Fig. 4: Dux binding induces transcription at gene promoters.

a Comparison of TF activities between mDux GFP- (Control; labeled in blue) and mDux GFP + (DuxOE; labeled in red). Volcano plot showing the TOBIAS differential binding score on the x-axis and -log10 (p value) on the y-axis; each dot represents one TF. b Aggregated footprint plots for Dux. The aggregated plots are centered on the predicted binding sites for Dux between Control and DuxOE conditions (left: all genomic sites). The total possible binding sites for DuxOE (n = 12,095) are separated into bound and unbound sites (right). The dashed lines represent the edges of the Dux motif. c Change in expression of genes near Dux binding sites. The heatmap shows n = 2664 Dux binding sites found in gene promoters. Footprint log2(FC) and RNA log2(FC) represent the matched changes between Control and DuxOE for footprints and gene expression, respectively. Log2(FC) is calculated as log2(DuxOE/Control). The column Binding prediction depicts whether the binding site was predicted by TOBIAS to be bound/unbound in the DuxOE condition. d Genomic tracks indicating three exemplary Dux binding sites and their target gene promoters and respective tracks for corrected cutsite signals (red/blue), TOBIAS footprint scores (blue), detected motifs (black boxes), and gene locations (solid black boxes with arrows indicating gene strand). e Dux transcription factor network. The TF-TF network is built of all TFBS with binding in TF promoters with increasing strength in DuxOE (log2(FC) > 0). Sizes of nodes represent the level of the network starting with Dux (Large: Dux, Medium: 1st level, Small: 2nd level). Nodes are colored based on corresponding RNA level in the DuxOE condition. Directed edges indicate binding sites in the respective gene promoter found by the TOBIAS CreateNetwork module. f Correlation of the Dux transcription factor network to expression during development. The heatmap depicts the in vivo gene expression during developmental stages. The right-hand group annotation highlights the difference in mean expression for each timepoint. The heatmap is split into Dux and target genes of Dux. Source data are available in the Source Data file.