Fig. 5: SOX11 directly regulates multiple major modulators of the epigenome including the SWI/SNF remodeling complex. | Nature Communications

Fig. 5: SOX11 directly regulates multiple major modulators of the epigenome including the SWI/SNF remodeling complex.

From: SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry

Fig. 5

a Overlap (min. overlap = 20 bp) of the SOX11 CUT&RUN peaks (MACS2 peakcalling qval < 0.05) in IMR-32, CLB-GA, NGP cells and SH-EP cells after SOX11 overexpression (OE) for 48 h (one-tailed fisher test p-value<2.2e-16). b Heatmap profiles −2 kb and +2 kb around the transcription start site of early and late SOX11 targets in SH-EP, subdivided in upregulated and downregulated genes. On these regions the SOX11 CUT&RUN data in IMR-32, CLB-GA, NGP and SH-EP cells after SOX11 overexpression (SH-EP DOX) for 48 h are mapped and ranked according to the sums of the peak scores across all datasets in the heatmap. c Overlap of common SOX11 CUN&RUN peaks (common peaks in IMR-32, CLB-GA, NGP cells and SH-EP cells after SOX11 overexpression for 48 h) and early and late up- and downregulated genes in SH-EP after SOX11 overexpression for 48 h (adj p value <0.05, log FC > 0.5 or < −0.5) and overlap of common SOX11 CUT&RUN peaks with genes positively (POS COR) and negatively (NEG COR) correlated with SOX11 expression in NB tumor cohort (n  =  283, GSE8504717, p-value<0.05, one-tailed fisher test p-value<2.2e-16). d EnrichR analysis53 for overlap of common SOX11 CUT&RUN peaks (common peaks in IMR-32, CLB-GA, NGP cells and SH-EP cells after SOX11 overexpression for 48 h) and early upregulated genes in SH-EP after SOX11 overexpression for 48 h. Depicted is the combined Z-score which is computed by taking the log of the p-value from the Fisher exact test and multiplying that with the z-score of the deviation from the expected rank (size), as well as the number of genes that overlap with the enriched genesets (color). e. Binding of SOX11 at c-MYB, SMARCC1, CBX2, KDM1A, SMARCA4, HDAC2, ARID1A and TET1 in IMR-32, CLB-GA, NGP and SH-EP cells after SOX11 overexpression for 48 h. Signal represents log likelihood ratio for the ChIP signal compared to input signal (RPM normalised). All peaks are called by MACS2 (q < 0.05). For Fig. 5d source data are provided as Source Data file.

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