Fig. 3 | Scientific Reports

Fig. 3

From: G-quadruplex forming regions in GCK and TM6SF2 are targets for differential DNA methylation in metabolic disease and hepatocellular carcinoma patients

Fig. 3

Regulatory roles of GCK and TM6SF4 target regions. (A). Activating (H3K27ac, H3K4me1 and H3K4me3) and repressing (H3K27me3) histone modifications obtained from ChIP-seq experiments from ENCODE for H1-hESC (stem cells, red), HepG2 (hepatoblastoma, blue), NHLF (healthy lung, orange), K562 (blood, brown), NHEK (normal human epidermal keratinocytes, violet) and MCF7 (breast cancer, green) cell lines82 in GCK (left panel) and TM6SF2 (right panel). For the hg19 genome assembly ENCODE did not provide H3K4me1 data for MCF7 cells. Yellow highlighted areas represent the pyrosequencing regions. Here we showed a cell-type specific pattern of activating and repressing histone marks. (B). The CpG-free basic vector was used to test for a putative promoter function and the CpG-free promoter (containing a minimal promoter) vector to test for a putative enhancer function of the differentially methylated regions in a luciferase gene reporter assay in (C). GCK exon 7 and (D). in the TM6SF2 intron 2-exon 3 boundary, in a methylated and unmethylated state compared to the empty vector (EV). Pairwise comparison against empty vectors (Welch two sample t-test), *p < 0.05, **p < 0.01, ***p < 0.001.

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