Genome Biology | Abstract | gb-2007-8-6-r106 | Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction: "We demonstrate that the sonic hedgehog a (shha) paralogs sonic hedgehog b (tiggy winkle hedgehog; shhb) genes of fishes have a modified ar-C enhancer which specifies a diverged function at the embryonic midline. We have identified several conserved motifs indicative of putative transcription factor binding sites by a local alignment of ar-C enhancers of numerous vertebrate sequences. To trace the evolutionary changes among paralog enhancers, phylogenomic reconstruction was carried out and lineage-specific motif changes were identified. The relevance of the motif composition to observed developmental differences was studied through transgenic functional analyses. Altering and exchanging motifs between paralog enhancers resulted in the reversal of enhancer specificity in the floor plate and notochord. A model reconstructing enhancer divergence during vertebrate evolution was developed."
Comments (by sterding):
1. Enhancers ar-C in two paralogs of zebrafish shh gene are diverse in sequence conservation (fig.1) and in functionality (fig. 3); ar-C in shha enhances the expression of reporter gene in notochord, while reporter with ar-C in sshb shows expression in floor plate, additionally.
2. Local alignment of ar-C shows that 4 conserved motifs(C1,C2,C3,C4) in shha, while only 2 of them(C1,C3) present in sshb branch (fig. 4).
3. Experiment with mutation in specific motif shows that C1 are critical for notochord specificity, C3 is not so important from current result; C2 and C4 are floor plate repressor (fig. 5,6).