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Figure 1 | Genome Biology

Figure 1

From: Defining the chromatin signature of inducible genes in T cells

Figure 1

Inducible genes have higher levels of H3K9ac at their promoters. The H3K9ac levels determined from ChIP-on-chip experiments are plotted for genes grouped by their kinetics of expression (red, primary response genes; blue, secondary response genes; white, unchanged genes) and their basal expression levels (Log2 robust multichip average values from expression profiling). (a, b) Levels of H3K9ac were compared to either total genomic input DNA (a) or total H3 levels determined by ChIP-on-chip (b). (c) The proportion of promoters with a H3K9ac MAT score >35.2 (FDR <5%) was plotted for each of the gene groups. Three biological replicates were performed for each ChIP-on-chip and the data combined (a-c). (d, e) Real-time PCR was used to verify the results of microarrays (d) for a selected group of genes and to examine the H3K9ac levels for a set of well characterized inducible genes at the promoter region (e). In (d) the genes are plotted from the left to right in order of decreasing predicted H3K9ac score from the ChIP-on-chip data (with H3 levels as background control). The H3K9ac/total input (green bars), the H3/total input (hatched green bars) and the H3K9ac/H3 ratios (black bars) are shown (d, e). The averages of three independent experiments are plotted; n = 3; error bars = standard error of the mean. (f) Data from ChIP-Seq experiments on human CD4+ lymphocytes [28] were analyzed to determine the number of H3K9ac sequence tags that overlapped with the promoter region (-1 kb to +1 kb) of each gene and the data are plotted for the different gene groups. The basal expression levels of the genes are from a matching human CD4+ lymphocyte microarray analysis [GEO:GSE10437]. 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 (a, b, f).

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