Genome-wide identification of basic helix-loop helix and NF-1 motifs underlying GR binding sites in male rat hippocampus

Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell-type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites are dependent on the activity of additional signal activated transcription factors that prime chromatin towards context specific organization. We hypothesized a stress-context dependency for GR binding in hippocampus as a consequence of rapidly induced stress mediators priming chromatin accessibility. Using ChIP-seq to interrogate GR binding we found no effect of restraint stress-context on GR binding though analysis of sequences underlying GR binding sites revealed mechanistic detail for hippocampal GR function. We note enrichment of GR binding sites proximal to genes linked to structural and organizational roles, an absence of major tethering partners for GR, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix (bHLH) motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding sites and is proposed as a candidate lineage-determining transcription factor directing hippocampal chromatin access for GR. Of our GR binding sites 54% additionally contained halfsites for NF-1 that we propose as a collaborative or general transcription factor involved in hippocampal GR function. Our findings imply a dose-dependent and context-independent action of GR in the hippocampus. Alterations in the expression or activity of NF-1/bHLH factors may play an as yet undetermined role in glucocorticoid-related disease susceptibility and outcome by altering GR access to hippocampal binding sites.