Selenium status affects selenoprotein expression, reproduction, and F1 generation locomotor activity in zebrafish (Danio rerio).

Se is an essential trace element, and is incorporated into selenoproteins which play important roles in human health. Mammalian selenoprotein-coding genes are often present as paralogues in teleost fish, and it is unclear whether the expression patterns or functions of these fish paralogues reflect their mammalian orthologues. Using the model species zebrafish (Danio rerio; ZF), we aimed to assess how dietary Se affects key parameters in Se metabolism and utilisation including glutathione peroxidase (GPX) activity, the mRNA expression of key Se-dependent proteins (gpx1a, gpx1b, sepp1a and sepp1b), oxidative status, reproductive success and F1 generation locomotor activity. From 27 d until 254 d post-fertilisation, ZF were fed diets with graded levels of Se ranging from deficient ( < 0·10 mg/kg) to toxic (30 mg/kg). The mRNA expression of gpx1a and gpx1b and GPX activity responded in a similar manner to changes in Se status. GPX activity and mRNA levels were lowest when dietary Se levels (0·3 mg/kg) resulted in the maximum growth of ZF, and a proposed bimodal mechanism in response to Se status below and above this dietary Se level was identified. The expression of the sepp1 paralogues differed, with only sepp1a responding to Se status. High dietary Se supplementation (30 mg/kg) decreased reproductive success, while the offspring of ZF fed above 0·3 mg Se/kg diet had lower locomotor activity than the other groups. Overall, the novel finding of low selenoprotein expression and activity coinciding with maximum body growth suggests that even small Se-induced variations in redox status may influence cellular growth rates.

Zebrafish enhancer trap line showing maternal and neural expression of kctd15a.

Potassium channel tetramerization domain containing proteins (KCTDs), which share a conserved BTB (Bric-a-brac, Tramtrack, Broad complex) domain at their N-terminus, are known to be involved in both developmental and neural processes. However, the developmental expression patterns and functional roles of most vertebrate KCTDs remain unknown. Using enhancer-trapping technology, we have identified a transgenic zebrafish line (ub49) where the vector insertion is in close proximity to kctd15a, and where transgenic marker (eGFP) expression closely reflects endogenous kctd15a expression. Both ub49 and kctd15a show strong maternal expression that suggests a functional role during epiboly and gastrulation. At later developmental stages, expression of eGFP in ub49 also shares the same spatiotemporal features as kctd15a in several neural tissues, including cranial placode precursors, retina, and different areas of the developing brain. In the retina, we observed eGFP labeling of the inner nuclear layer (INL), including a heterogenous population of amacrine cells, and both laminae of the inner plexiform layer (IPL). This expression pattern suggests that Kctd15a proteins have several context-dependent functional roles in both developmental and neural processes. The enhancer trap line, which is the first transgenic reporter of Kctd gene expression in vertebrates, also provides a novel tool to study kctd15a function in vivo.

Zebrafish transgenic lines co-expressing a hybrid Gal4 activator and eGFP in tissue-restricted patterns.

We have used a Tol2-derived trapping vector, carrying a hybrid Gal4 gene and a UAS:eGFP reporter cassette, to identify 16 transgenic zebrafish lines expressing the fluorescent marker eGFP in tissue-restricted patterns during development. Most lines show co-expression of eGFP and a hybrid Gal4 transcription activator containing a truncated VP16 domain that facilitate induction of other UAS-transgenes (UAS:RFP). Notably, many of the transgenic lines are expressed in particular areas of the central nervous system, such as the retina. We mapped the genomic positions of most of the activated insertions, and for three retina-specific lines we also demonstrate that eGFP reports the expression of particular endogenous genes. One of the identified zebrafish genes shows expression in ventral retina, and encodes a protein containing a repulsive guidance molecule (RGM) domain, suggesting a role in axonal guidance during optic nerve formation. Among the lines labeling other tissues, three show early co-expression of eGFP and Gal4-VP16 in blood vessels, erythrocytes and other hematopoietic cells. Interestingly, the activated insertion in the erythrocyte line was mapped to a site near the globin cluster on chromosome 3. All the reported lines co-expressing eGFP and the hybrid Gal4 activator may have potential as genetic tools to study developmental processes.

Autoregulatory binding sites in the zebrafish six3a promoter region define a new recognition sequence for Six3 proteins.

The homeodomain (HD) transcription factor Six3, which is a member of the Six/Sine oculis family, is essential for development of the eyes and forebrain in vertebrates. It has recently been claimed that the HDs of Six3 and other members of the Six family have a common recognition sequence, TGATAC. However, a different recognition sequence including the typical TAAT core motif, which has not yet been fully defined, has also been proposed for the Six3 HD in mice. Our study of the zebrafish orthologue six3a, which has an identical HD, shows that it binds in vitro to multiple TAAT-containing sites within its promoter region. Comparison of the different binding affinities for these sequences identifies three high-affinity sites with a common TAATGTC motif. Notably, this new recognition sequence, which is supported by our analysis of the influence of single-nucleotide substitutions on the DNA-binding affinity, is distinct from all of the DNA-binding specificities previously described in surveys of HDs. In addition, our comparison of Six3a HD binding to the novel TAATGTC motif and the common recognition sequence of Six family HDs (TGATAC) shows very similar affinities, suggesting two distinct DNA-binding modes. Transient reporter assays of the six3a promoter in zebrafish embryos also indicate that the three high-affinity sites are involved in autoregulation. In support of this, chromatin immunoprecipitation experiments show enrichment of Six3a binding to a six3a promoter fragment containing two clustered high-affinity sites. These findings provide strong evidence that the TAATGTC motif is an important target sequence for vertebrate Six3 proteins in vivo.

Labelling and targeted ablation of specific bipolar cell types in the zebrafish retina.

BACKGROUND: Development of a functional retina depends on regulated differentiation of several types of neurons and generation of a highly complex network between the different types of neurons. In addition, each type of retinal neuron includes several distinct morphological types. Very little is known about the mechanisms responsible for generating this diversity of retinal neurons, which may also display specific patterns of regional distribution. RESULTS: In a screen in zebrafish, using a trapping vector carrying an engineered yeast Gal4 transcription activator and a UAS:eGFP reporter cassette, we have identified two transgenic lines of zebrafish co-expressing eGFP and Gal4 in specific subsets of retinal bipolar cells. The eGFP-labelling facilitated analysis of axon terminals within the inner plexiform layer of the adult retina and showed that the fluorescent bipolar cells correspond to previously defined morphological types. Strong regional restriction of eGFP-positive bipolar cells to the central part of the retina surrounding the optic nerve was observed in adult zebrafish. Furthermore, we achieved specific ablation of the labelled bipolar cells in 5 days old larvae, using a bacterial nitroreductase gene under Gal4-UAS control in combination with the prodrug metronidazole. Following prodrug treatment, nitroreductase expressing bipolar cells were efficiently ablated without affecting surrounding retina architecture, and recovery occurred within a few days due to increased generation of new bipolar cells. CONCLUSION: This report shows that enhancer trapping can be applied to label distinct morphological types of bipolar cells in the zebrafish retina. The genetic labelling of these cells yielded co-expression of a modified Gal4 transcription activator and the fluorescent marker eGFP. Our work also demonstrates the potential utility of the Gal4-UAS system for induction of other transgenes, including a bacterial nitroreductase fusion gene, which can facilitate analysis of bipolar cell differentiation and how the retina recovers from specific ablation of these cells.

Distinct expression of two foxg1 paralogues in zebrafish.

The forkhead proteins (Fox) act as transcription factors in many biological processes in a wide range of species. One member of this superfamily, Foxg1, has essential roles in the development of eyes, telencephalon, ears and olfactory system. Zebrafish foxg1 has been reported to have similar roles as the mouse orthologue Foxg1. However, no data has been reported about possible zebrafish foxg1 paralogues. In this study we identified one zebrafish foxg1 paralogue by enhancer trapping, which we designate foxg1b. A more diverged paralogue, foxg1c, was identified by homology searches. Sequence comparisons indicate that both foxg1b and foxg1c are less related to mouse than the previously characterized foxg1. We report that foxg1b is expressed in a regionally restricted pattern within the developing eye, mainly in the dorsal-nasal retina, which is similar to the retinal expression of mouse Foxg1. By contrast, foxg1c is only expressed transiently in the eyes and forebrain between 14 and 20h post-fertilization, while expression was detected exclusively in the developing inner ear at later stages. Our results suggest that foxg1b and foxg1c have undergone expression pattern divergence during evolution that has resulted in functional specialization.

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.

We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding elements (HCNEs), their developmental regulatory target genes, and phylogenetically and functionally unrelated "bystander" genes. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are expressed in patterns that are different from those of the target genes. Reporter insertions distal to zebrafish developmental regulatory genes pax6.1/2, rx3, id1, and fgf8 and miRNA genes mirn9-1 and mirn9-5 recapitulate the expression patterns of these genes even if located inside or beyond bystander genes, suggesting that the regulatory domain of a developmental regulatory gene can extend into and beyond adjacent transcriptional units. We termed these chromosomal segments genomic regulatory blocks (GRBs). After whole genome duplication in teleosts, GRBs, including HCNEs and target genes, were often maintained in both copies, while bystander genes were typically lost from one GRB, strongly suggesting that evolutionary pressure acts to keep the single-copy GRBs of higher vertebrates intact. We show that loss of bystander genes and other mutational events suffered by duplicated GRBs in teleost genomes permits target gene identification and HCNE/target gene assignment. These findings explain the absence of evolutionary breakpoints from large vertebrate chromosomal segments and will aid in the recognition of position effect mutations within human GRBs.

Duplicate sfrp1 genes in zebrafish: sfrp1a is dynamically expressed in the developing central nervous system, gut and lateral line.

The secreted frizzled-related proteins (Sfrp) are a family of soluble proteins with diverse biological functions having the capacity to bind Wnt ligands, to modulate Wnt signalling, and to signal directly via the Wnt receptor, Frizzled. In an enhancer trap screen for embryonic expression in zebrafish we identified an sfrp1 gene. Previous studies suggest an important role for sfrp1 in eye development, however, no data have been reported using the zebrafish model. In this paper, we describe duplicate sfrp1 genes in zebrafish and present a detailed analysis of the expression profile of both genes. Whole mount in situ hybridisation analyses of sfrp1a during embryonic and larval development revealed a dynamic expression profile, including: the central nervous system, where sfrp1a was regionally expressed throughout the brain and developing eye; the posterior gut, from the time of endodermal cell condensation; the lateral line, where sfrp1a was expressed in the migrating primordia and interneuromast cells that give rise to the sensory organs. Other sites included the blastoderm, segmenting mesoderm, olfactory placode, developing ear, pronephros and fin-bud. We have also analysed sfrp1b expression during embryonic development. Surprisingly this gene exhibited a divergent expression profile being limited to the yolk syncytium under the elongating tail-bud, which later covered the distal yolk extension, and transiently in the tail-bud mesenchyme. Overall, our studies provide a basis for future analyses of these developmentally important factors using the zebrafish model.

Large-scale enhancer detection in the zebrafish genome.

Murine retroviral vectors carrying an enhancer detection cassette were used to generate 95 transgenic lines of fish in which reporter expression is observed in distinct patterns during embryonic development. We mapped 65 insertion sites to the as yet unfinished zebrafish genome sequence. Many integrations map close to previously known developmental genes, including transcription factors of the Pax, Hox, Sox, Pou, Otx, Emx, zinc-finger and bHLH gene families. In most cases, the activated provirus is located in, or within a 15 kb interval around, the corresponding transcriptional unit. The exceptions include four insertions into a gene desert on chromosome 20 upstream of sox11b, and an insertion upstream of otx1. In these cases, the activated insertions are found at a distance of between 32 kb and 132 kb from the coding region. These as well as seven other insertions described here identify genes that have recently been associated with ultra conserved non-coding elements found in all vertebrate genomes.