Fig. 3
From: Nickel-induced transcriptional changes persist post exposure through epigenetic reprogramming
H3K4me3 profiles at persistently upregulated (PU) genes. a Genome browser image showing expression levels (RNA-Seq) of DSP, a representative PU-A gene. b Genome browser image showing H3K4me3 at DSP. c, d Scatter plots showing changes in H3K4me3 levels in all-genes (grey) and PU-A genes (red). x-Axes in c and d show changes in the levels of H3K4me3 in Ni-E cells compared to UT cells. y-Axis in c shows changes in the levels of H3K4me3 in Ni-W cells compared to UT cells, and y-axis in d shows changes in the levels of H3K4me3 in Ni-W cells compared to Ni-E cells. Intensity of red dots represents the gene expression values in UT cells, with darker colors indicating higher expression values. e Quantitation of the scatter plots c and d. f Box plot showing H3K4me3 levels at all-genes and PU-A genes. PU-A genes show higher H3K4me3 enrichment in untreated cells. g Genome browser image showing expression levels (RNA-Seq) of CADM3, a representative PU-B gene. h Genome browser image showing H3K4me3 at CADM3. i, j Scatter plots showing changes in H3K4me3 levels in all-genes (grey) and PU-B genes (red). x-Axes in i and j show changes in the levels of H3K4me3 in Ni-E cells compared to UT cells. y-Axis in i shows changes in the levels of H3K4me3 in Ni-W cells compared to UT cells, and y-axis in j shows changes in the levels of H3K4me3 in Ni-W cells compared to Ni-E cells. Intensity of red dots represents the gene expression values in UT cells, with darker colors indicating higher expression. k Quantitation of the scatter plots i and j. P values were calculated using one-tailed Student’s t-test. n.s.not significant. PU-A (persistently upregulated-A), genes upregulated during nickel exposure with the increased expression continuing after the termination of exposure; PU-B (persistently upregulated-B), genes upregulated after the termination of nickel exposure; CDS, chromatin dynamic score (see “Methods” for details)