Fig. 5.

Gli3 regulates expression of Wnt pathway components. (A,B) Volcano plot of differentially expressed transcripts in control versus Foxg1Gli3T^Flag/+ foreguts, as determined by Log₂FC≥|1| (P<0.05) at E10.5 (A) and E11.5 (B). Dashed lines indicate FC and P value thresholds. (C) Venn diagram intersecting genes differentially expressed in Foxg1Cre;Gli3T^Flag/+ mutants with genes known to be involved in human or mouse tracheal chondrogenesis (Shefchek et al., 2020; Sinner et al., 2019). TM, tracheomalacia-associated genes. (D) Genome browser views of Gli3-3xFlag (GSE133710), Foxf1 (GSE77159) and H3K4me3 (GSE119885) ChiP-seq data, as well as ATAC-seq data (GSE119885) on Foxf1, Sox9, Rspo2 and Notum loci. Gli3 and Foxf1 bind the Foxf1, Sox9 and Notum loci, but only Foxf1 shows direct binding of the Rspo2 locus along with significant ATAC and H3K4me3 peaks, suggesting active transcription. Statistically significant ChIP peaks are underlined in red.