A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins

Abstract

Despite their evolutionary, developmental, and functional importance the origin of vertebrate paired appendages remains uncertain. In mice, a single enhancer termed ZRS is solely responsible for Shh expression in limbs. Here, zebrafish and mouse transgenic assays trace the functional equivalence of ZRS across the gnathostome phylogeny. CRISPR/Cas9-mediated deletion of the medaka-ZRS and enhancer assays reveal the existence of ZRS shadow enhancers in both teleost and human genomes. Deletion of both ZRS and shadow ZRS abolish shh expression and completely truncate pectoral fin formation. Strikingly, deletion of ZRS results in an almost complete ablation of the dorsal fin. This finding indicates that a ZRS-Shh regulatory module is shared by paired and median fins, and that paired fins likely emerged by the co‐option of developmental programs established in the median fins of stem gnathostomes. Shh function was later reinforced in pectoral fin development with the recruitment of shadow enhancers, conferring additional robustness.

A critical appraisal of appendage disparity and homology in fishes

“…One hypothesis is that these two genes could have evolved through the duplication of a Tbx4/5 gene that controlled the position of the ancestral paired fin (Agulnik et al, 1996;Hadzhiev et al, 2007;Onimaru & Kuraku, 2018;Ruvinsky & Gibson-Brown, 2000;Tanaka et al, 2002). As previously mentioned, some authors have also proposed that the origin of the paired fins can be explained by the lateral redeployment of developmental mechanisms originally associated with the median fins (Crotwell et al, 2001;Crotwell & Mabee, 2007;Freitas et al, 2014Freitas et al, , 2006Letelier et al, 2018). This hypothesis is supported by the similarities in molecular signalling pathways between developing median and paired fins (Abe et al, 2007;Freitas et al, 2014Freitas et al, , 2006.…”

An evolutionary perspective of regulatory landscape dynamics in development and disease

“…Similarly, the genomic region around the Sonic hedgehog (Shh) gene emerged by a chromosome rearrangement at the base of the vertebrate lineage, which allowed the recruitment and incorporation of the Lmbr1 gene to the Shh TAD [3,41]. The intron 5 of Lmbr1 became a substrate for the emergence of the Shh longdistance ZRS enhancer, a critical CRE for unpaired and paired fin evolution [42]. Interestingly, a recent study investigating hindbrain boundary formation in different fish species provides a more detailed picture about the molecular events leading to novel morphological structures [43··].…”

A Highly ConservedShhEnhancer Coordinates Hypothalamic and Craniofacial Development

“…The deep conservation and early stages of expression mediated by these Shh enhancers suggest a fundamental role in generating ancient, shared vertebrate characteristics. Studies to date show a modular composition of the Shh regulatory domain and thus, for at least some of the cis-regulators, there is a simple relationship of a single enhancer to a distinct spatial domain of expression (Jeong et al, 2006;Lettice et al, 2014); although, in other instances, secondary enhancers provide compensatory low levels of expression (Letelier et al, 2018;Tsukiji et al, 2014).…”