Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

Abstract

Glucocorticoids are potent steroid hormones that regulate immunity and metabolism by activating the transcription factor (TF) activity of glucocorticoid receptor (GR). Previous models have proposed that DNA binding motifs and sites of chromatin accessibility predetermine GR binding and activity. However, there are vast excesses of both features relative to the number of GR binding sites. Thus, these features alone are unlikely to account for the specificity of GR binding and activity. To identify genomic and epigenetic contributions to GR binding specificity and the downstream changes resultant from GR binding, we performed hundreds of genome-wide measurements of TF binding, epigenetic state, and gene expression across a 12-h time course of glucocorticoid exposure. We found that glucocorticoid treatment induces GR to bind to nearly all pre-established enhancers within minutes. However, GR binds to only a small fraction of the set of accessible sites that lack enhancer marks. Once GR is bound to enhancers, a combination of enhancer motif composition and interactions between enhancers then determines the strength and persistence of GR binding, which consequently correlates with dramatic shifts in enhancer activation. Over the course of several hours, highly coordinated changes in TF binding and histone modification occupancy occur specifically within enhancers, and these changes correlate with changes in the expression of nearby genes. Following GR binding, changes in the binding of other TFs precede changes in chromatin accessibility, suggesting that other TFs are also sensitive to genomic features beyond that of accessibility.

Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of transcription factors from a single experiment

“…As expected, H3K27ac deposition is temporally lagged behind its canonical acetyl-transferase p300 [29,60,51]. Additionally, the enhancer marks H3K4me1 and H3K4me2 show strong enrichment of GR by 30min but the promoter mark H3K4me3 shows only modest enrichment, further supporting the finding that GR binds primarily at enhancers [44] (Supp. Fig.…”

“…Although these data sets are less precise and are not direct readouts of polymerase initiation, the popularity of these data make them readily available. To determine whether TFEA could adequately infer TF activity from these datasets, we analyzed a timeseries dataset from ENCODE [19,44] in which cells were treated with dexamethasone (Dex)-a known activator of the glucocorticoid receptor (GR). TFEA correctly identifies GR as the key responding TF from the datasets that most closely capture RNA polymerase initiation (including p300, H3K27ac, and DNA accessibility), and does not identify GR for the transcriptionally repressive mark H3K9me3 (Figure 6a) [40,44].…”

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

“…Studies of transcription factor redistribution in association with transcriptional induction will, however, need to carefully account for the hyper-ChIPable nature of regulatory regions that are subject to the rapid repressive and chromatin remodeling effects of glucocorticoids. Indeed, whereas numerous studies have reported on chromatin structure remodeling in association with GR signaling (Voss et al 2011;Jubb et al 2017;McDowell et al 2018), our MNase data indicate that remodeling at some sites is associated with changes in intranucleosomal accessibility (e.g. PTPRK, Fig.…”

Locally acting transcription factors are required for p53-dependent cis-regulatory element activity

“…p53 is a pioneer transcription factor and can mediate context-dependent chromatin remodeling at CREs (10,48,54). Despite this activity, the large majority of p53 genomic binding events occur within regions that are accessible before p53 engagement (10,48,54,59), similar to what is observed for glucocorticoid receptor binding (66). These regions also contain chromatin modifications associated with active CRE, including H3K27ac and H3K4me1/2 before p53 binding (1,48,54,59,60,60).…”