Pluto Bioinformatics

GSE131165: Genome-wide enhancer profiling identifies novel Shh regulated gene targets in the developing cochlear duct

Bulk RNA sequencing

The development of the mammalian inner ears is a highly dynamic process that is dependent on the interplay of multiple signaling molecules. Previous studies demonstrated the role of Shh in the initiation and outgrowth of the cochlea. However, the gene targets of Shh in the cochlea largely remain unknown. We show in this study, Shh responsive genes that are loss in the cochlea of Smoecko mutant (Smo null) and upregulated in Shh-P1 mutant embryos through comparative RNA-seq profiling. We performed a genome-wide cis-regulatory element (cRE) study (via ATAC-seq and Gli2 ChIP-seq) and identified potential cREs that are targets of the Shh signaling pathway in the cochlea. Our data unravel novel Shh signaling regulated gene targets that have important functional roles in the development of the cochlea. SOURCE: Douglas,J,Epstein University of Pennsylvania