Transcriptional regulation using the Q system in transgenic zebrafish.

Methods to label cell populations selectively or to modify their gene expression are critical tools in the study of developmental or physiological processes in vivo. A variety of approaches have been applied to the zebrafish model, capitalizing on Tol2 transposition to generate transgenic lines with high efficiency. Here we describe the adoption of the Q system of Neurospora crassa, which includes the QF transcription factor and the upstream activating sequence (QUAS) to which it binds. These components function as a bipartite regulatory system similar to that of yeast Gal4/UAS, producing robust expression in transient assays of zebrafish embryos injected with plasmids and in stable transgenic lines. An important advantage, however, is that QUAS-regulated transgenes appear far less susceptible to transcriptional silencing even after seven generations. This chapter describes some of the Q system reagents that have been developed for zebrafish, as well as the use of the QF transcription factor for isolation of tissue-specific driver lines from gene/enhancer trap screens. Additional strategies successfully implemented in invertebrate models, such as a truncated QF transcription factor (QF2) or the reassembly of a split QF, are also discussed. The provided information, and available Gateway-based vectors, should enable those working with the zebrafish model to implement the Q system with minimal effort or to use it in combination with Gal4, Cre, or other regulatory systems for further refinement of transcriptional control.

Genetic analysis of digestive physiology using fluorescent phospholipid reporters.

Zebrafish are a valuable model for mammalian lipid metabolism; larvae process lipids similarly through the intestine and hepatobiliary system and respond to drugs that block cholesterol synthesis in humans. After ingestion of fluorescently quenched phospholipids, endogenous lipase activity and rapid transport of cleavage products results in intense gall bladder fluorescence. Genetic screening identifies zebrafish mutants, such as fat free, that show normal digestive organ morphology but severely reduced phospholipid and cholesterol processing. Thus, fluorescent lipids provide a sensitive readout of lipid metabolism and are a powerful tool for identifying genes that mediate vertebrate digestive physiology.

Asymmetric nodal signaling in the zebrafish diencephalon positions the pineal organ.

The vertebrate brain develops from a bilaterally symmetric neural tube but later displays profound anatomical and functional asymmetries. Despite considerable progress in deciphering mechanisms of visceral organ laterality, the genetic pathways regulating brain asymmetries are unknown. In zebrafish, genes implicated in laterality of the viscera (cyclops/nodal, antivin/lefty and pitx2) are coexpressed on the left side of the embryonic dorsal diencephalon, within a region corresponding to the presumptive epiphysis or pineal organ. Asymmetric gene expression in the brain requires an intact midline and Nodal-related factors. RNA-mediated rescue of mutants defective in Nodal signaling corrects tissue patterning at gastrulation, but fails to restore left-sided gene expression in the diencephalon. Such embryos develop into viable adults with seemingly normal brain morphology. However, the pineal organ, which typically emanates at a left-to-medial site from the dorsal diencephalic roof, becomes displaced in position. Thus, a conserved signaling pathway regulating visceral laterality also underlies an anatomical asymmetry of the zebrafish forebrain.

The bHLH transcription factor hand2 plays parallel roles in zebrafish heart and pectoral fin development.

The precursors of several organs reside within the lateral plate mesoderm of vertebrate embryos. Here, we demonstrate that the zebrafish hands off locus is essential for the development of two structures derived from the lateral plate mesoderm - the heart and the pectoral fin. hands off mutant embryos have defects in myocardial development from an early stage: they produce a reduced number of myocardial precursors, and the myocardial tissue that does form is improperly patterned and fails to maintain tbx5 expression. A similar array of defects is observed in the differentiation of the pectoral fin mesenchyme: small fin buds form in a delayed fashion, anteroposterior patterning of the fin mesenchyme is absent and tbx5 expression is poorly maintained. Defects in these mesodermal structures are preceded by the aberrant morphogenesis of both the cardiogenic and forelimb-forming regions of the lateral plate mesoderm. Molecular analysis of two hands off alleles indicates that the hands off locus encodes the bHLH transcription factor Hand2, which is expressed in the lateral plate mesoderm starting at the completion of gastrulation. Thus, these studies reveal early functions for Hand2 in several cellular processes and highlight a genetic parallel between heart and forelimb development.

Genes dependent on zebrafish cyclops function identified by AFLP differential gene expression screen.

Zebrafish cyclops (cyc) encodes a Transforming Growth Factor beta (TGFbeta) signaling factor closely related to mouse Nodal. By comparing amplified fragment length polymorphisms (AFLP) from cyc mutant and wild-type cDNA pools, we devised a differential gene expression screen to isolate genes whose expression is dependent on Cyc signaling. We report two genes not previously described in the zebrafish that were identified using this approach. The first gene, crestin, is expressed predominantly in premigratory and migrating neural crest cells during somitogenesis stages. crestin expression is reduced in cyc mutants initially but recovers by late somitogenesis. The second gene encodes the zebrafish homologue of the calcium-binding protein, calreticulin. Zebrafish calreticulin is highly expressed in the hatching gland and in the floor plate, tissues that are affected in cyc mutants. During gastrulation, calreticulin transcripts are found in the dorsal mesendoderm, in the same cells that express the cyc gene. Expression is reduced in cyc mutants and is abolished by the one-eyed pinhead (oep) mutation that is presumed to prevent Nodal signaling. The identification of calreticulin suggests that a differential screen between wild-type and mutant cDNA is a useful approach to reveal regulation of unexpected gene expression in response to cellular signals. genesis 26:86-97, 2000.

Patterning the zebrafish axial skeleton requires early chordin function.

Members of the bone morphogenetic protein (BMP) family actively promote ventral cell fates, such as epidermis and blood, in the vertebrate gastrula. More dorsally, the organizer region counteracts BMP signalling through secretion of BMP-binding antagonists chordin and noggin, allowing dorsally derived tissues such as neurectoderm and somitic muscle to develop. BMPs also function in skeletal development and regeneration of bone following injury. Noggin antagonism is thought to prevent osteogenesis at sites of joint formation, whereas chordin has not yet been implicated in skeletogenesis. Analyses of zebrafish mutants have confirmed the action of chordin (chd) in opposing ventralizing signals at gastrulation. Some ventralized mutants recover and develop into fertile adults, thereby revealing a requirement for chd function for the later processes of fin and caudal skeletal patterning. We observe in mutants the misexpression of genes encoding BMPs and putative downstream genes, and ectopic sclerotomal cells. Through injections of chd mRNA into the early embryo, we restored wild-type gene expression patterns, and the resultant fish, although genotypically mutant, developed normal axial skeletons and fins. Our results demonstrate that chordin function during gastrulation is important for the correct morphogenesis of the adult zebrafish skeleton.

Maternal and zygotic activity of the zebrafish ogon locus antagonizes BMP signaling.

The dorsal-ventral axis of vertebrate embryos is thought to be specified by a gradient of bone morphogenetic protein (BMP) activity, which, in part, arises through the interaction of dorsally expressed antagonists Chordin and Noggin with the ventralizing BMPs. The zebrafish mercedes(tm305), ogon(m60), and short tail(b180) mutations produce ventralized phenotypes, including expanded bmp2b/4 expression domains. We find that the three mutations are allelic and that the locus they define, renamed ogon (ogo), maps to linkage group 25. The ogo(m60) and ogo(b180) mutations are deficiencies and thus represent null alleles, whereas the ENU-induced allele ogo(tm305) retains partial function. Aspects of the ogo(m60) and ogo(tm305) mutant phenotypes are fully suppressed by overexpression of BMP antagonists. Moreover, swirl(tc300), a null mutation in bmp2b, is epistatic to ogo(m60) mutation, providing further evidence that ogo normally functions in a BMP-dependent manner. Embryonic patterning is highly sensitive to maternal and zygotic ogo gene dosage, especially when the level of zygotic chordin activity is also reduced. However, elimination of the zygotic activity of both genes does not result in a completely ventralized embryo. Thus, while ogo and chordin are required to limit activity of BMPs, additional mechanisms must exist to block these ventralizing signals. We have ruled out zebrafish noggin homologues as candidates for the ogo gene, including a newly identified gene, nog1, which is specifically expressed in the gastrula organizer. The results suggest that ogo encodes an as yet unidentified dorsalizing factor that mediates dorsoventral patterning by directly or indirectly antagonizing BMP activity.

Characterization of Ca2+-dependent phospholipase A2 activity during zebrafish embryogenesis.

We have developed a simple fluorescent assay for detection of phospholipase A2 (PLA2) activity in zebrafish embryos that utilizes a fluorescent phosphatidylcholine substrate. By using this assay in conjunction with selective PLA2 inhibitors and Western blot analysis, we identified the principal activity in zebrafish embryogenesis as characteristic of the Ca2+-dependent cytosolic PLA2 (cPLA2) subtype. Embryonic cPLA2 activity remained constant from the 1-cell stage until the onset of somitogenesis, at which time it increased sharply. This increase was preceded by the expression of a previously identified zebrafish cPLA2 homologue (Nalefski, E., Sultzman, L., Martin, D., Kriz, R., Towler, P., Knopf, J., and Clark, J. (1994) J. Biol. Chem. 269, 18239-18249). By using a quenched BODIPY-labeled phosphatidylcholine that fluoresces only upon cleavage by PLA2, lipase activity was visualized in the cells of living embryos where it localized to perinuclear membranes.

Induction of the zebrafish ventral brain and floorplate requires cyclops/nodal signalling.

Zebrafish cyclops (cyc) mutations cause deficiencies in the dorsal mesendoderm and ventral neural tube, leading to neural defects and cyclopia. Here we report that cyc encodes a transforming growth factor-beta (TGF-beta)-related intercellular signalling molecule that is similar to mouse nodal. cyc is expressed in dorsal mesendoderm at gastrulation and in the prechordal plate until early somitogenesis. Expression reappears transiently in the left lateral-plate mesoderm, and in an unprecedented asymmetric pattern in the left forebrain. Injection of cyc RNA non-autonomously restores sonic hedgehog-expressing cells of the ventral brain and floorplate that are absent in cyc mutants, whereas inducing activities are abolished by cyc, a mutation of a conserved cysteine in the mature ligand. Our results indicate that cyc provides an essential non-cell-autonomous signal at gastrulation, leading to induction of the floorplate and ventral brain.

Genetic interactions in zebrafish midline development.

Mutational analyses have shown that the genes no tail (ntl, Brachyury homolog), floating head (flh, a Not homeobox gene), and cyclops (cyc) play direct and essential roles in the development of midline structures in the zebrafish. In both ntl and flh mutants a notochord does not develop, and in cyc mutants the floor plate is nearly entirely missing. We made double mutants to learn how these genes might interact. Midline development is disrupted to a greater extent in cyc;flh double mutants than in either cyc or flh single mutants; their effects appear additive. Both the notochord and floor plate are completely lacking, and other phenotypic disturbances suggest that midline signaling functions are severely reduced. On the other hand, trunk midline defects in flh;ntl double mutants are not additive, but are most often similar to those in ntl single mutants. This finding reveals that loss of ntl function can suppress phenotypic defects due to mutation at flh, and we interpret it to mean that the wild-type allele of ntl (ntl+) functions upstream to flh in a regulatory hierarchy. Loss of function of ntl also strongly suppresses the floor plate deficiency in cyc mutants, for we found trunk floor plate to be present in cyc;ntl double mutants. From these findings we propose that ntl+ plays an early role in cell fate choice at the dorsal midline, mediated by the Ntl protein acting to antagonize floor plate development as well as to promote notochord development.

Temporal separation in the specification of primary and secondary motoneurons in zebrafish.

In zebrafish there are two populations of motoneurons, primary and secondary, that are temporally separate in their development. To determine if midline cells play a role in the specification of these neurons, we analyzed both secondary and primary motoneurons in mutants lacking floor plate, notochord, or both floor plate and notochord. Our data show that the specification of secondary motoneurons, those most similar to motoneurons in birds and mammals, depends on the presence of either a differentiated floor plate or notochord. In the absence of both of these structures, secondary motoneurons fail to form. In contrast, primary motoneurons, early developing motoneurons found in fish and amphibians, can develop in the absence of both floor plate and notochord. A spatial correspondence is found between secondary motoneurons and sonic hedgehog-expressing floor plate and notochord. In contrast, primary motoneuronal specification depends on the presence of sonic hedgehog in gastrula axial mesoderm, the tissue that will give rise to the notochord. These results suggest that both primary and secondary motoneurons are specified by signals from midline tissues, but at very different stages of embryonic development.

Loss of cerebum function ventralizes the zebrafish embryo.

Recent studies implicate ventrally derived signals, in addition to dorsal ones emanating from the organizer, in patterning the vertebrate gastrula. We have identified five overlapping deficiencies that uncover the zebrafish cerebum locus and dramatically alter dorsal-ventral polarity at gastrulation. Consistent with the properties of experimentally ventralized amphibian embryos, cerebum mutants exhibit reduced neurectodermal gene expression domains and an increase in derivatives of ventral mesoderm. Structures derived from paraxial and lateral mesoderm also are reduced; however, dorsal axial mesodermal derivatives, such as the hatching gland and notochord, are largely spared. The pleiotropic action of cerebum deficiencies, and the differential response of affected tissues, suggest that the cerebum gene may normally function as an inhibitor of ventralizing signals, a function previously ascribed to Noggin and Chordin in Xenopus. Analysis of the cerebum phenotype provides genetic evidence for the existence of ventralizing signals in the zebrafish gastrula and for antagonists of those signals.

Differential regulation of chordin expression domains in mutant zebrafish.

Patterning along the dorsal-ventral (D-V) axis of Xenopus and Drosophila embryos is believed to occur through a conserved molecular mechanism, with homologous proteins Chordin and Short gastrulation (Sog) antagonizing signaling by bone morphogenetic protein 4 (BMP-4) and Decapentaplegic (Dpp), respectively. We have isolated a zebrafish gene that is highly homologous to chordin and sog within cysteine-rich domains and exhibits conserved aspects of expression and function. As in Xenopus embryos, zebrafish chordin is expressed in the organizer region and transiently in axial mesoderm. Injection of zebrafish chordin mRNA to the ventral side of Xenopus embryos induced secondary axes. Ectopic overexpression in zebrafish resulted in an expansion of paraxial mesoderm and neurectoderm at the expense of more lateral and ventral derivatives, producing a range of defects similar to those of dorsalized zebrafish mutants (Mullins et al., 1996). In accordance with the proposed function of chordin in D-V patterning, dorsalized zebrafish mutants showed expanded domains of chordin expression by midgastrulation, while some ventralized mutants had reduced expression; however, in all mutants examined, early organizer expression was unaltered. In contrast to Xenopus, zebrafish chordin is also expressed in paraxial mesoderm and ectoderm and in localized regions of the developing brain, suggesting that there are additional roles for chordin in zebrafish embryonic development. Surprisingly, paraxial mesodermal expression of chordin appeared unaltered in spadetail mutants that later lack trunk muscle (Kimmel et al., 1989), while axial mesodermal expression was affected. This finding reveals an unexpected function for spadetail in midline mesoderm and in differential regulation of chordin expression during gastrulation.

Cell-autonomous shift from axial to paraxial mesodermal development in zebrafish floating head mutants.

Zebrafish floating head mutant embryos lack notochord and develop somitic muscle in its place. This may result from incorrect specification of the notochord domain at gastrulation, or from respecification of notochord progenitors to form muscle. In genetic mosaics, floating head acts cell autonomously. Transplanted wild-type cells differentiate into notochord in mutant hosts; however, cells from floating head mutant donors produce muscle rather than notochord in wild-type hosts. Consistent with respecification, markers of axial mesoderm are initially expressed in floating head mutant gastrulas, but expression does not persist. Axial cells also inappropriately express markers of paraxial mesoderm. Thus, single cells in the mutant midline transiently co-express genes that are normally specific to either axial or paraxial mesoderm. Since floating head mutants produce some floor plate in the ventral neural tube, midline mesoderm may also retain early signaling capabilities. Our results suggest that wild-type floating head provides an essential step in maintaining, rather than initiating, development of notochord-forming axial mesoderm.

A homeobox gene essential for zebrafish notochord development.

The notochord is a midline mesodermal structure with an essential patterning function in all vertebrate embryos. Zebrafish floating head (flh) mutants lack a notochord, but develop with prechordal plate and other mesodermal derivatives, indicating that flh functions specifically in notochord development. We show that floating head is the zebrafish homologue of Xnot, a homeobox gene expressed in the amphibian organizer and notochord. We propose that flh regulates notochord precursor cell fate.

Goosecoid expression in neurectoderm and mesendoderm is disrupted in zebrafish cyclops gastrulas.

RNA from goosecoid, a homeobox-containing gene expressed during gastrulation in the anterior mesoderm of vertebrate embryos, can generate organizer activity when injected into ventral mesoderm, resulting in a secondary body axis; it is not yet understood, however, how goosecoid performs its organizer function. We report here that in the zebrafish gastrula, a domain of goosecoid expression arises in presumptive anterior neurectoderm which lies directly above goosecoid-expressing mesendodermal cells. From this position, goosecoid expression then spreads gradually across the ectodermal layer. In cyclops mutant embryos, which lack a ventral anterior brain, expression of goosecoid is abnormal in the mesendoderm and completely absent in the overlying neurectoderm. These results indicate that cyclops is required for correct specification of the mesendoderm and suggest that goosecoid expression in the ectoderm may result from vertical induction from the mesoderm. We propose that in the gastrula head, goosecoid may be important in organizing the ventral neurectoderm.

no tail (ntl) is the zebrafish homologue of the mouse T (Brachyury) gene.

The mouse T (Brachyury) gene is required for normal mesoderm development and the extension of the body axis. Recently, two mutant alleles of a zebrafish gene, no tail (ntl), have been isolated (Halpern, M. E., Ho., R. K., Walker, C. and Kimmel, C. B. (1993) Cell 75, 99-111). ntl mutant embryos resemble mouse T/T mutant embryos in that they lack a differentiated notochord and the caudal region of their bodies. We report here that this phenotype is caused by mutation of the zebrafish homologue of the T gene. While ntl embryos express mutant mRNA, they show no nuclear protein product. Later, expression of mRNA in mutants, but not in wild types, is greatly reduced along the dorsal midline where the notochord normally forms. This suggests that the protein is required for maintaining transcription of its own gene.

Induction of muscle pioneers and floor plate is distinguished by the zebrafish no tail mutation.

Dorsal mesoderm is thought to provide important signals for axis formation and neural differentiation in vertebrate embryos. We have examined induction and patterning in a zebrafish mutant, no tail, that lacks a derivative of dorsal mesoderm, the notochord. Despite the absence of a differentiated notochord, development of the central nervous system including floor plate appears normal, likely owing to the presence of notochord precursor cells. In contrast, somites are misshapen, and muscle pioneer cells are absent. Wild-type cells transplanted into mutant hosts can autonomously differentiate into notochord and thereby rescue somitic defects, suggesting that interactions between notochord and paraxial mesoderm are necessary for proper somite patterning. Thus, cells derived from dorsal mesoderm may have multiple signaling functions during zebrafish embryogenesis.