Fig 3. Conserved role of Pax3 in the regulation (“regul.”) of somitic/myogenic gene expression.

(A-B) Heatmap of genes up-regulated upon 1-day and 6-day Pax3 induction. Changes are relative to noninduced Pax3 cells and were obtained by the analysis of 3 independent biological replicates. Selected genes and biological processes affected by Pax3 are indicated on the right side of the heatmaps. (C-D) GO analysis of up-regulated Pax3 genes: 1-day and 6-day samples using DAVID. (E) Analysis of Meox1 expression in the somites of WT and Pax3-null;Pax7-het E9.5 embryos using ISH. Red square represents the zoomed region (middle panel). Dashed red line indicates the section displayed in the right panel. (F) Representative FACS analysis of 2-day Pax3-induced EB cultures shows up-regulation of VCAM1 (y-axis). PDGFRα expression is shown on the x-axis. (G) Comparison of transcriptional changes for selected genes associated with Hedgehog and Notch signaling (“sign.”) pathways upon Pax3 expression in differentiating mouse and human ES cells. Data were extracted from RNA-seq analysis of 1-day and 6-day Pax3-induced (+dox) and noninduced (no dox) cultures. Bars represent fold induction (+dox/no dox) of each sample’s mean. *p < 0.05, **p < 0.01, ***p < 0.001. Numerical values are available in S1 Data. BMP, bone morphogenetic protein; develop., development; diff., differentiation; diff. expr., differentially expressed; dox, doxycycline; E, embryonic day; EB, embryoid body; excr., excretion; FACS, fluorescence-activated cell sorting; GO, gene ontology; ISH, in situ hybridization; Meox1, mesenchyme homeobox 1; morph., morphogenesis; Neuron., neuronal; Pax, paired box; PDGFRα, platelet-derived growth factor receptor alpha; pos reg, positive regulation; pos regul transcr RNA pol II prom, positive regulation of transcription from RNA pol II promoter; VCAM1, vascular cell adhesion molecule 1; WT, wild-type.