Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

Abstract

The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied AR and GR in an equivalent cellular context. Analysis of chromatin and sequence features suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the results of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in selectively guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared between AR and GR shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, we find that shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.

Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changes

“…For U2OS-GR cells, the following ChIP-seq datasets were downloaded from the Sequence Read Archive or ArrayExpress: GR replicate 1 (1 μM Dex, 1.5 h; Sequence Read Archive accession SRX256867 / SRX256891 ; [ 65 ]), GR replicate 2 (1 μM Dex, 1.5 h; ArrayExpress accession E-MTAB-9616 ; [ 66 , 67 Preprint ]), H3K27ac (1 μM Dex or EtOH, 1.5 h; ArrayExpress accession E-MTAB-9617 ; [ 66 ]).…”

Glucocorticoid receptor activation induces gene-specific transcriptional memory and universally reversible changes in chromatin accessibility

“…For A549 cells, the following ChIP-seq datasets were downloaded from the Gene Expression Omnibus (GEO): GR (2 replicates; 100 nM Dex or EtOH for 3h; GSE79431, [43]), H3K27ac (100 nM Dex, 0h/4h; GSM2421694/GSM2421873; [44]), H3K4me3 (100 nM Dex, 0h/4h; GSM2421504/GSM2421914; [44]), H3K27me3 (100 nM Dex or EtOH, 1h; GSM1003455/GSM1003577; [44]) and p300 (100 nM Dex, 0h/4h; GSM2421805/ GSM2421479; [44]). For U2OS-GR cells, the following ChIP-seq datasets were downloaded from the Sequence Read Archive (SRA) or ArrayExpress: GR replicate 1 (1 µM Dex, 1.5h; SRA accession SRX256867/SRX256891; [45]), GR replicate 2 (1 µM Dex, 1.5h; ArrayExpress accession E-MTAB-9616; [46], H3K27ac (1 µM Dex or EtOH, 1.5h; ArrayExpress accession E-MTAB-9617; [46]). 4C-seq 4C template preparation from 5 million A549 cells treated as indicated in the figure legend was done as described in [47] using Csp6I (Thermo Fisher Scientific) and DpnII (Thermo Fisher Scientific) as primary and secondary restriction enzymes, respectively.…”

“…(d) Same as for (c) except that RPKM-normalized GR ChIP-seq read coverage (1 μM Dex, 1.5h) in U2OS-GR cells is shown (data from [45]). (e) Same as for (c) except that RPKM-normalized H3K27ac ChIP-seq read coverage (1 μM Dex or EtOH, 1.5h) in U2OS-GR cells is shown (data from [46]). (f) Stacked bar graphs showing the percentage of genes in U2OS-GR cells of each category (upregulated, downregulated and nonregulated) that have at least one peak for each type as indicated (opening, closing and non-changing sites and GR peaks) within +/-50 kb around the TSS.…”

Androgen Receptor-Dependent Mechanisms Mediating Drug Resistance in Prostate Cancer

“…Mechanistically, GR may bind an overlapping set of AR target genes [ 102 , 103 , 104 ] and may thereby bypass AR blockage but allows the activation of a part of the AR transcriptome landscape. Dexamethasone, a GR agonist, has been shown to decrease the GR protein level in AR-null PCa cells (DU145 and HH870), which resulted in inhibited growth.…”