Figure 3: ATAC-Seq and Histone ChIP-Seq of Both Cell Types Accurately Map Out Epigenomic Profiles That Corroborate the Corresponding Transcriptomes

(A) Overlap of loci for assay in transposase accessible chromatin–sequencing (ATAC-seq) (open chromatin) and chromatin immunoprecipitation–sequencing (ChIP-seq) for H3K4me3 (active promoters) and H3K27me3 (repressed domains) in Venn diagrams. (B) Distribution of ATAC-seq and histone ChIP-seq peaks around transcription start sites (TSS) of genes. ATAC (red), H3K4me3 (green), and H3K27me3 (blue) peaks are plotted to show their enrichment around TSS. The x-axis shows the distance in kilobase centered on gene TSS; the y-axis depicts the enrichment of peaks. (C) Genome-wide density plots showing that ATAC-seq and H3K4me3 enrichment at TSS correspond well to genes that are highly expressed, whereas H3K27me3 are more spread out across TSS of genes that are lowly expressed. Blue indicates density signals for ATAC, H3K4me3, and H3K27me3 enrichment at each TSS gene locus ±5 kb represented in each row. Purple indicates expression level in fragments per kilobase of exon per million fragments mapped (FPKM), of the corresponding gene in each row. RNA-seq = ribonucleic acid–sequencing.