Inducible genes have higher RNA polymerase II occupancy at promoter regions. (a) Data from ChIP-Seq experiments with human CD4+ lymphocytes was used to determine the levels of Pol II at the promoters (-0.25 kb to +0.25 kb) of primary (red), secondary (blue) and unchanged (white) genes within each basal expression bin (Log2 robust multichip average values from expression profiling). The bar marks the median score, the edges of the boxes the second and third interquartile ranges and the whiskers the first and fourth interquartile ranges. (b) The percentage of promoters with tag counts equal to or greater than the median level (13) for the unchanged genes in the basal expression Log2 6 to 7 bin were plotted for each subgroup. (c) From the same data source the number of sequencing tags for H3K4me3 and H3K27me27, H3K9ac, H4K16ac, H2BK20ac, H2AK9ac and Pol II, overlapping -1 to +1 kb from the TSS, were counted for primary response genes with basal expression values between Log2 3 and 6. The logs of the sequence counts were median centered and normalized and heatmaps for the primary response genes were generated by uncentered correlation, complete linkage clustering. The major clusters are marked and the genes are colored according to their basal expression level (green, log2 3 to 4; black, log2 4 to 5; red, log2 5 to 6). In the cluster diagram, green indicates low tag counts and red indicates high tag counts. (d) ChIP assays were performed with antibodies against the CTD repeat of Pol II using unstimulated EL-4 T cells and detected by real-time PCR analysis. The data are presented as the ratio of immunoprecipitated DNA to the total input DNA and show Pol II occupancy at the promoter (green bars) and 2 kb downstream of the promoter (black bars). The mean and standard error of three independent experiments are shown.