Fig. 3: Brd7 loss alters chromatin accessibility and modulates immune regulatory enhancer elements.

A ATAC-seq was performed in Control (shNTC) and Brd7-KD (Brd7-sh1 and Brd7-sh4) 4T07-TGL cells. Chromatin accessibility heat maps for gained (top panel) and lost (bottom panel) peaks in Brd7-KD 4T07-TGL cells. Peaks were rank ordered by intensity per million mapped reads (RPM). B Overall aggregated enrichment signals within 3 kb of peak centers for differentially accessible regions. C Genomic annotation of gained peaks (left panel) and lost peaks (right panel). D GO analysis of overlap between upregulated genes in Brd7-KD samples (RNAseq) and genes associated with gained ATAC-seq peaks in Brd7-KD samples. E Top 13 gained peak motifs from these overlapping loci and corresponding transcriptional factors. F GO analysis of overlap between downregulated genes in Brd7-KD samples (RNAseq) and genes associated with lost ATAC-seq peaks in Brd7-KD samples showing enrichment for immune regulation pathways. G Top 8 enriched binding motifs from these overlapping loci and predicted transcriptional factors. H Heatmap showing ChIP-Seq signals for H3K27ac peak regions, rank ordered by intensity per million mapped reads (RPM). I Overall H3K27ac peak signal between − 3 kb and 10 kb relative to peak center for gained or lost peaks in Brd7-KO cells. J Genomic annotation of gained (left panel) and lost (right panel) H3K27ac peak distribution. K, L Gene Ontology (GO) analysis of overlap between upregulated genes (RNAseq) and genes associated with gained H3K27ac peaks in Brd7-KO samples (K; N = 224)) and between downregulated genes (RNAseq) and genes associated with lost H3K27ac peaks in Brd7-KO samples (L; N = 55). M, N Top binding motifs in Brd7-KO cells associated with lost (M) and gained (N) H3K27ac and predicted transcriptional factors.