Extended Data Fig. 10: Chromatin and gene-expression alterations after loss of chromatin accessibility at superenhancers.

a, Boxplots showing log₂(fold-change) of all differential regions annotated as superenhancers (n = 444) over time after dTAG47 treatment in the different HAP1 dTAG cell lines. First and third quartiles are denoted by lower and upper hinges, center is median. The upper/lower whisker extendes to the largest/ smallest value no further than 1.5* inter-quartile range. Data points beyond are plotted individually. b, Heatmap of log₂(fold-change) of ATAC-seq and H3K27ac ChIP-seq signal in SMARCA4^dTAG and SMARCA4^KOSMARCA2^dTAG cells after dTAG47 treatment versus DMSO control for the genomic regions differentially accessible in any cell line after dTAG47 treatment (cluster 1 – 11). c, Violin plots of log₂(fold-change) from RNA-seq experiments for all regions, active enhancer and superenhancer regions showing a decrease in accessibility (ATAC-seq) and either a decrease (log₂(fold-change) < 1) in H3K27 acetylation ChIP-signal at 24 h (red) or no response (log₂(fold-change) >-1 and < 1) in H3K27 acetylation ChIP-signal at 24 h (blue) in SMARCA4^dTAG, SMARCA4^KOSMARCA2^dTAG and SMARCC1^KOSMARCC2^dTAG cells after dTAG47 treatment (n = 2 independent experiments). First and third quartiles are denoted by lower and upper hinges, center is median. The upper/lower whisker extendes to the largest/ smallest value no further than 1.5* inter-quartile range. Data points beyond are plotted individually. Differential genes were defined as Padj < 0.01 und log₂(fold-change) > 1.