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Genome-Wide Identification of Basic Helix–Loop–Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus

Authors: Pooley, John R; Flynn, Ben P; Grøntved, Lars; Baek, Songjoon; Guertin, Michael J; Kershaw, Yvonne M; Birnie, Matthew T; +6 Authors
APC: 3,101.76 EUR

Genome-Wide Identification of Basic Helix–Loop–Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus

Abstract

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 toward 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 chromatin immunoprecipitation sequencing to interrogate GR binding, we found no effect of restraint stress context on GR binding, although 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 GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix 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 GRs. Of our GR binding sites, 54% additionally contained half-sites for nuclear factor (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 GRs in the hippocampus. Alterations in the expression or activity of NF-1/basic helix-loop-helix factors may play an as yet undetermined role in glucocorticoid-related disease susceptibility and outcome by altering GR access to hippocampal binding sites.

Countries
Denmark, United Kingdom
Keywords

Male, 570, Physiological, Hippocampus/metabolism, Amino Acid Motifs, Receptors, Glucocorticoid/chemistry, Stress, Hippocampus, Receptors, Glucocorticoid, Stress, Physiological, NFI Transcription Factors/metabolism, Receptors, Animals, Immunoprecipitation, Glucocorticoid/chemistry, Research Articles, Binding Sites, Genome, Chromatin/genetics, Helix-Loop-Helix Motifs, 500, Chromatin, Rats, NFI Transcription Factors, Gene Expression Regulation, Disease Susceptibility, Sequence Analysis, Protein Binding

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    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    25
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
25
Top 10%
Average
Top 10%
Green
hybrid