Gli3R-mediated inhibition of hedgehog signaling alters the embryonic transcriptome in zebrafish

Hedgehog signaling is a conserved developmental pathway that patterns diverse tissues during vertebrate embryogenesis. In zebrafish, disruptions to the hedgehog pathway cause well-characterized defects in specific cell types including neurons and glia derived from the ventral neural tube. We inhibited hedgehog signaling by overexpressing the Gli3 repressor ubiquitously and performed bulk RNA sequencing of 30 h postfertilization zebrafish embryos. Consistent with known roles of hedgehog signaling, we observed reduced expression of genes marking lateral floor plate, motor neurons, Kolmer-Agduhr cells, dopaminergic neurons, slow muscle cells, and anterior pituitary. Gene set enrichment analysis using marker genes derived from the Daniocell atlas also revealed downregulation of genes marking H+-ATPase-rich ionocytes, which are located in the embryonic skin and are responsible for osmotic homeostasis. Reduced expression of ionocyte-specific transporter genes and the transcription factor foxi3a suggests that Gli activity may play a previously unrecognized role in the specification of this cell type.