Fig. 4
From: High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing
Allele-dependent transcriptional regulation at rs13215402. a TF enrichment at SNP rs13215402 site by ChIP-seq analysis. The SNP region is occupied by multiple TFs including AR, FOXA1, HOXB13, and active enhancer epigenetic marks including H3K4me1/2 and H3K27ac. b TF enrichment at SNP rs13215402 site by ChIP-AS-qPCR analysis. Allele A of this SNP has lower FOXA1 occupancy than allele G in LNCaP cells. The P values were calculated using the two-tailed Student’s t-test, mean ± s.d. c, d Luciferase reporter assay at rs13215402 site. The relative luciferase activity for allele A is lower than allele G both under ETH and DHT treatment in LNCaP cells. The P values were calculated using the two-tailed Student’s t-test, mean ± s.d. e Suppression of RGS17 expression through allele-specific CRISPRi assay. Compared to non-target control (NTC), interference of either allele A or G downregulated RGS17 expression, with allele G showing statistical significance. The P values were calculated using the two-tailed Student’s t-test, mean ± s.d. f Elevated RGS17 expression after converting genotype of rs13215402 G/A to G/G in 22Rv1 cells by CRISPR/Cas9. Compared to parental cell line 22Rv1 with G/A genotype, two subclones of 22Rv1 with G/G genotype show threefold increase of RGS17 expression. The P values were calculated using the two-tailed Student’s t-test, mean ± s.d. g eQTL analysis between rs13215402 and RGS17. Compared to G/G genotype, the A/A genotype is associated with lower expression of RGS17 in benign prostate tissues22. The upper, middle, and lower bounds of boxes represent the 75th, 50th, and 25th percentile of the values, respectively. The whiskers represent 95th to 5th percentile. The P values were calculated using the correlation/trend test (genotype association test in Golden Helix)
