Fig. 5
From: Nickel-induced transcriptional changes persist post exposure through epigenetic reprogramming
H3K4me3 profiles at the persistently downregulated (PD) genes. a Genome browser image showing expression levels (RNA-Seq) of CDKN2B, a representative PD-A gene. b Genome browser image showing H3K4me3 at CDKN2B. c, d Scatter plots showing changes in H3K4me3 levels in all-genes (grey) and PD-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, darker colors indicating higher expression values. e Quantitation of c and d. f Genome browser image showing expression levels (RNA-Seq) of SELENBP1, a representative PD-B gene. g Genome browser image showing H3K4me3 at SELENBP1. h, i Scatter plots showing changes in H3K4me3 levels in all-genes (grey) and PD-B genes (red). x-Axes in h and i show changes in the levels of H3K4me3 in Ni-E cells compared to UT cells. y-Axis in h shows changes in the levels of H3K4me3 in Ni-W cells compared to UT cells, and y-axis in i 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. j Quantitation of h and i. P values were calculated using one-tailed Student’s t-test. n.s. not significant. PD-A (persistently downregulated-A), genes downregulated during nickel exposure with the downregulation continuing after the termination of exposure; PD-B (persistently downregulated-B), genes downregulated after the termination of nickel exposure; CDS, chromatin dynamic score (see “Methods” for details)