Fig. 2
From: Nickel-induced transcriptional changes persist post exposure through epigenetic reprogramming
H3K4me3 profiles at the transiently upregulated (TU) genes. a Genome browser image showing expression levels (RNA-Seq) of GATM, a representative TU gene. b Genome browser image showing H3K4me3 at GATM. c, d Scatter plots showing changes in H3K4me3 levels at all the genes in the genome (all-genes) (grey) and TU 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 gene expression values in UT cells, with darker colors indicating higher expression. e Quantitation of the scatter plots c and d. f Box plot showing H3K4me3 levels at all-genes and TU genes. TU genes show higher H3K4me3 enrichment in untreated cells. P values were calculated using one-tailed Student’s t-test. n.s. not significant. TU (transiently upregulated), genes upregulated during nickel exposure, with the expression reverting to normal levels after the termination of exposure; CDS, chromatin dynamic score (see “Methods” for details)