BRG1 occupancy profiling by high throughput sequencing from control and PTEN knockdown 22RV-1 cells

To identify the downstream targets and pathways mediated by BRG1, chromatin immunoprecipitation followed by sequencing (ChIP–seq) was performed in control and PTEN-knockdown 22RV-1 cells. Total 6279 genes showed the enhanced BRG1 occupancies in PTEN-knockdown cells as compared to that in control cells. Genome-wide analysis revealed that PTEN loss lead to increase BRG1 intervals specifically localized at enhancers, but not distal promoter regions. We therefore reasoned ablation of BRG1 might impair enhancer configurations in PTEN-deficient cells. Lentivirus-mediated RNA interference was used to knockdown PTEN expression in prostate cancer cell line 22RV-1. The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against BRG1 (abcam, ab110641).