Extended Data Fig. 4: Effects of PBRM1 loss on the genomic occupancy of PBAF subunits.

a) Altered SMARCA4 peaks were linked to promoters of the nearest genes by ChIP-Enrich (defined as ± 2.5 kb of TSS) and the log 2 fold change (left) or difference in gene expression (right) after PBRM1 KO in 786-O cells (n = 1527 genes mapped to gained regions and n = 134 genes mapped to lost regions). P-values were computed by two-sided Wilcoxon test. Boxplots presented as median values + /- 25%. Lower whisker is the smallest observation greater than or equal to 25% quantile - 1.5 × interquantile range (IQR). Upper whisker represents the largest observation less than or equal to 75% + 1.5 × IQR. b) Peak regions of all the PBAF subunits were merged, and differences in occupancies of the various PBAF subunits between parental (WT) and PBRM1 knockout (KO) 786-O cells were plotted against the differences in PBRM1 occupancy for all regions. Many regions with large changes in SMARCA4 and ARID2 occupancy have no corresponding changes in PBRM1 occupancy, suggesting that these regions are located away from PBRM1 binding sites. Shown are the spearman correlation coefficients of the changes in the occupancy of PBAF subunits after PBRM1 KO. c) Spearman correlation of changes in chromatin occupancy between parental (WT) and PBRM1 knockout (KO) 786-O cells for all PBAF bound regions.