Fig. 4. The enhancer transcriptionally regulates the lncRNA hub.

a Expression level of PCAT1 is plotted against the DHS intensity at rs72725854 regions across eight cell lines from ENCODE data. b Expression level of PCAT1 is plotted against the nascent-RNA signal derived from GRO-seq in LNCaP and MCF7 cell lines. c q-RT-PCRs show the relative fold changes of pre-mRNAs of various lncRNAs and MYC upon constitutive CRISPR blocking of the rs72725854 region with scr or specific gRNAs in LNCaP cells using dCas9-KRAB. Error bars denote SEM from three biological replicates. d, e Expression of PCAT1, PVT1, and MYC in patient tumor samples with different alleles of rs72725854 namely; AA, AT, and TT at pan-cancer level (from PCAWG) (d) and in prostate adenocarcinomas (from PCAWG) (e). Each dot represents a sample and the color indicates relative copy number status of the gene (0 is neutral, 1 is amplified, 2 is high-level amplified, −1 is deleted, −2 is deep deletion). The boxplots in d and e depict the minima (Q1-1.5*IQR), first quartile, median, third quartile, and maxima (Q3 + 1.5*IQR). f The survival analysis of prostate cancer patients exhibiting genetic alteration (copy number or mutations) vs. no alteration in PCAT1 (top), PVT1 (center) and MYC (bottom) genes irrespective of the genotype at rs72725854. The number of patients at each time interval in the cases with alteration (with) and the cases without alteration (without) of the respective gene is given below each plot. The data shown here were obtained from three different prostate cancer cohorts (see “Methods” and Supplementary Fig. 3f). p-values were calculated by Student’s two-tailed unpaired t-test in c. *p < 0.05, **p < 0.01 and ^nsp > 0.05. The p-values in f were calculated by log-rank test. Source data are provided as a Source Data file.