Fig. 3: SMARCA4 is present at centromeres, and this pattern changes in PBRM1 KOs.

a Simplified flowchart describing the mapping strategy to centromeric and pericentromeric sequences (detailed version in Supplementary Fig. 6). b Representative genome tracks displaying coverage of reads from CENP-B (purple), PBRM1 (blue), SMARCA4 (green) and IgG control (grey) CUT&RUN sequencing in RPE1 parental cells across the centromere. c Venn diagram indicating the overlap of significantly enriched SMARCA4 and PBRM1 peaks in centromeric and pericentromeric regions in RPE1 parental cells. d Stacked colour bar representing the genomic distribution of enriched PBRM1 and SMARCA4 peaks, categorised by feature, within centromeric and pericentromeric regions. e CUT&RUN and ChIP-seq signal heatmaps (PBRM1 – top, blue; SMARCA4 – bottom, green) in the indicated cell lines +/−5kb from the centre of RPE1 PBRM1 or SMARCA4 CUT&RUN peaks in the centromere and pericentromere, versus the IgG or input control (grey) of each experiment. Peaks are ordered by signal of the left-most heatmap, i.e. CUT&RUN peaks. An average signal plot is shown at the top of each heatmap. f Representative genome tracks displaying mapping locations of enriched k-mers across the centromere and pericentromere from analysis of CENP-B (purple), PBRM1 (blue), and SMARCA4 (green) CUT&RUN sequencing in RPE1 parental cells. g Venn diagram indicating the overlap of enriched k-mers (FC > 2) in centromeric and pericentromeric regions, in SMARCA4 and PBRM1 in RPE1 parental cells. h CENP-B motif detection following motif analysis of CENP-B-enriched k-mers compared to a shuffled control, where CENP-B k-mer sequences were shuffled maintaining 3-mer frequencies. i Percentage of enriched k-mers that map to specific regions in the centromere and pericentromere in each dataset, including SMARCA4 k-mers enriched in SMARCA4 KO cells (negative control).