Dynamic Nucleosome-Depleted Regions at Androgen Receptor Enhancers in the Absence of Ligand in Prostate Cancer Cells

Abstract

Nucleosome positioning at transcription start sites is known to regulate gene expression by altering DNA accessibility to transcription factors; however, its role at enhancers is poorly understood. We investigated nucleosome positioning at the androgen receptor (AR) enhancers of TMPRSS2, KLK2, and KLK3/PSA in prostate cancer cells. Surprisingly, a population of enhancer modules in androgen-deprived cultures showed nucleosome-depleted regions (NDRs) in all three loci. Under androgen-deprived conditions, NDRs at the TMPRSS2 enhancer were maintained by the pioneer AR transcriptional collaborator GATA-2. Androgen treatment resulted in AR occupancy, an increased number of enhancer modules with NDRs without changes in footprint width, increased levels of histone H3 acetylation (AcH3), and dimethylation (H3K4me2) at nucleosomes flanking the NDRs. Our data suggest that, in the absence of ligand, AR enhancers exist in an equilibrium in which a percentage of modules are occupied by nucleosomes while others display NDRs. We propose that androgen treatment leads to the disruption of the equilibrium toward a nucleosome-depleted state, rather than to enhancer de novo “remodeling.” This allows the recruitment of histone modifiers, chromatin remodelers, and ultimately gene activation. The “receptive” state described here could help explain AR signaling activation under very low ligand concentrations.

ACKNOWLEDGMENTS

We thank the USC Epigenome Center and its support from the Norris Foundation for high-throughput sequencing and data processing. This work was supported by the Whittier Foundation and grants from the NIH to G.A.C. (R01 CA 109147 and R01 CA 136924), U.S. National Institutes of Health grants to C.A.-V. (T32 CA009320) and P.A.J. (R37 CA082422), and a grant from The Concern Foundation to L.J.

The funding agencies had no role in study design, data collection and analysis, the decision to publish, or preparation of the manuscript.

We thank Phillippa Taberlay for critical reading of the manuscript and Suhn Kyong Rhie for helping with statistical analyses.

C.A.-V., J.L., P.A.J., and G.A.C. designed experiments; C.A.-V., J.L., and L.J. performed experiments; C.A.-V., J.L., and B.P.B. analyzed data; and C.A.-V., J.L., B.F., P.A.J., and G.A.C. wrote this report.

We have no conflict of interest to declare.