Figure 4.
esBAF regulates NDRs and flanking nucleosome occupancy of promoters and TTSs. (A–C) Aggregation plot of relative nucleosome occupancy upon EGFP knockdown (KD) or Smarca4 knockdown over TSSs (A), TTSs (B), or Ctcf-binding sites (C) ±2 kb in ESCs. Ctcf-binding sites were based on published data (Chen et al. 2008). P-values indicating the statistical significance of changes in nucleosome occupancy are indicated. To calculate P-values, a standard t-test summing reads from −500 to −240 upstream of TSSs and +240 to +500 downstream from TTSs in EGFP knockdown and Smarca4 knockdown was performed. (D) Aggregation plot of relative nucleosome occupancy upon EGFP knockdown or Smarca4 knockdown over DHSs grouped by changes in ncRNA levels in Smarca4 knockdown ESCs. Displayed are the top 25% of DHSs with increased ncRNA levels upon Smarca4 knockdown and the bottom 25% of DHSs with decreased or no change in ncRNA levels upon Smarca4 knockdown. (E) Log2 fold change of Smarca4 knockdown/EGFP knockdown ncRNA expression originating from annotated DHSs (left panel) or upstream of TSSs (right panel) from averaged ESC RNA-seq experiments, sorted by the log2 fold change of Smarca4 knockdown/EGFP knockdown nucleosome occupancy adjacent to DHSs or upstream of TSSs (−1 position). (F,G) Receiver of operating characteristic (ROC) curves for changes in nucleosome occupancy relative to changes in expression for DHSs (F) and TSSs (G). The P-values indicating the significance of changes in flanking nucleosome occupancy curves relative to scrambled data are shown.