Fig. 6 | Nature Communications

Fig. 6

From: A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells

Fig. 6

The bromodomain mediates BRD9 targeting to chromatin. a Representative immunoblotting analysis of a cellular fractionation assay in mouse ESC lysates after treatment with either DMSO or I-BRD9 at 3 or 10 µM for 24 h. Molecular weights from ladder are indicated. b Quantification of BRD9 chromatin fraction signal normalized to the loading control, Histone H3. Average of three independent experiments; error bars represent one standard deviation from the mean. Source data are provided as Source Data file. c Heat map of BRD9 ChIP signal ± 3 kb surrounding the BRD9 peak center in DMSO- or I-BRD9-treated ESCs, ranked according to BRD9 read density in DMSO. d Scatterplot of log2-transformed BRD9 ChIP tags in DMSO- and I-BRD9-treated ESCs. Blue and red correspond to 1.5-fold decrease or increase of BRD9 tag count in I-BRD9-treated ESCs, respectively (Poisson p value < 0.0001). e Venn diagram overlap of differentially decreased BRD9 ChIP sites after 6 and 24 h of I-BRD9 addition. f Histogram of BRD9 ChIP reads ± 2 kb surrounding the BRD9 peak center in DMSO and after 6 or 24 h of I-BRD9 treatment. g Representative genome browser tracks showing the progressive decrease in BRD9 ChIP reads with I-BRD9 treatment at 6 and 24-h time points. h Heat map of log2 FC in mRNA expression for genes annotated to BRD9 ChIP binding sites. Sites are ranked by degree of BRD9 ChIP signal loss after 24 h of I-BRD9 treatment, as indicated by an orange gradient. i Scatterplot of log2-transformed BRD9 ChIP tags in DMSO- and I-BRD9-treated ESCs at sites that are annotated to the genes that are significantly changed upon I-BRD9 treatment. Red line indicates y = x and corresponds to no change. j As in i, but for BRG1 ChIP tags in DMSO- and I-BRD9-treated ESCs. k Histogram of BRG1 ChIP reads ± 1 kb surrounding the BRG1 peak center in DMSO and after 24 h of I-BRD9 treatment, at sites annotated to I-BRD9 DEGs. Numbers of ChIP sites and of genes annotated to these sites are indicated