Fig. 6: The binding of BAF complexes to chromatin is responsible for many of the observed expression changes of the SS transcriptome after blocking SUMOylation.

A Gene ontology analysis of genes associated with significantly reduced SMARCA4 ChIP-seq signals after TAK-981 treatment in HS-SY-II cells. B Venn diagrams overlap in significantly downregulated genes among the different noted experiments. The significance of the gene set overlap (p value) was calculated with Chi-squared test under the assumption of 17,611 expressed transcripts. C Overlap of the 100 most significantly downregulated genes following SS18::SSX knockdown by Banito et al.²² with significantly reduced SMARCA4 ChIP-seq signals. D Gene ontology analysis of genes associated with significantly upregulated SMARCA4 ChIP-seq signals after TAK-981 treatment in HS-SY-II cells. E Venn diagram of the overlap of significantly enhanced SS18::SSX and SMARCA4 ChIP-seq signals in HS-SY-II cells. The significance of the gene set overlap (p value) was calculated with Chi-square test under the assumption of 17,611 expressed transcripts. F Volcano plot of the reduced and increased SMARCA4 ChIP-seq signals plotted with the genes of commonly reduced (dark orange dots) or commonly enhanced (dark green dots) SS18::SSX ChIP-seq signals. G Genes related to the mesenchymal phenotype associated with increased SMARC4A ChIP-seq signals (green dots). padj = adjusted p values. For (A, C, D, F, G) the p values were adjusted using a False Discovery Rate (FDR) multiple testing correction method.