Experimental workflow. A subset of 47 conserved non-coding elements (CNEs, [26]) were randomly selected (A), and tested for enhancer activity using transgenesis in zebrafish and mice (B). Transgenic expression was decomposed into major homologous anatomical terms, and systematically compared between mouse and zebrafish embryos to identify cases of differences in trans environments (C). Finally, 26 of these CNEs could be associated to putative target genes, for which endogenous gene expression data were gathered to detect changes in gene expression between zebrafish and mouse that were consistent with trans-changes between the two species (D).

Comparison of enhancer activity of different CNEs in mice and zebrafish. A, B) Expression driven by the Hs608 enhancer shows mouse-specific expression (A) in the dorsal root ganglia and spinal cord (arrow), and zebrafish-specific expression (B) in the forebrain (asterisk). C, D) The Hs278 enhancer drives expression in hindbrain (arrow) and spinal cord (asterisk) in mouse (C) but only in spinal cord in zebrafish embryos (D). E, F) The Hs123 enhancer drives similar expression in the forebrain of mouse (E) and zebrafish (F, arrow).

Examples of a change in endogenous gene expression associated to different enhancer activities in mouse and zebrafish.A) Expression driven by the Hs382 enhancer is detected in DRG (arrow) in mouse. B) This expression is coincident with the Hs382 target gene, Znf536 (arrow). C) In zebrafish, the Hs382 enhancer does not drive expression in DRGs (arrow). This contrasts with a positive control for DRG expression (inset, arrow; Tg(3.1neurog1:GFP)sb2). D) This absence coincides with lack of expression of Znf536 in DRG (arrow).

Examples of a change in endogenous gene expression associated to different enhancer activities in mouse and zebrafish.A) Expression driven by the Hs382 enhancer is detected in DRG (arrow) in mouse. B) This expression is coincident with the Hs382 target gene, Znf536 (arrow). C) In zebrafish, the Hs382 enhancer does not drive expression in DRGs (arrow). This contrasts with a positive control for DRG expression (inset, arrow; Tg(3.1neurog1:GFP)sb2). D) This absence coincides with lack of expression of Znf536 in DRG (arrow).

Additional file 9. Synteny, enhancer activity in mice and target gene expression in mice and zebrafish for the Hs215 and Hs335 CNEs. A) Relative position of Hs215 and Hs335 CNEs and their respective target genes isl1 and ntm. Hs335 is not detected by alignment in the zebrafish genome. B) Expression driven by the Hs215 enhancer in the eye, spinal cord, dorsal root ganglia and cranial nerve is shared by its target gene, islt1, in mice (C; inset is part of another section from the same embryo sowing expression in the eye) and zebrafish (D). E) Expression driven by the Hs335 enhancer in the spinal cord and limbs is shared with its corresponding target gene ntm (F; inset is part of another section from the same embryo sowing expression in the limb) but it does not coincide with the ntm ortholog in zebrafish (G).

In situ hybridization performed in 24hpf zebrafish embryos for gsx2 and znf423 genes. A) gsx2 expression is detected in hindbrain and forebrain at 24hpf and 48hpf (B). C) At 22hpf znf423 gene is expressed in the forebrain, hindbrain, eye and spinal cord. D) At 48hpf znf423 gene is detected in the forebrain, midbrain, hindbrain and eye.

Enhancer activity of CNEs absent from the lineage of teleost fishes in mice and in zebrafish. A and B) Expression of Hs240 is shared by zebrafish and mice in the forebrain, being singularly expressed in the zebrafish hindbrain. C and D) The Hs426 enhancer shows similar expression in mice and zebrafish (otic vesicle, forebrain and hindbrain). E and F) A species specific expression of the Hs312 enhancer is observed in the hindbrain and midbrain of mice (E) being shared by zebrafish (F) in the spinalcord, limbs and forebrain. G and H) The expression of the H752 enhancer is shared by mice and zebrafish in muscle being mice specific for the dorsal root ganglia, trigeminal ganglion and spinal cord.