Fig. 5: Functional experiments in skate fin samples.

a, Outline of a skate and a mouse embryo and their homologous appendages, used in our comparative analyses. A, anterior; P, posterior. The distal (Di) and proximal (Pr) regions of the fin/limb are indicated. b, In situ hybridization reveals the opposite expression pattern of many hox genes and the gli3 gene in the pectoral fin. n = 8 animals for each gene. Scale bar, 1 mm. The images of hoxa2 and gli3 were adapted from ref. ¹. c, UCSC Genome Browser view showing HiChIP, RNA-seq and ATAC–seq data around the hoxa cluster in skate. The anterior-specific open chromatin region between the hoxa1 and hoxa2 genes is marked with a dotted rectangle (see ‘A skate-specific hoxa fin enhancer’ section). Green denotes the most conserved regions with the elephant shark (Callorhinchus milii; Cmil) genome. Ant. pec. fin, anterior pectoral fin; post. pec. fin, posterior pectoral fin. d, GFP expression driven by the anterior-specific open chromatin region between the hoxa1 and hoxa2 genes from skate and shark in transgenic assays in zebrafish. The brain expression induced by the midbrain enhancer:egfp indicates a successful injection of the mini-Tol2 vector⁶¹ with the skate or shark hox enhancer as a positive control. Note that only the skate enhancer drives expression on the pectoral fin (5 eGFP-positive embryos at 48 h after fertilization (h.p.f.) out of 18 F₀ embryos for the skate enhancer (left), in contrast to 0 out of 31 F₀ embryos for the shark enhancer (right)). In F₁ stable embryos, the GFP is driven to the pectoral fin with a clear anterior pattern at 96 h after fertilization (middle). Scale bars, 250 µm.