Extended Data Fig. 5: SWI/SNF binding to chromatin but not complex assembly is lost upon ARID1A loss.
(a) BAF155-2 and BRG1-2 at BAF155/BRG1 binding sites in control and ARID1A KO MCF7 cells (n=1). (b) Box plot representing mean signal across differential BAF155-2 or BRG1-2 after ARID1A KO at BAF155/BRG1 sites. (c) Cropped western blots of co-immunoprecipitation of BRG1 with subunits of the SWI/SNF complex in control and ARID1A KO MCF7. (d) Plot of the fold change between control and ARID1A KO of ATAC-seq sites vs. similar fold change of BAF155/BRG1 sites; n=14838 peaks, R and P values calculated using spearman correlation from ggpubr package in R. (e) BAF155-2 and BRG1-2 at differential accessible sites in control and ARID1A KO MCF7. (f) Box plot representing mean signal across differential BAF155-2 or BRG1-2 after ARID1A KO at lost accessible sites. (g) ChIP-qPCR analysis of ER, FOXA1, and GATA3 in shared loci in control and ARID1A KO cells. (h) ChIP-qPCR analysis of FOS, JUN, and IgG control. (i) ChIP-seq tracks of BRG1 and BAF155 in control and ARID1A KO cells (n=1). For (g) and (h), error bars=mean ±SEM, n=3 biologically independent samples, center values are means. P values, Student’s two-sided t test. For the box plots P-values, Mann-Whitney U test (Wilcoxon rank-sum test, two-sided) and effect size (rosenthal’s coefficient) are shown. The log2FC which is calculated as log2 (mean KO / mean Control) is also indicated (n=6). Box shows 25th, median and 75th percentiles with whiskers extending to ± 1.5 * IQR.
