Fig. 3
From: Acute depletion of CTCF rewires genome-wide chromatin accessibility
CTCF-dependent chromatin accessibility regulates gene expression either through a promoter or enhancer-promoter loops. A Volcano plots of chromatin accessibility changes at gene promoters. Differential ATAC-seq peaks were defined at cutoffs of ILog2 fold change > 1 and an adjusted p value < 0.05. A total of 480 genes with decreased promoter ATAC signals and 4150 genes with increased promoter ATAC signals are shown. B Genomic heatmap of normalized ATAC-seq signals centered at ATAC-seq DARs with consistent gene expression changes. C Heatmap of expression levels and ATAC-seq signals at promoters of genes with consistent changes upon CTCF depletion (z-score was calculated independently by either expression or ATAC-seq signal). D Screenshot of the CTCF promoter with ATAC-seq tracks in CTCFAID cells with or without IAA treatment. Averaged tracks are combined analyses of three individual clones. E Q-PCR analysis of CTCF mRNA expression after CTCF protein depletion for 24 and 48 h and washout from three biological replicates of clones 27, 35, and 42