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 them in an equivalent cellular context. Analysis of chromatin and sequence 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 result 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 guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, 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

“… (A) Heat map visualization and mean signal plot of ATAC-seq (normalized), GR ChIP-seq (RPKM-normalized; 1 μM Dex, 1.5 h; data from reference 65 ) and H3K27ac ChIP-seq (RPKM-normalized; 1 μM Dex or EtOH, 1.5 h; data from reference 66 ) read coverage in U2OS-GR cells at sites of increasing (“opening”), non-changing (“non-changing”) and decreasing (“closing”) chromatin accessibility upon hormone treatment (±2 kb around center). Heat maps are sorted by GR ChIP-seq signal in descending order.…”

“…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 ]).…”

“…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]). 4C-seq 4C template preparation from 5 million A549 cells treated as indicated in the figure legend was done as described in reference 47 using Csp6I (Thermo Fisher Scientific) and DpnII (Thermo Fisher Scientific) as primary and secondary restriction enzymes, respectively.…”

MECHANISMS IN ENDOCRINOLOGY: Local and systemic effects of glucocorticoids on metabolism: new lessons from animal models

“…Reciprocity between AR and GR may explain, at least in part, why adipogenesis is impaired in preadipocytes lacking GR in vitro, but their implantation into male mice yields fully formed fat pads (97). AR and GR share many genomic binding sites, but AR/GR specificity depends on many other factors, including the DNA sequence of the response element, nearby enhancers, chromatin accessibility (145) and potentially by the expression of co-factors such as Bag1 and Ppid (146). This situation is further complicated by glucocorticoid-induced GR resistance: for example, leukocytes from Cushing's patients exhibit subtle changes in the distribution of GR splice variants that reduce dexamethasone binding (147).…”

Transcriptome profiling of theCaenorhabditis elegansintestine reveals that ELT-2 negatively and positively regulates intestinal gene expression within the context of a gene regulatory network

“…To further complicate matters, robust TF occupancy alone is sometimes not sufficient for transcriptional activation. An association with other factors, a critical phosphorylation event, or TF dynamics may be required to stimulate recruitment of RNA Polymerase II following successful TF binding (Meijsing et al 2009;Ucar et al 2009;Lickwar et al 2012;Kulik et al 2021).…”