An AR-ERG co-mediated chromatin interactome defines the transcriptional network in prostate cancer cells

An aberrant androgen receptor (AR) transcriptional network underpins prostate cancer development. Even though the AR cistrome had been extensively studied in prostate cancers, information pertaining to the spatial architecture of the AR transcriptional circuitry remains limited due to the absence of an AR-associated chromatin interactome map. To resolve this, we utilized chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to profile AR-associated and ERG-associated long range chromatin interactions in an ERG fusion positive prostate cancer cell line. We identified ERG-associated long range chromatin interactions as an elemental component in the AR-associated chromatin interactome, acting in concert, to achieve coordinated regulation of AR target genes. In addition, we characterized the epigenetic signature of the AR/ERG anchor binding sites and implicated AR and ERG associated chromatin loopings for facilitating fusion gene formation in prostate cancers. Taken together, our results revealed the presence of an AR/ERG defined higher order chromatin structure exploited for driving prostate cancer progression. Overall design: Chromatin interaction analysis coupled with Pair End Tags of AR and ERG: ChIP using anti-AR antibody and anti-ERG antibody, followed by close proximity ligations. ChIA-PET libraries were generated from VCaP cells treated with 100nM DHT. GRO-seq was performed as described previously (Core, Waterfall et al. 2008) with limited modifications. GRO-seq and RNA-PET libraries were generated from VCaP cells grown in phenol red-free RPMI medium and treated with 100 nM DHT as the timepoints indicated. The libraries of RNAs were prepared for Illumina sequencing.