Fig. 2: BRG1 positively regulates nascent transcription by facilitating RNA polymerases II binding to chromatin.
From: Acute depletion of BRG1 reveals its primary function as an activator of transcription
a Violin plots show a positive correlation between BRG1 TSS binding and gene expression in wild-type T cells, with 11,206 peaks assessed by a two-sided Wilcoxon rank sum test. b MA plot of RNA-seq shows gene expression changes from 17,595 genes after 10-h BRG1 depletion. Red and blue dots mark significant expression decreases and increases; a black line indicates no change. Significance was determined by a two-sided ROTS test with P < 0.05 and fold-change >1.5. c MA plot of PRO-seq data shows differential nascent transcription in 35,976 genes post 10-h BRG1 depletion. Red (decreased) and blue (increased) dots indicate significant gene changes, with a horizontal black line showing no change, as identified by a two-sided ROTS test (P < 0.05, fold-change > 1.3). d Genome browser snapshot compares PRO-seq and RNA-seq between wild-type (red) and BRG1-depleted (blue) cells. e PRO-seq read density compared at TSS, gene body, and intergenic areas between wild type (blue) and AID (red) samples, normalized by region size. f Violin plots show fold-change in BRG1 TSS binding across genes with differential transcription, analyzed by a two-sided Wilcoxon rank sum test. Groups are increased (6), decreased (395), and unchanged (249 genes; P > 0.5, log2 fold-change < 0.05), based on proximity within ± 2 kb of the TSS. g Violin plots illustrate PRO-seq signal fold-changes at 5’ (within 1000 bp of TSS) and 3’ (within 1000 bp of TTS) regions between BRG1-depleted and wild-type cells, with 881 and 157 sites showing decreased signals after BRG1 depletion, respectively, assessed by a two-sided Wilcoxon rank sum test. h, MA plot shows Pol II binding variations across 42,467 sites following BRG1 depletion, with red and blue dots marking sites with significant decreases and increases, respectively, determined by a two-sided ROTS test at P < 0.05 and fold-change > 1.3. i Violin plot shows Pol II binding changes at 5’ (within 1000 bp of TSS) and 3’ (within 1000 bp of TTS) after 10-h BRG1 depletion, with 993 and 393 fewer sites at 5’ and 3’, respectively, in BRG1-depleted cells versus wild type, assessed by a two-sided Wilcoxon rank sum test.
