Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments.

In this paper we focus on the detection of differentially expressed genes according to changes in hybridization signals using statistical tests. These tests were applied to 14 208 zebrafish cDNA clones that were immobilized on a nylon support and hybridized with radioactively labeled target mRNA from wild-type and lithium-treated zebrafish embryos. The methods were evaluated with respect to 16 control clones that correspond to eight different genes which are known to be involved in dorso-ventral axis specification. Moreover, 4608 Arabidopsis thaliana clones on the same array were used to judge statistical significance of expression changes and to control the false positive rates of the test decisions. Utilizing this special array design we show that differential expression of a high proportion of cDNA clones (15/16) and the respective genes (7/8) were identified, with a false positive error of <5% using the constant control data. Furthermore, we investigated the influence of the number of repetitions of experiments on the accuracy of the procedures with experimental and simulated data. Our results suggest that the detection of differential expression with repeated hybridization experiments is an accurate and sensitive way of identifying even small expression changes (1:1.5) of a large number of genes in parallel.

Expression of brain subtype creatine kinase in the zebrafish embryo.

Creatine kinases (CK) play crucial roles in intracellular energy transfer. We have isolated a cDNA from zebrafish embryos, which encodes a CK highly related to the mammalian brain subtype creatine kinase (BCK). The bck mRNA is expressed maternally in the zebrafish embryo and transcripts are distributed uniformly in blastula and gastrula stages. Expression becomes restricted to the prechordal plate and the nervous system during subsequent somitogenesis stages. bck transcripts are abundant in primary neurons in the developing central nervous system of the 1-day-old embryo. While some bck expression persists in the hindbrain, expression vanishes in the spinal cord of the 2-day-old embryo. In summary, the expression pattern of bck is highly dynamic and suggests a role for bck during gastrulation and neuronal differentiation.

Identification of nodal signaling targets by array analysis of induced complex probes.

Nodal signaling controls germ layer formation, left-right asymmetry, and patterning of the brain in the vertebrate embryo. Cellular responses to Nodal signals are complex and include changes in gene expression, cell morphology, and migratory behavior. Only little is known about the genes regulated by Nodal signaling. We designed a subtractive screening strategy by using a constitutively active Nodal receptor to identify putative target genes of Nodal signals in the early gastrula of zebrafish embryos. By quantitative analysis of macro-array hybridizations, 132 genes corresponding to 1.4% of genes on the entire macro-array were identified, which were enriched in the Nodal-induced probe pool. These genes encode components of signal transduction pathways, transcription regulators, proteins involved in protein metabolism but also cytoskeletal components and metabolic enzymes, suggesting dramatic changes of cell physiology in gastrula cells in response to Nodal signals.

A crucial component of the endoderm formation pathway, CASANOVA, is encoded by a novel sox-related gene.

casanova (cas) mutant zebrafish embryos lack endoderm and develop cardia bifida. In a substractive screen for Nodal-responsive genes, we isolated an HMG box-containing gene, 10J3, which is expressed in the endoderm. The cas phenotype is rescued by overexpression of 10J3 and can be mimicked by 10J3-directed morpholinos. Furthermore, we identified a mutation within 10J3 coding sequence that cosegregates with the cas phenotype, clearly demonstrating that cas is encoded by 10J3. Epistasis experiments are consistent with an instructive role for cas in endoderm formation downstream of Nodal signals and upstream of sox17. In the absence of cas activity, endoderm progenitors differentiate into mesodermal derivatives. Thus, cas is an HMG box-containing gene involved in the fate decision between endoderm and mesoderm that acts downstream of Nodal signals.

Expression of the anti-dorsalizing morphogenetic protein gene in the zebrafish embryo.

The BMP3 related anti-dorsalizing morphogenetic protein (ADMP) has been proposed to function in the organizer of chick and Xenopus embryos. We report here the cloning and expression pattern of a zebrafish admp gene. The gene is expressed in involuting cells of the embryonic shield, but not in the non-involuting forerunner cells. During gastrulation, admp transcripts are detected in the posterior prechordal plate, in the notochord primordium and in cells of the dorsal blastoderm margin. Expression is also detectable in the neuroectoderm overlying the posterior prechordal plate. Expression persists in the tail bud until the end of somitogenesis while expression in other areas disappears during early somitogenesis stages.

Predictability of dorso-ventral asymmetry in the cleavage stage zebrafish embryo: an analysis using lithium sensitivity as a dorso-ventral marker.

The dorso-ventral axis in zebrafish first becomes apparent at gastrulation, when the future ventral side appears thinner than the dorsal side. The exact time of establishment of the dorso-ventral axis is not known. We show here that the dorso-ventral axis is specified as early as the 32 cell stage. Using lithium as a marker for dorso-ventral asymmetry, we show that lithium-sensitivity is a characteristic of future ventral cell, but not future dorsal cells, and that there is an asymmetric lithium-sensitivity along the long axis of the 32 cell stage embryo. Consequently, the dorso-ventral axis corresponds to the long axis of the embryo. Because the effect of lithium treatment is short-lived, the dorso-ventral axis must be specified in zebrafish already at the 32 cell stage.