Fig. 5: Direct effects of the ABC variant rs4810856 on ZEB1 affinity, target genes expression and cell proliferation. | Nature Communications

Fig. 5: Direct effects of the ABC variant rs4810856 on ZEB1 affinity, target genes expression and cell proliferation.

From: Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk

Fig. 5

CRISPR/Cas9 mediated single variant mutation of rs4810856 in SW480 and HCT116 cells. The genotype of rs4810856 was converted from CC to CT in SW480 cells (a), and from CT to TT in HCT116 cells (b). c Chromatin enrichment of ZEB1 at the rs4810856 in parental (SW480[CC] and HCT116[CT]) and mutated cells (SW480[CT] and HCT116[TT]). Data were presented as the median (minimum to maximum) and normalized to the input from three repeated experiments, each with three replicates. IgG served as negative control. ***P < 0.0001 were calculated by a two-sided Student’s t-test. d Expression of target genes in parental and mutated cells. Data were presented as the mean ± SEM of triplicate experiments, each with 3 technical replicates. ***P < 0.0001, **P < 0.001 were calculated by a two-sided Student’s t-test. e The effects of ZEB1 knockdown on target genes expression in parental and mutated cells. The center line of the box presentation as the median, box limits indicated upper and lower quartiles, and whiskers indicated the maximum and minimum. ***P < 0.0001, **P < 0.001 were calculated by a two-sided Student’s t-test, from three independent experiments with three technical replicates. f Enrichment quantification of allele-specific 3 C profiles in CRISPR/Cas9 editing cell lines with different rs4810856 genotypes depict the relative interaction frequencies between DNA fragment containing rs4810856 as the anchor and representative BssKI enzyme cutting sites indicated by dot plot. Data were shown as the mean ± SD of triplicate experiments. **P < 0.001, *P < 0.01 were calculated by a two-sided Student’s t-test. g The direct effect of rs4810856 genotype on cell proliferation. Results were shown as the means ± SEM from triplicate experiments. ***P < 0.0001, **P < 0.001 were calculated by a two-sided Student’s t-test. h The direct effect of rs4810856 genotype on colony formation ability. The results presented colony formation ability relative to control cells (set to 100%). Data were shown as the median (minimum to maximum) from triplicate experiments. ***P < 0.0001 were calculated by a two-sided Student’s t-test. Source data are provided with this paper.

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