Figure 3

Inducible genes have higher levels of H3K4me3 and lower levels of H3K27me3. (a, b) Data from ChIP-Seq experiments with human CD4+ lymphocytes [28] were analyzed to determine the levels of H3K4me3 (a) and H3K27me3 (b) on different gene groups. The number of sequencing tags that overlapped with the promoter region (-1 kb to +1 kb) of each gene was used to score the genes and the data are plotted for the genes grouped by their kinetics of response to activation (red, primary response genes; blue, secondary response genes; white, unchanged genes) and basal expression levels (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. (c, d) ChIP was performed with antibodies against H3K4me3 (green bars) and H3K27me3 (black bars) using unstimulated EL-4 T cells and analyzed by real-time PCR, with primers designed against the promoter region. The data are presented as a ratio of immunoprecipitated DNA to total input DNA. The mean and standard error of three independent experiments are shown. (e) From the same data source used in (a) the number of sequencing tags for mono, di and tri-methylated H3K4 and H3K27, 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.