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Strickland BA, Ansari SA, Dantoft W, Uhlenhaut NH. How to tame your genes: mechanisms of inflammatory gene repression by glucocorticoids. FEBS Lett 2022; 596:2596-2616. [PMID: 35612756 DOI: 10.1002/1873-3468.14409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/24/2022] [Accepted: 05/18/2022] [Indexed: 01/08/2023]
Abstract
Glucocorticoids (GCs) are widely used therapeutic agents to treat a broad range of inflammatory conditions. Their functional effects are elicited by binding to the glucocorticoid receptor (GR), which regulates transcription of distinct gene networks in response to ligand. However, the mechanisms governing various aspects of undesired side effects versus beneficial immunomodulation upon GR activation remain complex and incompletely understood. In this review, we discuss emerging models of inflammatory gene regulation by GR, highlighting GR's regulatory specificity conferred by context-dependent changes in chromatin architecture and transcription factor or co-regulator dynamics. GR controls both gene activation and repression, with the repression mechanism being central to favorable clinical outcomes. We describe current knowledge about 3D genome organization and its role in spatiotemporal transcriptional control by GR. Looking beyond, we summarize the evidence for dynamics in gene regulation by GR through cooperative convergence of epigenetic modifications, transcription factor crosstalk, molecular condensate formation and chromatin looping. Further characterizing these genomic events will reframe our understanding of mechanisms of transcriptional repression by GR.
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Affiliation(s)
- Benjamin A Strickland
- Metabolic Programming, Technische Universitaet Muenchen (TUM), School of Life Sciences Weihenstephan, ZIEL - Institute for Food and Health, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Suhail A Ansari
- Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Widad Dantoft
- Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - N Henriette Uhlenhaut
- Metabolic Programming, Technische Universitaet Muenchen (TUM), School of Life Sciences Weihenstephan, ZIEL - Institute for Food and Health, Gregor-Mendel-Str. 2, 85354, Freising, Germany.,Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
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Weems JC, Slaughter BD, Unruh JR, Weaver KJ, Miller BD, Delventhal KM, Conaway JW, Conaway RC. A role for the Cockayne Syndrome B (CSB)-Elongin ubiquitin ligase complex in signal-dependent RNA polymerase II transcription. J Biol Chem 2021; 297:100862. [PMID: 34116057 PMCID: PMC8294581 DOI: 10.1016/j.jbc.2021.100862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/19/2022] Open
Abstract
The Elongin complex was originally identified as an RNA polymerase II (RNAPII) elongation factor and subsequently as the substrate recognition component of a Cullin-RING E3 ubiquitin ligase. More recent evidence indicates that the Elongin ubiquitin ligase assembles with the Cockayne syndrome B helicase (CSB) in response to DNA damage and can target stalled polymerases for ubiquitylation and removal from the genome. In this report, we present evidence that the CSB-Elongin ubiquitin ligase pathway has roles beyond the DNA damage response in the activation of RNAPII-mediated transcription. We observed that assembly of the CSB-Elongin ubiquitin ligase is induced not just by DNA damage, but also by a variety of signals that activate RNAPII-mediated transcription, including endoplasmic reticulum (ER) stress, amino acid starvation, retinoic acid, glucocorticoids, and doxycycline treatment of cells carrying several copies of a doxycycline-inducible reporter. Using glucocorticoid receptor (GR)-regulated genes as a model, we showed that glucocorticoid-induced transcription is accompanied by rapid recruitment of CSB and the Elongin ubiquitin ligase to target genes in a step that depends upon the presence of transcribing RNAPII on those genes. Consistent with the idea that the CSB-Elongin pathway plays a direct role in GR-regulated transcription, mouse cells lacking the Elongin subunit Elongin A exhibit delays in both RNAPII accumulation on and dismissal from target genes following glucocorticoid addition and withdrawal, respectively. Taken together, our findings bring to light a new role for the CSB-Elongin pathway in RNAPII-mediated transcription.
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Affiliation(s)
- Juston C Weems
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Kyle J Weaver
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Brandon D Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Kym M Delventhal
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
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Stavreva DA, Coulon A, Baek S, Sung MH, John S, Stixova L, Tesikova M, Hakim O, Miranda T, Hawkins M, Stamatoyannopoulos JA, Chow CC, Hager GL. Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing. Genome Res 2015; 25:845-57. [PMID: 25677181 PMCID: PMC4448681 DOI: 10.1101/gr.184168.114] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/05/2015] [Indexed: 12/20/2022]
Abstract
Although physiological steroid levels are often pulsatile (ultradian), the genomic effects of this pulsatility are poorly understood. By utilizing glucocorticoid receptor (GR) signaling as a model system, we uncovered striking spatiotemporal relationships between receptor loading, lifetimes of the DNase I hypersensitivity sites (DHSs), long-range interactions, and gene regulation. We found that hormone-induced DHSs were enriched within ± 50 kb of GR-responsive genes and displayed a broad spectrum of lifetimes upon hormone withdrawal. These lifetimes dictate the strength of the DHS interactions with gene targets and contribute to gene regulation from a distance. Our results demonstrate that pulsatile and constant hormone stimulations induce unique, treatment-specific patterns of gene and regulatory element activation. These modes of activation have implications for corticosteroid function in vivo and for steroid therapies in various clinical settings.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Antoine Coulon
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Sam John
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Lenka Stixova
- Department of Molecular Cytology and Cytometry, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
| | - Martina Tesikova
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Tina Miranda
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Mary Hawkins
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | | | - Carson C Chow
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
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Zarzer CA, Puchinger MG, Köhler G, Kügler P. Differentiation between genomic and non-genomic feedback controls yields an HPA axis model featuring hypercortisolism as an irreversible bistable switch. Theor Biol Med Model 2013; 10:65. [PMID: 24209391 PMCID: PMC3879227 DOI: 10.1186/1742-4682-10-65] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/29/2013] [Indexed: 01/30/2023] Open
Abstract
Background The hypothalamic-pituitary-adrenal axis (HPA axis) is a major part of the neuroendocrine system responsible for the regulation of the response to physical or mental stress and for the control of the synthesis of the stress hormone cortisol. Dysfunctions of the HPA axis characterized by either low (hypocortisolism) or increased (hypercortisolism) cortisol levels are implicated in various pathological conditions. Their understanding and therapeutic correction may be supported by mathematical modeling and simulation of the HPA axis. Methods Mass action and Michaelis Menten enzyme kinetics were used to provide a mechanistic description of the feedback mechanisms within the pituitary gland cells by which cortisol inhibits its own production. A separation of the nucleus from the cytoplasm by compartments enabled a differentiation between slow genomic and fast non-genomic processes. The model in parts was trained against time resolved ACTH stress response data from an in vitro cell culture of murine AtT-20 pituitary tumor cells and analyzed by bifurcation discovery tools. Results A recently found pituitary gland cell membrane receptor that mediates rapid non-genomic actions of glucocorticoids has been incorporated into our model of the HPA axis. As a consequence of the distinction between genomic and non-genomic feedback processes our model possesses an extended dynamic repertoire in comparison to existing HPA models. In particular, our model exhibits limit cycle oscillations and bistable behavior associated to hypocortisolism but also features a (second) bistable switch which captures irreversible transitions in hypercortisolism to elevated cortisol levels. Conclusions Model predictive control and inverse bifurcation analysis have been previously applied in the simulation-based design of therapeutic strategies for the correction of hypocortisolism. Given the HPA model extension presented in this paper, these techniques may also be used in the study of hypercortisolism. As an example, we show how sparsity enforcing penalization may suggest network interventions that allow the return from elevated cortisol levels back to nominal ones.
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Affiliation(s)
| | | | | | - Philipp Kügler
- Institute for Applied Mathematics and Statistics, University of Hohenheim, Schloss, 70599 Stuttgart, Germany.
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Miranda TB, Morris SA, Hager GL. Complex genomic interactions in the dynamic regulation of transcription by the glucocorticoid receptor. Mol Cell Endocrinol 2013; 380:16-24. [PMID: 23499945 PMCID: PMC3724757 DOI: 10.1016/j.mce.2013.03.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/26/2013] [Accepted: 03/03/2013] [Indexed: 12/13/2022]
Abstract
The glucocorticoid receptor regulates transcriptional output through complex interactions with the genome. These events require continuous remodeling of chromatin, interactions of the glucocorticoid receptor with chaperones and other accessory factors, and recycling of the receptor by the proteasome. Therefore, the cohort of factors expressed in a particular cell type can determine the physiological outcome upon treatment with glucocorticoid hormones. In addition, circadian and ultradian cycling of hormones can also affect GR response. Here we will discuss revision of the classical static model of GR binding to response elements to incorporate recent findings from single cell and genome-wide analyses of GR regulation. We will highlight how these studies have changed our views on the dynamics of GR recruitment and its modulation of gene expression.
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The use of saliva for assessment of cortisol pulsatile secretion by deconvolution analysis. Psychoneuroendocrinology 2013; 38:1090-101. [PMID: 23246325 DOI: 10.1016/j.psyneuen.2012.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/20/2022]
Abstract
Cortisol is the key effector molecule of the HPA axis and is secreted in a pulsatile manner in all species studied. In order to understand cortisol signalling in health and disease, detailed analysis of hormone pulsatility is necessary. To dissect cortisol pulsatility in plasma deconvolution techniques have been applied. Blood sampling is a labour-intensive, expensive and invasive technique that causes stress and alters HPA axis activity. Therefore saliva has been extensively investigated as an alternative sample to measure cortisol. Here we use state of the art deconvolution algorithms to investigate cortisol pulsatility in saliva. Blood and saliva samples were obtained at 15-min intervals over an 8h period in 18 healthy men to analyse their diurnal cortisol levels. A multiparameter deconvolution technique was used to generate statistically significant models of cortisol secretion and elimination in plasma and saliva. The models consisted of estimates of the number, amplitude, duration and frequency of secretory bursts as well as the elimination half-life (t1/2) in a subject specific manner. No significant differences were noted between plasma and saliva with regard to the observed secretory bursts (7.8±1.5 vs. 7.0±1.4) and the interpeak interval (59.6±10.5 min vs. 61.0±11.5 min). Moreover a strong positive correlation between the numbers of peaks in both fluids was observed (r=0.83, P<0.0001). Monte Carlo simulations revealed an 84% temporal concordance between plasma and saliva peaks in all donors (P<0.05) with a mean of 1.3±0.8 plasma peaks unmatched in saliva. The percentage concordance increased to 90% when concording only the morning cortisol peaks in plasma and saliva up to 11:00 h. The deconvolution of the most distinct component of cortisol diurnal rhythm-cortisol awakening response (CAR), revealed an average 2.5±1.1 peaks based on the individual time for cortisol to return to baseline levels. In conclusion, deconvolution analysis of plasma and salivary cortisol concentration time series showed a close correlation and similar pulsatile characteristics between saliva and plasma cortisol. Similarly, Monte Carlo simulations revealed a high concordance between the peaks in these coupled time series suggesting that saliva is a suitable medium for subsequent deconvolution analysis yielding accurate and reliable models of cortisol secretion in particular during the morning hours.
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Trifonova ST, Zimmer J, Turner JD, Muller CP. Diurnal redistribution of human lymphocytes and their temporal associations with salivary cortisol. Chronobiol Int 2013; 30:669-81. [DOI: 10.3109/07420528.2013.775654] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Stavreva DA, George AA, Klausmeyer P, Varticovski L, Sack D, Voss TC, Schiltz RL, Blazer VS, Iwanowicz LR, Hager GL. Prevalent glucocorticoid and androgen activity in US water sources. Sci Rep 2012; 2:937. [PMID: 23226835 PMCID: PMC3515810 DOI: 10.1038/srep00937] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/12/2012] [Indexed: 11/17/2022] Open
Abstract
Contamination of the environment with endocrine disrupting chemicals (EDCs) is a major health concern. The presence of estrogenic compounds in water and their deleterious effect are well documented. However, detection and monitoring of other classes of EDCs is limited. Here we utilize a high-throughput live cell assay based on sub-cellular relocalization of GFP-tagged glucocorticoid and androgen receptors (GFP-GR and GFP-AR), in combination with gene transcription analysis, to screen for glucocorticoid and androgen activity in water samples. We report previously unrecognized glucocorticoid activity in 27%, and androgen activity in 35% of tested water sources from 14 states in the US. Steroids of both classes impact body development, metabolism, and interfere with reproductive, endocrine, and immune systems. This prevalent contamination could negatively affect wildlife and human populations.
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Affiliation(s)
- Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression Building 41, B602 41 Library Dr. National Cancer Institute, NIH Bethesda, MD 20892-5055
| | - Anuja A. George
- Laboratory of Receptor Biology and Gene Expression Building 41, B602 41 Library Dr. National Cancer Institute, NIH Bethesda, MD 20892-5055
- Current address: Department of Pharmacology UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Paul Klausmeyer
- Natural Products Support Group SAIC-Frederick, Inc Frederick National Laboratory for Cancer Research Frederick, MD 21702
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression Building 41, B602 41 Library Dr. National Cancer Institute, NIH Bethesda, MD 20892-5055
| | - Daniel Sack
- Laboratory of Receptor Biology and Gene Expression Building 41, B602 41 Library Dr. National Cancer Institute, NIH Bethesda, MD 20892-5055
| | - Ty C. Voss
- Laboratory of Receptor Biology and Gene Expression Building 41, B602 41 Library Dr. National Cancer Institute, NIH Bethesda, MD 20892-5055
| | - R. Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression Building 41, B602 41 Library Dr. National Cancer Institute, NIH Bethesda, MD 20892-5055
| | - Vicki S. Blazer
- USGS-BRD Leetown Science Center 11649 Leetown Road Kearneysville, WV 25430
| | - Luke R. Iwanowicz
- USGS-BRD Leetown Science Center 11649 Leetown Road Kearneysville, WV 25430
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression Building 41, B602 41 Library Dr. National Cancer Institute, NIH Bethesda, MD 20892-5055
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The crucial role of pulsatile activity of the HPA axis for continuous dynamic equilibration. Nat Rev Neurosci 2010; 11:710-8. [DOI: 10.1038/nrn2914] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Stavreva DA, Wiench M, John S, Conway-Campbell BL, McKenna MA, Pooley JR, Johnson TA, Voss TC, Lightman SL, Hager GL. Ultradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription. Nat Cell Biol 2009; 11:1093-102. [PMID: 19684579 DOI: 10.1038/ncb1922] [Citation(s) in RCA: 264] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 05/22/2009] [Indexed: 01/10/2023]
Abstract
Studies on glucocorticoid receptor (GR) action typically assess gene responses by long-term stimulation with synthetic hormones. As corticosteroids are released from adrenal glands in a circadian and high-frequency (ultradian) mode, such treatments may not provide an accurate assessment of physiological hormone action. Here we demonstrate that ultradian hormone stimulation induces cyclic GR-mediated transcriptional regulation, or gene pulsing, both in cultured cells and in animal models. Equilibrium receptor-occupancy of regulatory elements precisely tracks the ligand pulses. Nascent RNA transcripts from GR-regulated genes are released in distinct quanta, demonstrating a profound difference between the transcriptional programs induced by ultradian and constant stimulation. Gene pulsing is driven by rapid GR exchange with response elements and by GR recycling through the chaperone machinery, which promotes GR activation and reactivation in response to the ultradian hormone release, thus coupling promoter activity to the naturally occurring fluctuations in hormone levels. The GR signalling pathway has been optimized for a prompt and timely response to fluctuations in hormone levels, indicating that biologically accurate regulation of gene targets by GR requires an ultradian mode of hormone stimulation.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-5055, USA
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George AA, Louis Schiltz R, Hager GL. Dynamic access of the glucocorticoid receptor to response elements in chromatin. Int J Biochem Cell Biol 2009; 41:214-24. [PMID: 18930837 PMCID: PMC2632576 DOI: 10.1016/j.biocel.2008.09.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 09/22/2008] [Accepted: 09/23/2008] [Indexed: 12/22/2022]
Abstract
Transcriptional activation as a rate-limiting step of gene expression is often triggered by an environmental stimulus that is transmitted through a signaling cascade to specific transcription factors. Transcription factors must then find appropriate target genes in the context of chromatin. Subsequent modulation of local chromatin domains is now recognized as a major mechanism of gene regulation. The interactions of transcription factors with chromatin structures have recently been observed to be highly dynamic, with residence times measured in seconds. Thus, the concept of static, multi-protein complexes forming at regulatory elements in the genome has been replaced by a new paradigm that envisages rapid and continuous exchange events with the template. These highly dynamic interactions are a property of both DNA-protein and protein-protein interactions and are inherent to every stage of the transcriptional response. In this review we discuss the dynamics of a nuclear receptor, and its transcriptional response in the chromatin context.
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Affiliation(s)
- Anuja A. George
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - R. Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
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