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.Nucleosomes are the basic units of eukaryotic chromatin, each one containing ϳ146 bp of DNA wrapped around an octamer of histone core proteins, which in turn are separated by linker DNA sequences of variable length (39). Nucleosomes play a pivotal role in chromatin structure, and their differential occupancy at promoters (transcription start sites) regulates gene expression by altering DNA accessibility (39). For instance, a nucleosome-depleted region (NDR) at transcriptional start sites correlates with gene expression, whereas the positioning of a nucleosome over the transcriptional start site results in gene repression (23). In contrast, the role of nucleosome positioning at other regulatory regions, particularly distal ones such as enhancers, is less well characterized. Interestingly, nucleosome turnover was recently shown to be increased at genes and regulatory elements (9), suggesting that this process may control nucleosome density and the existence of NDRs.Enhancers are nondirectional regulatory elements that control promoter activity at a distance on linear DNA. Several histone marks, including mono-and dimethylated H3K4 (H3K4me1 and H3K4me2) and acetylated H3K9,14 (AcH3), have been shown to correlate or be associated with regions that display enhancer activity, although H3K4me2 and AcH3, along with the trimethylation version of H3K4 (H3K4me3), are also located at transcriptional start sites (16,44). Enhancers generally contain DNA recognition motifs for transcription factors which, upon binding, regulate gene expression by looping to the transcriptional start sites of their target genes.The androgen receptor (AR) is a ligan...

FoxA1 Specifies Unique Androgen and Glucocorticoid Receptor Binding Events in Prostate Cancer Cells

“…Enhancers that bind AR exhibit nucleosomedepleted regions already in the absence of androgen (29). Together, these findings raise the question as to the role of the ligand in instructing the AR to bind to appropriate chromatin loci.…”

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

“…FAIRE-seq relies on enhanced sensitivity to DNA breakage of nucleosome-depleted regions (Giresi et al 2007; Nagy and Price 2009). Rather than using a nuclease, methyltransferase-based footprinting, with the CpG methyltransferase M.SssI (Gal-Yam et al 2006;Lin et al 2007;Bouazoune et al 2009;Kelly et al 2010) or GpC methyltransferase M.CviPI Wolff et al 2010;Andreu-Vieyra et al 2011;Taberlay et al 2011;You et al 2011), uses the placement of a biochemical mark (i.e., methylation) on DNA to assess nucleosome occupancy. Since GpC dinucleotides are not endogenously methylated, NOMe-seq provides both nucleosome positioning and DNA methylation within the same individual DNA strand.…”

“…Nuclei from IMR90 Cold Spring Harbor Laboratory Press on May 12, 2018 -Published by genome.cshlp.org Downloaded from cells (ATCC) were isolated as previously described . Previous publications using locus-specific NOMe-seq have used the minimal amount of M.CviPI that resulted in optimal footprinting of the specific region of interest: 100 units (Wolff et al 2010), 200 units You et al 2011), or 200 + 100 units (Andreu-Vieyra et al 2011). Since whole-genome NOMe-seq required accurate footprinting of a variety of genomic regions, we performed a dose response curve ( Fig.…”

Myogenic Enhancers Regulate Expression of the Facioscapulohumeral Muscular Dystrophy-Associated DUX4 Gene

“…Active tissue-specific enhancers are gener- ally devoid of CpG methylation and may also show lower nucleosome occupancy (49 -51). To determine the DNA methylation status and nucleosome occupancy of DME1 and DME2 in FSHD myocytes, we performed NOMe-seq, a recently pioneered technique that has been instrumental in assessing specific chromatin states both for single loci and across the genome (39,(50)(51)(52)(53). Taking advantage of the fact that mammalian cells lack GpC methylation, intact nuclei are incubated with the GpC methyltransferase M.CviPI, which methylates GpC dinucleotides not associated with nucleosomes or tightly bound transcription factors while leaving nucleosomal or transcription factor-occupied sites unmethylated.…”