Fig. 3: Acute depletion of BRG1 results in significantly decreased chromatin accessibility at BRG1 binding sites in mouse T cells.
From: Acute depletion of BRG1 reveals its primary function as an activator of transcription
a Average profiles of the normalized DNase-seq tag density around TSSs in BRG1-depleted and wild-type cells. Cells depleted of BRG1 for 10 h as described in Fig. 1a were subjected to DNase-seq assay. The red line refers to the BRG1-depleted sample and the blue line refers to wild wild-type sample. The total number of DHSs identified in wild-type and AID CD4 + T cells is 37,572. b The DNase-seq signal heatmap for both BRG1-depleted and wild-type samples based on the order ranked by the DNase-seq reads density at the 42,404 TSSs. The color level indicates the DNase-seq reads density level. c Genome browser view of ChIC-seq BRG1 binding and DNase-seq chromatin accessibility profiles, with blue for wild type and red for BRG1-depleted cells. d Volcano plots depict DNase-seq read density shifts at DHSs following acute BRG1 depletion (left) and conditional Brg1 deletion (right) in T cells. Blue and red dots indicate significant DHS increases and decreases, respectively, assessed by a two-sided ROTS test (P < 0.05, fold-change>1.3). e, f, Violin plots compare chromatin accessibility among low, medium, and high BRG1 binding groups in wild-type T cells at nonTSS (> 5 kb from TSS, panel (e)) and TSS (≤ 2 kb from TSS, panel (f)) regions, using only DHSs that overlap with BRG1 peaks. Group separation was based on BRG1 binding intensity, with P values determined by two-sided Wilcoxon rank sum tests. g, h, Violin plots illustrate chromatin accessibility changes at non-TSS (g) and TSS (h) DHSs in T cells post 10-h acute BRG1 depletion. DHSs were categorized by the extent of BRG1 binding reduction (more, medium, less) compared between BRG1-depleted and wild-type cells, with P values from two-sided Wilcoxon rank sum tests.
