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Bedell VM, Dubey P, Lee HB, Bailey DS, Anderson JL, Jamieson-Lucy A, Xiao R, Leonard EV, Falk MJ, Pack MA, Mullins M, Farber SA, Eckenhoff RG, Ekker SC. Zebrafishology, study design guidelines for rigorous and reproducible data using zebrafish. Commun Biol 2025; 8:739. [PMID: 40360750 PMCID: PMC12075475 DOI: 10.1038/s42003-025-07496-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 01/08/2025] [Indexed: 05/15/2025] Open
Abstract
The zebrafish (Danio rerio) is one of the most widely used research model organisms funded by the United States' National Institutes of Health, second only to the mouse. Here, we discuss the advantages and unique qualities of this model organism. Additionally, we discuss key aspects of experimental design and statistical approaches that apply to studies using the zebrafish model organism. Finally, we list critical details that should be considered in the design of zebrafish experiments to enhance rigor and data reproducibility. These guidelines are designed to aid new researchers, journal editors, and manuscript reviewers in supporting the publication of the highest-quality zebrafish research.
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Affiliation(s)
- Victoria M Bedell
- Department of Anesthesiology and Critical Care, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Priya Dubey
- Department of Anesthesiology and Critical Care, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Han B Lee
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Dondra S Bailey
- Department of Natural Sciences, Coppin State University, Baltimore, MD, USA
| | - Jennifer L Anderson
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Allison Jamieson-Lucy
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rui Xiao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elvin V Leonard
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael A Pack
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mary Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Steven A Farber
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Roderic G Eckenhoff
- Department of Anesthesiology and Critical Care, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephen C Ekker
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Department of Molecular Biosciences and Dell Medical School Department of Pediatrics, University of Texas, Austin, TX, USA
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2
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Kroll F, Donnelly J, Özcan GG, Mackay E, Rihel J. Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer's disease risk genes. eLife 2025; 13:RP96839. [PMID: 39960847 PMCID: PMC11832171 DOI: 10.7554/elife.96839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2025] Open
Abstract
By exposing genes associated with disease, genomic studies provide hundreds of starting points that should lead to druggable processes. However, our ability to systematically translate these genomic findings into biological pathways remains limited. Here, we combine rapid loss-of-function mutagenesis of Alzheimer's risk genes and behavioural pharmacology in zebrafish to predict disrupted processes and candidate therapeutics. FramebyFrame, our expanded package for the analysis of larval behaviours, revealed that decreased night-time sleep was common to F0 knockouts of all four late-onset Alzheimer's risk genes tested. We developed an online tool, ZOLTAR, which compares any behavioural fingerprint to a library of fingerprints from larvae treated with 3677 compounds. ZOLTAR successfully predicted that sorl1 mutants have disrupted serotonin signalling and identified betamethasone as a drug which normalises the excessive day-time sleep of presenilin-2 knockout larvae with minimal side effects. Predictive behavioural pharmacology offers a general framework to rapidly link disease-associated genes to druggable pathways.
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Affiliation(s)
- François Kroll
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
- Institut de la Vision, Sorbonne UniversitéParisFrance
| | - Joshua Donnelly
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Güliz Gürel Özcan
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Eirinn Mackay
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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3
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Jarayseh T, Debaenst S, De Saffel H, Rosseel T, Milazzo M, Bek JW, Hudson DM, Van Nieuwerburgh F, Gansemans Y, Josipovic I, Boone MN, Witten PE, Willaert A, Coucke PJ. Bmpr1aa modulates the severity of the skeletal phenotype in an fkbp10-deficient Bruck syndrome zebrafish model. J Bone Miner Res 2024; 40:154-166. [PMID: 39566080 DOI: 10.1093/jbmr/zjae185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 10/23/2024] [Accepted: 11/19/2024] [Indexed: 11/22/2024]
Abstract
Rare monogenic disorders often exhibit significant phenotypic variability among individuals sharing identical genetic mutations. Bruck syndrome (BS), a prime example, is characterized by bone fragility and congenital contractures, although with a pronounced variability among family members. BS arises from recessive biallelic mutations in FKBP10 or PLOD2. FKBP65, the protein encoded by FKBP10, collaborates with the LH2 enzyme (PLOD2) in type I collagen telopeptide lysine hydroxylation, crucial for collagen cross-linking. To identify potential modifier genes and to investigate the mechanistic role of FKBP10 in BS pathogenesis, we established an fkbp10a knockout zebrafish model. Mass-spectrometry analysis in fkbp10a-/- mutants revealed a generally decreased type I collagen lysyl hydroxylation, paralleled by a wide skeletal variability similar to human patients. Ultrastructural examination of the skeleton in severely affected mutants showed enlarged type I collagen fibrils and disturbed elastin layers. Whole-exome sequencing of 7 mildly and 7 severely affected mutant zebrafish siblings, followed by single nucleotide polymorphism-based linkage analysis, indicated a linked region on chromosome 13, which segregates with phenotypic severity. Transcriptome analysis identified 6 differentially expressed genes (DEGs) between mildly and severely affected mutants. The convergence of genes within the linked region and DEGs highlighted bmpr1aa as a potential modifier gene, as its reduced expression correlates with increased skeletal severity. In summary, our study provides deeper insights into the role of FKBP10 in BS pathogenesis. Additionally, we identified a pivotal gene that influences phenotypic severity in a zebrafish model of BS. These findings hold promise for novel treatments in the field of bone diseases.
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Affiliation(s)
- Tamara Jarayseh
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Sophie Debaenst
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Hanna De Saffel
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Toon Rosseel
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Mauro Milazzo
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Jan Willem Bek
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - David M Hudson
- Department of Orthopaedics and Sports Medicine, University of Washington, WA 98195, Seattle, United States
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000, Ghent, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000, Ghent, Belgium
| | - Iván Josipovic
- Radiation Physics Research GroupCentre for X-ray Tomography (UGCT), Ghent University, 9000, Ghent, Belgium
| | - Matthieu N Boone
- Radiation Physics Research GroupCentre for X-ray Tomography (UGCT), Ghent University, 9000, Ghent, Belgium
| | | | - Andy Willaert
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Paul J Coucke
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
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4
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Zhang L, Li H, Shi M, Ren K, Zhang W, Cheng Y, Wang Y, Xia XQ. FishSNP: a high quality cross-species SNP database of fishes. Sci Data 2024; 11:286. [PMID: 38461307 PMCID: PMC10924876 DOI: 10.1038/s41597-024-03111-8] [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: 09/20/2023] [Accepted: 03/04/2024] [Indexed: 03/11/2024] Open
Abstract
The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP ( http://bioinfo.ihb.ac.cn/fishsnp ), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mijuan Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Keyi Ren
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Wanting Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yingyin Cheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Qin Xia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Bin JM, Suminaite D, Benito-Kwiecinski SK, Kegel L, Rubio-Brotons M, Early JJ, Soong D, Livesey MR, Poole RJ, Lyons DA. Importin 13-dependent axon diameter growth regulates conduction speeds along myelinated CNS axons. Nat Commun 2024; 15:1790. [PMID: 38413580 PMCID: PMC10899189 DOI: 10.1038/s41467-024-45908-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
Axon diameter influences the conduction properties of myelinated axons, both directly, and indirectly through effects on myelin. However, we have limited understanding of mechanisms controlling axon diameter growth in the central nervous system, preventing systematic dissection of how manipulating diameter affects myelination and conduction along individual axons. Here we establish zebrafish to study axon diameter. We find that importin 13b is required for axon diameter growth, but does not affect cell body size or axon length. Using neuron-specific ipo13b mutants, we assess how reduced axon diameter affects myelination and conduction, and find no changes to myelin thickness, precision of action potential propagation, or ability to sustain high frequency firing. However, increases in conduction speed that occur along single myelinated axons with development are tightly linked to their growth in diameter. This suggests that axon diameter growth is a major driver of increases in conduction speeds along myelinated axons over time.
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Affiliation(s)
- Jenea M Bin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK.
| | - Daumante Suminaite
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | | | - Linde Kegel
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Maria Rubio-Brotons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Jason J Early
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Daniel Soong
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Matthew R Livesey
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - David A Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK.
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6
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Xu J, Casanave R, Chitre AS, Wang Q, Nguyen KM, Blake C, Wagle M, Cheng R, Polesskaya O, Palmer AA, Guo S. Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556529. [PMID: 37732200 PMCID: PMC10508786 DOI: 10.1101/2023.09.06.556529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Behavioral diversity is critical for population fitness. Individual differences in risk-taking are observed across species, but underlying genetic mechanisms and conservation are largely unknown. We examined dark avoidance in larval zebrafish, a motivated behavior reflecting an approach-avoidance conflict. Brain-wide calcium imaging revealed significant neural activity differences between approach-inclined versus avoidance-inclined individuals. We used a population of ∼6,000 to perform the first genome-wide association study (GWAS) in zebrafish, which identified 34 genomic regions harboring many genes that are involved in synaptic transmission and human psychiatric diseases. We used CRISPR to study several causal genes: serotonin receptor-1b ( htr1b ), nitric oxide synthase-1 ( nos1 ), and stress-induced phosphoprotein-1 ( stip1 ). We further identified 52 conserved elements containing 66 GWAS significant variants. One encoded an exonic regulatory element that influenced tissue-specific nos1 expression. Together, these findings reveal new genetic loci and establish a powerful, scalable animal system to probe mechanisms underlying motivation, a critical dimension of psychiatric diseases.
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7
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Hodorovich DR, Lindsley PM, Berry AA, Burton DF, Marsden KC. Morphological and sensorimotor phenotypes in a zebrafish CHARGE syndrome model are domain-dependent. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12839. [PMID: 36717082 PMCID: PMC10242184 DOI: 10.1111/gbb.12839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 02/01/2023]
Abstract
CHARGE syndrome is a heterogeneous disorder characterized by a spectrum of defects affecting multiple tissues and behavioral difficulties such as autism, attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, anxiety, and sensory deficits. Most CHARGE cases arise from de novo, loss-of-function mutations in chromodomain-helicase-DNA-binding-protein-7 (CHD7). CHD7 is required for processes such as neuronal differentiation and neural crest cell migration, but how CHD7 affects neural circuit function to regulate behavior is unclear. To investigate the pathophysiology of behavioral symptoms in CHARGE, we established a mutant chd7 zebrafish line that recapitulates multiple CHARGE phenotypes including ear, cardiac, and craniofacial defects. Using a panel of behavioral assays, we found that chd7 mutants have specific auditory and visual behavior deficits that are independent of defects in sensory structures. Mauthner cell-dependent short-latency acoustic startle responses are normal in chd7 mutants, while Mauthner-independent long-latency responses are reduced. Responses to sudden decreases in light are also reduced in mutants, while responses to sudden increases in light are normal, suggesting that the retinal OFF pathway may be affected. Furthermore, by analyzing multiple chd7 alleles we observed that the penetrance of morphological and behavioral phenotypes is influenced by genetic background but that it also depends on the mutation location, with a chromodomain mutation causing the highest penetrance. This pattern is consistent with analysis of a CHARGE patient dataset in which symptom penetrance was highest in subjects with mutations in the CHD7 chromodomains. These results provide new insight into the heterogeneity of CHARGE and will inform future work to define CHD7-dependent neurobehavioral mechanisms.
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Affiliation(s)
- Dana R. Hodorovich
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Patrick M. Lindsley
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- University of Virginia School of Medicine, University of VirginiaCharlottesvilleVAUSA
| | - Austen A. Berry
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- BiogenDurhamNCUSA
| | - Derek F. Burton
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Washington UniversitySt. LouisMOUSA
| | - Kurt C. Marsden
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Washington UniversitySt. LouisMOUSA
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8
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McConnell SC, Hernandez KM, Andrade J, de Jong JLO. Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes. Sci Rep 2023; 13:7777. [PMID: 37179373 PMCID: PMC10183018 DOI: 10.1038/s41598-023-34467-3] [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: 01/19/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
Immune genes have evolved to maintain exceptional diversity, offering robust defense against pathogens. We performed genomic assembly to examine immune gene variation in zebrafish. Gene pathway analysis identified immune genes as significantly enriched among genes with evidence of positive selection. A large subset of genes was absent from analysis of coding sequences due to apparent lack of reads, prompting us to examine genes overlapping zero coverage regions (ZCRs), defined as 2 kb stretches without mapped reads. Immune genes were identified as highly enriched within ZCRs, including over 60% of major histocompatibility complex (MHC) genes and NOD-like receptor (NLR) genes, mediators of direct and indirect pathogen recognition. This variation was most highly concentrated throughout one arm of chromosome 4 carrying a large cluster of NLR genes, associated with large-scale structural variation covering more than half of the chromosome. Our genomic assemblies uncovered alternative haplotypes and distinct complements of immune genes among individual zebrafish, including the MHC Class II locus on chromosome 8 and the NLR gene cluster on chromosome 4. While previous studies have shown marked variation in NLR genes between vertebrate species, our study highlights extensive variation in NLR gene regions between individuals of the same species. Taken together, these findings provide evidence of immune gene variation on a scale previously unknown in other vertebrate species and raise questions about potential impact on immune function.
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Affiliation(s)
- Sean C McConnell
- Section of Hematology-Oncology and Stem Cell Transplant, Department of Pediatrics, The University of Chicago, Chicago, IL, 60637, USA
| | - Kyle M Hernandez
- Center for Research Informatics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Medicine, Computational Biomedicine and Biomedical Data Science, Center for Translational Data Science, The University of Chicago, Chicago, IL, 60637, USA
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, IL, 60637, USA
- Kite Pharma, Santa Monica, CA, 90404, USA
| | - Jill L O de Jong
- Section of Hematology-Oncology and Stem Cell Transplant, Department of Pediatrics, The University of Chicago, Chicago, IL, 60637, USA.
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9
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Niescierowicz K, Pryszcz L, Navarrete C, Tralle E, Sulej A, Abu Nahia K, Kasprzyk ME, Misztal K, Pateria A, Pakuła A, Bochtler M, Winata C. Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish. Nat Commun 2022; 13:5520. [PMID: 36127363 PMCID: PMC9489775 DOI: 10.1038/s41467-022-33260-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery reveals pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3'-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning are found to contain multiple editing sites. Adar knockdown or overexpression affect gene expression by 12 hpf. Analysis of adar-/- zygotic mutants further reveals that the previously described role of Adar in mammals in regulating the innate immune response is conserved in zebrafish. Our study therefore establishes distinct maternal and zygotic functions of RNA editing by Adar in embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes, and in the regulation of the innate immune response, respectively.
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Affiliation(s)
| | - Leszek Pryszcz
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Cristina Navarrete
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Eugeniusz Tralle
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Karim Abu Nahia
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Marta Elżbieta Kasprzyk
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Misztal
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Abhishek Pateria
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Adrianna Pakuła
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland. .,Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland.
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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10
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Osorio-Méndez D, Miller A, Begeman IJ, Kurth A, Hagle R, Rolph D, Dickson AL, Chen CH, Halloran M, Poss KD, Kang J. Voltage-gated sodium channel scn8a is required for innervation and regeneration of amputated adult zebrafish fins. Proc Natl Acad Sci U S A 2022; 119:e2200342119. [PMID: 35867745 PMCID: PMC9282381 DOI: 10.1073/pnas.2200342119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Teleost fishes and urodele amphibians can regenerate amputated appendages, whereas this ability is restricted to digit tips in adult mammals. One key component of appendage regeneration is reinnervation of the wound area. However, how innervation is regulated in injured appendages of adult vertebrates has seen limited research attention. From a forward genetics screen for temperature-sensitive defects in zebrafish fin regeneration, we identified a mutation that disrupted regeneration while also inducing paralysis at the restrictive temperature. Genetic mapping and complementation tests identify a mutation in the major neuronal voltage-gated sodium channel (VGSC) gene scn8ab. Conditional disruption of scn8ab impairs early regenerative events, including blastema formation, but does not affect morphogenesis of established regenerates. Whereas scn8ab mutations reduced neural activity as expected, they also disrupted axon regrowth and patterning in fin regenerates, resulting in hypoinnervation. Our findings indicate that the activity of VGSCs plays a proregenerative role by promoting innervation of appendage stumps.
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Affiliation(s)
- Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Andrew Miller
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705
| | - Ian J. Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Ryan Hagle
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Daniela Rolph
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Amy L. Dickson
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Chen-Hui Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Mary Halloran
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705
| | - Kenneth D. Poss
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
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11
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Hageter J, Waalkes M, Starkey J, Copeland H, Price H, Bays L, Showman C, Laverty S, Bergeron SA, Horstick EJ. Environmental and Molecular Modulation of Motor Individuality in Larval Zebrafish. Front Behav Neurosci 2021; 15:777778. [PMID: 34938167 PMCID: PMC8685292 DOI: 10.3389/fnbeh.2021.777778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
Innate behavioral biases such as human handedness are a ubiquitous form of inter-individual variation that are not strictly hardwired into the genome and are influenced by diverse internal and external cues. Yet, genetic and environmental factors modulating behavioral variation remain poorly understood, especially in vertebrates. To identify genetic and environmental factors that influence behavioral variation, we take advantage of larval zebrafish light-search behavior. During light-search, individuals preferentially turn in leftward or rightward loops, in which directional bias is sustained and non-heritable. Our previous work has shown that bias is maintained by a habenula-rostral PT circuit and genes associated with Notch signaling. Here we use a medium-throughput recording strategy and unbiased analysis to show that significant individual to individual variation exists in wildtype larval zebrafish turning preference. We classify stable left, right, and unbiased turning types, with most individuals exhibiting a directional preference. We show unbiased behavior is not due to a loss of photo-responsiveness but reduced persistence in same-direction turning. Raising larvae at elevated temperature selectively reduces the leftward turning type and impacts rostral PT neurons, specifically. Exposure to conspecifics, variable salinity, environmental enrichment, and physical disturbance does not significantly impact inter-individual turning bias. Pharmacological manipulation of Notch signaling disrupts habenula development and turn bias individuality in a dose dependent manner, establishing a direct role of Notch signaling. Last, a mutant allele of a known Notch pathway affecter gene, gsx2, disrupts turn bias individuality, implicating that brain regions independent of the previously established habenula-rostral PT likely contribute to inter-individual variation. These results establish that larval zebrafish is a powerful vertebrate model for inter-individual variation with established neural targets showing sensitivity to specific environmental and gene signaling disruptions. Our results provide new insight into how variation is generated in the vertebrate nervous system.
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Affiliation(s)
- John Hageter
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Matthew Waalkes
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Jacob Starkey
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Haylee Copeland
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Heather Price
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Logan Bays
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Casey Showman
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Sean Laverty
- Department of Mathematics and Statistics, University of Central Oklahoma, Edmond, OK, United States
| | - Sadie A. Bergeron
- Department of Biology, West Virginia University, Morgantown, WV, United States
- Department of Neuroscience, West Virginia University, Morgantown, WV, United States
| | - Eric J. Horstick
- Department of Biology, West Virginia University, Morgantown, WV, United States
- Department of Neuroscience, West Virginia University, Morgantown, WV, United States
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12
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Stewart S, Le Bleu HK, Yette GA, Henner AL, Robbins AE, Braunstein JA, Stankunas K. longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth. Development 2021; 148:dev199384. [PMID: 34061172 PMCID: PMC8217709 DOI: 10.1242/dev.199384] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022]
Abstract
Organs stop growing to achieve a characteristic size and shape in scale with the body of an animal. Likewise, regenerating organs sense injury extents to instruct appropriate replacement growth. Fish fins exemplify both phenomena through their tremendous diversity of form and remarkably robust regeneration. The classic zebrafish mutant longfint2 develops and regenerates dramatically elongated fins and underlying ray skeleton. We show longfint2 chromosome 2 overexpresses the ether-a-go-go-related voltage-gated potassium channel kcnh2a. Genetic disruption of kcnh2a in cis rescues longfint2, indicating longfint2 is a regulatory kcnh2a allele. We find longfint2 fin overgrowth originates from prolonged outgrowth periods by showing Kcnh2a chemical inhibition during late stage regeneration fully suppresses overgrowth. Cell transplantations demonstrate longfint2-ectopic kcnh2a acts tissue autonomously within the fin intra-ray mesenchymal lineage. Temporal inhibition of the Ca2+-dependent phosphatase calcineurin indicates it likewise entirely acts late in regeneration to attenuate fin outgrowth. Epistasis experiments suggest longfint2-expressed Kcnh2a inhibits calcineurin output to supersede growth cessation signals. We conclude ion signaling within the growth-determining mesenchyme lineage controls fin size by tuning outgrowth periods rather than altering positional information or cell-level growth potency.
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Affiliation(s)
- Scott Stewart
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Heather K. Le Bleu
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Gabriel A. Yette
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Astra L. Henner
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Amy E. Robbins
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Joshua A. Braunstein
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Kryn Stankunas
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
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13
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Suurväli J, Whiteley AR, Zheng Y, Gharbi K, Leptin M, Wiehe T. The Laboratory Domestication of Zebrafish: From Diverse Populations to Inbred Substrains. Mol Biol Evol 2021; 37:1056-1069. [PMID: 31808937 PMCID: PMC7086173 DOI: 10.1093/molbev/msz289] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of “personalized medicine.” Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behavior, and physiology, for modeling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species. Here, we use restriction site-associated DNA sequencing to genetically characterize wild populations of zebrafish from India, Nepal, and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity, and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish, there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic, and evolutionary studies in Danio rerio.
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Affiliation(s)
- Jaanus Suurväli
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Andrew R Whiteley
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Yichen Zheng
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Maria Leptin
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Thomas Wiehe
- Institute for Genetics, University of Cologne, Cologne, Germany
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14
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A fish is not a mouse: understanding differences in background genetics is critical for reproducibility. Lab Anim (NY) 2020; 50:19-25. [PMID: 33268901 DOI: 10.1038/s41684-020-00683-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023]
Abstract
Poorly controlled background genetics in animal models contributes to the lack of reproducibility that is increasingly recognized in biomedical research. The laboratory zebrafish, Danio rerio, has been an important model organism for decades in many research areas, yet inbred strains and traditionally managed outbred stocks are not available for this species. Sometimes incorrectly referred to as 'inbred strains' or 'strains', zebrafish wild-type lines possess background genetics that are often not well characterized, and breeding practices for these lines have not been consistent over time or among institutions. In this Perspective, we trace key milestones in the history of one of the most widely used genetic backgrounds, the AB line, to illustrate the dynamic complexity within an example background that is largely invisible when reading the scientific literature. Failure to adequately control for genetic background compromises the validity of experimental outcomes. We therefore propose that authors provide as much specific detail about the origin and genetic makeup of zebrafish lines as is reasonable and possible, and that the terms used to describe background genetics be applied in a way that is consistent with other fish and mammalian model organisms. We strongly encourage the adoption of genetic monitoring for the characterization of existing zebrafish lines, to help detect genetic contamination in breeding colonies and to verify the level of genetic heterogeneity in breeding colonies over time. Careful attention to background genetics will improve transparency and reproducibility, therefore improving the utility of the zebrafish as a model organism.
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15
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Torres-Sánchez M. Variation under domestication in animal models: the case of the Mexican axolotl. BMC Genomics 2020; 21:827. [PMID: 33228551 PMCID: PMC7685626 DOI: 10.1186/s12864-020-07248-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864. RESULTS Using gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations. CONCLUSIONS Awareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.
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Affiliation(s)
- María Torres-Sánchez
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center & Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA.
- Present address: Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA.
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16
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Marshall-Phelps KL, Kegel L, Baraban M, Ruhwedel T, Almeida RG, Rubio-Brotons M, Klingseisen A, Benito-Kwiecinski SK, Early JJ, Bin JM, Suminaite D, Livesey MR, Möbius W, Poole RJ, Lyons DA. Neuronal activity disrupts myelinated axon integrity in the absence of NKCC1b. J Cell Biol 2020; 219:e201909022. [PMID: 32364583 PMCID: PMC7337504 DOI: 10.1083/jcb.201909022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/09/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Through a genetic screen in zebrafish, we identified a mutant with disruption to myelin in both the CNS and PNS caused by a mutation in a previously uncharacterized gene, slc12a2b, predicted to encode a Na+, K+, and Cl- (NKCC) cotransporter, NKCC1b. slc12a2b/NKCC1b mutants exhibited a severe and progressive pathology in the PNS, characterized by dysmyelination and swelling of the periaxonal space at the axon-myelin interface. Cell-type-specific loss of slc12a2b/NKCC1b in either neurons or myelinating Schwann cells recapitulated these pathologies. Given that NKCC1 is critical for ion homeostasis, we asked whether the disruption to myelinated axons in slc12a2b/NKCC1b mutants is affected by neuronal activity. Strikingly, we found that blocking neuronal activity completely prevented and could even rescue the pathology in slc12a2b/NKCC1b mutants. Together, our data indicate that NKCC1b is required to maintain neuronal activity-related solute homeostasis at the axon-myelin interface, and the integrity of myelinated axons.
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Affiliation(s)
| | - Linde Kegel
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Marion Baraban
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Torben Ruhwedel
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Rafael G. Almeida
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Anna Klingseisen
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Jason J. Early
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Jenea M. Bin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Daumante Suminaite
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Matthew R. Livesey
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Wiebke Möbius
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Richard J. Poole
- Department of Cell and Developmental Biology, University College London, London, UK
| | - David A. Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
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17
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Bian C, Chen W, Ruan Z, Hu Z, Huang Y, Lv Y, Xu T, Li J, Shi Q, Ge W. Genome and Transcriptome Sequencing of casper and roy Zebrafish Mutants Provides Novel Genetic Clues for Iridophore Loss. Int J Mol Sci 2020; 21:ijms21072385. [PMID: 32235607 PMCID: PMC7177266 DOI: 10.3390/ijms21072385] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/16/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
casper has been a widely used transparent mutant of zebrafish. It possesses a combined loss of reflective iridophores and light-absorbing melanophores, which gives rise to its almost transparent trunk throughout larval and adult stages. Nevertheless, genomic causal mutations of this transparent phenotype are poorly defined. To identify the potential genetic basis of this fascinating morphological phenotype, we constructed genome maps by performing genome sequencing of 28 zebrafish individuals including wild-type AB strain, roy orbison (roy), and casper mutants. A total of 4.3 million high-quality and high-confidence homozygous single nucleotide polymorphisms (SNPs) were detected in the present study. We also identified a 6.0-Mb linkage disequilibrium block specifically in both roy and casper that was composed of 39 functional genes, of which the mpv17 gene was potentially involved in the regulation of iridophore formation and maintenance. This is the first report of high-confidence genomic mutations in the mpv17 gene of roy and casper that potentially leads to defective splicing as one major molecular clue for the iridophore loss. Additionally, comparative transcriptomic analyses of skin tissues from the AB, roy and casper groups revealed detailed transcriptional changes of several core genes that may be involved in melanophore and iridophore degeneration. In summary, our updated genome and transcriptome sequencing of the casper and roy mutants provides novel genetic clues for the iridophore loss. These new genomic variation maps will offer a solid genetic basis for expanding the zebrafish mutant database and in-depth investigation into pigmentation of animals.
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Affiliation(s)
- Chao Bian
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China; (C.B.); (W.C.); (Z.H.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; (Z.R.); (Y.H.); (Y.L.); (T.X.); (J.L.)
| | - Weiting Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China; (C.B.); (W.C.); (Z.H.)
- School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Zhiqiang Ruan
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; (Z.R.); (Y.H.); (Y.L.); (T.X.); (J.L.)
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Zhe Hu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China; (C.B.); (W.C.); (Z.H.)
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; (Z.R.); (Y.H.); (Y.L.); (T.X.); (J.L.)
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; (Z.R.); (Y.H.); (Y.L.); (T.X.); (J.L.)
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; (Z.R.); (Y.H.); (Y.L.); (T.X.); (J.L.)
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; (Z.R.); (Y.H.); (Y.L.); (T.X.); (J.L.)
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; (Z.R.); (Y.H.); (Y.L.); (T.X.); (J.L.)
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Correspondence: (Q.S.); (W.G.); Tel.: +86-185-6627-9826 (Q.S.); +853-8822-4998 (W.G.)
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China; (C.B.); (W.C.); (Z.H.)
- Correspondence: (Q.S.); (W.G.); Tel.: +86-185-6627-9826 (Q.S.); +853-8822-4998 (W.G.)
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18
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Espino-Saldaña AE, Durán-Ríos K, Olivares-Hernandez E, Rodríguez-Ortiz R, Arellano-Carbajal F, Martínez-Torres A. Temporal and spatial expression of zebrafish mctp genes and evaluation of frameshift alleles of mctp2b. Gene 2020; 738:144371. [PMID: 32001375 DOI: 10.1016/j.gene.2020.144371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 01/28/2023]
Abstract
MCTPs (multiple C2 domain proteins with two transmembrane regions) have been proposed as novel endoplasmic reticulum calcium sensors; however, their function remains largely unknown. Here we report the structure of the four mctp genes from zebrafish (mctp1a, mctp1b, mctp2a and mctp2b), their diversity, expression pattern during embryonic development and in adult tissue and the effect of knocking down the expression of Mctp2b by CRISPR/Cas9. The four mctp genes are expressed from early development and exhibit differential expression patterns but are found mainly in the nervous and muscular systems. Mctp2b tagged with fluorescent proteins and expressed in HEK-293 cells and neurons of the fish spinal cord localized mostly in the endoplasmic reticulum but also in lysosomes and late and recycling endosomes. Knocking down mctp2b expression impaired embryonic development, suggesting that the functional participation of this gene is relevant, at least during the early stages of development.
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Affiliation(s)
- Angeles E Espino-Saldaña
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Juriquilla, Querétaro, 76230, Mexico; Universidad Autónoma de Querétaro, Facultad de Ciencias Naturales, Av. de las Ciencias S/N, Querétaro, Mexico
| | - Karina Durán-Ríos
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Juriquilla, Querétaro, 76230, Mexico
| | - Eduardo Olivares-Hernandez
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Juriquilla, Querétaro, 76230, Mexico
| | - Roberto Rodríguez-Ortiz
- CONACYT- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Juriquilla, Querétaro, 76230, Mexico
| | - Fausto Arellano-Carbajal
- Universidad Autónoma de Querétaro, Facultad de Ciencias Naturales, Av. de las Ciencias S/N, Querétaro, Mexico
| | - Ataulfo Martínez-Torres
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Juriquilla, Querétaro, 76230, Mexico.
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19
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Early life exposure to cortisol in zebrafish (Danio rerio): similarities and differences in behaviour and physiology between larvae of the AB and TL strains. Behav Pharmacol 2020; 30:260-271. [PMID: 30724799 DOI: 10.1097/fbp.0000000000000470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Maternal stress and early life stress affect development. Zebrafish (Danio rerio) are ideally suited to study this, as embryos develop externally into free-feeding larvae. The objective of this study was therefore to assess the effects of increased levels of cortisol, mimicking thereby maternal stress, on larval physiology and behaviour. We studied the effects in two common zebrafish strains, that is, AB and Tupfel long-fin (TL), to assess strain dependency of effects. Fertilized eggs were exposed to a cortisol-containing medium (1.1 μmol/l) or control medium from 0 to 6 h following fertilization, after which at 5-day following fertilization, larval behaviour and baseline hypothalamus-pituitary-interrenal cells axis functioning were measured. The data confirmed earlier observed differences between AB larvae and TL larvae: a lower hypothalamus-pituitary-interrenal axis activity in TL larvae than AB larvae, and slower habituation to repeated acoustic/vibrational stimuli in TL larvae than AB larvae. Following cortisol treatment, increased baseline levels of cortisol were found in AB larvae but not TL larvae. At the behavioural level, increased thigmotaxis or 'wall hugging' was found in AB larvae, but decreased thigmotaxis in TL larvae; however, both AB larvae and TL larvae showed decreased habituation to repeated acoustic/vibrational stimuli. The data emphasize that strain is a critical factor in zebrafish research. The habituation data suggest a robust effect of cortisol exposure, which is likely an adaptive response to increase the likelihood of detecting or responding to potentially threatening stimuli. This may enhance early life survival. Along with other studies, our study underlines the notion that zebrafish may be a powerful model animal to study the effects of maternal and early life stress on life history.
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20
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Klingseisen A, Ristoiu AM, Kegel L, Sherman DL, Rubio-Brotons M, Almeida RG, Koudelka S, Benito-Kwiecinski SK, Poole RJ, Brophy PJ, Lyons DA. Oligodendrocyte Neurofascin Independently Regulates Both Myelin Targeting and Sheath Growth in the CNS. Dev Cell 2019; 51:730-744.e6. [PMID: 31761670 PMCID: PMC6912162 DOI: 10.1016/j.devcel.2019.10.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/10/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023]
Abstract
Selection of the correct targets for myelination and regulation of myelin sheath growth are essential for central nervous system (CNS) formation and function. Through a genetic screen in zebrafish and complementary analyses in mice, we find that loss of oligodendrocyte Neurofascin leads to mistargeting of myelin to cell bodies, without affecting targeting to axons. In addition, loss of Neurofascin reduces CNS myelination by impairing myelin sheath growth. Time-lapse imaging reveals that the distinct myelinating processes of individual oligodendrocytes can engage in target selection and sheath growth at the same time and that Neurofascin concomitantly regulates targeting and growth. Disruption to Caspr, the neuronal binding partner of oligodendrocyte Neurofascin, also impairs myelin sheath growth, likely reflecting its association in an adhesion complex at the axon-glial interface with Neurofascin. Caspr does not, however, affect myelin targeting, further indicating that Neurofascin independently regulates distinct aspects of CNS myelination by individual oligodendrocytes in vivo. Single oligodendrocytes coordinate myelin targeting and growth at the same time Oligodendrocyte Neurofascin prevents myelination of cell bodies Oligodendrocyte Neurofascin promotes myelin sheath growth The neuronal binding partner of Neurofascin, Caspr, promotes myelin sheath growth
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Affiliation(s)
- Anna Klingseisen
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ana-Maria Ristoiu
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Linde Kegel
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Diane L Sherman
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Maria Rubio-Brotons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Rafael G Almeida
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Sigrid Koudelka
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | | | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Peter J Brophy
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - David A Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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Hulke ML, Siefert JC, Sansam CL, Koren A. Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development. Genome Biol Evol 2019; 11:1663-1678. [PMID: 31076752 PMCID: PMC6582765 DOI: 10.1093/gbe/evz098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2019] [Indexed: 02/06/2023] Open
Abstract
The DNA replication timing program is modulated throughout development and is also one of the main factors influencing the distribution of mutation rates across the genome. However, the relationship between the mutagenic influence of replication timing and its developmental plasticity remains unexplored. Here, we studied the distribution of copy number variations (CNVs) and single nucleotide polymorphisms across the zebrafish genome in relation to changes in DNA replication timing during embryonic development in this model vertebrate species. We show that CNV sites exhibit strong replication timing plasticity during development, replicating significantly early during early development but significantly late during more advanced developmental stages. Reciprocally, genomic regions that changed their replication timing during development contained a higher proportion of CNVs than developmentally constant regions. Developmentally plastic CNV sites, in particular those that become delayed in their replication timing, were enriched for the clustered protocadherins, a set of genes important for neuronal development that have undergone extensive genetic and epigenetic diversification during zebrafish evolution. In contrast, single nucleotide polymorphism sites replicated consistently early throughout embryonic development, highlighting a unique aspect of the zebrafish genome. Our results uncover a hitherto unrecognized interface between development and evolution.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University
| | - Joseph C Siefert
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation.,Department of Cell Biology, University of Oklahoma Health Sciences Center
| | - Christopher L Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation.,Department of Cell Biology, University of Oklahoma Health Sciences Center
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University
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22
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Holden LA, Wilson C, Heineman Z, Dobrinski KP, Brown KH. An Interrogation of Shared and Unique Copy Number Variants Across Genetically Distinct Zebrafish Strains. Zebrafish 2018; 16:29-36. [PMID: 30418105 DOI: 10.1089/zeb.2018.1644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Zebrafish (Danio rerio) are a widely utilized model system for human disorders, but common laboratory strains have distinct behavioral and physiological differences. Accompanying these known strain differences, commonly used "wildtype" zebrafish strains have both shared and unique suites of single nucleotide polymorphisms and copy number variants (CNVs). Despite this, genomic variation is often ignored in study design, and the actual strain used is often not adequately reported. The goal of this study was to assess CNVs across three common laboratory strains of zebrafish-AB, Tubingen (TU), and WIK-and provide these data as a tool for the zebrafish community. Herein we identified 1351 CNV regions within the most recent genome assembly (GRCz11) covering 1.9% of the zebrafish genome (31.7 Mb). CNVs were found across all chromosomes, and 2200 genes (5121 transcripts) lie within ±5 kb of identified CNVs, pointing to likely cis regulatory actions of CNVs on nearby gene neighbors. We have created a Public Session accessible on the UCSC Genome Browser to view CNVs from this study titled "danRer11 zebrafish CNV across strains" as a tool for the zebrafish community.
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Affiliation(s)
- Lindsay A Holden
- 1 Department of Biology, Portland State University, Portland, Oregon
| | - Charles Wilson
- 1 Department of Biology, Portland State University, Portland, Oregon
| | - Zachary Heineman
- 1 Department of Biology, Portland State University, Portland, Oregon
| | | | - Kim H Brown
- 1 Department of Biology, Portland State University, Portland, Oregon
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23
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Balik-Meisner M, Truong L, Scholl EH, La Du JK, Tanguay RL, Reif DM. Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:067010. [PMID: 29968567 PMCID: PMC6084885 DOI: 10.1289/ehp2662] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Modern societies are exposed to vast numbers of potentially hazardous chemicals. Despite demonstrated linkages between chemical exposure and severe health effects, there are limited, often conflicting, data on how adverse health effects of exposure differ across individuals. OBJECTIVES We tested the hypothesis that population variability in response to certain chemicals could elucidate a role for gene-environment interactions (GxE) in differential susceptibility. METHODS High-throughput screening (HTS) data on thousands of chemicals in genetically heterogeneous zebrafish were leveraged to identify a candidate chemical (Abamectin) with response patterns indicative of population susceptibility differences. We tested the prediction by generating genome-wide sequence data for 276 individual zebrafish displaying susceptible (Affected) vs. resistant (Unaffected) phenotypes following identical chemical exposure. RESULTS We found GxE associated with differential susceptibility in the sox7 promoter region and then confirmed gene expression differences between phenotypic response classes. CONCLUSIONS The results for Abamectin in zebrafish demonstrate that GxE associated with naturally occurring, population genetic variation play a significant role in mediating individual response to chemical exposure. https://doi.org/10.1289/EHP2662.
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Affiliation(s)
- Michele Balik-Meisner
- Bioinformatics Research Center, Center for Human Health and the Environment, Dept. of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Lisa Truong
- Sinnhuber Aquatic Research Laboratory, Dept. of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, Center for Human Health and the Environment, Dept. of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Jane K La Du
- Sinnhuber Aquatic Research Laboratory, Dept. of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, USA
| | - Robert L Tanguay
- Sinnhuber Aquatic Research Laboratory, Dept. of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, USA
| | - David M Reif
- Bioinformatics Research Center, Center for Human Health and the Environment, Dept. of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
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24
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Balik-Meisner M, Truong L, Scholl EH, Tanguay RL, Reif DM. Population genetic diversity in zebrafish lines. Mamm Genome 2018; 29:90-100. [PMID: 29368091 PMCID: PMC5851690 DOI: 10.1007/s00335-018-9735-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/17/2018] [Indexed: 12/27/2022]
Abstract
Toxicological and pharmacological researchers have seized upon the many benefits of zebrafish, including the short generation time, well-characterized development, and early maturation as clear embryos. A major difference from many model organisms is that standard husbandry practices in zebrafish are designed to maintain population diversity. While this diversity is attractive for translational applications in human and ecological health, it raises critical questions on how interindividual genetic variation might contribute to chemical exposure or disease susceptibility differences. Findings from pooled samples of zebrafish support this supposition of diversity yet cannot directly measure allele frequencies for reference versus alternate alleles. Using the Tanguay lab Tropical 5D zebrafish line (T5D), we performed whole genome sequencing on a large group (n = 276) of individual zebrafish embryos. Paired-end reads were collected on an Illumina 3000HT, then aligned to the most recent zebrafish reference genome (GRCz10). These data were used to compare observed population genetic variation across species (humans, mice, zebrafish), then across lines within zebrafish. We found more single nucleotide polymorphisms (SNPs) in T5D than have been reported in SNP databases for any of the WIK, TU, TL, or AB lines. We theorize that some subset of the novel SNPs may be shared with other zebrafish lines but have not been identified in other studies due to the limitations of capturing population diversity in pooled sequencing strategies. We establish T5D as a model that is representative of diversity levels within laboratory zebrafish lines and demonstrate that experimental design and analysis can exert major effects when characterizing genetic diversity in heterogeneous populations.
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Affiliation(s)
- Michele Balik-Meisner
- Bioinformatics Research Center, Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Ricks Hall 344, 1 Lampe Drive, Box 7566, Raleigh, NC, 27695, USA
| | - Lisa Truong
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Ricks Hall 344, 1 Lampe Drive, Box 7566, Raleigh, NC, 27695, USA
| | - Robert L Tanguay
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA
| | - David M Reif
- Bioinformatics Research Center, Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Ricks Hall 344, 1 Lampe Drive, Box 7566, Raleigh, NC, 27695, USA.
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25
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van den Bos R, Zethof J, Flik G, Gorissen M. Light regimes differentially affect baseline transcript abundance of stress-axis and (neuro)development-related genes in zebrafish ( Danio rerio, Hamilton 1822) AB and TL larvae. Biol Open 2017; 6:1692-1697. [PMID: 28982701 PMCID: PMC5703615 DOI: 10.1242/bio.028969] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many strains of zebrafish (Danio rerio) are readily available. Earlier we observed differences between AB and Tupfel long-fin (TL) larvae regarding baseline hypothalamus-pituitary-interrenal (HPI) axis activity and (neuro)development. Light regimes, i.e. 14 h light:10 h dark and 24 h continuous dark or light, affect hatching rate and larval growth. Here, we assessed baseline transcript abundance of HPI-axis-related genes and (neuro)development-related genes of AB and TL larvae (5 days post fertilisation) using these light regimes. A principal component analysis revealed that in AB larvae the baseline expression of HPI-axis-related genes was higher the more hours of light, while the expression of (neuro)development-related genes was higher under 14 h light:10 h dark than under both continuous light or dark. In TL larvae, a complex pattern emerged regarding baseline expression of HPI-axis-related and (neuro)development-related genes. These data extend data of earlier studies by showing that light regimes affect gene-expression in larvae, and more importantly so, strengthen the notion of differences between larvae of the AB and TL strain. The latter finding adds to the growing database of phenotypical differences between zebrafish of the AB and TL strain. Summary: This study shows gene expression levels of zebrafish AB and TL larvae differ in relation to light regimes, strengthening earlier observations: AB and TL are not interchangeable strains.
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Affiliation(s)
- Ruud van den Bos
- Radboud University, Institute for Water and Wetland Research, Department of Animal Ecology and Physiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jan Zethof
- Radboud University, Institute for Water and Wetland Research, Department of Animal Ecology and Physiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Gert Flik
- Radboud University, Institute for Water and Wetland Research, Department of Animal Ecology and Physiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Marnix Gorissen
- Radboud University, Institute for Water and Wetland Research, Department of Animal Ecology and Physiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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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: 1.0] [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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27
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McGuigan K, Aw E. How does mutation affect the distribution of phenotypes? Evolution 2017; 71:2445-2456. [PMID: 28884791 DOI: 10.1111/evo.13358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/27/2017] [Accepted: 08/29/2017] [Indexed: 12/14/2022]
Abstract
The potential for mutational processes to influence patterns of neutral or adaptive phenotypic evolution is not well understood. If mutations are directionally biased, shifting trait means in a particular direction, or if mutation generates more variance in some directions of multivariate trait space than others, mutation itself might be a source of bias in phenotypic evolution. Here, we use mutagenesis to investigate the affect of mutation on trait mean and (co)variances in zebrafish, Danio rerio. Mutation altered the relationship between age and both prolonged swimming speed and body shape. These observations suggest that mutational effects on ontogeny or aging have the potential to generate variance across the phenome. Mutations had a far greater effect in males than females, although whether this is a reflection of sex-specific ontogeny or aging remains to be determined. In males, mutations generated positive covariance between swimming speed, size, and body shape suggesting the potential for mutation to affect the evolutionary covariation of these traits. Overall, our observations suggest that mutation does not generate equal variance in all directions of phenotypic space or in each sex, and that pervasive variation in ontogeny or aging within a cohort could affect the variation available to evolution.
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Affiliation(s)
- Katrina McGuigan
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072
| | - Ernest Aw
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072
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Abstract
Zebrafish have been extensively used for studying vertebrate development and modeling human diseases such as cancer. In the last two decades, they have also emerged as an important model for developmental toxicology research and, more recently, for studying the developmental origins of health and disease (DOHaD). It is widely recognized that epigenetic mechanisms mediate the persistent effects of exposure to chemicals during sensitive windows of development. There is considerable interest in understanding the epigenetic mechanisms associated with DOHaD using zebrafish as a model system. This review summarizes our current knowledge on the effects of environmental chemicals on DNA methylation, histone modifications and noncoding RNAs in the context of DOHaD, and suggest some key considerations in designing experiments for characterizating the mechanisms of action.
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Affiliation(s)
- Neelakanteswar Aluru
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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29
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Further characterisation of differences between TL and AB zebrafish (Danio rerio): Gene expression, physiology and behaviour at day 5 of the larval stage. PLoS One 2017; 12:e0175420. [PMID: 28419104 PMCID: PMC5395159 DOI: 10.1371/journal.pone.0175420] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/24/2017] [Indexed: 11/19/2022] Open
Abstract
Zebrafish (Danio rerio) have become popular as model organism in research. Many strains are readily available, which not only differ morphologically, but also genetically, physiologically and behaviourally. Here, we focus on the AB and Tupfel long-fin (TL) strain for which we have previously shown that adults differ in baseline hypothalamus-pituitary-interrenal (HPI)-axis activity (AB higher than TL) affecting inhibitory avoidance behaviour (absent in AB). To assess whether strain differences are already present in early life stages, we compared baseline HPI-axis related gene expression as well as cortisol levels, (neuro)development related as well as (innate) immune system related gene expression, and light-dark as well as startle behaviour in larvae 5 days post fertilisation. The data show that AB and TL larvae differ in baseline HPI-axis activity (AB higher than TL), expression of (neuro)development and immune system related genes (AB higher than TL), habituation to acoustic/vibrational stimuli (AB habituate faster than TL) and light-dark induced changes in motor behaviour (AB stronger than TL). Our data show that already in larval stages differences exist between zebrafish of the AB and TL strain confirming and extending data of earlier studies. To what extent the mutation in connexin 41.8, leading to spots rather than stripes in TL, but also (possibly) affecting eye, heart and brain function, is involved in the expression of (some of) these differences needs to be studied. These results emphasise that differences between strains need to be taken into account to enhance reproducibility both within, and between, laboratories.
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30
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Shin M, Male I, Beane TJ, Villefranc JA, Kok FO, Zhu LJ, Lawson ND. Correction: Vegfc acts through ERK to induce sprouting and differentiation of trunk lymphatic progenitors. Development 2017; 144:531. [PMID: 28143848 DOI: 10.1242/dev.148569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Chatterjee A, Lagisz M, Rodger EJ, Zhen L, Stockwell PA, Duncan EJ, Horsfield JA, Jeyakani J, Mathavan S, Ozaki Y, Nakagawa S. Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive' hypothesis. Gene 2016; 590:307-16. [PMID: 27259666 DOI: 10.1016/j.gene.2016.05.042] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/20/2016] [Accepted: 05/29/2016] [Indexed: 12/17/2022]
Abstract
The sex drive hypothesis predicts that stronger selection on male traits has resulted in masculinization of the genome. Here we test whether such masculinizing effects can be detected at the level of the transcriptome and methylome in the adult zebrafish brain. Although methylation is globally similar, we identified 914 specific differentially methylated CpGs (DMCs) between males and females (435 were hypermethylated and 479 were hypomethylated in males compared to females). These DMCs were prevalent in gene body, intergenic regions and CpG island shores. We also discovered 15 distinct CpG clusters with striking sex-specific DNA methylation differences. In contrast, at transcriptome level, more female-biased genes than male-biased genes were expressed, giving little support for the male sex drive hypothesis. Our study provides genome-wide methylome and transcriptome assessment and sheds light on sex-specific epigenetic patterns and in zebrafish for the first time.
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Affiliation(s)
- Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
| | - Malgorzata Lagisz
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9054, New Zealand; Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, 2052 Sydney, NSW, Australia.
| | - Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
| | - Li Zhen
- LKC School of Medicine, Nanyang Technological University and Human Genetics Division, Genome Institute of Singapore, Singapore.
| | - Peter A Stockwell
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand.
| | - Elizabeth J Duncan
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand.
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
| | - Justin Jeyakani
- LKC School of Medicine, Nanyang Technological University and Human Genetics Division, Genome Institute of Singapore, Singapore.
| | - Sinnakaruppan Mathavan
- LKC School of Medicine, Nanyang Technological University and Human Genetics Division, Genome Institute of Singapore, Singapore.
| | - Yuichi Ozaki
- Department of Biology, Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8521, Japan.
| | - Shinichi Nakagawa
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9054, New Zealand; Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, 2052 Sydney, NSW, Australia; Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
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