Figure 7

Role of other factors in differential gene regulation. (a) AR, AR-V7, FOXA1, HOXB13, NFIB, CTCF, cMYC average ChIP-seq signal intensity per every 10 bp bin at common, AR and AR-V7 binding sites identified in Fig. 3, panel a. Data were generated from LNCaP cells and ChIP signals plotted are within ± 1 kb from the center of AR and AR-V7 binding sites using publicly available data listed in STable 1. (b–d) qPCR analysis measuring gene expression upon HOXB13 depletion using the method previously described for FOXA1. All qPCR plots are expression values normalized to 18S on the y-axis and corresponding treatment on the x-axis. Data are plotted as mean of three biological replicates from the same experiment and error bars are SEM. Each experiment was performed a minimum of three times and a representative experiment is shown here. (e) Venn diagram showing number of AR and AR-V7 binding sites in LNCaP AR-V7 cells overlapping FOXA1 binding sites in LNCaP cells (peaks with a local FC > 5 and at least a base pair overlap). (f) Venn diagram showing number of AR and AR-V7 binding sites in LNCaP AR-V7 cells overlapping HOXB13 binding sites in LNCaP cells (peaks with a local FC > 5 and at least a base pair overlap). (g) Consensus sequence reported by HOMER motif analysis of all AR-V7 peaks identified from LNCaP AR-V7. Motif enrichment p value for de novo motif and known half ARE motif were calculated using cumulative binomial distribution. Venn diagrams (e,f) are plotted as symmetrical circles and not proportional to numbers.