Genome-wide behavior of IRF8 during monocyte/macrophage differentiation. Tot2 cells were transduced with empty MSCV-puro or MSCV-IRF8-puro vectors. Transduced cells were selected by puromycin. (A) Summary of the locations of IRF8 ChIP-seq peaks in IRF8-transduced Tot2 cells. ChIP-seq for IRF8 was performed on day 3. (B) Correlation between IRF8 binding and gene expression changes. Gene expression profiling by microarray was performed in biological duplicates on day 4. Genes were ranked in order of fold induction by IRF8. The frequencies of the presence of promoter-proximal or -distal IRF8 ChIP-seq peak(s) per gene were calculated in a sliding window comprising 1000 ranked genes. (C) The frequencies of genes with promoter-proximal and/or -distal IRF8 binding among the IRF8-upregulated genes. FC indicates fold change. (D) De novo DNA motif analysis of promoter-proximal (left panel) and promotor-distal (right panel) IRF8 binding sites in IRF8-upregulated genes. Numbers indicate the percentage of the ChIP-seq peaks containing the motif. The background frequency is shown in parentheses. (E) Heatmaps of promoter-distal IRF8 binding, H3K4me1, and PU.1 binding. ChIP-seq analyses for H3K4me1 and PU.1 were performed on day 3. Each horizontal line represents the density of indicated ChIP-seq tags in the 10-kb region centered on the promoter-distal IRF8 peak summit. “Cells: MSCV” indicates MSCV-puro–transduced cells. “Cells: IRF8” indicates MSCV-IRF8-puro–transduced cells. (F) Cumulative H3K4me1 and PU.1 levels around IRF8 ChIP-seq peak positions. Histograms of averaged ChIP-seq tag densities are presented.