Fig. 1

BAF controls the open chromatin landscape in epidermal differentiation. a Workflow of on-plate ATAC-seq analysis in control (CTRLi) and BRG1/BRM depletion (BAFi) conditions in primary human keratinocyte differentiation. b UCSC genome browser tracks showing replicates of ATAC-seq, generated from individual wells of differentiating human keratinocytes growing on a 96-well plate, in control (green tracks, n = 2) and BAF loss (red tracks, n = 2) conditions at the ZNF750 TF locus. Published DNase-seq in normal human epidermal keratinocyte (NHEK) cells from publically available ENCODE data (beige track) is also included as reference. An example of a decreased peak with BAF loss is shaded in blue, and an example of an increased peak is shaded in red. c Pie chart showing the distribution of the total 152,110 ATAC-seq peaks relative to gain and loss with BAFi. d–f Scatter plots showing the ATAC-Seq signal correlation between BAFi versus CTRLi, as well as between technical replicates. g Heatmap showing the cell-type specificity of both BAF-dependent and BAF-independent ATAC-seq peaks, as compared to DNase hypersensitive sites (DHS) open chromatin accessibility in 14 representative cell lines. h Boxplot showing the z-score distribution of BAF-dependent ATAC-seq peaks, as compared to all and gained ATAC-seq peaks. The lost ATAC-seq peaks with BAFi are highly enriched with keratinocyte-specific open chromatin regions (p < 10^-600, Kolmogorov–Smirnov test). TF transcription factor, ENCODE encyclopedia of DNA elements.