Figure 1. Gene expression profiles of transcription factors and signaling molecules analyzed in this study.

(A) Spatial and temporal expression profiles. The expression of 21 genes encoding transcription factors (goosecoid, nk2.2, tbx2.3, nk1, foxA, brachyury, foxG, onecut/hnf6, irxA, hox7, dlx, smad6, msx, id, oasis, deadringer, otx, gfi, pax2/5/8, atbf1, unc4), 13 signaling molecules (nodal, lefty, bmp2/4, chordin, fgfA, fgfr1, glypican5, admp2, bmp1, wnt8, univin, wnt5, Delta), 2 RNA binding proteins (rkhd, ptb), 3 differentiation genes (cyIIIa, 29D, tubulinß3) and a mitochondrial gene (cytochrome oxidase) is depicted above a scheme of early development of the sea urchin embryo. The genes are classified into 5 groups according to the timing of their expression. (1) Maternal cytochrome oxidase transcripts show a graded distribution in cleaving embryos. (2,3) Starting at the early blastula stage, nodal and lefty are the first zygotic genes to be expressed in a restricted pattern along the D/V axis, followed by bmp2/4 and goosecoid before hatching (4,5). (6–9) After hatching, expression of fgfr1 and chordin is initiated ventrally while nk2.2 and tbx2/3 start to be expressed dorsally. (10–26) At mesenchyme blastula stage foxA, brachyury, foxG, Delta, nk1, onecut, fgfA, glypican5, irxA, hox7, dlx, smad6, msx, id, oasis, admp2, and CyIII start to be expressed in a restricted pattern. (27–36) A restricted expression is established slightly later at the early gastrula stage for ptb, bmp1, dri, otx, rkhd, gfi1, pax2/5/8, wnt8, univin, and for atbf1, unc4 and wnt5 (37–39). (40–43) tubulinß3 and 29D are expressed in the presumptive ciliary band or dorsal ectoderm starting at prism/early pluteus stages while foxG is expressed in a ventral subdomain of the ciliary band and Delta in individual cells within the ciliary band and facial ectoderm. (B) (1) Two color double in situ hybridization showing that foxG is expressed ventrally. (2,15,16) nk2.2 is expressed in two discrete regions along the D/V axis. At the late blastula stage, the territory with the strongest expression is located on the ventral side while at mesenchyme blastula stage, the highest level of transcripts is detected on the dorsal side. (3–6) Two color double in situ hybridization with chordin shows that dlx, msx, irxA and smad6 are expressed on the dorsal side. (7–13) One color double in situs hybridizations confirm that id and hox7 are expressed on the dorsal side. (C) At late gastrula stage, differences in expression of marker genes along the A/V and D/V axes identify differently specified territories within the ventral ectoderm. (1)The NK1 homeobox gene is expressed in a trapezoidal domain that abuts the stomodeal domain and the lateral ectodermal regions that express fgfA and pax2/5/8. (2) brachyury is expressed in a group of 30 cells located in the center of the ventral ectoderm and that likely constitute the stomodeal precursors. (3–5) This group of cells is surrounded by a large belt of goosecoid and foxG expressing cells that are themselves surrounded by a thinner belt of onecut/hnf6 expressing ciliary band precursors. (D) Nested expression domains are also apparent within the dorsal ectoderm and ciliary band. (1) irxA is expressed in a medial sub domain of the dorsal ectoderm that abuts the ciliary band. Note that irxA is also expressed in the stomodeal region at this stage. (2,3) Genes like admp2 and msx are expressed in nested patterns in the dorsal most region that corresponds to the presumptive apex of the larva. (4) nk2.2, like tbx2/3, is expressed in most cells of the dorsal ectoderm. (5,6) Onecut is expressed in the whole ciliary band, while pax2/5/8 is expressed in the vegetal portion of the presumptive ciliary band. (E) A set of ectodermal genes including onecut/hnf6, glypican5, fgfA, univin and wnt8 are expressed broadly in the ectoderm at blastula stages and subsequently restricted to either the dorsal ectoderm (glypican5) or the ciliary band (onecut/hnf6, fgfA, univin, wnt8). (F) Expression of several ciliary band genes including onecut, gfi1, foxG, egip, fgfA, pax2/5/8, univin, wnt8, dri, otx and of the dorsal marker glypican5 critically relies on the activity of the transcription factor SoxB1. V, ventral, D, dorsal, L, lateral. lv, lateral view, vv, vegetal pole view, fv, frontal view.