The Zebrafish Information Network: the zebrafish model organism database

Sprague, Judy

doi:10.1093/nar/gkj086

Cited by 267 publications

(209 citation statements)

References 3 publications

(2 reference statements)

Supporting

Mentioning

202

Contrasting

Order By: Relevance

“…The approach was informed by a number of considerations including (i) the selection of developmental stages that will likely be screened for dysregulated protein expression in large scale mutagenesis or chemical screens, (ii) the simplicity of sample preparation and analytical methodology (mindful of their possible adaptation to high throughput screening), (iii) the eminent quality of mass spectrometric protein identifications, (iv) the accessibility of the protein data in a fully searchable database and their integration with existing genomics and genetics resources provided to the zebrafish research community through the ZFIN database (32), and (v) the comprehensive categorization of proteins by functional classes to facilitate the selection of candidate proteins, for example for the design of targeted quantitative mass spectrometry assays (29). Our approach yielded 1384 unique proteins at 72 or 120 hpf by 2D LC-ESI-MS/MS and 477 unique proteins at 72 or 120 hpf by 2D PAGE-MALDI-TOF/TOF, which showed an overlap of about 30%.…”

Section: Discussionmentioning

confidence: 99%

“…The data are accessible on line in a fully searchable database that links protein identifications to existing resources including the ZFIN database (32). This new resource should allow the selection of candidate proteins for targeted quantitation (29) in mutagenesis and chemical screens and may refine systematic genetic network analysis in vertebrate development and biology.…”

Section: Fig 1 Estimated Sensitivity and Error Of Protein Identificmentioning

confidence: 99%

See 1 more Smart Citation

Analysis of the Zebrafish Proteome during Embryonic Development

Lucitt

Price

Pizarro

et al. 2008

Molecular & Cellular Proteomics

116

View full text Add to dashboard Cite

The model organism zebrafish (Danio rerio) is particularly amenable to studies deciphering regulatory genetic networks in vertebrate development, biology, and pharmacology. Unraveling the functional dynamics of such networks requires precise quantitation of protein expression during organismal growth, which is incrementally challenging with progressive complexity of the systems. In an approach toward such quantitative studies of dynamic network behavior, we applied mass spectrometric methodology and rigorous statistical analysis to create comprehensive, high quality profiles of proteins expressed at two stages of zebrafish development. Proteins of embryos 72 and 120 h postfertilization (hpf) were isolated and analyzed both by two-dimensional (2D) LC followed by ESI-MS/MS and by 2D PAGE followed by MALDI-TOF/TOF protein identification. We detected 1384 proteins from 327,906 peptide sequence identifications at 72 and 120 hpf with false identification rates of less than 1% using 2D LC-ESI-MS/MS. These included only ϳ30% of proteins that were identified by 2D PAGE-MALDI-TOF/TOF. Roughly 10% of all detected proteins were derived from hypothetical or predicted gene models or were entirely unannotated. Comparison of proteins expression by 2D DIGE revealed that proteins involved in energy production and transcription/translation were relatively more abundant at 72 hpf consistent with faster synthesis of cellular proteins during organismal growth at this time compared with 120 hpf. The data are accessible in a database that links protein identifications to existing resources including the Zebrafish Information Network database. This new resource should facilitate the selection of candidate proteins for targeted quantitation and refine systematic genetic network analysis in vertebrate development and biology. Molecular & Cellular Proteomics 7:981-994, 2008.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Fig 1 Estimated Sensitivity and Error Of Protein Identificmentioning

confidence: 99%

Analysis of the Zebrafish Proteome during Embryonic Development

Lucitt

Price

Pizarro

et al. 2008

Molecular & Cellular Proteomics

116

View full text Add to dashboard Cite

show abstract

“…Mosaic gene expression is a hallmark of embryonic development in notably mouse (Rossant and Tam, 2009) and zebrafish (Sprague et al, 2003;Lunde et al, 2004;Sprague et al, 2006) and may be at the origin of lineage specification. Whole-mount in situ hybridization of MBT + embryos showed that sox3 was ubiquitously expressed (Fig.…”

Section: Mosaic Klf4 Expression In Embryos Correlates With Co-detectimentioning

confidence: 99%

“…Based on genome-wide data from mouse and human embryonic stem cells (Azuara et al, 2006;Bernstein et al, 2006;Pan et al, 2007), as well as in hematopoietic progenitors (Cui et al, 2009), such H3K4/K27me3 "bivalent" state would predict that non-klf4 expressing cells are programmed for later upregulation of the gene. Indeed, klf4 is strongly upregulated post-MBT (Sprague et al, 2003;Sprague et al, 2006;O'Boyle et al, 2007). Interestingly, recent genome-wide H3K4me3 and H3K27me3 promoter mapping data in mouse embryos reveals co-enrichment of these marks on developmentally-regulated genes (Dahl et al, 2010).…”

Section: Epigenetic States Of Embryonic Genes In Relation To Developmmentioning

confidence: 99%

Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos

Lindeman¹,

Winata²,

Aanes³

et al. 2010

Int. J. Dev. Biol.

View full text Add to dashboard Cite

Embryo development proceeds from a cascade of gene activation and repression events controlled by epigenetic modifications of DNA and histones. Little is known about epigenetic states in the developing zebrafish, despite its importance as a model organism. We report here DNA methylation and histone modification profiles of promoters of developmentallyregulated genes (pou5f1, sox2, sox3, klf4, nnr, otx1b, nes, vasa), as well as tert and bactin2, in zebrafish embryos at the mid-late blastula transition, shortly after embryonic genome activation. We identify four classes of promoters based on the following profiles: (i) those enriched in marks of active genes (H3K9ac, H4ac, H3K4me3) without transcriptionally repressing H3K9me3 or H3K27me3; (ii) those enriched in H3K9ac, H4ac and H3K27me3, without H3K9me3; one such gene was klf4, shown by in situ hybridization to be mosaically expressed, likely accounting for the detection of both activating and repressive marks on its promoter; (iii) those enriched in H3K4me3 and H3K27me3 without acetylation; and (iv) those enriched in all histone modifications examined. Culture of embryo-derived cells under differentiation conditions leads to H3K9 and H4 deacetylation and H3K9 and H3K27 trimethylation on genes that are inactivated, yielding an epigenetic profile similar to those of fibroblasts or muscle. All promoters however retain H3K4me3, indicating an uncoupling of H3K4me3 occupancy and gene expression. All non-CpG island developmentallyregulated promoters are DNA unmethylated in embryos, but hypermethylated in fibroblasts. Our results suggest that differentially expressed embryonic genes are regulated by various patterns of histone modifications on unmethylated DNA, which create a developmentally permissive chromatin state.

show abstract

“…Zebrafish have surged in importance as an animal model in almost every field of medicine, [9][10][11] owing to their publicly available genomic sequence, 12 their external fertilization, rapid development, accessibility of embryos (larvae) and the evolutionary conservation of the vertebrate body plan. Their precocious development of vision and remarkable evolutionary conservation of the eye make the zebrafish retina an excellent model for human visual disorders.…”

Section: Introductionmentioning

confidence: 99%

Gucy2f zebrafish knockdown – a model for Gucy2d-related leber congenital amaurosis

et al. 2012

View full text Add to dashboard Cite

Mutations in retinal-specific guanylate cyclase (Gucy2d) are associated with Leber congenital amaurosis-1 (LCA1). Zebrafish offer unique advantages relative to rodents, including their excellent color vision, precocious retinal development, robust visual testing strategies, low cost, relatively easy transgenesis and shortened experimental times. In this study we will demonstrate the feasibility of using gene-targeting in the zebrafish as a model for the photoreceptor-specific GUCY2D-related LCA1, by reporting the visual phenotype and retinal histology resulting from Gucy2f knockdown. Gucy2f zebrafish LCA-orthologous cDNA was identified and isolated by PCR amplification. Its expression pattern was determined by whole-mount in-situ hybridization and its function was studied by gene knockdown using two different morpholino-modified oligos (MO), one that blocks translation of Gucy2f and one that blocks splicing of Gucy2f. Visual function was assessed with an optomotor assay on 6-days-postfertilization larvae, and by analyzing changes in retinal histology. Gucy2f knockdown resulted in significantly lower vision as measured by the optomotor response compared with uninjected and control MO-injected zebrafish larvae. Histological changes in the Gucy2f-knockdown larvae included loss and shortening of cone and rod outer segments. A zebrafish model of Gucy2f-related LCA1 displays early visual dysfunction and photoreceptor layer dystrophy. This study serves as proof of concept for the use of zebrafish as a simple, inexpensive model with excellent vision on which further study of LCA-related genes is possible. Keywords: leber congenital amaurosis; animal model; GUCY2D; optomotor assay INTRODUCTION Leber congenital amaurosis (LCA) is a family of severe, early-onset, autosomal-recessive forms of pediatric blindness. LCA has been linked to more than 16 genes, often exhibiting clinical heterogeneity. 1,2 LCA1 is caused by mutations in the gene GUCY2D, which encodes the retinal Gucy2d-1 (GC1) and accounts for B20% of all cases of LCA. 3 LCA2 is caused by mutations in the RPE65 gene, which is expressed in the retinal pigment epithelium. Breakthrough research has demonstrated visual improvement following gene therapy trials in humans with LCA2. 4,5 Human trials relied on a decade of proof-of-concept studies in canine and rodent models. 6-8 Unlike LCA2, in which gene therapy is aimed at correcting an RPE defect, searching for gene therapy for LCA1 will involve an attempt at treating the photoreceptors. European Journal of Human GeneticsResearch in inherited retinal disease relies heavily on animal models, commonly mammals such as mice and dogs. These animal models have significant advantages, including the availability of knockout technology. Two specific drawbacks slow the applicability of rodent or canine models for study of relatively rare genetic diseases such as LCA and other retinal dystrophies. The first difficulty is the high cost and length of time required to create a new knockout line; thus, it is applicable only for comm...

show abstract

The Zebrafish Information Network: the zebrafish model organism database

Cited by 267 publications

References 3 publications

Analysis of the Zebrafish Proteome during Embryonic Development

Analysis of the Zebrafish Proteome during Embryonic Development

Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos

Gucy2f zebrafish knockdown – a model for Gucy2d-related leber congenital amaurosis

Contact Info

Product

Resources

About