Fig. 4: The SNP rs2297440-associated enhancer promotes glioma progression by regulating SOX18 expression.
From: Systematic decoding of functional enhancer connectomes and risk variants in human glioma
a, H3K27ac signal at the rs2297440-associated enhancer in normal brain, glioma tissues and glioma cell lines. b, The relative mRNA expression of RTEL1 in U251 cells after the rs2297440-associated enhancer KO. c, MTT assay showing the proliferation of enhancer KO (eKO) U251 cells. d, Colony formation assay in WT and eKO U251 cells. e, Scatter plots of differential expression of genes interacting with the rs2297440-associated enhancer between WT and eKO cells. f, The relative mRNA expression of SOX18 in U251 cells after enhancer KO. g, Top: genome architecture mapping contact matrix of the chr20: 62,500–64,200 kb genomic window, showing increased interaction between the rs2297440 locus and the SOX18 gene in glioma compared with normal brain tissues. Bottom: confirmation of 3C-PCR and Sanger sequencing detected contacting genomic fragments for SOX18 and rs2297440 locus. h, PCR–agarose gel electrophoresis of the ligation products of SOX18 TSS region and rs2297440 locus in U251, LN229 and U87 cells. This PCR–agarose gel electrophoresis was carried out once (n = 1). i, Relative connection frequency measured by 3C-qPCR in U251 WT cells and enhancer KO (eKO1 and eKO2) cell lines. Data represent mean ± s.d. of three independent experiments. Statistical significance was determined by two-sided t-test. NS, not significant.
