation(s)
- Gianluca D'Agati
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Rosanna Beltre
- Hematology&Oncology, Children's Hospital Boston, Boston, MA, United States
| | - Anna Sessa
- Hematology&Oncology, Children's Hospital Boston, Boston, MA, United States
| | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Yi Zhou
- Hematology&Oncology, Children's Hospital Boston, Boston, MA, United States
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
| | - Richard M White
- Cancer Biology&Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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Chen J, Wu X, Yao L, Yan L, Zhang L, Qiu J, Liu X, Jia S, Meng A. Impairment of Cargo Transportation Caused by gbf1 Mutation Disrupts Vascular Integrity and Causes Hemorrhage in Zebrafish Embryos. J Biol Chem 2016; 292:2315-2327. [PMID: 28003365 DOI: 10.1074/jbc.m116.767608] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/19/2016] [Indexed: 12/11/2022] Open
Abstract
ADP-ribosylation factor GTPases are activated by guanine nucleotide exchange factors including Gbf1 (Golgi brefeldin A-resistant factor 1) and play important roles in regulating organelle structure and cargo-selective vesicle trafficking. However, the developmental role of Gbf1 in vertebrates remains elusive. In this study, we report the zebrafish mutant line tsu3994 that arises from N-ethyl-N-nitrosourea (ENU)-mediated mutagenesis and is characterized by prominent intracerebral and trunk hemorrhage. The mutant embryos develop hemorrhage accompanied by fewer pigments and shorter caudal fin at day 2 of development. The hemorrhage phenotype is caused by vascular breakage in a cell autonomous fashion. Positional cloning identifies a T → G nucleotide substitution in the 23rd exon of the gbf1 locus, resulting in a leucine → arginine substitution (L1246R) in the HDS2 domain. The mutant phenotype is mimicked by gbf1 knockouts and morphants, suggesting a nature of loss of function. Experimental results in mammalian cells show that the mutant form Gbf1(L1246R) is unable to be recruited to the Golgi apparatus and fails to activate Arf1 for recruiting COPI complex. The hemorrhage in tsu3994 mutants can be prevented partially and temporally by treating with the endoplasmic reticulum stress/apoptosis inhibitor tauroursodeoxycholic acid or by knocking down the proapoptotic gene baxb Therefore, endothelial endoplasmic reticulum stress and subsequent apoptosis induced by gbf1 deficiency may account for the vascular collapse and hemorrhage.
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Affiliation(s)
- Jing Chen
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaotong Wu
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Likun Yao
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lu Yan
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lin Zhang
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Juhui Qiu
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xingfeng Liu
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- From the Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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10
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Don EK, de Jong-Curtain TA, Doggett K, Hall TE, Heng B, Badrock AP, Winnick C, Nicholson GA, Guillemin GJ, Currie PD, Hesselson D, Heath JK, Cole NJ. Genetic basis of hindlimb loss in a naturally occurring vertebrate model. Biol Open 2016; 5:359-66. [PMID: 26892237 PMCID: PMC4810746 DOI: 10.1242/bio.016295] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Here we genetically characterise pelvic finless, a naturally occurring model of hindlimb loss in zebrafish that lacks pelvic fin structures, which are homologous to tetrapod hindlimbs, but displays no other abnormalities. Using a hybrid positional cloning and next generation sequencing approach, we identified mutations in the nuclear localisation signal (NLS) of T-box transcription factor 4 (Tbx4) that impair nuclear localisation of the protein, resulting in altered gene expression patterns during pelvic fin development and the failure of pelvic fin development. Using a TALEN-induced tbx4 knockout allele we confirm that mutations within the Tbx4 NLS (A78V; G79A) are sufficient to disrupt pelvic fin development. By combining histological, genetic, and cellular approaches we show that the hindlimb initiation gene tbx4 has an evolutionarily conserved, essential role in pelvic fin development. In addition, our novel viable model of hindlimb deficiency is likely to facilitate the elucidation of the detailed molecular mechanisms through which Tbx4 functions during pelvic fin and hindlimb development. Summary: Here we genetically characterise mutations in tbx4 which underlie pelvic finless, a naturally occurring model of hindlimb loss in zebrafish that lacks pelvic fin structures.
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Affiliation(s)
- Emily K Don
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia Department of Anatomy & Histology, School of Medical Sciences and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Karen Doggett
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Thomas E Hall
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Benjamin Heng
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Andrew P Badrock
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Claire Winnick
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Gilles J Guillemin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel Hesselson
- Garvan Institute of Medical Research, Diabetes and Metabolism Division, Sydney, New South Wales 2010, Australia St. Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Joan K Heath
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Nicholas J Cole
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia Department of Anatomy & Histology, School of Medical Sciences and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
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11
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Wei Y, Xu J, Zhang W, Wen Z, Liu F. RNA polymerase III component Rpc9 regulates hematopoietic stem and progenitor cell maintenance in zebrafish. Development 2016; 143:2103-10. [DOI: 10.1242/dev.126797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 04/25/2016] [Indexed: 12/18/2022]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are capable of self-renewal and replenishing all lineages of blood cells throughout the lifetime and thus critical for tissue homeostasis. However, the mechanism regulating HSPC development is still incompletely understood. Here, we isolate a zebrafish mutant with defective T lymphopoiesis and positional cloning identifies that Rpc9, a component of DNA-directed RNA polymerase III (Pol III) complex, is responsible for the mutant phenotype. Further analysis shows that rpc9-deficiency leads to the impairment of HSPCs and their derivatives in zebrafish embryos. Excessive apoptosis is observed in the caudal hematopoietic tissue (CHT, the equivalent of fetal liver in mammals) of rpc9−/− embryos and the hematopoietic defects in rpc9−/− embryos can be fully rescued by suppression of p53. Thus, our work illustrate that Rpc9, a component of Pol III, plays an important tissue-specific role in HSPC maintenance during zebrafish embryogenesis and that it might be conserved across vertebrates including mammals.
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Affiliation(s)
- Yonglong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Xu
- State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Wenqing Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, China
| | - Zilong Wen
- State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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12
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Wang K, Fang X, Ma N, Lin Q, Huang Z, Liu W, Xu M, Chen X, Zhang W, Zhang Y. Myeloperoxidase-deficient zebrafish show an augmented inflammatory response to challenge with Candida albicans. FISH & SHELLFISH IMMUNOLOGY 2015; 44:109-116. [PMID: 25665803 DOI: 10.1016/j.fsi.2015.01.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 06/04/2023]
Abstract
Myeloperoxidase is a key component of neutrophil granules involved in killing engulfed microorganisms. We obtained a zebrafish mutant (smu681) lacking Sudan black staining by large-scale screening, which was a neutrophil-replete but myeloperoxidase-deficient mutant. When infiltrated with Candida albicans, smu681 embryos and sibling embryos showed similar survival after infection. Proliferation of C. albicans was more rapid in smu681 embryos than in sibling embryos, although it was eventually suppressed. In addition, the number of neutrophils accumulating at the site of infection was significantly larger in mutant embryos than in sibling embryos, and mutant embryos showed increased expression of several inflammatory cytokines after C. albicans infection. These findings indicate that myeloperoxidase deficiency alters the inflammatory response to fungal infection.
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Affiliation(s)
- Kun Wang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China
| | - Xiao Fang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China
| | - Ning Ma
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China
| | - Qing Lin
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China
| | - Zhibin Huang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China
| | - Wei Liu
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China
| | - Mengchang Xu
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China
| | - Xiaohui Chen
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China
| | - Wenqing Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China.
| | - Yiyue Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, PR China.
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13
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14
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Kroeger PT, Wingert RA. Using zebrafish to study podocyte genesis during kidney development and regeneration. Genesis 2014; 52:771-92. [PMID: 24920186 DOI: 10.1002/dvg.22798] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/08/2014] [Accepted: 06/09/2014] [Indexed: 12/21/2022]
Abstract
During development, vertebrates form a progression of up to three different kidneys that are comprised of functional units termed nephrons. Nephron composition is highly conserved across species, and an increasing appreciation of the similarities between zebrafish and mammalian nephron cell types has positioned the zebrafish as a relevant genetic system for nephrogenesis studies. A key component of the nephron blood filter is a specialized epithelial cell known as the podocyte. Podocyte research is of the utmost importance as a vast majority of renal diseases initiate with the dysfunction or loss of podocytes, resulting in a condition known as proteinuria that causes nephron degeneration and eventually leads to kidney failure. Understanding how podocytes develop during organogenesis may elucidate new ways to promote nephron health by stimulating podocyte replacement in kidney disease patients. In this review, we discuss how the zebrafish model can be used to study kidney development, and how zebrafish research has provided new insights into podocyte lineage specification and differentiation. Further, we discuss the recent discovery of podocyte regeneration in adult zebrafish, and explore how continued basic research using zebrafish can provide important knowledge about podocyte genesis in embryonic and adult environments. genesis 52:771-792, 2014. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Paul T Kroeger
- Department of Biological Sciences and Center for Zebrafish Research, University of Notre Dame, Notre Dame, Indiana, 46556
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15
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McConnell SC, Restaino AC, de Jong JL. Multiple divergent haplotypes express completely distinct sets of class I MHC genes in zebrafish. Immunogenetics 2014; 66:199-213. [PMID: 24291825 PMCID: PMC3965299 DOI: 10.1007/s00251-013-0749-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 11/16/2013] [Indexed: 12/12/2022]
Abstract
The zebrafish is an important animal model for stem cell biology, cancer, and immunology research. Histocompatibility represents a key intersection of these disciplines; however, histocompatibility in zebrafish remains poorly understood. We examined a set of diverse zebrafish class I major histocompatibility complex (MHC) genes that segregate with specific haplotypes at chromosome 19, and for which donor-recipient matching has been shown to improve engraftment after hematopoietic transplantation. Using flanking gene polymorphisms, we identified six distinct chromosome 19 haplotypes. We describe several novel class I U lineage genes and characterize their sequence properties, expression, and haplotype distribution. Altogether, ten full-length zebrafish class I genes were analyzed, mhc1uba through mhc1uka. Expression data and sequence properties indicate that most are candidate classical genes. Several substitutions in putative peptide anchor residues, often shared with deduced MHC molecules from additional teleost species, suggest flexibility in antigen binding. All ten zebrafish class I genes were uniquely assigned among the six haplotypes, with dominant or codominant expression of one to three genes per haplotype. Interestingly, while the divergent MHC haplotypes display variable gene copy number and content, the different genes appear to have ancient origin, with extremely high levels of sequence diversity. Furthermore, haplotype variability extends beyond the MHC genes to include divergent forms of psmb8. The many disparate haplotypes at this locus therefore represent a remarkable form of genomic region configuration polymorphism. Defining the functional MHC genes within these divergent class I haplotypes in zebrafish will provide an important foundation for future studies in immunology and transplantation.
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Affiliation(s)
- Sean C. McConnell
- Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Knapp Center for Biomedical Discovery, 900 E. 57St, Chicago, IL 60637
| | - Anthony C. Restaino
- Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Knapp Center for Biomedical Discovery, 900 E. 57St, Chicago, IL 60637
| | - Jill L.O. de Jong
- Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Knapp Center for Biomedical Discovery, 900 E. 57St, Chicago, IL 60637
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16
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Ryan S, Willer J, Marjoram L, Bagwell J, Mankiewicz J, Leshchiner I, Goessling W, Bagnat M, Katsanis N. Rapid identification of kidney cyst mutations by whole exome sequencing in zebrafish. Development 2013; 140:4445-51. [PMID: 24130329 DOI: 10.1242/dev.101170] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Forward genetic approaches in zebrafish have provided invaluable information about developmental processes. However, the relative difficulty of mapping and isolating mutations has limited the number of new genetic screens. Recent improvements in the annotation of the zebrafish genome coupled to a reduction in sequencing costs prompted the development of whole genome and RNA sequencing approaches for gene discovery. Here we describe a whole exome sequencing (WES) approach that allows rapid and cost-effective identification of mutations. We used our WES methodology to isolate four mutations that cause kidney cysts; we identified novel alleles in two ciliary genes as well as two novel mutants. The WES approach described here does not require specialized infrastructure or training and is therefore widely accessible. This methodology should thus help facilitate genetic screens and expedite the identification of mutants that can inform basic biological processes and the causality of genetic disorders in humans.
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Affiliation(s)
- Sean Ryan
- Department of Cell Biology, Duke University, 333 B, Nanaline Duke Building, Durham, NC 27710, USA
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17
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Varshney GK, Burgess SM. Mutagenesis and phenotyping resources in zebrafish for studying development and human disease. Brief Funct Genomics 2013; 13:82-94. [PMID: 24162064 DOI: 10.1093/bfgp/elt042] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The zebrafish (Danio rerio) is an important model organism for studying development and human disease. The zebrafish has an excellent reference genome and the functions of hundreds of genes have been tested using both forward and reverse genetic approaches. Recent years have seen an increasing number of large-scale mutagenesis projects and the number of mutants or gene knockouts in zebrafish has increased rapidly, including for the first time conditional knockout technologies. In addition, targeted mutagenesis techniques such as zinc finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short sequences (CRISPR) or CRISPR-associated (Cas), have all been shown to effectively target zebrafish genes as well as the first reported germline homologous recombination, further expanding the utility and power of zebrafish genetics. Given this explosion of mutagenesis resources, it is now possible to perform systematic, high-throughput phenotype analysis of all zebrafish gene knockouts.
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Affiliation(s)
- Gaurav Kumar Varshney
- Developmental Genomics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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18
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Henke K, Bowen ME, Harris MP. Perspectives for identification of mutations in the zebrafish: Making use of next-generation sequencing technologies for forward genetic approaches. Methods 2013; 62:185-96. [DOI: 10.1016/j.ymeth.2013.05.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 05/21/2013] [Accepted: 05/22/2013] [Indexed: 01/13/2023] Open
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Miller AC, Obholzer ND, Shah AN, Megason SG, Moens CB. RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res 2013; 23:679-86. [PMID: 23299976 PMCID: PMC3613584 DOI: 10.1101/gr.147322.112] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/18/2012] [Indexed: 11/24/2022]
Abstract
Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life; however, identifying the causal mutations from such screens has long been the bottleneck in the process, particularly in vertebrates. We have developed an RNA-seq-based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Furthermore, we develop an easily accessible bioinformatics pipeline allowing for implementation of all steps of the method. Overall, we show that RNA-seq is a fast, reliable, and cost-effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.
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Affiliation(s)
- Adam C. Miller
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Nikolaus D. Obholzer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Arish N. Shah
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sean G. Megason
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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20
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Li J, Li P, Carr A, Wang X, DeLaPaz A, Sun L, Lee E, Tomei E, Li L. Functional expression of SCL/TAL1 interrupting locus (Stil) protects retinal dopaminergic cells from neurotoxin-induced degeneration. J Biol Chem 2012; 288:886-93. [PMID: 23166330 DOI: 10.1074/jbc.m112.417089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We previously isolated a dominant mutation, night blindness b (nbb), which causes a late onset of retinal dopaminergic cell degeneration in zebrafish. In this study, we cloned the zebrafish nbb locus. Sequencing results revealed that nbb is a homolog of the vertebrate SCL/TAL1 interrupting locus (Stil). The Stil gene has been shown to play important roles in the regulation of vertebrate embryonic neural development and human cancer cell proliferation. In this study, we demonstrate that functional expression of Stil is also required for neural survival. In zebrafish, decreased expression of Stil resulted in increased toxic susceptibility of retinal dopaminergic cells to 6-hydroxydopamine. Increases in Stil-mediated Shh signaling transduction (i.e. by knocking down the Shh repressor Sufu) prevented dopaminergic cell death induced by neurotoxic insult. The data suggest that the oncogene Stil also plays important roles in neural protection.
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Affiliation(s)
- Jingling Li
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
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21
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Obholzer N, Swinburne IA, Schwab E, Nechiporuk AV, Nicolson T, Megason SG. Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing. Development 2012; 139:4280-90. [PMID: 23052906 DOI: 10.1242/dev.083931] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Forward genetic screens in zebrafish have identified >9000 mutants, many of which are potential disease models. Most mutants remain molecularly uncharacterized because of the high cost, time and labor investment required for positional cloning. These costs limit the benefit of previous genetic screens and discourage future screens. Drastic improvements in DNA sequencing technology could dramatically improve the efficiency of positional cloning in zebrafish and other model organisms, but the best strategy for cloning by sequencing has yet to be established. Using four zebrafish inner ear mutants, we developed and compared two approaches for 'cloning by sequencing': one based on bulk segregant linkage (BSFseq) and one based on homozygosity mapping (HMFseq). Using BSFseq we discovered that mutations in lmx1b and jagged1b cause abnormal ear morphogenesis. With HMFseq we validated that the disruption of cdh23 abolishes the ear's sensory functions and identified a candidate lesion in lhfpl5a predicted to cause nonsyndromic deafness. The success of HMFseq shows that the high intrastrain polymorphism rate in zebrafish eliminates the need for time-consuming map crosses. Additionally, we analyzed diversity in zebrafish laboratory strains to find areas of elevated diversity and areas of fixed homozygosity, reinforcing recent findings that genome diversity is clustered. We present a database of >15 million sequence variants that provides much of this approach's power. In our four test cases, only a single candidate single nucleotide polymorphism (SNP) remained after subtracting all database SNPs from a mutant's critical region. The saturation of the common SNP database and our open source analysis pipeline MegaMapper will improve the pace at which the zebrafish community makes unique discoveries relevant to human health.
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Affiliation(s)
- Nikolaus Obholzer
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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22
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Gupta VA, Kawahara G, Myers JA, Chen AT, Hall TE, Manzini MC, Currie PD, Zhou Y, Zon LI, Kunkel LM, Beggs AH. A splice site mutation in laminin-α2 results in a severe muscular dystrophy and growth abnormalities in zebrafish. PLoS One 2012; 7:e43794. [PMID: 22952766 PMCID: PMC3428294 DOI: 10.1371/journal.pone.0043794] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 07/24/2012] [Indexed: 11/18/2022] Open
Abstract
Congenital muscular dystrophy (CMD) is a clinically and genetically heterogeneous group of inherited muscle disorders. In patients, muscle weakness is usually present at or shortly after birth and is progressive in nature. Merosin deficient congenital muscular dystrophy (MDC1A) is a form of CMD caused by a defect in the laminin-α2 gene (LAMA2). Laminin-α2 is an extracellular matrix protein that interacts with the dystrophin-dystroglycan (DGC) complex in membranes providing stability to muscle fibers. In an N-ethyl-N-nitrosourea mutagenesis screen to develop zebrafish models of neuromuscular diseases, we identified a mutant fish that exhibits severe muscular dystrophy early in development. Genetic mapping identified a splice site mutation in the lama2 gene. This splice site is highly conserved in humans and this mutation results in mis-splicing of RNA and a loss of protein function. Homozygous lama2 mutant zebrafish, designated lama2cl501/cl501, exhibited reduced motor function and progressive degeneration of skeletal muscles and died at 8–15 days post fertilization. The skeletal muscles exhibited damaged myosepta and detachment of myofibers in the affected fish. Laminin-α2 deficiency also resulted in growth defects in the brain and eye of the mutant fish. This laminin-α2 deficient mutant fish represents a novel disease model to develop therapies for modulating splicing defects in congenital muscular dystrophies and to restore the muscle function in human patients with CMD.
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Affiliation(s)
- Vandana A. Gupta
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Genri Kawahara
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Jennifer A. Myers
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Aye T. Chen
- Stem Cell Program and Pediatric Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas E. Hall
- Australian Regenerative Medicine Institute, Monash University, Clayton Campus, Victoria, Australia
| | - M. Chiara Manzini
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Peter D. Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton Campus, Victoria, Australia
| | - Yi Zhou
- Stem Cell Program and Pediatric Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Leonard I. Zon
- Stem Cell Program and Pediatric Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, San Francisco, California, United States of America
| | - Louis M. Kunkel
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Alan H. Beggs
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
- * E-mail:
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