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Heart development is a complex process, starting from specification of cardiac precursors and formation of a linear tube to gradual progression to a functional beating organ. For normal heart development, many processes, including asymmetric positioning of the heart along the left-right (L/R) axis, cardiac growth, and cardiac valve morphogenesis must be completed successfully. Although heart development has been studied extensively, the mechanisms that control heart morphogenesis and valve formation are not fully understood. The pro-convertase FurinA is a key protein that functions in heart development in many vertebrates including zebrafish. How FurinA activity is regulated during heart development is not known. Through computational analysis of the zebrafish transcriptome, we identified a short sequence and structure RNA motif in a variant transcript of FurinA harbouring a long 3’untranslated region (3’UTR). The alternative 3’UTRfurinaisoform is expressed at embryonic stages preceding organ positioning. Reporter localization and RNA-binding assays show that thefurina3’UTR forms complexes with the conserved RNA-binding protein and translational repressor Ybx1. Conditional mutant zebrafish embryos affectingybx1show premature and increased Furin reporter protein expression, abnormal cardiac morphogenesis and heart looping defects. Our mutantybx1hearts have an expanded atrioventricular canal, abnormal sino-atrial valves and many mutant embryos show retrograde blood flow from the ventricle to the atrium. This is similar to human heart valve regurgitation patients. Our findings show an essential function for the 3’UTR element/Ybx1 regulon in translational repression of FurinA, revealing a new upstream regulatory mechanism that controls embryonic heart development, and demonstrates theybx1mutant as a model to study cardiac valve development and function.

During the first day of zebrafish development, ribonucleoprotein (RNP) complexes called germplasm form large aggregates that initially segregate asymmetrically during cleavage stages. After zygotic genome activation, the granules break into smaller fragments that associate with the nuclear membrane as perinuclear (germ) granules toward the end of gastrulation. The mechanisms underlying the highly dynamic behavior of germ granules are not well studied but thought to be facilitated by the cytoskeleton. Here, we present efficient mounting strategies using 3d-printed tools that generate wells on agarose-coated sample holders to allow high-resolution imaging of multiplexed embryos that are less than one day post-fertilization (dpf) on inverted (spinning disk confocal) as well as upright (lattice light-sheet and diSPIM) microscopes. In particular, our tools and methodology allow water dipping lenses to have direct access to mounted embryos, with no obstructions to the light path (e.g., through low melting agarose or methyl cellulose). Moreover, the multiplexed tight arrays of wells generated by our tools facilitate efficient mounting of early embryos (including cleavage stages) for live imaging. These methods and tools, together with new transgenic reporter lines, can facilitate the study of germ granule dynamics throughout their lifetime in detail, at high resolution and throughput, using live imaging technologies.

In many organisms, transcriptional and post-transcriptional regulation of components of pathways or processes has been reported. However, to date, there are few reports of translational co-regulation of multiple components of a developmental signaling pathway. Here, we show that an RNA element which we previously identified as a dorsal localization element (DLE) in the 3′UTR of zebrafish nodal-related1/squint (ndr1/sqt) ligand mRNA, is shared by the related ligand nodal-related2/cyclops (ndr2/cyc) and the nodal inhibitors, lefty1 (lft1) and lefty2 mRNAs. We investigated the activity of the DLEs through functional assays in live zebrafish embryos. The lft1 DLE localizes fluorescently labeled RNA similarly to the ndr1/sqt DLE. Similar to the ndr1/sqt 3′UTR, the lft1 and lft2 3′UTRs are bound by the RNA-binding protein (RBP) and translational repressor, Y-box binding protein 1 (Ybx1), whereas deletions in the DLE abolish binding to Ybx1. Analysis of zebrafish ybx1 mutants shows that Ybx1 represses lefty1 translation in embryos. CRISPR/Cas9-mediated inactivation of human YBX1 also results in human NODAL translational de-repression, suggesting broader conservation of the DLE RNA element/Ybx1 RBP module in regulation of Nodal signaling. Our findings demonstrate translational co-regulation of components of a signaling pathway by an RNA element conserved in both sequence and structure and an RBP, revealing a ‘translational regulon’.

Post-transcriptional gene regulation through the recognition of specific elements in mRNAs is an important determinant of gene expression. The cis elements are recognised by RNA binding proteins (RBPs) and/or small non-coding RNAs, which then orchestrate a range of processes such as mRNA localization, translational control, and degradation. RNA regulation is critical for development and disruptions in regulatory mechanisms can cause disease. While mutations in numerous RBPs have been linked to diseases in humans, the contribution of mutations in RNA elements to disease manifestation is largely unknown. Danio rerio (zebrafish), a fish model is a widely used vertebrate system to study development and disease. Here, we describe how state-of-the-art genomics tools combined with in vivo functional studies in zebrafish have facilitated the discovery of RNA elements, many of which are functionally conserved. We also highlight the potential of zebrafish to model human diseases and for drug discovery.

The spatial and temporal expression of steroidogenic genes in zebrafish has not been fully characterized. Since zebrafish are increasingly employed in endocrine and stress research, a better characterization of steroidogenic pathways is required to target specific steps in the biosynthetic pathways in the future. Here, we have systematically defined the temporal and spatial expression of steroidogenic enzymes involved in glucocorticoid biosynthesis (cyp21a2, cyp11c1, cyp11a1, cyp11a2, cyp17a1, cyp17a2, hsd3b1, hsd3b2), as well as the mitochondrial electron-providing co-factors ferredoxin (fdx1, fdx1b) during zebrafish development. Our studies showed an early expression of all these genes during embryogenesis. In larvae, expression of cyp11a2, cyp11c1, cyp17a2, cyp21a2, hsd3b1 and fdx1b can be detected in the interrenal gland, the zebrafish counterpart of the mammalian adrenal gland, whereas the fdx1 transcript is mainly found in the digestive system. Gene expression studies using quantitative RT-PCR and whole-mount in situ hybridization in the adult zebrafish brain revealed a wide expression of these genes throughout the encephalon, including neurogenic regions. Using ultra-high-performance liquid chromatography tandem mass spectrometry, we were able to demonstrate the presence of the glucocorticoid cortisol in the adult zebrafish brain. Moreover, we demonstrate de novo biosynthesis of cortisol and the neurosteroid THDOC in the adult zebrafish brain from radiolabeled pregnenolone. Taken together, our study is a comprehensive characterization of the steroidogenic genes and the fdx co-factors facilitating glucocorticoid biosynthesis in zebrafish. Furthermore, we provide additional evidence of de novo neurosteroid biosynthesizing in the brain of adult zebrafish facilitated by enzymes involved on glucocorticoid biosynthesis. Our work provides a valuable source for establishing the zebrafish as a translational model to understand the roles of the genes of glucocorticoid biosynthesis and fdx co-factors during embryonic development, stress and in brain homeostasis and function.

Congenital adrenal hyperplasia is a group of common inherited disorders leading to glucocorticoid deficiency. Most cases are caused by 21-hydroxylase deficiency (21OHD). The systemic consequences of imbalanced steroid hormone biosynthesis due to severe 21OHD remains poorly understood. Therefore, we developed a zebrafish model for 21OHD, which focuses on the impairment of glucocorticoid biosynthesis. A single 21-hydroxylase gene (cyp21a2) is annotated in the zebrafish genome based on sequence homology. Our in silico analysis of the 21-hydroxylase (Cyp21a2) protein sequence suggests a sufficient degree of similarity for the usage of zebrafish cyp21a2 to model aspects of human 21OHD in vivo. We determined the spatiotemporal expression patterns of cyp21a2 by whole-mount in situ hybridization and reverse transcription polymerase chain reaction throughout early development. Early cyp21a2 expression is restricted to the interrenal gland (zebrafish adrenal counterpart) and the brain. To further explore the in vivo consequences of 21OHD we created several cyp21a2 null-allele zebrafish lines by using a transcription activator–like effector nuclease genomic engineering strategy. Homozygous mutant zebrafish larvae showed an upregulation of the hypothalamic–pituitary–interrenal (HPI) axis and interrenal hyperplasia. Furthermore, Cyp21a2-deficient larvae had a typical steroid profile, with reduced concentrations of cortisol and increased concentrations of 17-hydroxyprogesterone and 21-deoxycortisol. Affected larvae showed an upregulation of the HPI axis and interrenal hyperplasia. Downregulation of the glucocorticoid-responsive genes pck1 and fkbp5 indicated systemic glucocorticoid deficiency. Our work demonstrates the crucial role of Cyp21a2 in glucocorticoid biosynthesis in zebrafish larvae and establishes an in vivo model allowing studies of systemic consequences of altered steroid hormone synthesis.

Pufferfish species of the Tetraodontidae family carry the smallest genomes among vertebrates. Their compressed genomes are thought to be enriched for functional DNA compared to larger vertebrate genomes, and they are important models for comparative genomics. The significance of pufferfish as model organisms in comparative genomics is due to the availability of two sequenced genomes, that of spotted green pufferfish (Tetraodon nigroviridis) and fugu (Takifugu rubripes). However, there is only a very limited utilization of pufferfish as an experimental model organism, due to the lack of established husbandry and developmental genetics protocols. In this study, we provide the first description of the normal embryonic development of Tetraodon nigroviridis. Embryos were obtained by in vitro fertilization of eggs, and subsequent development was monitored by brightfield microscopy at constant temperature. Tetraodon development was divided into distinct stages based on diagnostic morphological features, which were adopted from published literature on normal development of other fish species like medaka (Oryzias latipes), zebrafish (Danio rerio), and fugu. Tetraodon embryos show more similar morphologies to medaka than to zebrafish, reflecting its phylogenetic position. The early developmental stage series described in this study forms the foundation for the utilization of tetraodon as an experimental model organism for comparative developmental studies.

The spatial and temporal expression of steroidogenic genes in zebrafish has not been fully characterised. Because zebrafish are increasingly employed in endocrine and stress research, a better characterisation of steroidogenic pathways is required to target specific steps in the biosynthetic pathways. In the present study, we have systematically defined the temporal and spatial expression of steroidogenic enzymes involved in glucocorticoid biosynthesis (cyp21a2, cyp11c1, cyp11a1, cyp11a2, cyp17a1, cyp17a2, hsd3b1, hsd3b2), as well as the mitochondrial electron-providing ferredoxin co-factors (fdx1, fdx1b), during zebrafish development. Our studies showed an early expression of all these genes during embryogenesis. In larvae, expression of cyp11a2, cyp11c1, cyp17a2, cyp21a2, hsd3b1 and fdx1b can be detected in the interrenal gland, which is the zebrafish counterpart of the mammalian adrenal gland, whereas the fdx1 transcript is mainly found in the digestive system. Gene expression studies using quantitative reverse transcriptase-PCR and whole-mount in situ hybridisation in the adult zebrafish brain revealed a wide expression of these genes throughout the encephalon, including neurogenic regions. Using ultra-high-performance liquid chromatography tandem mass spectrometry, we were able to demonstrate the presence of the glucocorticoid cortisol in the adult zebrafish brain. Moreover, we demonstrate de novo biosynthesis of cortisol and the neurosteroid tetrahydrodeoxycorticosterone in the adult zebrafish brain from radiolabelled pregnenolone. Taken together, the present study comprises a comprehensive characterisation of the steroidogenic genes and the fdx co-factors facilitating glucocorticoid biosynthesis in zebrafish. Furthermore, we provide additional evidence of de novo neurosteroid biosynthesising in the brain of adult zebrafish facilitated by enzymes involved in glucocorticoid biosynthesis. Our study provides a valuable source for establishing the zebrafish as a translational model with respect to understanding the roles of the genes for glucocorticoid biosynthesis and fdx co-factors during embryonic development and stress, as well as in brain homeostasis and function.

Zebrafish embryos offer a unique combination of high-throughput capabilities and the complexity of the vertebrate animal for a variety of phenotypic screening applications. However, there is a need for automation of imaging technologies to exploit the potential of the transparent embryo. Here we report a high-throughput pipeline for registering domain-specific reporter expression in zebrafish embryos with the aim of mapping the interactions between cis-regulatory modules and core promoters. Automated microscopy coupled with custom-built embryo detection and segmentation software allowed the spatial registration of reporter activity for 202 enhancer-promoter combinations, based on images of thousands of embryos. The diversity of promoter-enhancer interaction specificities underscores the importance of the core promoter sequence in cis-regulatory interactions and provides a promoter resource for transgenic reporter studies. The technology described here is also suitable for the spatial analysis of fluorescence readouts in genetic, pharmaceutical or toxicological screens.

Radon 222 distributions during the 1993 North Atlantic Regional Experiment are simulated with the National Oceanic and Atmospheric Administration Aeronomy Laboratory three-dimensional regional transport model. The model domain covers the western part of the North Atlantic Ocean and part of the eastern United States and Canada. It horizontally elongates 4200 km in the east-west and north-south directions and vertically extends from the surface to 50 mbar. The model simulates emissions, transport, and radioactive decay of 222Rn. Advection, cloud transport, mixing in the planetary boundary layer, and diffusion are simulated and the emissions, boundary, and initial conditions are parameterized. The model results are analyzed to study the ability of the model to simulate 222Rn distribution in the troposphere. The analysis indicates that 222Rn simulations near the surface are dominated by emissions. At altitudes from 6 km) are dominated by side boundary conditions and the wind field. The impact of top boundary on 222Rn simulations is negligible provided the top is specified at an altitude well above the tropopause. Cloud mixing is important in the vertical transport of 222Rn from the surface to the free troposphere. Cloud effect is significant in 222Rn distributions at grid columns within or near which there are abundant clouds. The mean effect of cloud mixing cannot be appropriately represented by contrasting large-scale or long-term average 222Rn distributions simulated in cases with and without cloud mixing. Surface pressure fluctuation has substantial influence on 222Rn emission and concentration variabilities, but this effect is restricted to altitudes near the surface. The model-simulated 222Rn concentrations are compared with measurements made onboard the U.S. Department of Energy Gulfstream aircraft based at Halifax, Nova Scotia, to evaluate the quality of the simulations. The comparison indicates that the simulations and observations are usually within a factor of 2 of one another and significantly correlated with each other. The simulations are capable of capturing high 222Rn concentrations observed in continental plumes.

In this paper we describe a recently developed technique to collect samples for atmospheric 222Rn measurements suited for deployment on (research) aircraft. Following a technical description of the sampler we present measurements from nine flights during the 1993 North Atlantic Regional Experiment (NARE) intensive over the North Atlantic Ocean and over the continent in the vicinity of Nova Scotia and New Brunswick, Canada. Samples were taken both in the boundary layer and in the free troposphere up to about 5500 m (msl). Concentrations ranged from 0.01 to 1.66 Bq/m3 in the free troposphere, with means of 1.66 and 0.52 Bq/m3, respectively. Boundary layer 222Rn concentrations were strongly correlated with back trajectory origins confirming the use of 222Rn as tracer for continental air masses. Samples collected in the marine boundary layer (MBL) were found to be significantly correlated with aerosol particle, NOy, and O3 concentrations reaffirming the utility of radon as a tracer of continental boundary layer air. Radon concentrations for the MBL samples were not found to be significantly correlated with transit times from the continent as estimated from back trajectory analysis implying that variations in the radon concentrations are dominated by factors other than radioactive decay. It is suggested that this factor is the height of the continental boundary layer into which the radon is emitted. On the basis of the radioactive decay we estimated apparent 222Rn ages for our samples and discuss the inherent difficulties in reliable age estimates. A comparison with hydrocarbon ratio age estimates for a highly polluted plume of air encountered during the campaign shows a similar age range for these samples and suggests that simultaneous measurements of species with different chemical and physical properties might allow narrowing the uncertainties in such ages estimates.

The traditional model of transcription initiation nucleated by the TFIID complex has suffered significant erosion in the last decade. The discovery of cell-specific paralogs of TFIID subunits and a variety of complexes that replace TFIID in transcription initiation of protein coding genes have been paralleled by the description of diverse core promoter sequences. These observations suggest an additional level of regulation of developmental and tissue-specific gene expression at the core promoter level. Recent work suggests that this regulation may function through specific roles of distinct TBP-type factors and TBP-associated factors (TAFs), however the picture emerging is still far from complete. Here we summarize the proposed models of transcription initiation by alternative initiation complexes in distinct stages of developmental specialization during vertebrate ontogeny.

Maternal gene products drive early embryogenesis almost exclusively until the mid blastula transition (MBT) in many animal models including fish. However, the maternal contribution to embryogenesis does not stop at MBT, but continues to be an essential regulator of key developmental processes. The extent to which maternal effects contribute to embryonic and larval development is hard to estimate due to the technical difficulty of interfering with maternal gene products by conventional forward and reverse genetic tools. Therefore, novel methods to manipulate maternal factors in oocytes need to be developed. Here, we provide a proof of principle protocol for transplanting stage I-II zebrafish follicles into recipient mothers where donor stage I oocytes can develop to stage IV in 2 weeks and in 3 weeks they develop into mature eggs and produce viable offspring. Moreover, we show that simple microinjection of stage I-II follicles with RNA results in reporter gene expression in oocytes and paves the way for developing tools for interfering with maternal gene activity. This early stage oocyte transplantation protocol provides a means to study cellular and molecular aspects of oocyte development in the zebrafish.

Arthrogryposis, renal dysfunction and cholestasis syndrome (ARC) is a multisystem disorder associated with abnormalities in polarized liver and kidney cells. Mutations in VPS33B account for most cases of ARC. We identified mutations in VIPAR (also called C14ORF133) in individuals with ARC without VPS33B defects. We show that VIPAR forms a functional complex with VPS33B that interacts with RAB11A. Knockdown of vipar in zebrafish resulted in biliary excretion and E-cadherin defects similar to those in individuals with ARC. Vipar-and Vps33b-deficient mouse inner medullary collecting duct (mIMDC-3) cells expressed membrane proteins abnormally and had structural and functional tight junction defects. Abnormal Ceacam5 expression was due to mis-sorting toward lysosomal degradation, but reduced E-cadherin levels were associated with transcriptional downregulation. The VPS33B-VIPAR complex thus has diverse functions in the pathways regulating apical-basolateral polarity in the liver and kidney. Children Liver Disease Foundation Framework 6 IP EUTRACC (LSGH CT 2006037445) European Molecular Biology Organization (EMBO) (ASTF 121:2007) European Science Foundation (ESF) European Commission (2008) UK Research & Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) (BB/H002308/1) ARC syndrome association Children Living with Inherited Metabolic Diseases (CLIMB) Birmingham Children's Hospital Research Foundation (BCHRF) WellChild Wellcome Trust European Commission United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD) (ZIAHD008807) United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK) (R01DK035652) NIH National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK) (P30DK034928)