Zebrafish nodal-related genes are implicated in axial patterning and establishing left-right asymmetry

Odd skipped related 1 is a negative feedback regulator of nodal-induced endoderm development

BACKGROUND

Early embryo patterning is orchestrated by tightly regulated morphogen gradients. The Nodal morphogen patterns the mesendoderm, giving rise to all endoderm and head and trunk mesoderm. High Nodal concentrations favor endoderm differentiation while lower promote mesoderm differentiation. Nodal signaling is controlled by both positive and negative feedback regulation to ensure robust developmental patterning.

RESULTS

Here we identify odd skipped related 1 (osr1), a zinc finger transcription factor, as a new element in Nodal feedback regulation affecting endoderm development. We show that osr1 expression in zebrafish germ ring mesendoderm requires Nodal signaling; osr1 expression was lost in embryos lacking Nodal signaling. Conversely, osr1 expression was ectopically induced by the activation of Nodal signaling. Furthermore we demonstrate that osr1 responds directly to Nodal signaling. Additionally, osr1 knockdown generated excess endoderm cells marked by sox32 expression while expression of osr1 mRNA was not affected in sox32-deficient embryos.

CONCLUSIONS

Our findings identify osr1 as a Nodal-induced, negative feedback regulator of Nodal signaling that acts at the earliest stages of endoderm differentiation to limit the number of endoderm progenitors. As such, we propose that osr1 represents a novel network motif controlling the output of Nodal signaling to regulate mesendoderm patterning.

Evolutionary conservation of early mesoderm specification by mechanotransduction in Bilateria

The modulation of developmental biochemical pathways by mechanical cues is an emerging feature of animal development, but its evolutionary origins have not been explored. Here we show that a common mechanosensitive pathway involving β-catenin specifies early mesodermal identity at gastrulation in zebrafish and Drosophila. Mechanical strains developed by zebrafish epiboly and Drosophila mesoderm invagination trigger the phosphorylation of β-catenin–tyrosine-667. This leads to the release of β-catenin into the cytoplasm and nucleus, where it triggers and maintains, respectively, the expression of zebrafish brachyury orthologue notail and of Drosophila Twist, both crucial transcription factors for early mesoderm identity. The role of the β-catenin mechanosensitive pathway in mesoderm identity has been conserved over the large evolutionary distance separating zebrafish and Drosophila. This suggests mesoderm mechanical induction dating back to at least the last bilaterian common ancestor more than 570 million years ago, the period during which mesoderm is thought to have emerged.

Mechanical cues can induce morphogenetic processes during development. Here the authors show that mechanical changes during embryonic development in both zebrafish and Drosophila lead to nuclear localization of β-catenin, which regulates genes required for early mesoderm development in both species.

A Nodal-independent and tissue-intrinsic mechanism controls heart-looping chirality

Breaking left-right symmetry in bilateria is a major event during embryo development that is required for asymmetric organ position, directional organ looping and lateralized organ function in the adult. Asymmetric expression of Nodal-related genes is hypothesized to be the driving force behind regulation of organ laterality. Here we identify a Nodal-independent mechanism that drives asymmetric heart looping in zebrafish embryos. In a unique mutant defective for the Nodal-related southpaw gene, preferential dextral looping in the heart is maintained, whereas gut and brain asymmetries are randomized. As genetic and pharmacological inhibition of Nodal signalling does not abolish heart asymmetry, a yet undiscovered mechanism controls heart chirality. This mechanism is tissue intrinsic, as explanted hearts maintain ex vivo retain chiral looping behaviour and require actin polymerization and myosin II activity. We find that Nodal signalling regulates actin gene expression, supporting a model in which Nodal signalling amplifies this tissue-intrinsic mechanism of heart looping.

Early left-right asymmetries during axial morphogenesis in the chick embryo

The primitive node is the "hub" of early left-right patterning in the chick embryo: (1) it undergoes asymmetrical morphogenesis immediately after its appearance at Stage 4; (2) it is closely linked to the emerging asymmetrical expression of nodal and shh at Stage 5; and (3) its asymmetry is spatiotemporally related to the emerging notochord, the midline barrier maintaining molecular left-right patterning from Stage 6 onward. Here, we study the correlation of node asymmetry to notochord marker expression using high-resolution histology, and we test pharmacological inhibition of shh signaling using cyclopamine at Stages 4 and 5. Just as noggin expression mirrors an intriguing structural continuity between the right node shoulder and the notochord, shh expression in the left node shoulder confirms a similar continuity with the future floor plate. Shh inhibition at Stage 4 or 5 suppressed nodal in both its paraxial or lateral plate mesoderm domains, respectively, and resulted in randomized heart looping. Thus, the "primordial" paraxial nodal asymmetry at Stage 4/5 (1) appears to be dependent on, but not instructed by, shh signaling and (2) may be fixed by asymmetrical roots of the notochord and the floor plate, thereby adding further twists to the node's pivotal role during left-right patterning.

FGF signaling is required for brain left-right asymmetry and brain midline formation

Early disruption of FGF signaling alters left-right (LR) asymmetry throughout the embryo. Here we uncover a role for FGF signaling that specifically disrupts brain asymmetry, independent of normal lateral plate mesoderm (LPM) asymmetry. When FGF signaling is inhibited during mid-somitogenesis, asymmetrically expressed LPM markers southpaw and lefty2 are not affected. However, asymmetrically expressed brain markers lefty1 and cyclops become bilateral. We show that FGF signaling controls expression of six3b and six7, two transcription factors required for repression of asymmetric lefty1 in the brain. We found that Z0-1, atypical PKC (aPKC) and β-catenin protein distribution revealed a midline structure in the forebrain that is dependent on a balance of FGF signaling. Ectopic activation of FGF signaling leads to overexpression of six3b, loss of organized midline adherins junctions and bilateral loss of lefty1 expression. Reducing FGF signaling leads to a reduction in six3b and six7 expression, an increase in cell boundary formation in the brain midline, and bilateral expression of lefty1. Together, these results suggest a novel role for FGF signaling in the brain to control LR asymmetry, six transcription factor expressions, and a midline barrier structure.

Trb3 regulates LR axis formation in zebrafish embryos

Tribless family proteins are pseudokinases that lack DFG (Asp-Phe-Gly) motif in the functional kinase domain, regulating Akt and BMP pathways, insulin metabolism, hypoxia, and ubiquitination. This report concerns expression patterns and functional roles of trb3 in zebrafish embryonic development. trb3 is evolutionarily well-conserved and located on zebrafish chromosome 11. Spatiotemporal expression studies show that trb3 transcripts are abundant throughout embryogenesis, but confined to mesendodermal cells during the late blastula phase. Over-expression of trb3 ventralizes the embryos while a knockdown of trb3 using morpholino alters positioning of the heart, liver, and pancreatic buds as well as gut looping. Furthermore, constitutive activation of TGF-signaling with TARAM-A* (TGF-related type I receptor) significantly increases the level of trb3 transcripts during the late blastula phase. Over-expression of trb3 reduces the level of smurf1 transcripts, a member of TGF-signaling. We thus propose that Trb3 governs left-right (LR) axis patterning as a component of TGF-signaling in vertebrate embryonic development.

The integrator complex subunit 6 (Ints6) confines the dorsal organizer in vertebrate embryogenesis

Dorsoventral patterning of the embryonic axis relies upon the mutual antagonism of competing signaling pathways to establish a balance between ventralizing BMP signaling and dorsal cell fate specification mediated by the organizer. In zebrafish, the initial embryo-wide domain of BMP signaling is refined into a morphogenetic gradient following activation dorsally of a maternal Wnt pathway. The accumulation of β-catenin in nuclei on the dorsal side of the embryo then leads to repression of BMP signaling dorsally and the induction of dorsal cell fates mediated by Nodal and FGF signaling. A separate Wnt pathway operates zygotically via Wnt8a to limit dorsal cell fate specification and maintain the expression of ventralizing genes in ventrolateral domains. We have isolated a recessive dorsalizing maternal-effect mutation disrupting the gene encoding Integrator Complex Subunit 6 (Ints6). Due to widespread de-repression of dorsal organizer genes, embryos from mutant mothers fail to maintain expression of BMP ligands, fail to fully express vox and ved, two mediators of Wnt8a, display delayed cell movements during gastrulation, and severe dorsalization. Consistent with radial dorsalization, affected embryos display multiple independent axial domains along with ectopic dorsal forerunner cells. Limiting Nodal signaling or restoring BMP signaling restores wild-type patterning to affected embryos. Our results are consistent with a novel role for Ints6 in restricting the vertebrate organizer to a dorsal domain in embryonic patterning.

Araf kinase antagonizes Nodal-Smad2 activity in mesendoderm development by directly phosphorylating the Smad2 linker region

Smad2/3-mediated transforming growth factor β signalling and the Ras-Raf-Mek-Erk cascade have important roles in stem cell and development and tissue homeostasis. However, it remains unknown whether Raf kinases directly crosstalk with Smad2/3 signalling and how this would regulate embryonic development. Here we show that Araf antagonizes mesendoderm induction and patterning activity of Nodal/Smad2 signals in vertebrate embryos by directly inhibiting Smad2 signalling. Knockdown of araf in zebrafish embryos leads to an increase of activated Smad2 with a decrease in linker phosphorylation; consequently, the embryos have excess mesendoderm precursors and are dorsalized. Mechanistically, Araf physically binds to and phosphorylates Smad2 in the linker region with S253 being indispensable in a Mek/Erk-independent manner, thereby attenuating Smad2 signalling by accelerating degradation of activated Smad2. Our findings open avenues for investigating the potential significance of Raf regulation of transforming growth factor β signalling in versatile biological and pathological processes in the future.

An essential role for maternal control of Nodal signaling

Growth factor signaling is essential for pattern formation, growth, differentiation, and maintenance of stem cell pluripotency. Nodal-related signaling factors are required for axis formation and germ layer specification from sea urchins to mammals. Maternal transcripts of the zebrafish Nodal factor, Squint (Sqt), are localized to future embryonic dorsal. The mechanisms by which maternal sqt/nodal RNA is localized and regulated have been unclear. Here, we show that maternal control of Nodal signaling via the conserved Y box-binding protein 1 (Ybx1) is essential. We identified Ybx1 via a proteomic screen. Ybx1 recognizes the 3’ untranslated region (UTR) of sqt RNA and prevents premature translation and Sqt/Nodal signaling. Maternal-effect mutations in zebrafish ybx1 lead to deregulated Nodal signaling, gastrulation failure, and embryonic lethality. Implanted Nodal-coated beads phenocopy ybx1 mutant defects. Thus, Ybx1 prevents ectopic Nodal activity, revealing a new paradigm in the regulation of Nodal signaling, which is likely to be conserved.

DOI:http://dx.doi.org/10.7554/eLife.00683.001

In many organisms, embryonic development is controlled in part by RNAs that are deposited into the egg as it forms inside the mother. These ‘maternal RNAs’ may localize to particular regions of the egg or embryo, where they are then exclusively translated into protein and carry out their specific function. This helps to establish asymmetry in the developing organism—that is, to produce tissues that will eventually become the top or bottom, front or back, and left or right of the organism.

One such maternal RNA encodes Nodal, a key signaling molecule that is conserved across vertebrate and some invertebrate organisms. In zebrafish, the equivalent RNA is called squint, and plays an important role in embryonic development. The squint RNA deposited by the mother localizes to the dorsal region—the embryo’s back—and signals that region to make dorsal tissues, but how squint is regulated is not well understood. Now, Kumari et al. identify a protein that controls the positioning of squint RNA, and find that it can also prevent this RNA from being translated into protein.

The squint RNA contains a ‘dorsal localization element’ that recruits it to the dorsal cells of the embryo by the 4-cell stage (i.e., within two cell divisions after the egg is fertilized). Kumari et al. identified a protein called Ybx1 that could bind to this element: this protein may help to correctly position RNAs in many other organisms, including fruit flies and mammals. Strikingly, embryos formed abnormally when their maternally derived Ybx1 protein was mutant, and these mutations also prevented the squint RNA from localizing properly. This suggests that maternally derived Ybx1 protein directly regulates the squint RNA.

As well as positioning the squint RNA correctly, the embryo must translate this RNA into protein at the right time. In embryos with mutant maternal Ybx1 protein, the Squint protein could be detected at the 16-cell stage, whereas in wild-type embryos this protein is not translated until the 256-cell stage; this indicates that Ybx1 protein might normally repress the translation of the squint RNA. Indeed, Kumari et al. found that Ybx1 binds to another protein—eIF4E—that recruits mRNAs to the ribosome (the cell’s translational machinery). Ybx1 might therefore prevent eIF4E from associating with other components of the ribosomal complex, and initiating the translation of the squint RNA, until additional signals have been received. It will be interesting to determine how widespread this regulatory mechanism is in other organisms.

DOI:http://dx.doi.org/10.7554/eLife.00683.002

Normal function of Myf5 during gastrulation is required for pharyngeal arch cartilage development in zebrafish embryos

Myf5, a myogenic regulatory factor, plays a key role in regulating muscle differentiation. However, it is not known if Myf5 has a regulatory role during early embryogenesis. Here, we used myf5-morpholino oligonucleotides [MO] to knock down myf5 expression and demonstrated a series of results pointing to the functional roles of Myf5 during early embryogenesis: (1) reduced head size resulting from abnormal morphology in the cranial skeleton; (2) decreased expressions of the cranial neural crest (CNC) markers foxd3, sox9a, dlx2, and col2a1; (3) defect in the chondrogenic neural crest similar to that of fgf3 morphants; (4) reduced fgf3/fgf8 transcripts in the cephalic mesoderm rescued by co-injection of myf5 wobble-mismatched mRNA together with myf5-MO1 during 12 h postfertilization; (5) abnormal patterns of axial and non-axial mesoderm causing expansion of the dorsal organizer, and (6) increased bmp4 gradient, but reduced fgf3/fgf8 marginal gradient, during gastrulation. Interestingly, overexpression of fgf3 could rescue the cranial cartilage defects caused by myf5-MO1, suggesting that Myf5 modulates craniofacial cartilage development through the fgf3 signaling pathway. Together, the loss of Myf5 function results in a cascade effect that begins with abnormal formation of the dorsal organizer during gastrulation, causing, in turn, defects in the CNC and cranial cartilage of myf5-knockdown embryos.

Expression and regulation of miR-17a and miR-430b in zebrafish ovarian follicles

MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate gene expression and control many developmental and physiological processes. Oocyte maturation in fish is mainly regulated by luteinizing hormone (LH) and maturation-inducing hormone (MIH). In addition, growth factors, including members of the transforming growth factor β (TGF-β) superfamily, have also been shown to play important roles in regulating oocyte maturation. In this study, we determined the expression and regulation of two miRNAs, miR-17a and miR-430b, which potentially target signalling molecules in the TGF-β pathway, in zebrafish ovarian follicles. Using real-time PCR, we observed that miR-17a and miR-430b levels in follicular cells were significantly lower in late vitellogenic and full grown follicles than in early vitellogenic follicles. Treatment with a LH analog, human chorionic gonadotropin, significantly down-regulated miR-17a and miR-430b expression in follicular cells but had no effect on their expression in oocytes. Forskolin also inhibited follicular cell miR-430b expression; however, no significant changes in miR-17a levels were observed after Forskolin treatment. Finally, MIH did not affect the expression of these miRNAs either in follicular cells or oocytes at the time points tested. These findings suggest that miR-17a and miR-430b may be involved in the regulation of follicle development and oocyte maturation in zebrafish.

Deep mRNA sequencing analysis to capture the transcriptome landscape of zebrafish embryos and larvae

Transcriptome analysis is a powerful tool to obtain large amount genome-scale gene expression profiles. Despite its extensive usage to diverse biological problems in the last decade, transcriptomic researches approaching the zebrafish embryonic development have been very limited. Several recent studies have made great progress in this direction, yet the large gap still exists, especially regarding to the transcriptome dynamics of embryonic stages from early gastrulation onwards. Here, we present a comprehensive analysis about the transcriptomes of 9 different stages covering 7 major periods (cleavage, blastula, gastrula, segmentation, pharyngula, hatching and early larval stage) in zebrafish development, by recruiting the RNA-sequencing technology. We detected the expression for at least 24,065 genes in at least one of the 9 stages. We identified 16,130 genes that were significantly differentially expressed between stages and were subsequently classified into six clusters. Each revealed gene cluster had distinct expression patterns and characteristic functional pathways, providing a framework for the understanding of the developmental transcriptome dynamics. Over 4000 genes were identified as preferentially expressed in one of the stages, which could be of high relevance to stage-specific developmental and molecular events. Among the 68 transcription factor families active during development, most had enhanced average expression levels and thus might be crucial for embryogenesis, whereas the inactivation of the other families was likely required by the activation of the zygotic genome. We discussed our RNA-seq data together with previous findings about the Wnt signaling pathway and some other genes with known functions, to show how our data could be used to advance our understanding about these developmental functional elements. Our study provides ample information for further study about the molecular and cellular mechanisms underlying vertebrate development.

Lethal giant larvae 2 regulates development of the ciliated organ Kupffer's vesicle

Motile cilia perform crucial functions during embryonic development and throughout adult life. Development of organs containing motile cilia involves regulation of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis) in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis is not yet fully understood, and it remains unclear whether these processes are coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently in ciliated organs. Lgl proteins are involved in establishing cell polarity and have been implicated in vesicle trafficking. Here, we identified a role for Lgl2 in development of ciliated epithelia in Kupffer's vesicle, which directs left-right asymmetry of the embryo; the otic vesicles, which give rise to the inner ear; and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed loss of the adherens junction component E-cadherin at lateral membranes. Genetic interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin and mediate lumen formation that is uncoupled from cilia formation. These results uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis and ciliogenesis and indicate that these processes are genetically separable in zebrafish.

Anteroposterior and dorsoventral patterning are coordinated by an identical patterning clock

Establishment of the body plan in vertebrates depends on the temporally coordinated patterning of tissues along the body axes. We have previously shown that dorsoventral (DV) tissues are temporally patterned progressively from anterior to posterior by a BMP signaling pathway. Here we report that DV patterning along the zebrafish anteroposterior (AP) axis is temporally coordinated with AP patterning by an identical patterning clock. We altered AP patterning by inhibiting or activating FGF, Wnt or retinoic acid signaling combined with inhibition of BMP signaling at a series of developmental time points, which revealed that the temporal progression of DV patterning is directly coordinated with AP patterning. We investigated how these signaling pathways are integrated and suggest a model for how DV and AP patterning are temporally coordinated. It has been shown that in Xenopus dorsal tissues FGF and Wnt signaling quell BMP signaling by degrading phosphorylated (P) Smad1/5, the BMP pathway signal transducer, via phosphorylation of the Smad1/5 linker region. We show that in zebrafish FGF/MAPK, but not Wnt/GSK3, phosphorylation of the Smad1/5 linker region localizes to a ventral vegetal gastrula region that could coordinate DV patterning with AP patterning ventrally without degrading P-Smad1/5. Furthermore, we demonstrate that alteration of the MAPK phosphorylation sites in the Smad5 linker causes precocious patterning of DV tissues along the AP axis during gastrulation. Thus, DV and AP patterning are intimately coordinated to allow cells to acquire both positional and temporal information simultaneously.

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes

A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning) that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST) have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction.

We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT) dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics techniques and will help biologists systematically integrate prior knowledge from diverse systems to direct targeted experiments in their organism of study.

Due to technical and ethical challenges many human diseases or biological processes are studied in model organisms. Discoveries in these organisms are then transferred back to human or other model organisms. Traditional methods for transferring novel gene function annotations have relied on finding genes with high sequence similarity believed to share evolutionary ancestry. However, sequence similarity does not guarantee a shared functional role in molecular pathways. In this study, we show that functional genomics can complement traditional sequence similarity measures to improve the transfer of gene annotations between organisms. We coupled our knowledge transfer method with current state-of-the-art machine learning algorithms and predicted gene function for 11,000 biological processes across six organisms. We experimentally validated our prediction of wnt5b's involvement in the determination of left-right heart asymmetry in zebrafish. Our results show that functional knowledge transfer can improve the coverage and accuracy of machine learning methods used for gene function prediction in a diverse set of organisms. Such an approach can be applied to additional organisms, and will be especially beneficial in organisms that have high-throughput genomic data with sparse annotations.

Paraxial left-sided nodal expression and the start of left-right patterning in the early chick embryo

A common element during early left-right patterning of the vertebrate body is left-sided nodal expression in the early-somite stage lateral plate mesoderm. Leftward cell movements near the node of the gastrulating chick embryo recently offered a plausible mechanism for breaking the presomite-stage molecular symmetry in those vertebrates which lack rotating cilia on the notochord or equivalent tissues. However, the temporal and functional relationships between generation of the known morphological node asymmetry, onset of leftward cell movements and establishment of stable molecular asymmetry in the chick remain unresolved. This study uses high-resolution light microscopy and in situ gene expression analysis to show that intranodal cell rearrangement during the phase of counter-clockwise node torsion at stage 4+ is immediately followed by symmetry loss and rearrangement of shh and fgf8 expression in node epiblast between stages 5- and 5+. Surprisingly, left-sided nodal expression starts at stage 5-, too, but lies in the paraxial mesoderm next to the forming notochordal plate, and can be rendered symmetrical by minimal mechanical disturbance of distant tissue integrity at stage 4. The "premature" paraxial nodal expression together with morphological and molecular asymmetries in, and near, midline compartments occurring at defined substages of early gastrulation help to identify a new narrow time window for early steps in left-right patterning in the chick and support the concept of a causal relationship between a-still enigmatic-chiral (motor) protein, cell movements and incipient left-right asymmetry in the amniote embryo.

Dorsal activity of maternal squint is mediated by a non-coding function of the RNA

Despite extensive study, the earliest steps of vertebrate axis formation are only beginning to be elucidated. We previously showed that asymmetric localization of maternal transcripts of the conserved zebrafish TGFβ factor Squint (Sqt) in 4-cell stage embryos predicts dorsal, preceding nuclear accumulation of β-catenin. Cell ablations and antisense oligonucleotides that deplete Sqt lead to dorsal deficiencies, suggesting that localized maternal sqt functions in dorsal specification. However, based upon analysis of sqt and Nodal signaling mutants, the function and mechanism of maternal sqt was debated. Here, we show that sqt RNA may function independently of Sqt protein in dorsal specification. sqt insertion mutants express localized maternal sqt RNA. Overexpression of mutant/non-coding sqt RNA and, particularly, the sqt 3'UTR, leads to ectopic nuclear β-catenin accumulation and expands dorsal gene expression. Dorsal activity of sqt RNA requires Wnt/β-catenin but not Oep-dependent Nodal signaling. Unexpectedly, sqt ATG morpholinos block both sqt RNA localization and translation and abolish nuclear β-catenin, providing a mechanism for the loss of dorsal identity in sqt morphants and placing maternal sqt RNA upstream of β-catenin. The loss of early dorsal gene expression can be rescued by the sqt 3'UTR. Our findings identify new non-coding functions for the Nodal genes and support a model wherein sqt RNA acts as a scaffold to bind and deliver/sequester maternal factors to future embryonic dorsal.

Molecular and functional characterization of grass carp squint/nodal-related 1: a potential regulator of activin signaling in teleost pituitary cells

Nodal, a member of the transforming growth factor-β superfamily, plays important roles in embryogenesis in vertebrates, including fish. However, the functional characterization of the fish nodal-related gene in nonembryonic cells is still unclear. In teleost, three nodal-related genes, nodal-related (ndr)1/squint, ndr2/cyclops, and ndr3/southpaw have been reported. In this study, a full-length cDNA for grass carp squint (gcSqt) was cloned, and its transcript was detected in the selected organs, including pituitary, brain, heart, head kidney, kidney, spleen, and gonad. To further define its functional role, recombinant grass carp squint (rgcSQT) was produced in Escherichia coli in a homodimer form. Furthermore, we examined the effects of rgcSQT on activin and its receptor gene expression with the use of grass carp pituitary cell as a model. Results showed that rgcSQT stimulated the mRNA expression of activin βA and βB subunit, as well as activin receptor ActRIB and ActRIIB. These findings not only contribute to the understanding of nonembryonic functions of nodal gene in fish, but they also provide new insight into the regulation of activin signaling in vertebrates.

The formation and positioning of cilia in Ciona intestinalis embryos in relation to the generation and evolution of chordate left-right asymmetry

In the early mouse embryo monocilia on the ventral node rotate to generate a leftward flow of fluid. This nodal flow is essential for the left-sided expression of nodal and pitx2, and for subsequent asymmetric organ patterning. Equivalent left fluid flow has been identified in other vertebrates, including Xenopus and zebrafish, indicating it is an ancient vertebrate mechanism. Asymmetric nodal and Pitx expression have also been identified in several invertebrates, including the vertebrates' nearest relatives, the urochordates. However whether cilia regulate this asymmetric gene expression remains unknown, and previous studies in urochordates have not identified any cilia prior to the larval stage, when asymmetry is already long established. Here we use Scanning and Transmission Electron Microscopy and immunofluorescence to investigate cilia in the urochordate Ciona intestinalis. We show that single cilia are transiently present on each ectoderm cell of the late neurula/early tailbud stage embryo, a time point just before onset of asymmetric nodal expression. Mapping the position of each cilium on these cells shows they are posteriorly positioned, something also described for mouse node cilia. The C. intestinalis cilia have a 9+0 ring ultrastructure, however we find no evidence of structures associated with motility such as dynein arms, radial spokes or nexin. Furthermore the 9+0 ring structure becomes disorganised immediately after the cilia have exited the cell, indicative of cilia which are not capable of motility. Our results indicate that although cilia are present prior to molecular asymmetries, they are not motile and hence cannot be operating in the same way as the flow-generating cilia of the vertebrate node. We conclude that the cilia may have a role in the development of C. intestinalis left-right asymmetry but that this would have to be in a sensory capacity, perhaps as mechanosensors as hypothesised in two-cilia physical models of vertebrate cilia-driven asymmetry.

Using zebrafish to learn statistical analysis and Mendelian genetics

This project was developed to promote understanding of how mathematics and statistical analysis are used as tools in genetic research. It gives students the opportunity to carry out hypothesis-driven experiments in the classroom: students generate hypotheses about Mendelian and non-Mendelian inheritance patterns, gather raw data, and test their hypotheses using chi-square statistical analysis. In the first protocol, students are challenged to analyze inheritance patterns using GloFish, brightly colored, commercially available, transgenic zebrafish that express Green, Yellow, or Red Fluorescent Protein throughout their muscles. In the second protocol, students learn about genetic screens, microscopy, and developmental biology by analyzing the inheritance patterns of mutations that cause developmental defects. The difficulty of the experiments can be adapted for middle school to upper level undergraduate students. Since the GloFish experiments use only fish and materials that can be purchased from pet stores, they should be accessible to many schools. For each protocol, we provide detailed instructions, ideas for how the experiments fit into an undergraduate curriculum, raw data, and example analyses. Our plan is to have these protocols form the basis of a growing and adaptable educational tool available on the Zebrafish in the Classroom Web site.

Correct anteroposterior patterning of the zebrafish neurectoderm in the absence of the early dorsal organizer

Background

The embryonic organizer (i.e., Spemann organizer) has a pivotal role in the establishment of the dorsoventral (DV) axis through the coordination of BMP signaling. However, as impaired organizer function also results in anterior and posterior truncations, it is of interest to determine if proper anteroposterior (AP) pattern can be obtained even in the absence of early organizer signaling.

Results

Using the ventralized, maternal effect ichabod (ich) mutant, and by inhibiting BMP signaling in ich embryos, we provide conclusive evidence that AP patterning is independent of the organizer in zebrafish, and is governed by TGFβ, FGF, and Wnt signals emanating from the germ-ring. The expression patterns of neurectodermal markers in embryos with impaired BMP signaling show that the directionality of such signals is oriented along the animal-vegetal axis, which is essentially concordant with the AP axis. In addition, we find that in embryos inhibited in both Wnt and BMP signaling, the AP pattern of such markers is unchanged from that of the normal untreated embryo. These embryos develop radially organized trunk and head tissues, with an outer neurectodermal layer containing diffusely positioned neuronal precursors. Such organization is reflective of the presumed eumetazoan ancestor and might provide clues for the evolution of centralization in the nervous system.

Conclusions

Using a zebrafish mutant deficient in the induction of the embryonic organizer, we demonstrate that the AP patterning of the neuroectoderm during gastrulation is independent of DV patterning. Our results provide further support for Nieuwkoop's "two step model" of embryonic induction. We also show that the zebrafish embryo can form a radial diffuse neural sheath in the absence of both BMP signaling and the early organizer.

The zebrafish maternal-effect gene mission impossible encodes the DEAH-box helicase Dhx16 and is essential for the expression of downstream endodermal genes

Early animal embryonic development requires maternal products that drive developmental processes prior to the activation of the zygotic genome at the mid-blastula transition. During and after this transition, maternal products may continue to act within incipient zygotic developmental programs. Mechanisms that control maternally-inherited products to spatially and temporally restrict developmental responses remain poorly understood, but necessarily depend on posttranscriptional regulation. We report the functional analysis and molecular identification of the zebrafish maternal-effect gene mission impossible (mis). Our studies suggest requirements for maternally-derived mis function in events that occur during gastrulation, including cell movement and the activation of some endodermal target genes. Cell transplantation experiments show that the cell movement defect is cell autonomous. Within the endoderm induction pathway, mis is not required for the activation of early zygotic genes, but is essential to implement nodal activity downstream of casanova/sox 32 but upstream of sox17 expression. Activation of nodal signaling in blastoderm explants shows that the requirement for mis function in endoderm gene induction is independent of the underlying yolk cell. Positional cloning of mis, including genetic rescue and complementation analysis, shows that it encodes the DEAH-box RNA helicase Dhx16, shown in other systems to act in RNA regulatory processes such as splicing and translational control. Analysis of a previously identified insertional dhx16 mutation shows that the zygotic component of this gene is also essential for embryonic viability. Our studies provide a striking example of the interweaving of maternal and zygotic genetic functions during the egg-to-embryo transition. Maternal RNA helicases have long been known to be involved in the development of the animal germ line, but our findings add to growing evidence that these factors may also control specific gene expression programs in somatic tissues.

Embryonic mesoderm and endoderm induction requires the actions of non-embryonic Nodal-related ligands and Mxtx2

Vertebrate mesoderm and endoderm formation requires signaling by Nodal-related ligands from the TGFβ superfamily. The factors that initiate Nodal-related gene transcription are unknown in most species and the relative contributions of Nodal-related ligands from embryonic, extraembryonic and maternal sources remain uncertain. In zebrafish, signals from the yolk syncytial layer (YSL), an extraembryonic domain, are required for mesoderm and endoderm induction, and YSL expression of nodal-related 1 (ndr1) and ndr2 accounts for a portion of this activity. A variable requirement of maternally derived Ndr1 for dorsal and anterior axis formation has also been documented. Here we show that Mxtx2 directly activates expression of ndr2 via binding to its first intron and is required for ndr2 expression in the YSL. Mxtx2 is also required for the Nodal signaling-independent expression component of the no tail a (ntla) gene, which is required for posterior (tail) mesoderm formation. Therefore, Mxtx2 defines a new pathway upstream of Nodal signaling and posterior mesoderm formation. We further show that the co-disruption of extraembryonic Ndr2, extraembryonic Ndr1 and maternal Ndr1 eliminates endoderm and anterior (head and trunk) mesoderm, recapitulating the loss of Nodal signaling phenotype. Therefore, non-embryonic sources of Nodal-related ligands account for the complete spectrum of early Nodal signaling requirements. In summary, the induction of mesoderm and endoderm depends upon the combined actions of Mxtx2 and Nodal-related ligands from non-embryonic sources.

Activin/nodal signaling and pluripotency

Maintenance of a pluripotent cell population during mammalian embryogenesis is crucial for the proper generation of extraembryonic and embryonic tissues to ensure intrauterine survival and fetal development. Pluripotent stem cells derived from early stage mammalian embryos are known as "embryonic stem cells." Such embryo-derived stem cells can proliferate indefinitely in vitro and give rise to derivatives of all three primary germ layers. Their potential for clinical and commercial applications has sparked great excitement within scientific and lay communities. Identification of the signaling pathways controlling stem cell pluripotency and differentiation provides knowledge-based approaches to manipulate stem cells for regenerative medicine. One of the signaling cascades that has been identified in the control of stem cell pluripotency and differentiation is the Activin/Nodal pathway. Here, we describe the differences among pluripotent cell types and discuss the latest findings on the molecular mechanisms involving Activin/Nodal signaling in controlling their pluripotency and differentiation.

Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element

RNA localization is emerging as a general principle of sub-cellular protein localization and cellular organization. However, the sequence and structural requirements in many RNA localization elements remain poorly understood. Whereas transcription factor-binding sites in DNA can be recognized as short degenerate motifs, and consensus binding sites readily inferred, protein-binding sites in RNA often contain structural features, and can be difficult to infer. We previously showed that zebrafish squint/nodal-related 1 (sqt/ndr1) RNA localizes to the future dorsal side of the embryo. Interestingly, mammalian nodal RNA can also localize to dorsal when injected into zebrafish embryos, suggesting that the sequence motif(s) may be conserved, even though the fish and mammal UTRs cannot be aligned. To define potential sequence and structural features, we obtained ndr1 3′-UTR sequences from approximately 50 fishes that are closely, or distantly, related to zebrafish, for high-resolution phylogenetic footprinting. We identify conserved sequence and structural motifs within the zebrafish/carp family and catfish. We find that two novel motifs, a single-stranded AGCAC motif and a small stem-loop, are required for efficient sqt RNA localization. These findings show that comparative sequencing in the zebrafish/carp family is an efficient approach for identifying weak consensus binding sites for RNA regulatory proteins.

Forming and interpreting gradients in the early Xenopus embryo

The amphibian embryo provides a powerful model system to study morphogen gradients because of the ease with which it is possible to manipulate the early embryo. In particular, it is possible to introduce exogenous sources of morphogen, to follow the progression of the signal, to monitor the cellular response to induction, and to up- or down-regulate molecules that are involved in all aspects of long-range signaling. In this article, I discuss the evidence that gradients exist in the early amphibian embryo, the way in which morphogens might traverse a field of cells, and the way in which different concentrations of morphogens might be interpreted to activate the expression of different genes.

Nodal morphogens

Nodal signals belong to the TGF-beta superfamily and are essential for the induction of mesoderm and endoderm and the determination of the left-right axis. Nodal signals can act as morphogens-they have concentration-dependent effects and can act at a distance from their source of production. Nodal and its feedback inhibitor Lefty form an activator/inhibitor pair that behaves similarly to postulated reaction-diffusion models of tissue patterning. Nodal morphogen activity is also regulated by microRNAs, convertases, TGF-beta signals, coreceptors, and trafficking factors. This article describes how Nodal morphogens pattern embryonic fields and discusses how Nodal morphogen signaling is modulated.

Characterization of an lhx1a transgenic reporter in zebrafish

The LIM-domain containing transcription factor, Lhx1, is involved in the regulation of early gastrulation cell movements, kidney organogenesis and other processes in vertebrate model organisms. To follow the expression of this gene in live embryos, we created transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) under the control of lhx1a regulatory regions. Tg(lhx1a:EGFP)(pt303) recapitulates the expression of endogenous lhx1a beginning at early gastrula stages through 72 hours of development with only few exceptions. In addition, over-expression of the Nodal ligand, ndr1, results in the concomitant expansion of the transgene and endogenous lhx1a expression. Treatment of Tg(lhx1a:EGFP)(pt303) embryos with the small molecule SB-431542, an inhibitor of Nodal signaling, results in the loss of both transgene and endogenous lhx1a expression. These experiments suggest that Tg(lhx1a:EGFP)(pt303) is regulated in a manner similar to endogenous lhx1a. Therefore, this reporter can be utilized not only for monitoring lhx1a expression, but also for numerous applications, including chemical genetics screening.

The zebrafish dyrk1b gene is important for endoderm formation

Nodal-signaling is required for specification of mesoderm, endoderm, establishing left-right asymmetry, and craniofacial development. Wdr68 is a WD40-repeat domain-containing protein recently shown to be required for endothelin-1 (edn1) expression and subsequent lower jaw development. Previous reports detected the Wdr68 protein in multiprotein complexes containing mammalian members of the dual-specificity tyrosine-regulated kinase (dyrk) family. Here we describe the characterization of the zebrafish dyrk1b homolog. We report the detection of a physical interaction between Dyrk1b and Wdr68. We also found perturbations of nodal signaling in dyrk1b antisense morpholino knockdown (dyrk1b-MO) animals. Specifically, we found reduced expression of lft1 and lft2 (lft1/2) during gastrulation and a near complete loss of the later asymmetric lft1/2 expression domains. Although wdr68-MO animals did not display lft1/2 expression defects during gastrulation, they displayed a near complete loss of the later asymmetric lft1/2 expression domains. While expression of ndr1 was not substantially effected during gastrulation, ndr2 expression was moderately reduced in dyrk1b-MO animals. Analysis of additional downstream components of the nodal signaling pathway in dyrk1b-MO animals revealed modestly expanded expression of the dorsal axial mesoderm marker gsc while the pan-mesodermal marker bik was largely unaffected. The endodermal markers cas and sox17 were also moderately reduced in dyrk1b-MO animals. Notably, and similar to defects previously reported for wdr68 mutant animals, we also found reduced expression of the pharyngeal pouch marker edn1 in dyrk1b-MO animals. Taken together, these data reveal a role for dyrk1b in endoderm formation and craniofacial patterning in the zebrafish.

hnRNP I is required to generate the Ca2+ signal that causes egg activation in zebrafish

Egg activation is an important cellular event required to prevent polyspermy and initiate development of the zygote. Egg activation in all animals examined is elicited by a rise in free Ca(2+) in the egg cytosol at fertilization. This Ca(2+) rise is crucial for all subsequent egg activation steps, such as cortical granule exocytosis, which modifies the vitelline membrane to prevent polyspermy. The cytosolic Ca(2+) rise is primarily initiated by inositol 1,4,5-trisphosphate (IP(3))-mediated Ca(2+) release from the endoplasmic reticulum. The genes involved in regulating the IP(3)-mediated Ca(2+) release during egg activation remain largely unknown. Here we report on a zebrafish maternal-effect mutant, brom bones, which is defective in the cytosolic Ca(2+) rise and subsequent egg activation events, including cortical granule exocytosis and cytoplasmic segregation. We show that the egg activation defects in brom bones can be rescued by providing Ca(2+) or the Ca(2+)-release messenger IP(3), suggesting that brom bones is a regulator of IP(3)-mediated Ca(2+) release at fertilization. Interestingly, brom bones mutant embryos also display defects in dorsoventral axis formation accompanied by a disorganized cortical microtubule network, which is known to be crucial for dorsal axis formation. We provide evidence that the impaired microtubule organization is associated with non-exocytosed cortical granules from the earlier egg activation defect. Positional cloning of the brom bones gene reveals that a premature stop codon in the gene encoding hnRNP I (referred to here as hnrnp I) underlies the abnormalities. Our studies therefore reveal an important new role of hnrnp I in regulating the fundamental process of IP(3)-mediated Ca(2+) release at egg activation.

Deciphering the role of Shh signaling in axial defects produced by ethanol exposure

BACKGROUND

The phenotype of embryos exposed to ethanol is complex and likely due to multiple alterations in developmental pathways. We have previously demonstrated that Sonic hedgehog signaling (Shh-s) was reduced in both chicken and zebrafish embryos when exposed to ethanol.

METHODS

There are many tissues affected by embryonic ethanol exposure, and in this article we explore the development of axial tissues, using zebrafish embryos. We then compare these effects to the phenotypes produced by exposure to two drugs that also inhibit Shh-s: cyclopamine and forskolin.

RESULTS

We found alterations in the development of the notochord and somites produced by all three compounds, although only ethanol produced developmental delay of epiboly. Upon observation of early developing embryos, muscle pioneer cells were completely lost in cyclopamine-treated embryos, and reduced, but less so, in embryos treated with forskolin and ethanol. Ethanol treatment produced a dose-dependent reduction in total body length that may be linked to epiboly delay seen earlier during development. Despite the differences between cyclopamine and forskolin, we found that shh mRNA injection rescued the short body length, the alteration in somite shape, and the cyclopia produced by ethanol exposure.

CONCLUSIONS

Taken together, each teratogen produced a unique set of phenotypic changes in the body axis, suggesting that each compound affects Shh-s and also produces a distinctive set of molecular alterations. However, addition of exogenous Shh to ethanol treated zebrafish prevented many of the gross physical phenotypes, suggesting that the suppression of Shh-s is one of the major effects of ethanol exposure.

Zic-associated holoprosencephaly: zebrafish Zic1 controls midline formation and forebrain patterning by regulating Nodal, Hedgehog, and retinoic acid signaling

Holoprosencephaly (HPE) is the most frequently observed human embryonic forebrain defect. Recent evidence indicates that the two major forms of HPE, classic HPE and midline interhemispheric (MIH) HPE, are elicited by two different mechanisms. The only gene known to be associated with both forms of HPE is Zic2. We used the zebrafish Danio rerio as a model system to study Zic knockdown during midline formation by looking at the close homolog Zic1, which is expressed in an overlapping fashion with Zic2. Zic1 knockdown in zebrafish leads to a strong midline defect including partial cyclopia due to attenuated Nodal and Hedgehog signaling in the anterior ventral diencephalon. Strikingly, we were able to show that Zic1 is also required for maintaining early forebrain expression of the retinoic acid (RA)-degrading enzyme cyp26a1. Zic1 LOF leads to increased RA levels in the forebrain, subsequent ventralization of the optic vesicle and down-regulation of genes involved in dorsal BMP signaling. Repression of BMP signaling in dorsal forebrain has been implicated in causing MIH HPE. This work provides a mechanistical explanation at the molecular level of why Zic factors are associated with both major forms of HPE.

Rock2 controls TGFbeta signaling and inhibits mesoderm induction in zebrafish embryos

The Rho-associated serine/threonine kinases Rock1 and Rock2 play important roles in cell contraction, adhesion, migration, proliferation and apoptosis. Here we report that Rock2 acts as a negative regulator of the TGFbeta signaling pathway. Mechanistically, Rock2 binds to and accelerates the lysosomal degradation of TGFbeta type I receptors internalized from the cell surface in mammalian cells. The inhibitory effect of Rock2 on TGFbeta signaling requires its kinase activity. In zebrafish embryos, injection of rock2a mRNA attenuates the expression of mesodermal markers during late blastulation and blocks the induction of mesoderm by ectopic Nodal signals. By contrast, overexpression of a dominant negative form of zebrafish rock2a, dnrock2a, has an opposite effect on mesoderm induction, suggesting that Rock2 proteins are endogenous inhibitors for mesoderm induction. Thus, our data have unraveled previously unidentified functions of Rock2, in controlling TGFbeta signaling as well as in regulating embryonic patterning.

Is left-right asymmetry a form of planar cell polarity?

Consistent left-right (LR) patterning is a clinically important embryonic process. However, key questions remain about the origin of asymmetry and its amplification across cell fields. Planar cell polarity (PCP) solves a similar morphogenetic problem, and although core PCP proteins have yet to be implicated in embryonic LR asymmetry, studies of mutations affecting planar polarity, together with exciting new data in cell and developmental biology, provide a new perspective on LR patterning. Here we propose testable models for the hypothesis that LR asymmetry propagates as a type of PCP that imposes coherent orientation onto cell fields, and that the cue that orients this polarization is a chiral intracellular structure.

Identification of common and unique modifiers of zebrafish midline bifurcation and cyclopia

Loss of the zebrafish Nodal-related protein Squint causes a spectrum of phenotypes including cyclopia and midline bifurcations (MB). Here we examine MBs and their relation to cyclopia in maternal-zygotic squint (MZsqt) mutants. There is a concordance of MB with cyclopia in MZsqt embryos. Heat treatment and depletion of Hsp90a are "common" risk factors, each of which increases the incidence of both phenotypes. Midline identity is specified on both sides of MBs, and deep-layer cells are initially lacking within bifurcations, whereas enveloping layer cells are intact. Bifurcations do not appear until the completion of gastrulation and are preceded by gaps in the expression of wnt5b, an essential regulator of dorsal convergence. The incidence of early MBs and wnt5b expression defects in heated MZsqt embryos is high, but there is also substantial recovery. Wnt5b depletion increases the incidence of MB, but not cyclopia, and as such Wnt5b is a "unique" risk factor for MB. Reciprocally, depletion of Wnt11 or Hsp90b increases cyclopia only. In summary, we find that MB arises after gastrulation in regions that fail to express wnt5b, and we show that two complex dysmorphologies - MB and cyclopia - can be promoted by either common or unique risk factors.

The pro-domain of the zebrafish Nodal-related protein Cyclops regulates its signaling activities

Nodal proteins are secreted signaling factors of the transforming growth factor β (TGFβ) family with essential roles in embryonic development in vertebrates. Mutations affecting the Nodal factors have severe consequences in mammals and fish. Furthermore, increased Nodal levels have been associated with melanoma tumor progression. Like other TGFβ-related proteins, Nodal factors consist of a pro-domain and a mature domain. The pro-domain of mouse Nodal protein stabilizes its precursor. However, the mechanisms by which the pro-domains exert their activities are unknown. Here, we characterize the zebrafish Nodal-related factor Cyclops (Cyc) and find unexpected functions for the pro-domain in regulating Cyc activity. We identified a lysosome-targeting region in the Cyc pro-domain that destabilizes the precursor and restricts Cyc activity, revealing the molecular basis for the short-range signaling activities of Cyc. We show that both the pro- and mature-domains of Cyc regulate its stability. We also characterize a mutation in the pro-domain of human NODAL (hNODAL) that underlies congenital heterotaxia. Heterologous expression of mutant hNODAL increases expression of Nodal-response genes. Our studies reveal unexpected roles for the pro-domain of the Nodal factors and provide a possible mechanism for familial heterotaxia.

Tbx2b is required for the development of the parapineal organ

Structural differences between the left and right sides of the brain exist throughout the vertebrate lineage. By studying the zebrafish pineal complex, which exhibits notable asymmetries, both the genes and the cell movements that result in left-right differences can be characterized. The pineal complex consists of the midline pineal organ and the left-sided parapineal organ. The parapineal is responsible for instructing the asymmetric architecture of the bilateral habenulae, the brain nuclei that flank the pineal complex. Using in vivo time-lapse confocal microscopy, we find that the cells that form the parapineal organ migrate as a cluster of cells from the pineal complex anlage to the left side of the brain. In a screen for mutations that disrupted brain laterality, we identified a nonsense mutation in the T-box2b (tbx2b) gene, which encodes a transcription factor expressed in the pineal complex anlage. The tbx2b mutant makes fewer parapineal cells, and they remain as individuals near the midline rather than migrating leftward as a group. The reduced number and incorrect placement of parapineal cells result in symmetric development of the adjacent habenular nuclei. We conclude that tbx2b functions to specify the correct number of parapineal cells and to regulate their asymmetric migration.

Ttrap is an essential modulator of Smad3-dependent Nodal signaling during zebrafish gastrulation and left-right axis determination

During vertebrate development, signaling by the TGFbeta ligand Nodal is critical for mesoderm formation, correct positioning of the anterior-posterior axis, normal anterior and midline patterning, and left-right asymmetric development of the heart and viscera. Stimulation of Alk4/EGF-CFC receptor complexes by Nodal activates Smad2/3, leading to left-sided expression of target genes that promote asymmetric placement of certain internal organs. We identified Ttrap as a novel Alk4- and Smad3-interacting protein that controls gastrulation movements and left-right axis determination in zebrafish. Morpholino-mediated Ttrap knockdown increases Smad3 activity, leading to ectopic expression of snail1a and apparent repression of e-cadherin, thereby perturbing cell movements during convergent extension, epiboly and node formation. Thus, although the role of Smad proteins in mediating Nodal signaling is well-documented, the functional characterization of Ttrap provides insight into a novel Smad partner that plays an essential role in the fine-tuning of this signal transduction cascade.

Rasl11b knock down in zebrafish suppresses one-eyed-pinhead mutant phenotype

The EGF-CFC factor Oep/Cripto1/Frl1 has been implicated in embryogenesis and several human cancers. During vertebrate development, Oep/Cripto1/Frl1 has been shown to act as an essential coreceptor in the TGFβ/Nodal pathway, which is crucial for germ layer formation. Although studies in cell cultures suggest that Oep/Cripto1/Frl1 is also implicated in other pathways, in vivo it is solely regarded as a Nodal coreceptor. We have found that Rasl11b, a small GTPase belonging to a Ras subfamily of putative tumor suppressor genes, modulates Oep function in zebrafish independently of the Nodal pathway. rasl11b down regulation partially rescues endodermal and prechordal plate defects of zygotic oep^−/− mutants (Zoep). Rasl11b inhibitory action was only observed in oep-deficient backgrounds, suggesting that normal oep expression prevents Rasl11b function. Surprisingly, rasl11b down regulation does not rescue mesendodermal defects in other Nodal pathway mutants, nor does it influence the phosphorylation state of the downstream effector Smad2. Thus, Rasl11b modifies the effect of Oep on mesendoderm development independently of the main known Oep output: the Nodal signaling pathway. This data suggests a new branch of Oep signaling that has implications for germ layer development, as well as for studies of Oep/Frl1/Cripto1 dysfunction, such as that found in tumors.

Nodal signals mediate interactions between the extra-embryonic and embryonic tissues in zebrafish

In many vertebrates, extra-embryonic tissues are important signaling centers that induce and pattern the germ layers. In teleosts, the mechanism by which the extra-embryonic yolk syncytial layer (YSL) patterns the embryo is not understood. Although the Nodal-related protein Squint is expressed in the YSL, its role in this tissue is not known. We generated a series of stable transgenic lines with GFP under the control of squint genomic sequences. In all species, nodal-related genes induce their own expression through a positive feedback loop. We show that two tissue specific enhancers in the zebrafish squint gene mediate the response to Nodal signals. Expression in the blastomeres depends upon a conserved Nodal response element (NRE) in the squint first intron, while expression in the extra-embryonic enveloping layer (EVL) is mediated by an element upstream of the transcription start site. Targeted depletion experiments demonstrate that the zebrafish Nodal-related proteins Squint and Cyclops are required in the YSL for endoderm and head mesoderm formation. Thus, Nodal signals mediate interactions between embryonic and extra-embryonic tissues in zebrafish that maintain nodal-related gene expression in the margin. Our results demonstrate a high degree of functional conservation between the extra-embryonic tissues of mouse and zebrafish.

Six3 represses nodal activity to establish early brain asymmetry in zebrafish

The vertebrate brain is anatomically and functionally asymmetric; however, the molecular mechanisms that establish left-right brain patterning are largely unknown. In zebrafish, asymmetric left-sided Nodal signaling within the developing dorsal diencephalon is required for determining the direction of epithalamic asymmetries. Here, we show that Six3, a transcription factor essential for forebrain formation and associated with holoprosencephaly in humans, regulates diencephalic Nodal activity during initial establishment of brain asymmetry. Reduction of Six3 function causes brain-specific deregulation of Nodal pathway activity, resulting in epithalamic laterality defects. Based on misexpression and genetic epistasis experiments, we propose that Six3 acts in the neuroectoderm to establish a prepattern of bilateral repression of Nodal activity. Subsequently, Nodal signaling from the left lateral plate mesoderm alleviates this repression ipsilaterally. Our data reveal a Six3-dependent mechanism for establishment of correct brain laterality and provide an entry point to understanding the genetic regulation of Nodal signaling in the brain.