Supplementary Figure 11: Identification of AR late-response genes regulated by PCAT1.
From: Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer
(a) qPCR validation of androgen late-response genes (with AR and LSD1 binding within ±10 kb of the TSS). (b) Expression of androgen late-response genes after PCAT1 knockdown. (c) Expression of androgen late-response genes with PCAT1 overexpression. (d) Outlier analysis shows that GNMT is upregulated in prostate cancer tumors as compared to normal prostate tissues. Inset tables quantify expression for ‘positive’ and ‘negative’ samples defined using a cutoff at the 75th percentile (red dashed line). Statistical significance was determined using χ2 tests. (e–j) Regulatory regions of androgen late-response genes for ChIP–qPCR. The highlighted AR and LSD1 peak regions were used to design primers for ChIP–qPCR. (k) AR and LSD1 occupancy at enhancers of androgen late-response genes after PCAT1 knockdown. (l) PCAT1 ChIRP enriches for human PCAT1 RNA. (m) PCAT1 ChIRP–qPCR in LNCaP cells. Enhancers of DHCR24 and GNMT are regions that interact with PCAT1. The KLK2 enhancer served as a negative control. P value was calculated by Student’s t test in l and one-way ANOVA in m: *P < 0.05, **P < 0.01.
