3D genome in CRPC

Chromatin interactions between regulatory elements, promoters and genes in threedimensional (3D) nuclear space orchestrate cell-type specific gene-expression signatures by modulating RNA Polymerase II (RNA Pol II) activity. This process is dysregulated in cancers. We applied chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) to define the 3D genomic architecture underlying RNA Pol II associated transcription in normal prostate cells and prostate cancer (PCa). By integrative analysis with multiple datasets, we show that RNA Pol II associated chromatin interactions are strongly associated with the acetylation of Histone H3 at lysine 27 (H3K27ac), a mark of active enhancers that is sculpted by the combinatorial action of tissue-specific master transcription factors such as the androgen receptor (AR) and pioneer factors including FOXA1. These master regulators in turn auto-regulate themselves through binding their own enhancers. RNA Pol II associated chromatin interactions are insulated by RAD21 associated chromatin interactions marked by the insulator protein CTCF. By combining analyses from cell lines and metastatic castration resistant PCa (mCRPC) specimens, we show that AR locus amplification is associated with concomitant amplification of its enhancers and augmented chromatin interactions contributing to AR over-expression. We deconvolute the transcriptional regulation of PCa biomarkers (KLK3), lineage restricted genes (KRT8, KRT18, HOXB13, ZBTB16), drug targets (EZH2) and oncogenes (MYC). Critically, we also show that germ-line PCa predisposing SNPs from genome-wide association studies (GWAS) significantly overlap with RNA Pol II associated chromatin interactions in normal prostate cells; this overlap is progressively lost as PCa develops and ultimately disappears when PCa cells change their lineage identity. Our studies implicate changes in 3D genome organization as a critical determinant of aberrant transcriptional regulation in PCa.