Wnt signaling affects cell-fate specification processes throughout embryonic development. Here we take advantage of the well-studied gene regulatory networks (GRNs) that control pregastrular sea urchin embryogenesis to reveal the gene regulatory functions of the entire Wnt-signaling system. Five wnt genes, three frizzled genes, two secreted frizzled-related protein 1 genes, and two Dickkopf genes are expressed in dynamic spatial patterns in the pregastrular embryo of Strongylocentrotus purpuratus. We present a comprehensive analysis of these genes in each embryonic domain. Total functions of the Wnt-signaling system in regulatory gene expression throughout the embryo were studied by use of the Porcupine inhibitor C59, which interferes with zygotic Wnt ligand secretion. Morpholino-mediated knockdown of each expressed Wnt ligand demonstrated that individual Wnt ligands are functionally distinct, despite their partially overlapping spatial expression. They target specific embryonic domains and affect particular regulatory genes. The sum of the effects of blocking expression of individual wnt genes is shown to equal C59 effects. Remarkably, zygotic Wnt-signaling inputs are required for only three general aspects of embryonic specification: the broad activation of endodermal GRNs, the regional specification of the immediately adjacent stripe of ectoderm, and the restriction of the apical neurogenic domain. All Wnt signaling in this pregastrular embryo is short range (and/or autocrine). Furthermore, we show that the transcriptional drivers of wnt genes execute important specification functions in the embryonic domains targeted by the ligands, thus connecting the expression and function of wnt genes by encoded crossregulatory interactions within the specific regional GRNs. embryonic interdomain signaling | developmental GRNs | Wnt system regulatory functions | Porcupine T he formation of spatial patterns of gene expression and the development of the body plan are controlled by gene regulatory networks (GRNs). Signaling interactions have a particular role in these networks, in that they provide the means of communication between cell-fate specification processes operating in separate cellular domains. The timing, location, and function of each signaling interaction is determined by GRN linkages that control the expression of signaling ligands and receptors as well as the expression of regulatory genes in response to a combination of signaling inputs and cell fate-specific transcription factors. Cell-fate specification GRNs active during pregastrular development of the sea urchin Strongylocentrotus purpuratus are particularly well understood. During the first 30 h of sea urchin embryogenesis, more than 15 gene-expression domains are formed, and specifically expressed regulatory genes have been identified for each domain. In most cases, the regulatory mechanisms determining their spatial expression patterns have been resolved. Thus, fairly complete GRN models have been constructed for the majority of cell-fate domains in ...