Fig. 4: SWI/SNF enrichment at a subset of centromeric chromatin marks is altered in a PBRM1-dependent manner.

a Venn diagram indicating the overlap of significantly enriched peaks (top, orange) or k-mers (bottom, red) in the centromere and pericentromere, of SMARCA4 and PBRM1 in RPE1 parental cells, and SMARCA4 in PBRM1 knockout (KO) cells. Venn diagrams show enriched peaks or k-mers found in at least two of three independent biological replicates, versus their IgG controls. The colour corresponds to the total number of enriched peaks or k-mers in each region of the Venn diagram (count). b Representative genome tracks displaying coverage of reads from PBRM1 (blue), SMARCA4 (green), and IgG control (grey) CUT&RUN sequencing in RPE1 parental cells and SMARCA4 in PBRM1 knockout cells (light green), showing an example of peaks gained (left) or lost (right) in the PBRM1 knockout cells. One representative independent biological replicate is shown, with boxes underneath representing peaks that were called as significantly enriched (q < 0.01) in at least two of three replicates versus their IgG control. Genomic location is indicated at the top and centromeric annotation is shown above the tracks. c Schematic showing PBRM1 specific, PBRM1 non-specific and KO specific categories of peaks from CUT&RUN sequencing. Example graphics for called peaks are shown for each category. d CUT&RUN signal heatmaps representing the three categories of peaks in the centromere and pericentromere. Signal +/− 5 kb from the centre of each peak is shown for PBRM1 (blue) and SMARCA4 in parental RPE1 (green), SMARCA4 in PBRM1 knockout cells (light green), and IgG control (grey). Peaks are ordered by signal of the left-most heatmap for each condition. An average signal plot is shown at the top of each heatmap. e Stacked colour bar representing the genomic distribution of the three categories of peaks, categorised by feature, within centromere and pericentromere regions.