title: 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.
authors.affiliation: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom.
authors.forename: John R
authors.initials: JR
authors.lastname: Pooley
authors.affiliation: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom.
authors.forename: Ben P
authors.initials: BP
authors.lastname: Flynn
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.
authors.forename: Lars
authors.initials: L
authors.lastname: Grøntved
authors.affiliation: Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Songjoon
authors.initials: S
authors.lastname: Baek
authors.affiliation: University of Virginia School of Medicine, Charlottesville, Virginia 22908.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Guertin
authors.affiliation: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom.
authors.forename: Yvonne M
authors.initials: YM
authors.lastname: Kershaw
authors.affiliation: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Birnie
authors.affiliation: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom.
authors.forename: Annie
authors.initials: A
authors.lastname: Pellatt
authors.affiliation: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom.
authors.forename: Caroline A
authors.initials: CA
authors.lastname: Rivers
authors.affiliation: Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: R Louis
authors.initials: RL
authors.lastname: Schiltz
authors.affiliation: Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Gordon L
authors.initials: GL
authors.lastname: Hager
authors.affiliation: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom.
authors.forename: Stafford L
authors.initials: SL
authors.lastname: Lightman
authors.affiliation: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom.
authors.forename: Becky L
authors.initials: BL
authors.lastname: Conway-Campbell
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D004198:Disease Susceptibility; D005786:Gene Expression Regulation; D016678:Genome; D018257:Helix-Loop-Helix Motifs; D006624:Hippocampus / Q000378:metabolism*; D047468:Immunoprecipitation; D008297:Male; D051839:NFI Transcription Factors / Q000378:metabolism*; D011485:Protein Binding; D051381:Rats; D011965:Receptors, Glucocorticoid / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017421:Sequence Analysis; D013312:Stress, Physiological
chemical_list: D002843:Chromatin; D051839:NFI Transcription Factors; D011965:Receptors, Glucocorticoid