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. Author manuscript; available in PMC: 2013 Jul 20.
Published in final edited form as: Cell. 2012 Jul 20;150(2):279–290. doi: 10.1016/j.cell.2012.05.043

Figure 4. Promoter and Chromatin Properties of Co-Expressed Genes.

Figure 4

(A) The distribution of CpG-island promoters was determined for each class from Figure 3 on the basis of expression kinetics of chromatin-associated transcripts. Levels of histone H3K4me3, H3K27me3, and RNA polymerase II at the promoters in unstimulated cells is shown. ChIP-Seq values represent the signal within a 1 kb window centered on the TSS. Each column is normalized to the average enrichment at all inducible promoters, and color-coded according to percentile.

(B) The number of genes that contain CpG island (red) or LCG (blue) promoters within each co-expressed class is shown.

(C) The quantitative distributions of promoter-associated histone H3K4me3 (top) and RNA polymerase II (bottom) in unstimulated cells is shown for each class subdivided by promoter CpG content. The scale of the boxplots represents the intensity of ChIP-Seq peaks as determined in De Santa et al. (2009).

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