Figure 4: Polymorphisms at 8q24.21 affect HIF binding and chromatin accessibility. | Nature Communications

Figure 4: Polymorphisms at 8q24.21 affect HIF binding and chromatin accessibility.

From: Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer

Figure 4

ChIP and FAIRE assays in cells that are heterozygous for SNP rs35252396. (a) Allele-specific qPCR for rs35252396 using DNA samples from RCC4 (left) and primary renal tubular (PTC, right) cells derived from HIF-1α, HIF-2α (only in RCC4) and HIF-1β ChIP experiments. Input DNA was used as a control and genomic DNA from homozygous cell lines was used for positive controls for the alleles (AC/AC-Caki1 cells and CG/CG-786-O cells). A shift of the qPCR signals towards the minor allele CG indicates enrichment for the risk allele. Data are from three independent ChIP experiments (RCC4) or one ChIP experiment per PTC culture exposed to DMOG for 16 h from four different individuals. (b) Ratios of qPCRs signals from a. The mean ratio of minor allele CG/major allele AC for the input DNA (before immunoprecipitation) was arbitrarily set to 1. Data are mean±s.d.. Data are from three independent ChIP experiments (RCC4) or one ChIP experiment per PTC culture exposed to DMOG for 16 h from four different individuals (three to four technical replicates for each experiment). *One-sample t-test, P<0.05. (c) Allele-specific qPCR for rs35252396 using FAIRE and input DNA samples from RCC4 (left) and primary renal tubular (PTC, right) cells. Results are from two independent experiments (RCC4) or one FAIRE experiment per PTC culture from four different individuals. DNA from homozygous cell lines was used for positive controls for the homozygous alleles (AC/AC and CG/CG). Signals of the positive controls for the homozygous alleles are similar in RCC4 (left) and PTC (right) because these samples were analysed by allele specific in the same qPCR experiment. (d) Ratios of qPCRs signals from c. The mean ratio minor allele CG/major allele AC for the input DNA was arbitrarily set to 1. Data are mean ±s.d. from two independent experiments (RCC4) or one FAIRE experiment per PTC culture from four different individuals (8–10 technical replicates each). *One-sample t-test, P<0.05.

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