Fig. 2

Comparison between methylation and expression data for macrophage (MAC) and dendritic cell (DC) differentiation and maturation. a Heatmap of significant changes between monocyte (MOs)-to-immature DC (iDC) and MO-to-immature MAC (iMAC) differentiation (left) and two additional heatmaps showing significant changes between iDC-to-mature DC (mDC) , and iMAC-to-mature MAC (mMAC) maturation. The heatmaps include all the genes displaying significant expression changes (>2-fold or <0.5-fold change; p < 0.01 and false discovery rate < 0.05). A scale is shown at the bottom, wherein expression values range from −3 (lower expression levels, blue) to +3 (higher expression levels, red). b Venn diagrams showing the degree of overlap of genes upregulated and downregulated between MO-to-iDC and MO-to-iMAC differentiation and iDC-to-mDC and iMAC-to-mMAC activation. c Scatterplots showing the relationship between the log₂-transformed fold change (FC) in expression and the log₂-transformed FC in DNA methylation. d Correlation between DNA methylation and expression data (the mean value for all CpG sites within a given sequence region is shown) for all the significantly demethylated genes organized by genomic location [intergenic, promoter (1,500 and 200 upstream of the transcription start site (TSS), 5′ untranslated region (UTR), first exon, gene body, and 3′UTR)]. e Box-plots representing the DNA methylation and expression values of all genes that are demethylated during DC and MAC differentiation and whose upregulation is stronger in the maturation step than in the previous differentiation step. f Diagram showing the proportion of genes among the DC-specific, MAC-specific and those that are demethylated in both processes with no significant changes in expression during the differentiation step and upregulated during the lipopolysaccharide (LPS)-dependent activation step. g Time-course analysis of DNA methylation and expression in two selected genes (IL1B and CCL20) during DC and MAC differentiation/maturation, among those displaying no changes in the differentiation step and a sharp increase in the maturation step. h Chromatin immunoprecipitation assays in IL1B and CCL20 with anti-histone H3K27me3 and anti-histone H3K9me3 in MOs, and in a time-course manner in differentiation to iDCs and iMACs, as well as mDCs and mMACs (120 h + LPS). The Y-axis shows the relative enrichment in arbitrary units