Fig 1

(A) Two-color whole mount in situ hybridization of embryonic zebrafish hindbrains for otx2 (purple, anterior region, far left), krox20 (purple segments, center) and aldh1a2 (red, far right) transcripts from 11 to 14 hpf. otx2 marks the midbrain-hindbrain boundary (MHB), krox20 marks r3 and r5 and aldh1a2 marks the RA production region. Embryos are flat-mounted and shown in dorsal view with anterior to the left. Scale bars: 100 μm. (B) Illustration depicting convergent-extension of the hindbrain. The entire rectangular region, including r1-7 and the RA production region, constitutes the morphogen domain. The hindbrain narrows in the L-R direction (width) and elongates in the A-P direction. (C) Gene regulatory network used to model hindbrain patterning in r2-6. Genes and morphogens with black font were previously used for modeling the r3-r5 pattern [17], while additional factors considered in this model are shown in orange font. Pointed arrows depict up-regulation/activation and blunt arrows depict down-regulation/inhibition. Two morphogens, retinoic acid (RA) and Fibroblast Growth Factor (FGF) diffuse and form two distinct gradients to govern downstream gene expression. (D) Illustration depicting r2-6 and distinct identities (i.e. gene expression signatures) underlying selective cell sorting. Cells in r3 and r5 (blue) express krox20 and cells in r4 (red) express hoxb1a, while both krox20 and hoxb1a levels are low in r2 and r6. Cells in r6 (purple) have high vhnf1 expression. Cells with the same segmental identity attract each other and cells with different identities repulse each other.