The genome-wide AR interactome in prostate cancer cells. (A) Circos (Krzywinski et al. 2009) view of the AR interactome landscape in Chromosome 1. From innermost to outermost: (1) AR ultra-long-range looping (>1 Mbp), FISH-validated loops are highlighted in black, and the locations of the three FISH probes P1, P2, and P3 are annotated; (2) chromatin state track; (3) AR-Gene Linking; (4) AR target genes; (5) GRO-seq signal 2 h after DHT; (6) RNA-seq signal 6 h after DHT. (B) FISH analysis for the intra-Chromosome 1 interaction (16934619–21771843). (C) Summary of the validation rate of FISH experiments from examining 180 cells. (D) Breakdown of AR binding sites (ARBS) according to their associated type of chromatin interaction model classification from our previous study (Fullwood et al. 2009). (E) The fraction of ARanchor in either intra-genic regions or inter-genic regions whose targets genes were defined by ChIA-PET interaction matching the nearest gene. (Only Nearest) The nearest gene is the only target gene, (Contain Nearest) the nearest gene is one of the target genes, (Only Distal) the nearest gene is not one of the target genes. (F) Bar plot (Wickham 2009) showing the fraction of genes from different categories that are up-regulated after DHT. The genes with AR looping in their TSS show more up-regulation events than genes with only ARalone in proximal 5 kbp to TSS and random genes. (G) Snapshot representation (from top to bottom) of the AR binding peak profile (defined by ChIP-seq), AR self-ligation peak profile (defined by ChIA-PET), AR-associated chromatin interaction profile (defined by ChIA-PET), transcriptional rate profiles (defined by GRO-seq), and steady-state mRNA level profiles (defined by RNA-seq) associated with the androgen-regulated gene, FKBP5.
