Transgenic zebrafish containing sqt genomic sequences driving expression of a reporter gene are provided. This line faithfully reproduces the spatiotemporal expression pattern of endogenous sqt, and at the late blastula stage is expressed in the YSL as well as in the blastomeres. The data show that expression in embryonic and extra-embryonic tissues is controlled by separable regulatory elements, including at least two elements that mediate the response to Nodal signals in different cell types. An element upstream of the transcription start site mediates the response to Nodal signaling specifically in the EVL cells. By contrast, a conserved Nodal response element (NRE) in the first introns is required for transgene expression in the blastomeres. The data show that expression of the transgene in the blastomeres depends on Nodal signaling activity. Furthermore, expression of sqt and cyc in the blastomeres depends upon Nodal signals from the YSL. These experiments suggest that Nodal signals in the YSL act to induce nodal-related gene expression in the embryo margin by activating the Nodal autoregulatory pathway. Targeted depletion of Nodal signals from the YSL results in embryos lacking endoderm and head mesoderm, similar to the defects observed in mice lacking Nodal function in the visceral endoderm. Thus, the data provides strong genetic evidence for the functional conservation between the YSL and the visceral endoderm. This suggests a common evolutionary origin for teleost and mammalian extra-embryonic tissues, despite their profound morphological differences.