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Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
Open accessAbstract
The glucocorticoid steroid hormone cortisol is released by the adrenal glands in response to stress and serves as a messenger in circadian rhythms. Transcriptional responses to this hormonal signal are mediated by the glucocorticoid receptor (GR). We determined GR binding throughout the human genome by using chromatin immunoprecipitation followed by next-generation DNA sequencing, and measured related changes in gene expression with mRNA sequencing in response to the glucocorticoid dexamethasone (DEX). We identified 4392 genomic positions occupied by the GR and 234 genes with significant changes in expression in response to DEX. This genomic census revealed striking differences between gene activation and repression by the GR. While genes activated with DEX treatment have GR bound within a median distance of 11 kb from the transcriptional start site (TSS), the nearest GR binding for genes repressed with DEX treatment is a median of 146 kb from the TSS, suggesting that DEX-mediated repression occurs independently of promoter-proximal GR binding. In addition to the dramatic differences in proximity of GR binding, we found differences in the kinetics of gene expression response for induced and repressed genes, with repression occurring substantially after induction. We also found that the GR can respond to different levels of corticosteroids in a gene-specific manner. For example, low doses of DEX selectively induced PER1 , a transcription factor involved in regulating circadian rhythms. Overall, the genome-wide determination and analysis of GR:DNA binding and transcriptional response to hormone reveals new insights into the complexities of gene regulatory activities managed by GR.
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“Through action on the cytosolic GC receptor (GR), GCs profoundly modulate the cellular transcriptional landscape,24 affecting up to 20% of all genes25”
From Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy (2023) · cites this paper as [24]
Experimental — accuracy not yet measuredIn the citing paper
“Protocols for ChIP-seq are similar to those for frozen tissue previously described by our lab115,116 and consistent with techniques recommended by the ENCODE Consortium (www.encodeproject.org/documents).”
From Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements (2023) · cites this paper as [116]
In the citing paper
“Ligand-activated GR induces or represses the transcription of thousands of genes through direct binding to DNA response elements, physically associating with other transcription factors, or both.”
From Corticosteroids (2016) · cites this paper as [22]
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“Comprehensive GR binding analyses revealed that many GR-binding sites identified are located far from the promoter proximal region of target genes and showed an unexpected difference between the activation and repressive functions of the GR [22].”
From Corticosteroids (2016) · cites this paper as [22]
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Metadata
- Authors
- Reddy, T. E., Pauli, F., Sprouse, R. O., Neff, N. F., Newberry, K. M., Garabedian, M. J., & Myers, R. M.
- Affiliations
- HudsonAlpha Institute for Biotechnology (US)
- Stanford Medicine (US)
- New York University (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-10-02
- Volume
- 19
- Issue
- 12
- Pages
- 2163-2171
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2792167
- OpenAlex
- W2113112889
- Cited by
- 543
- References
- 44
- Citations by year
- 2026: 16 · 2025: 15 · 2024: 32 · 2023: 35 · 2022: 25 · 2021: 28 · 2020: 29 · 2019: 35 · 2018: 34 · 2017: 47 · 2016: 49 · 2015: 41 · 2014: 32 · 2013: 35 · 2012: 38
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Philip Morris International
- National Institutes of Health
- National Human Genome Research Institute (U54HG004576)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Estrogen and related hormone effects
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Neuroscience › Behavioral Neuroscience › Stress Responses and Cortisol
- Keywords
- glucocorticoid receptor, dexamethasone, cortisol, transcriptional repression, transcriptional activation, Per1, circadian rhythm, hormone dose-response, gene expression regulation
- MeSH terms
- Binding Sites, Dexamethasone, Gene Expression Regulation, Humans, Lung, Proteins, Receptors, Glucocorticoid, RNA, Messenger, Genome, Sequence Analysis, DNA, Chromatin Immunoprecipitation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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