Insights into Negative Regulation by the Glucocorticoid Receptor from Genome-wide Profiling of Inflammatory Cistromes

Abstract

Summary How the glucocorticoid receptor (GR) activates some genes while potently repressing others remains an open question. There are three current models for suppression: trans-repression via GR ‘tethering’ to AP-1/NF-κB sites, direct GR association with inhibitory elements (nGREs), and GR recruitment of the corepressor GRIP1. To gain insights into GR suppression, we used genomic analyses and genome-wide profiling of GR, p65, and c-Jun in LPS-stimulated macrophages. We show that GR mediates both activation and repression at tethered sites, GREs, and GRIP1-bound elements, indicating that motif classification is insufficient to predict regulatory polarity of GR binding. Interestingly, sites of GR repression utilize GRIP1’s corepressor function and display reduced histone acetylation. Together, these findings suggest that while GR occupancy confers hormone responsiveness, the receptor itself may not participate in the regulatory effects. Furthermore, transcriptional outcome is not established by sequence, but is influenced by epigenetic regulators, context, and other unrecognized regulatory determinants.

Glucocorticoid-induced tethered transrepression requires SUMOylation of GR and formation of a SUMO-SMRT/NCoR1-HDAC3 repressing complex

“…S2), most likely because a repressing complex was assembled on the accessory SUMOylation site located at K294 (K277 in human), therefore leading to the conclusion that GR SUMOylation is instrumental in GC-induced repressing mechanisms involved in tethered repression. Note, however, that it is not excluded that additional factors could be marginally involved in these repressing mechanisms (13,20). Further experiments, performed with GR K310R and GR K310R/K294R double mutant mice to study the effect of GC on a variety of actual inflammatory models, will establish the importance of GR SUMOylation in tethered repression and more generally in GC-induced antiinflammatory processes.…”

Novel Mechanism of Positive versus Negative Regulation by Thyroid Hormone Receptor β1 (TRβ1) Identified by Genome-wide Profiling of Binding Sites in Mouse Liver

“…TR␤1 has been shown to bind to two half-sites separated by 1-6 base pairs in vitro (21), and several previously identified TREs fit this pattern. Previous ChIP-seq experiments have helped to confirm that the in vitro binding preference of nuclear receptors such as liver X receptor, glucocorticoid receptor and farnesoid X receptor are preserved in vivo (33,36,37). The nuclear receptor LXR is known to bind with high affinity to DR-4 elements (38 -40), whereas PPAR␣ binds to DR-1 elements (41,42), and FXR binds to IR-1 elements (36).…”

Cistrome-based Cooperation between Airway Epithelial Glucocorticoid Receptor and NF-κB Orchestrates Anti-inflammatory Effects

“…For example, genomewide analysis of GR interactions with DNA (i.e. chromatin-immunoprecipitation of GR followed by deep sequencing, or ChIP-seq) indicated that interactions between GR and inflammatory transcription factors do not necessarily lead to repressive regulatory outcomes (11)(12)(13)(14). Moreover, an increasing number of GR-induced genes are now recognized as contributing to inflammatory repression by GCs (15)(16)(17).…”