Fig. 4
Short CpG islands are enriched in early response genes. a Murine LPS-stimulated BMDCs (left panel) and heregulin-stimulated human breast adenocarcinoma cells (right panel) demonstrate an enrichment for short CpG islands immediately post-stimulation compared to later time points. b Stimulation-specific enrichment for longer CpG islands post-stimulation in MCF7 breast adenocarcinoma (left) and retinal pigment epithelial cells (right). Plotted are the top 250 up-regulated genes with the largest log2-fold changes between time points (early, 0 vs 1 hr and late, 1 vs 2 hr). CpG island size is truncated at 3 kb for clarity. Vertical dashed lines denote the median CpG island length for the most up-regulated genes in the relevant time-point comparison (early is orange and late is yellow). c Highly variable genes in unstimulated BMDCs mark early response genes. Gene expression noise (CV2, y-axis) in unstimulated BMDCs across CpG island genes binned into 0.5-kb intervals (x-axis). Points are coloured by the direction of differential expression between unstimulated cells and 1-h post-stimulation (blue for down-regulated, yellow for no change and red for up-regulated). Filled grey circles represent the mean CV2 within each size category for differential expression. BMDC bone marrow-derived dendritic cell, ER α oestrogen receptor α, HRG heregulin, LPS lipopolysaccharide, SWI/SNF switch/sucrose non-fermentable complex