Fig 2: ARID1A and ARID1B have unique and shared roles in the maintenance of chromatin accessibility.(A) Differential peak calls from ATAC-seq in HCT116 WT cells expressing shRNAs to scrambled control (WT) or ARID1B (ARID1B KD), or HCT116 ARID1A-/- cells expressing shRNAs to scrambled control (ARID1A-/-) or ARID1B (ARID1A-/- ARID1B KD). These cells were validated for the expression, complex association, and function of ARID1A and ARID1B (Figure 1—figure supplement 1A–D). Blue and red dots represent differential ATAC-seq peaks whose read density increased or decreased by 1.5 fold or more (FDR < 0.05), respectively, in two independent biological replicates. Numbers in the upper left and lower right corners refer to numbers of called peaks increased or decreased in accessibility. Percent of changed sites was calculated from total number of accessible sites (Figure 1—figure supplement 2A). Replicate experiments showed strong correlation (Figure 1—figure supplement 2B) and overlap with DNAseI Hypersensitivity data (Figure 1—figure supplement 2C). (B) FPKM expression of ARID1A and ARID1B quantified by RNA-seq of two biological replicates from wild-type (WT) and ARID1A-/- (ARID1A-/-) HCT116 cells. (C) ARID1B protein expression in wild-type (WT) and ARID1A-/- (ARID1A-/-) HCT116 cells expressing shRNAs to scrambled control (scr) or ARID1B (KD1, KD2). ARID1B levels are quantified relative to TBP control (Figure 1—figure supplement 1B). Values shown are averages from three biological replicates where error bars indicate standard deviation. (D) k-means clustering analysis of ATAC-seq read density (log2) from WT, ARID1B KD, ARID1A-/-, and ARID1A-/- ARID1B KD HCT116 cells. Reads are centered on the middle of the accessible peak ±0.5 kb. (E) Average ATAC-seq read density in WT, ARID1B KD, ARID1A-/-, and ARID1A-/- ARID1B KD HCT116 cells centered on accessible peaks from Clusters 1–7. (F) Fold change in RNA expression relative to WT HCT116 cells for the top 25% of expressed genes nearest to called accessible peaks from Clusters 1–7. Ns, not significant; *p<0.05; **p<0.01; ***p<0.001, ****p<0.0001. Gene Set Enrichment analysis of hallmark gene sets was performed on annotated sites from Clusters 1–7 (Figure 1—figure supplement 3).10.7554/eLife.30506.006Figure 1—source data 1.ARID1B protein expression in WT and ARID1A-/- HCT116 cells with ARID1B knockdown.ARID1B protein expression in wild-type (WT) and ARID1A-/- (ARID1A-/-) HCT116 cells expressing shRNAs to scrambled control (scr) or ARID1B (KD1, KD2) was quantified by western blotting. ARID1B levels were normalized to TBP control and then KD1 and KD2 were normalized to scrambled (scr) control in WT cells.10.7554/eLife.30506.007Figure 1—source data 2.Proliferation of WT and ARID1A-/- HCT116 cells with ARID1B knockdown.Relative proliferation over 9 days normalized to scrambled (scr) control at day 3, as determined by CellTiterGlo. Data shown from two independent biological replicates with averages and standard deviation.