Genomic Androgen Receptor-Occupied Regions with Different Functions, Defined by Histone Acetylation, Coregulators and Transcriptional Capacity
Figure 1
Characterization of ARORs and AcH3 regions on chromosome 19 and 20.
Three replicate ChIP-chip experiments identified 738 Androgen Receptor Occupied Regions (ARORs), 62 of which were common to all three replicates (L1 ARORs) and 127 common to only two of three (L2 ARORs), while two replicate ChIP-chip experiments identified 1,388 regions with acetylated histone H3 marks, 1,189 of which were present in both replicates (A). Genome plots are shown for the kallikrein locus (B) and three other AROR-containing loci (C), where AR-ChIP peaks are labeled, and raw log2 ratios [from 0 (1-fold) to 2 (4-fold)] for each replicate are shown in green (AR-ChIP) and blue (AcH3-ChIP). Panel (D) shows the genomic positioning of the 189 L1/L2 AROR peaks and 1,189 AcH3 peaks. A cumulative distribution plot (outer) shows that the distance from annotated transcription start sites (TSSs) is similar between ARORs, Estrogen Receptor Occupied Regions (ERORs) from [2], and randomly selected regions from the repeat-masked tiling array, while a majority of AcH3 peaks are located at or near TSSs. All three classes (AROR, EROR, and AcH3) are excluded from exons relative to randomly selected regions (insert). The selected ARORs were validated by independent ChIP-qPCR (E–G). C4-2B cell were incubated in phenol red-free RPMI 1640 containing 5% CSS for 3 days and then treated with 10 nM DHT or ethanol (EtOH) vehicle for 4 h. Conventional site-specific ChIP assays were performed with anti-AR antibody. Normal IgG was used in parallel. Twenty-one L1 ARORs (E), 7 L2 ARORs (F) and 4 negative control (NC) (see table S4) (G) regions were examined by TaqMan qPCR. Acetylated ARORs are indicated by asterisks. A042 (F) is the PSA enhancer and acted as a positive control. All values are presented as percentage of input.