Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

Abstract

The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes.

Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site

“…Sequence divergence in the wing regions contributes to differences in DNA binding 14–15 . The wing regions carry basic amino acids, which potentially recognize DNA structural features in the flanking regions of FOX binding sites, as previously observed for other transcription factor families 16–18 . For forkhead proteins, a recent analysis of HT-SELEX data demonstrated that binding specificity predictions improve for models that augment nucleotide sequence with DNA shape features 19 .…”

Glucocorticoid receptor control of transcription: precision and plasticity via allostery

“…2F). Finally, recent work has shown that sequences at the +8 and −8 positions flanking the GBS that alter DNA conformation also affect GR DBD structure, as assessed by NMR analysis in vitro and using a zinc-finger nuclease-generated, genomically integrated GBS-reporter system and endogenous GR in vivo 57 . Collectively, these studies suggest that DNA sequence-specific conformational states of GR result in the generation or stabilization of distinct patterns of GR surfaces, which serve as interaction platforms, driving alternative transcriptional outcomes.…”

Synergistic Regulation of Coregulator/Nuclear Receptor Interaction by Ligand and DNA

“…Natural and synthetic ligands, including FDA-approved drugs, bind to the NR LBD and affect NR activity through stabilizing specific LBD conformations that influence interactions with coregulators (Gronemeyer et al, 2004). NRs also bind DNA response elements of similar but varying sequences located in receptor target gene promoter regions via their DBD that also influence NR structure and activity (Meijsing et al, 2009; Schone et al, 2016; Watson et al, 2013). …”

“…No large LBD structural changes have been observed in crystal structures of isolated NR LBDs compared to DNA-bound full-length receptor complexes (Chandra et al, 2008; Chandra et al, 2013; Helsen and Claessens, 2014; Lou et al, 2014). However, studies on glucocorticoid receptor (GR) have revealed that DNA can act as an allosteric nuclear receptor ligand, functioning in part by affecting the conformation of the DBD (Meijsing et al, 2009; Schone et al, 2016; Watson et al, 2013). Extending this concept beyond the DBD, hydrogen/deuterium exchange mass spectrometry (HDX-MS) studies on the vitamin D receptor (VDR)-RXRα heterodimer have shown that DNA binding can impact the conformation of surfaces remote from the DBD, including the receptor dimerization and AF-2 coregulator interaction surfaces located in the LBD (Zhang et al, 2011).…”