A method that combines the chromatin immunoprecipitation (ChIP) and “promoter” arrays was developed to identify the genes whose promoters are regulated directly by androgen receptor (AR) or AR-ligand complexes (active AR) in hormone-sensitive LNCaP cells. We have developed promoter arrays containing 3083 unique promoter sequences including 28 known or suspected AR-binding sequences as previously described [1]. ChIP-captured DNA has been applied to these arrays in order to identify genes bound and activated by AR. In the presence of androgens, significant changes of acetylation of H3K9 and recruitment of pol II to the transcriptional complexes were experimentally quantified for the 3083 arrayed sequences. Representative genes identified by array hybridization were verified by quantitative PCR. Affymetrix expression arrays were used for analysis of transcriptional changes following addition of synthetic androgen R1881 to LNCaP cells. The expression changes were correlated with the promoter occupancy and presence of transcriptional complexes. Additionally ChIP with anti-polymerase II (pol II) and anti-acetylated histone revealed that pol II binding and H3K9ac changes correlated with AR binding. Overlapping gene subsets were delineated by standard and customized bioinformatic tools semi or quantitatively. These include DEGS, ARHB, BCL2L2 as well as NKX3.1 and PSA. Our data suggest that AR is bound to DNA even in the absence of androgens, and that androgen binding regulates a profile of genes involved in cell growth. Administration of androgens increases AR binding to the specific sites, pol II recruitment and acetylation of H3K9 and these overall changes potentates an increase in transcriptional regulatory activity in an AR-dependent manner. [1] Hayakawa et al. Hayakawa J, Mittal S, Wang Y, Korkmaz KS, Adamson E, English C, Omichi M, McClelland M, Mercola D. Identification of Promoters Bound by c-Jun/ATF2 during Rapid Large-Scale Gene Activation following Genotoxic Stress. Molecular Cell 6:521-35, 2004

[Proc Amer Assoc Cancer Res, Volume 46, 2005]