We describe the cloning of a new fibroblast growth factor receptor, SpFGFR1, that is differentially regulated at the level of transcript abundance during sea urchin embryogenesis. Sequence representing the conserved tyrosine kinase domain was obtained by reverse transcription-polymerase chain reaction using degenerate primers, and the entire open reading frame was obtained by standard cDNA library screening methods. SpFGFR contains a series of domains characteristic of FGFRs: three immunoglobulin-like motifs, an acid box, a transmembrane domain, a relatively long juxtamembrane sequence, a split tyrosine kinase domain, and two conserved intracellular tyrosine residues. Alternative splicing of SpFGFR generates two variants (Ig3L and Ig3S), which differ by insertion in the center of the Ig3 domain of 34 extra amino acids, encoded by an additional exon. Transcripts encoding both variants accumulate when morphogenesis begins with mesenchyme cell ingression and gastrulation. SpFGFR transcripts accumulate in all cell types of the embryo, although in situ hybridization shows that they are somewhat enriched in cells of oral ectoderm and endoderm. Transcripts encoding the Ig3S variant, whose structure resembles more closely that of vertebrate receptors, are enriched in endomesoderm, suggesting that the SpFGFR variants could play distinct roles in the sea urchin embryo.Cell-cell interactions are important in specifying cell fates in all embryos. Receptor-ligand combinations that activate signal transduction pathways are known mediators of these interactions in some cases and obvious candidates for signaling in others. Cell fate specification in sea urchin embryos is highly dependent on cell-cell interactions (reviewed in Refs. 1 and 2). For example, signaling among different blastomeres is known to begin during early cleavage since the developmental fates of tiers of early blastomeres are altered both by isolation and by transplantation into different signaling environments (3-6). Maintenance of positional information also requires continued signaling through blastula stage and, for determination of endodermal and secondary mesenchymal lineages, through early gastrula stages (7-9). In addition to positive inductive influences, signals sent from primary mesenchyme cells prevent pluripotent secondary mesenchyme cells from converting to a skeletogenic fate at the late gastrula stage (10), and unidentified signals repress expression of vegetal markers (11).The effect of LiCl on sea urchin development suggests the kinds of pathways that might mediate cell-cell interactions required to specify blastomere fates. Animal hemispheres (presumptive ectoderm) (12) and animal mesomere pairs isolated from 16-cell embryos (13) that are cultured in the presence of LiCl form spicules and guts, structures normally derived only from vegetal cells. Increasing LiCl concentration induces correspondingly increased levels of expression of vegetal molecular markers, which mimics the effect of transplantation of vegetal cells to the animal pole of c...