Fig. 6: IRX3 ablation alters SUMO occupancy at Wnt and Rho signaling genes.
From: IRX3 controls a SUMOylation-dependent differentiation switch in adipocyte precursor cells
ChIP-seq for SUMO2/3 was performed in ME3 control and IRX3-KO cells on days \(-\)1 and 1 of adipogenic differentiation (n \(=\) 2 biological replicates per condition). a Heatmap of SUMO2/3 ChIP-seq peak intensities clustered by shared and condition-specific peaks. See Supplementary Fig. 6, Supplementary Data 7. b MA plots showing differential SUMO2/3 peak intensity for IRX3-KO vs control (top) and day \(-\)1 vs day 1 (bottom). Blue dots, peaks with padj \( < \) 0.05; grey, non-significant; DESeq2 analysis with Benjamini-Hochberg correction. Beige ellipse, hypoSUMOylated regions in IRX3-KO on day 1; blue ellipse, hyperSUMOylated regions on day 1 vs day \(-\)1 in IRX3-KO. See Supplementary Data 7. c Number of significantly up- and downregulated SUMO peaks in b. d ClusterProfiler GO enrichment analysis of genes associated with increased SUMO occupancy in IRX3-KO cells on day 1 versus day \(-\)1; Benjamini-Hochberg correction, top 5 terms shown. See Supplementary Data 8. e ClusterProfiler GO enrichment analysis of genes with reduced SUMO occupancy in IRX3-KO vs control cells on day 1; Benjamini-Hochberg correction, top 15 terms shown. See also Supplementary Fig. 6 and Supplementary Data 8. f STREME motif enrichment analysis of SUMO peaks within Wnt pathway genes. Matching TOMTOM motifs are shown. See Supplementary Data 9–10. g Genome browser view of SUMO2/3 peaks at the Rspo2 promoter (top). Zoomed-in comparison with Unibind 2021 ChIP-seq tracks143 from relevant cell types showing peak overlap with transcription factors involved in osteogenesis and adipogenesis (bottom). h Relative Rspo2 mRNA levels in ME3 control vs IRX3-KO cells (top) and in response to ML-792 (bottom) on day 1 and day 9 (n = 3). ***padj \( < \) 0.001; two-way ANOVA with Holm–Sidak correction. i Relative expression of Wnt-responsive genes in IRX3-KO vs control cells on days 1 and 7 (n \(=\) 6). Genes upregulated and downregulated by Wnt signaling are shown in red and blue, respectively. **q \( < \) 0.01; multiple two-sided Mann-Whitney tests with FDR correction. Bar graphs show means \(\pm \,\)SD. Source data are provided in the Source Data file.
