Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

Howe, Kerstin; Clark, Matthew D.; Torroja, Carlos; Torrance, James; Berthelot, Camille; Muffato, Matthieu; Collins, John; Humphray, Sean; McLaren, Karen; Matthews, Lucy; McLaren, Stuart; Sealy, Ian; Cáccamo, Mario; Churcher, Carol; Scott, Carol; Barrett, Jeffrey C.; Koch, Romke; Rauch, Gerd Jörg; White, Simon; Chow, William; Kilian, Britt; Quintais, Leonor; Guerra-Assunção, José Afonso; Zhou, Yi; Gu, Yong; Yen, Jennifer; Vogel, Jan; Eyre, Tina A.; Banerjee, Ruby; Chi, Jianxiang; Fu, Beiyuan; Langley, Elizabeth; Maguire, Sean; Laird, Gavin K.; Lloyd, D. M.; Kenyon, Emma J.; Donaldson, Sarah; Sehra, Harminder; Almeida-King, Jeff; Loveland, Jane; Trevanion, Stephen J.; Jones, Matt; Quail, Mike; Willey, Dave; Hunt, Adrienne; Burton, John H.; Sims, Sarah; McLay, Kirsten; Plumb, Bob; Davis, Joy; Clee, Chris; Oliver, Karen; Clark, Richard; Riddle, Clare; Elliott, David; Threadgold, Glen; Harden, Glenn; Ware, Darren; Begum, Sharmin; Mortimore, Beverley; Kerry, Giselle; Heath, P. D.; Phillimore, Benjamin; Tracey, Alan S.; Corby, N.; Dunn, Matthew; Johnson, Christopher M.; Wood, Jonathan; Clark, S. Y.; Pelan, Sarah; Griffiths, Guy; Smith, Michelle; Glithero, Rebecca; Howden, Philip; Barker, Nicholas; Lloyd, Christine; Stevens, Christopher; Harley, Joanna; Holt, Karen; Panagiotidis, Georgios; Lovell, J.; Beasley, Helen; Henderson, Carl; Gordon, Daria; Auger, Katherine A.; Wright, Deborah; Collins, Joanna; Raisen, Claire; Dyer, Lauren; Leung, Kenric; Robertson, Lauren; Ambridge, Kirsty; Leongamornlert, Daniel; McGuire, Sarah Lea; Gilderthorp, Ruth; Griffiths, Chris; Manthravadi, Deepa; Nichol, Sarah; Barker, G. L.; Whitehead, Siobhan; Kay, Mike; Brown, J. Y.; Murnane, Clare; Gray, Emma; Humphries, Matthew; Sycamore, Neil; Barker, Darren; Saunders, David; Wallis, J. M.; Babbage, Anne; Hammond, S.; Mashreghi-Mohammadi, M.; Barr, Lucy; Martin, Sancha; Wray, Paul; Ellington, Andrew; Matthews, N.; Ellwood, Matthew; Woodmansey, Rebecca; Clark, Graham; Cooper, James D.; Tromans, A.; Grafham, Darren; Skuce, C. D.; Pandian, Richard; Andrews, Robert; Harrison, Elliot; Kimberley, A. M.; Garnett, J.; Fosker, Nigel; Hall, R. E.; Garner, P.; Kelly, Daniel; Bird, Christine P.; Palmer, Sophie; Gehring, Ines; Berger, Andrea; Dooley, Christopher M.; Ersan-Ürün, Zübeyde; Eser, Cigdem; Geiger, Horst; Geisler, Maria; Karotki, Lena; Kirn, A; Konantz, Judith; Konantz, Martina; Oberländer, Martina; Rudolph-Geiger, Silke; Teucke, Mathias; Lanz, Christa; Raddatz, Günter; Osoegawa, Kazutoyo; Zhu, Baoli; Rapp, Amanda; Widaa, Sara; Langford, Cordelia; Yang, Fengtang; Schuster, Stephan C.; Carter, Nigel P.; Harrow, Jennifer; Ning, Zemin; Herrero, Javier; Searle, Steve; Enright, Anton J.; Geisler, Robert; Plasterk, Ronald H.A.; Lee, Charles; Westerfield, Monte; Jong, Pieter J. de; Zon, Leonard I.; Postlethwait, John H.; Volhard, Christiane Nüsslein; Hubbard, Tim; Crollius, Hugues Roest; Rogers, Jane; Stemple, Derek L.

doi:10.1038/nature12813

Cited by 23 publications

(9 citation statements)

References 1 publication

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“…Zebrafish has become a powerful and widely used model organism as they are easy and cheap to maintain, are sensitive to neurotropic drugs, and a single pair can spawn 200-300 eggs in one week who grow to sexual maturity in only 3-4 months [37,38]. 70% of zebrafish genes have homologs in humans, 84% of human disease-related genes have homologs in zebrafish, and CNS protein-encoding genes have very similar functions with their human counterparts [39]. Moreover, the human retina is more closely related to the zebrafish retina than that of mice, which has rod-dominant vision unlike the cone-dominant vision found in humans and zebrafish [37].…”

Section: Introductionmentioning

confidence: 99%

Exploration of age-related mitochondrial dysfunction and the anti-aging effects of resveratrol in zebrafish retina

Wang

Luo

Jin

et al. 2019

Aging

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It is currently believed that aging is closely linked with mitochondrial dysfunction, and that resveratrol exhibits anti-aging and neuroprotective effects by improving mitochondrial function, even though the mechanisms are not well defined. This study explored mitochondrial quality (mitochondrial DNA integrity and copy number), mitochondrial function (fusion/fission, mitophagy/autophagy), antioxidant system and activity of the Akt/mTOR and Ampk/Sirt1/Pgc1α pathways, and inflammation in aging zebrafish retinas to identify the probable mechanisms of resveratrol’s anti-aging and neuroprotective effects. mtDNA integrity, mtDNA copy number, mitochondrial fusion regulators, mitophagy, and antioxidant-related genes were all decreased whereas Akt/mTOR activity and inflammation was increased upon aging in zebrafish retinas. Resveratrol was shown to not only increase mitochondrial quality and function, but also to suppress Akt/mTOR activity in zebrafish retinas. These results support the notion that mitochondrial dysfunction and increased Akt/mTOR activity are major players in age-related retinal neuropathy in zebrafish, and demonstrate a trend towards mitochondrial fragmentation in the aging retina. Importantly, resveratrol promoted mitochondrial function, up-regulating Ampk/Sirt1/Pgc1α, and down-regulated Akt/mTOR pathway activity in zebrafish retinas, suggesting that it may be able to prevent age-related oculopathy.

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Section: Introductionmentioning

confidence: 99%

Exploration of age-related mitochondrial dysfunction and the anti-aging effects of resveratrol in zebrafish retina

Wang

Luo

Jin

et al. 2019

Aging

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“…The zebrafish ( Danio rerio ) is a vertebrate in vivo model and a higher throughput alternative to mammalian models. Zebrafish have a high degree of functional conservation with humans, including metabolic processes 7,8 , a sequenced genome with extensive parity to humans, expression of proteins that are orthologous to those known to be involved in over 80% of human diseases 9 , and similarities in cardiac conduction and ion channel composition 10 resulting in heart rate responses that are predictive of myocardial membrane activity in humans 11 . Moreover, zebrafish embryo skin is permeable to small molecules permitting exposure to an array of drugs and/or toxicants 11–14 , some of which have been linked to changes in expression of human gene orthologues 15 .…”

Section: Introductionmentioning

confidence: 99%

High-Throughput Video Processing of Heart Rate Responses in Multiple Wild-type Embryonic Zebrafish per Imaging Field

Martin

Tennant

Conolly

et al. 2019

Sci Rep

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Heart rate assays in wild-type zebrafish embryos have been limited to analysis of one embryo per video/imaging field. Here we present for the first time a platform for high-throughput derivation of heart rate from multiple zebrafish (Danio rerio) embryos per imaging field, which is capable of quickly processing thousands of videos and ideal for multi-well platforms with multiple fish/well. This approach relies on use of 2-day post fertilization wild-type embryos, and uses only bright-field imaging, circumventing requirement for anesthesia or restraint, costly software/hardware, or fluorescently-labeled animals. Our original scripts (1) locate the heart and record pixel intensity fluctuations generated by each cardiac cycle using a robust image processing routine, and (2) process intensity data to derive heart rate. To demonstrate assay utility, we exposed embryos to the drugs epinephrine and clonidine, which increased or decreased heart rate, respectively. Exposure to organic extracts of air pollution-derived particulate matter, including diesel or biodiesel exhausts, or wood smoke, all complex environmental mixtures, decreased heart rate to varying degrees. Comparison against an established lower-throughput method indicated robust assay fidelity. As all code and executable files are publicly available, this approach may expedite cardiotoxicity screening of compounds as diverse as small molecule drugs and complex chemical mixtures.

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“…However, with over 26,000 genes in the genome, understanding the specific role of individual genes in heart development and disease is a massive undertaking [ 99 ]. To add to the complexity, there was a full genome duplication in teleost fish that has led to functional duplication or divergence for some genes [ 106 ]. In the post-genomic era, complete sequencing of the zebrafish genome and development of tools for gene knockdown and targeted genome modification has enabled functional characterization nearly any candidate gene [ 107 ].…”

Section: Experimental Approaches To Studying Chds In Zebrafishmentioning

confidence: 99%

Advances in the Study of Heart Development and Disease Using Zebrafish

Brown

Samsa

et al. 2016

JCDD

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Animal models of cardiovascular disease are key players in the translational medicine pipeline used to define the conserved genetic and molecular basis of disease. Congenital heart diseases (CHDs) are the most common type of human birth defect and feature structural abnormalities that arise during cardiac development and maturation. The zebrafish, Danio rerio, is a valuable vertebrate model organism, offering advantages over traditional mammalian models. These advantages include the rapid, stereotyped and external development of transparent embryos produced in large numbers from inexpensively housed adults, vast capacity for genetic manipulation, and amenability to high-throughput screening. With the help of modern genetics and a sequenced genome, zebrafish have led to insights in cardiovascular diseases ranging from CHDs to arrhythmia and cardiomyopathy. Here, we discuss the utility of zebrafish as a model system and summarize zebrafish cardiac morphogenesis with emphasis on parallels to human heart diseases. Additionally, we discuss the specific tools and experimental platforms utilized in the zebrafish model including forward screens, functional characterization of candidate genes, and high throughput applications.

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Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

Cited by 23 publications

References 1 publication

Exploration of age-related mitochondrial dysfunction and the anti-aging effects of resveratrol in zebrafish retina

Exploration of age-related mitochondrial dysfunction and the anti-aging effects of resveratrol in zebrafish retina

High-Throughput Video Processing of Heart Rate Responses in Multiple Wild-type Embryonic Zebrafish per Imaging Field

Advances in the Study of Heart Development and Disease Using Zebrafish

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