Fig. 4

Analysis of genome-wide distribution of H3K4me3 by EPAT-ChIP. Purified DNA previously immunoselected from an archival invasive breast carcinoma sample was subjected to massive parallel sequencing. Snapshots of ChIP-Seq data from UCSC Genome Browser showing the correspondence between standard PAT-ChIP (Std) and EPAT-ChIP (LRC) signals at promoters of the active genes VCL (a) and GAPDH (b) previously amplified by real-time qPCR. Identified peaks (black bars) are marked above the corresponding profile, CpG islands are reported as green bars, and Ref-Seq genes are indicated in blue. c Pie charts depicting the distribution across genomic features with relative percentage values shown on the right. Promoters are defined as − 3 Kb to + 3 Kb relative to the TSS, while Downstream as − 3 Kb relative to the end of 3′ UTR region. d Heatmaps illustrating H3K4me3 read densities from − 10 Kb to + 10 Kb relative to the TSS. e Distribution of H3K4me3 promoter peaks relative to the TSS. f Venn diagram showing common and unique peak-containing promoters identified by standard PAT-ChIP and EPAT-ChIP