A cluster of three long-range enhancers directs regionalShhexpression in the epithelial linings

Abstract

The sonic hedgehog (Shh) pathway plays indispensable roles in the morphogenesis of mouse epithelial linings of the oral cavity and respiratory and digestive tubes. However, no enhancers that regulate regional Shh expression within the epithelial linings have been identified so far. In this study, comparison of genomic sequences across mammalian species and teleost fishes revealed three novel conserved non-coding sequences (CNCSs) that cluster in a region 600 to 900 kb upstream of the transcriptional start site of the mouse Shh gene. These CNCSs drive regional transgenic lacZ reporter expression in the epithelial lining of the oral cavity, pharynx, lung and gut. Together, these enhancers recapitulate the endogenous Shh expression domain within the major epithelial linings. Notably, genomic arrangement of the three CNCSs shows co-linearity that mirrors the order of the epithelial expression domains along the anteroposterior body axis. The results suggest that the three CNCSs are epithelial lining-specific long-range Shh enhancers, and that their actions partition the continuous epithelial linings into three domains: ectoderm-derived oral cavity, endoderm-derived pharynx, and respiratory and digestive tubes of the mouse. Targeted deletion of the pharyngeal epithelium specific CNCS results in loss of endogenous Shh expression in the pharynx and postnatal lethality owing to hypoplasia of the soft palate, epiglottis and arytenoid. Thus, this long-range enhancer is indispensable for morphogenesis of the pharyngeal apparatus.

Temporal and spatial dissection of Shh signaling in genital tubercle development

“…Although Shh is expressed in both appendages, its expression in the ZPA and that in the hindgut are regulated by different enhancers. Hindgut Shh expression relies on DNA elements that are not conserved between mammals and the teleost fish medaka (Sagai et al, 2009), whereas those controlling ZPA Shh expression are highly conserved (Lettice et al, 2008;Sagai et al, 2005). These findings suggest a differential acquisition of Shh expression in the evolution of the two appendages.…”

GATA4 and GATA6 regulate pancreatic endoderm identity through inhibition of hedgehog signaling

“…The upregulation of hedgehog pathway expression in the pDKO mice suggested that Shh might be repressed by GATA4 and/or GATA6. An 806-bp MACS1 enhancer located ∼740 kb upstream from the Shh transcriptional start site has been shown to be sufficient for driving Shh expression specifically in the foregut endoderm (Anderson et al, 2014;Sagai et al, 2009). Using position weight matrix analysis we identified four putative GATA consensus elements within the MACS1 enhancer (Fig.…”

Sonic hedgehog patterning during cerebellar development

“…The spatial and temporal Shh expression pattern results from the combined action of multiple enhancer elements present in its extensive regulatory domain, controlling Shh transcription in different tissues [12][13][14][15][16]. However, only recently specific transcription factors have been discovered to directly control Shh enhancer activity.…”