ZFIN: enhancements and updates to the zebrafish model organism database

Bradford, Yvonne M.; Conlin, Tom; Dunn, Nathan; Fashena, David; Frazer, Ken; Howe, Douglas G.; Knight, Jonathan; Mani, Prita; Martin, R. D.; Moxon, Sierra; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruef, Barbara J.; Ruzicka, Leyla; Schaper, Holle Bauer; Schaper, Kevin; Shao, Xiang; Singer, Amy; Sprague, Judy; Sprunger, Brock; Slyke, Ceri E. Van; Westerfield, Monte

doi:10.1093/nar/gkq1077

Cited by 203 publications

(224 citation statements)

References 8 publications

(8 reference statements)

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“…S4) and the rpl7l1 mutant apparently has a mild phenotype (source: ZIRC). By contrast, its paralogue rpl7 has been demonstrated to be strongly and ubiquitously expressed (Bradford et al, 2011). A similar situation might occur in Drosophila, where RpL7 has been shown to be specifically required in neuroblasts to maintain their proliferation (Neumüller et al, 2011), whereas its counterpart (RpL7-like) displays ubiquitous expression.…”

Section: The Expression Of Genes Coding For Ribosomal Protein Is Crucmentioning

confidence: 85%

Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis

et al. 2013

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Investigating neural stem cell (NSC) behaviour in vivo, which is a major area of research, requires NSC models to be developed. We carried out a multilevel characterisation of the zebrafish embryo peripheral midbrain layer (PML) and identified a unique vertebrate progenitor population. Located dorsally in the transparent embryo midbrain, these large slow-amplifying progenitors (SAPs) are accessible for long-term in vivo imaging. They form a neuroepithelial layer adjacent to the optic tectum, which has transitory fast-amplifying progenitors (FAPs) at its margin. The presence of these SAPs and FAPs in separate domains provided the opportunity to data mine the ZFIN expression pattern database for SAP markers, which are coexpressed in the retina. Most of them are involved in nucleotide synthesis, or encode nucleolar and ribosomal proteins. A mutant for the cad gene, which is strongly expressed in the PML, reveals severe midbrain defects with massive apoptosis and sustained proliferation. We discuss how fish midbrain and retina progenitors might derive from ancient sister cell types and have specific features that are not shared with other SAPs.

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Section: The Expression Of Genes Coding For Ribosomal Protein Is Crucmentioning

confidence: 85%

Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis

et al. 2013

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“…To identify the molecular events underlying the synthesis of oxytocin, we screened the zebrafish model organism database (ZFIN) (Bradford et al, 2011) for transcriptional regulators expressed in the neurosecretory preoptic area (NPO), which includes neurons expressing the zebrafish homolog of oxytocin, termed oxytocin-like (Oxtl) (Blechman et al, 2007). One such candidate was the gene encoding the zebrafish ortholog of the transcriptional coactivator PGC-1␣ (LeMoine et al, 2010).…”

Section: Resultsmentioning

confidence: 99%

The Metabolic Regulator PGC-1α Directly Controls the Expression of the Hypothalamic Neuropeptide Oxytocin

Blechman¹,

Amir-Zilberstein²,

Gutnick³

et al. 2011

J. Neurosci.

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The transcriptional coactivator PGC-1␣ is a key regulator of cellular energy expenditure in peripheral tissues. Recent studies report that PGC-1␣-null mice develop late-onset obesity and that the neuronal inactivation of PGC-1␣ causes increased food intake. However, the exact role of PGC-1␣ in the CNS remains unclear. Here we show that PGC-1␣ directly regulates the expression of the hypothalamic neuropeptide oxytocin, a known central regulator of appetite. We developed a unique genetic approach in the zebrafish, allowing us to monitor and manipulate PGC-1␣ activity in oxytocinergic neurons. We found that PGC-1␣ is coexpressed with oxytocin in the zebrafish hypothalamus. Targeted knockdown of the zebrafish PGC-1␣ gene activity caused a marked decrease in oxytocin mRNA levels and inhibited the expression of a transgenic GFP reporter driven by the oxytocin promoter. The effect of PGC-1␣ loss of function on oxytocin gene activity was rescued by tissue-specific re-expression of either PGC-1␣ or oxytocin precursor in zebrafish oxytocinergic neurons. PGC-1␣ activated the oxytocin promoter in a heterologous cell culture system, and overexpression of PGC-1␣ induced ectopic expression of oxytocin in muscles and neurons. Finally, PGC-1␣ forms an in vivo complex with the oxytocin promoter in fed but not fasted animals. These findings demonstrate that PGC-1␣ is both necessary and sufficient for the production of oxytocin, implicating hypothalamic PGC-1␣ in the direct activation of a hypothalamic hormone known to control energy intake.

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“…The close phylogenetic relationship between goldfish and zebrafish (Saitoh et al, 2003, 2006) suggest that the well‐established molecular techniques, as well as mutant, morphant, and gene expression patterns, catalogued in The Zebrafish Model Organism Database (Bradford et al, 2011), can be directly applied to goldfish research (Mabee et al, 2007; Schlling and Webb, 2007; Tsai et al, 2013). Moreover, it was recently confirmed that these two teleost species are similar in terms of embryological development (Tsai et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems

Chang

Liu

et al. 2015

Developmental Dynamics

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Background: Artificial selection of postembryonic features is known to have established morphological variation in goldfish (Carassius auratus). Although previous studies have suggested that goldfish and zebrafish are almost directly comparable at the embryonic level, little is known at the postembryonic level. Results: Here, we categorized the postembryonic developmental process in the wild‐type goldfish into 11 different stages. We also report certain differences between the postembryonic developmental processes of goldfish and zebrafish, especially in the skeletal systems (scales and median fin skeletons), suggesting that postembryonic development underwent evolutionary divergence in these two teleost species. Conclusions: Our postembryonic staging system of wild‐type goldfish paves the way for careful and appropriate comparison with other teleost species. The staging system will also facilitate comparative ontogenic analyses between wild‐type and mutant goldfish strains, allowing us to closely study the relationship between artificial selection and molecular developmental mechanisms in vertebrates. Developmental Dynamics 244:1485–1518, 2015. © 2015 Wiley Periodicals, Inc.

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ZFIN: enhancements and updates to the zebrafish model organism database

Cited by 203 publications

References 8 publications

Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis

Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis

The Metabolic Regulator PGC-1α Directly Controls the Expression of the Hypothalamic Neuropeptide Oxytocin

Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems

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