Cryptic glucocorticoid receptor-binding sites pervade genomic NF-\u03baB response elements

William H Hudson,Kendall W Nettles,Douglas J Kojetin,David L Bain,Eric A Ortlund,Ian Mitchelle S De Vera,Emily R Weikum,Austin G Herbst,Jerome C Nwachukwu,Qin Yang

doi:10.1038/s41467-018-03780-1

Abstract

Glucocorticoids (GCs) are potent repressors of NF-κB activity, making them a preferred choice for treatment of inflammation-driven conditions. Despite the widespread use of GCs in the clinic, current models are inadequate to explain the role of the glucocorticoid receptor (GR) within this critical signaling pathway. GR binding directly to NF-κB itself—tethering in a DNA binding-independent manner—represents the standing model of how GCs inhibit NF-κB-driven transcription. We demonstrate that direct binding of GR to genomic NF-κB response elements (κBREs) mediates GR-driven repression of inflammatory gene expression. We report five crystal structures and solution NMR data of GR DBD-κBRE complexes, which reveal that GR recognizes a cryptic response element between the binding footprints of NF-κB subunits within κBREs. These cryptic sequences exhibit high sequence and functional conservation, suggesting that GR binding to κBREs is an evolutionarily conserved mechanism of controlling the inflammatory response.

Highlights

Glucocorticoids (GCs) are potent repressors of nuclear factor-κB (NF-κB) activity, making them a preferred choice for treatment of inflammation-driven conditions
Mutation had been reported to ablate the ability of glucocorticoid receptor (GR) to repress NF-κB-driven transcription[22,23]. In line with these results, we found that the S425G mutation hindered the ability of full-length GR to repress a constitutively active reporter gene preceded by 400 bp of the IL8 promoter, which contains a κB response elements (κBREs), but not a (+) GRE (Supplementary Figure 1a)
We hypothesized this effect could be due to direct binding of GR to DNA, given the similar effect seen at DNA-dependent nGREs17,19

Summary

Introduction

Glucocorticoids (GCs) are potent repressors of NF-κB activity, making them a preferred choice for treatment of inflammation-driven conditions. We demonstrate that direct binding of GR to genomic NF-κB response elements (κBREs) mediates GR-driven repression of inflammatory gene expression. The repressive effects of GR on pro-inflammatory transcription factors are generally thought to be DNA independent[3,5,6,15] In line with this hypothesis, GR has been shown in many circumstances to interact directly with NF-κB subunits and is believed to tether to NF-κB response elements (κBREs) without the use of its own DNA-binding capabilities[16]. We demonstrate that GR binds directly to κBREs and propose that direct GR–DNA interaction at these genomic loci are an important mechanism to repress the expression of proinflammatory genes

Methods

Results

Conclusion