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Seebacher F, Little AG. Thyroid hormone links environmental signals to DNA methylation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220506. [PMID: 38310936 PMCID: PMC10838643 DOI: 10.1098/rstb.2022.0506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/14/2023] [Indexed: 02/06/2024] Open
Abstract
Environmental conditions experienced within and across generations can impact individual phenotypes via so-called 'epigenetic' processes. Here we suggest that endocrine signalling acts as a 'sensor' linking environmental inputs to epigenetic modifications. We focus on thyroid hormone signalling and DNA methylation, but other mechanisms are likely to act in a similar manner. DNA methylation is one of the most important epigenetic mechanisms, which alters gene expression patterns by methylating cytosine bases via DNA methyltransferase enzymes. Thyroid hormone is mechanistically linked to DNA methylation, at least partly by regulating the activity of DNA methyltransferase 3a, which is the principal enzyme that mediates epigenetic responses to environmental change. Thyroid signalling is sensitive to natural and anthropogenic environmental impacts (e.g. light, temperature, endocrine-disrupting pollution), and here we propose that thyroid hormone acts as an environmental sensor to mediate epigenetic modifications. The nexus between thyroid hormone signalling and DNA methylation can integrate multiple environmental signals to modify phenotypes, and coordinate phenotypic plasticity at different time scales, such as within and across generations. These dynamics can have wide-ranging effects on health and fitness of animals, because they influence the time course of phenotypic adjustments and potentially the range of environmental stimuli that can elicit epigenetic responses. This article is part of the theme issue 'Endocrine responses to environmental variation: conceptual approaches and recent developments'.
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Affiliation(s)
- Frank Seebacher
- School of Life and Environmental Sciences A08, University of Sydney, New South Wales 2006, Australia
| | - Alexander G. Little
- Department of Biology, Life Sciences Building, McMaster University, Ontario, Canada L8S 4K1
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2
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Paluvai H, Shanmukha KD, Tyedmers J, Backs J. Insights into the function of HDAC3 and NCoR1/NCoR2 co-repressor complex in metabolic diseases. Front Mol Biosci 2023; 10:1190094. [PMID: 37674539 PMCID: PMC10477789 DOI: 10.3389/fmolb.2023.1190094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023] Open
Abstract
Histone deacetylase 3 (HDAC3) and nuclear receptor co-repressor (NCoR1/2) are epigenetic regulators that play a key role in gene expression and metabolism. HDAC3 is a class I histone deacetylase that functions as a transcriptional co-repressor, modulating gene expression by removing acetyl groups from histones and non-histone proteins. NCoR1, on the other hand, is a transcriptional co-repressor that interacts with nuclear hormone receptors, including peroxisome proliferator-activated receptor gamma (PPARγ) and liver X receptor (LXR), to regulate metabolic gene expression. Recent research has revealed a functional link between HDAC3 and NCoR1 in the regulation of metabolic gene expression. Genetic deletion of HDAC3 in mouse models has been shown to improve glucose intolerance and insulin sensitivity in the liver, skeletal muscle, and adipose tissue. Similarly, genetic deletion of NCoR1 has improved insulin resistance and reduced adiposity in mouse models. Dysregulation of this interaction has been associated with the development of cardio-metabolic diseases such as cardiovascular diseases, obesity and type 2 diabetes, suggesting that targeting this pathway may hold promise for the development of novel therapeutic interventions. In this review, we summarize the current understanding of individual functions of HDAC3 and NCoR1/2 and the co-repressor complex formation (HDAC3/NCoR1/2) in different metabolic tissues. Further studies are needed to thoroughly understand the mechanisms through which HDAC3, and NCoR1/2 govern metabolic processes and the implications for treating metabolic diseases.
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Affiliation(s)
- Harikrishnareddy Paluvai
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Kumar D. Shanmukha
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Jens Tyedmers
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Johannes Backs
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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3
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Toso A, Boulahtouf A, Escande A, Garoche C, Balaguer P. A comparative study of human and zebrafish glucocorticoid receptor activities of natural and pharmaceutical steroids. Front Endocrinol (Lausanne) 2023; 14:1235501. [PMID: 37654569 PMCID: PMC10466050 DOI: 10.3389/fendo.2023.1235501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Introduction The action of environmental steroids on the human glucocorticoid receptor (hGR) has been pointed out with the risk to impair physiological immune and metabolic processes regulated by this nuclear receptor. However, there is still a lack of mechanistic information regarding their ability to interact with GR in aquatic species. Methods To investigate ligand activation differences between hGR and zebrafish GR (zfGR), we tested several natural and synthetic steroids using reporter cell lines expressing hGR or zfGR. Results and discussion Almost all the glucocorticoids tested (dexamethasone, cortisol, bimedrazol, medrol, cortivazol and fluticasone) are agonists of the two receptors with similar potencies. The dissociated glucocorticoids, RU24782 and RU24858 are agonists of both zfGR and hGR but with a better potency for the latter. On the other hand, the synthetic glucocorticoid forbimenol and the mineralocorticoid aldosterone are agonist on hGR but antagonist on zfGR. The other steroids tested, androgens and progestins, are all antagonists of both GRs with equal or lower potency on zfGR than on hGR. Surprisingly, the lower efficacy and potency on zfGR of aldosterone, forbimenol and the dissociated glucocorticoids is not related to their affinity for the receptors which would suggest that it could be related to less efficacious recruitment of coactivators by zfGR compared to hGR.
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Affiliation(s)
- Anna Toso
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Abdelhay Boulahtouf
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Aurélie Escande
- UMR Hydrosciences Montpellier, Université de Montpellier, Montpellier, France
| | - Clémentine Garoche
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Patrick Balaguer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Université Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
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4
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Hare KS, Wood KM, Mustapha Y, Swanson KC, Steele MA. Colostrum insulin supplementation to neonatal Holstein bulls affects small intestinal histomorphology, mRNA expression, and enzymatic activity with minor influences on peripheral metabolism. J Dairy Sci 2023; 106:5054-5073. [PMID: 37268570 DOI: 10.3168/jds.2022-22965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/29/2022] [Indexed: 06/04/2023]
Abstract
The objectives of this study were to evaluate how varying colostral insulin concentrations influenced small intestinal development and peripheral metabolism in neonatal Holstein bulls. Insulin was supplemented to approximately 5× (70.0 μg/L; n = 16) or 10× (149.7 μg/L; n = 16) the basal colostrum insulin (12.9 μg/L; BI, n = 16) concentration to maintain equivalent macronutrient intake (crude fat: 4.1 ± 0.06%; crude protein: 11.7 ± 0.05%; and lactose: 1.9 ± 0.01%) among treatments. Colostrum was fed at 2, 14, and 26 h postnatal and blood metabolites and insulin concentration were measured at 0, 30, 60, 90, 120, 180, 240, 360, 480, and 600 min postprandial respective to the first and second colostrum meal. At 30 h postnatal, a subset of calves (n = 8/treatment) were killed to excise the gastrointestinal and visceral tissues. Gastrointestinal and visceral gross morphology and dry matter and small intestinal histomorphology, gene expression, and carbohydrase activity were assessed. Insulin supplementation tended to linearly reduce the glucose clearance rate following the first meal, whereas after the second meal, supplementation linearly increased the rate of glucose absorption and nonesterified fatty acid clearance rate, decreased the time to maximum glucose concentrations, and decreased the time to reach minimum nonesterified fatty acid concentrations. Additionally, insulin clearance rate was linearly increased by insulin supplementation following the second colostrum feeding. However, there were no overall differences between treatments in the concentrations of glucose, nonesterified fatty acids, or insulin in plasma or serum. With respect to macroscopic intestinal development, dry rumen tissue mass linearly decreased when insulin was supplemented in colostrum, and supplementation linearly increased duodenal dry tissue density (g dry matter/cm) while tending to increase duodenal dry tissue weight. Increasing the colostrum insulin concentration improved small intestinal histomorphological development in the distal small intestine, as ileal villi height and mucosal-serosal surface area index were increased by supplementing insulin. Lactase enzymatic activity linearly increased in the proximal jejunum while ileal isomaltase activity linearly decreased with insulin supplementation. These data indicate that changes in colostrum insulin concentrations rapidly affect gastrointestinal growth prioritization and carbohydrase activity. The changes in gastrointestinal ontology result in minor changes in postprandial metabolite availability and clearance.
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Affiliation(s)
- K S Hare
- Department of Animal Biosciences, Animal Science and Nutrition, Ontario Agricultural College University of Guelph, Guelph, ON, Canada N1G 1Y2
| | - K M Wood
- Department of Animal Biosciences, Animal Science and Nutrition, Ontario Agricultural College University of Guelph, Guelph, ON, Canada N1G 1Y2
| | - Y Mustapha
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108
| | - K C Swanson
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108
| | - M A Steele
- Department of Animal Biosciences, Animal Science and Nutrition, Ontario Agricultural College University of Guelph, Guelph, ON, Canada N1G 1Y2.
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Steinke I, Govindarajulu M, Pinky PD, Bloemer J, Yoo S, Ward T, Schaedig T, Young T, Wibowo FS, Suppiramaniam V, Amin RH. Selective PPAR-Delta/PPAR-Gamma Activation Improves Cognition in a Model of Alzheimer's Disease. Cells 2023; 12:1116. [PMID: 37190025 PMCID: PMC10136457 DOI: 10.3390/cells12081116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
Background: The continuously increasing association of Alzheimer's disease (AD) with increased mortality rates indicates an unmet medical need and the critical need for establishing novel molecular targets for therapeutic potential. Agonists for peroxisomal proliferator activating receptors (PPAR) are known to regulate energy in the body and have shown positive effects against Alzheimer's disease. There are three members of this class (delta, gamma, and alpha), with PPAR-gamma being the most studied, as these pharmaceutical agonists offer promise for AD because they reduce amyloid beta and tau pathologies, display anti-inflammatory properties, and improve cognition. However, they display poor brain bioavailability and are associated with several adverse side effects on human health, thus limiting their clinical application. Methods: We have developed a novel series of PPAR-delta and PPAR-gamma agonists in silico with AU9 as our lead compound that displays selective amino acid interactions focused upon avoiding the Tyr-473 epitope in the PPAR-gamma AF2 ligand binding domain. Results: This design helps to avoid the unwanted side effects of current PPAR-gamma agonists and improve behavioral deficits and synaptic plasticity while reducing amyloid-beta levels and inflammation in 3xTgAD animals. Conclusions: Our innovative in silico design of PPAR-delta/gamma agonists may offer new perspectives for this class of agonists for AD.
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Affiliation(s)
- Ian Steinke
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
| | - Manoj Govindarajulu
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
| | - Priyanka Das Pinky
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
| | - Jenna Bloemer
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY 10027, USA
| | - Sieun Yoo
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
| | - Tracey Ward
- Department of Pharmaceutical Sciences, Ferris State University, Big Rapids, MI 49307, USA
| | - Taylor Schaedig
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
| | - Taylor Young
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
| | - Fajar Setyo Wibowo
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
| | - Vishnu Suppiramaniam
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
- College of Science and Mathematics, Kennesaw State University, Kennesaw, GA 31044, USA
| | - Rajesh H. Amin
- Department of Drug Discovery and Development, Auburn University, Auburn, AL 36879, USA
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6
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Nuclear receptor: Structure and function. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 196:209-227. [PMID: 36813359 DOI: 10.1016/bs.pmbts.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ligand-dependent transcription factors are nuclear receptors (NRs) that regulate various critical cellular processes such as reproduction, metabolism, development, etc. NRs are classified into (subgroup 0 to subgroup 6) seven superfamilies based on ligand-binding characteristics. All NRs share a general domain structure (A/B, C, D, and E) with distinct essential functions. NRs as monomers, homodimers, or heterodimers bind to consensus DNA sequences known as Hormone Response Elements (HREs). Furthermore, nuclear receptor-binding efficiency depends on minor differences in the sequences of HREs, spacing between the two half-sites, and the flanking sequence of the response elements. NRs can trans-activate and repress their target genes. In positively regulated genes, ligand-bound NRs recruit coactivators to activate the target gene expression, and unliganded NRs cause transcriptional repression. On the other hand, NRs repress gene expression by different mechanisms: (i) ligand-dependent transcriptional repression, (ii) ligand-independent transcriptional repression. This chapter will briefly explain NR superfamilies, their structures, molecular mechanism of action and their role in pathophysiological conditions, etc. That could enable the discovery of new receptors and their ligands and may elucidate their roles in various physiological processes. In addition, therapeutic agonists and antagonists would be developed to control the dysregulation of nuclear receptor signaling.
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7
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Wang Q, Wang Z, Tian S, Wang L, Tang R, Yu Y, Ge J, Hou T, Hao H, Sun H. Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. J Chem Inf Model 2022; 62:3993-4007. [PMID: 36040137 DOI: 10.1021/acs.jcim.2c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of transcriptional activation/repression of the nuclear receptors (NRs) involves two main conformations of the NR protein, namely, the active (agonistic) and inactive (antagonistic) conformations. Binding of agonists or antagonists to the ligand-binding pocket (LBP) of NRs can regulate the downstream signaling pathways with different physiological effects. However, it is still hard to determine the molecular type of a LBP-bound ligand because both the agonists and antagonists bind to the same position of the protein. Therefore, it is necessary to develop precise and efficient methods to facilitate the discrimination of agonists and antagonists targeting the LBP of NRs. Here, combining structural and energetic analyses with machine-learning (ML) algorithms, we constructed a series of structure-based ML models to determine the molecular category of the LBP-bound ligands. We show that the proposed models work robustly and with high accuracy (ACC > 0.9) for determining the category of molecules derived from docking-based and crystallized poses. Furthermore, the models are also capable of determining the molecular category of ligands with dual opposite functions on different NRs (i.e., working as an agonist in one NR target, whereas functioning as an antagonist in another) with reasonable accuracy. The proposed method is expected to facilitate the determination of the molecular properties of ligands targeting the LBP of NRs with structural interpretation.
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Affiliation(s)
- Qinghua Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Sheng Tian
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, P. R. China
| | - Lingling Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Rongfan Tang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Yang Yu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Jingxuan Ge
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, 210009 Nanjing, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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8
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Aibara D, Takahashi S, Yagai T, Kim D, Brocker CN, Levi M, Matsusue K, Gonzalez FJ. Gene repression through epigenetic modulation by PPARA enhances hepatocellular proliferation. iScience 2022; 25:104196. [PMID: 35479397 PMCID: PMC9036120 DOI: 10.1016/j.isci.2022.104196] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 02/22/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022] Open
Abstract
Peroxisome proliferator-activated receptor α (PPARA) is a key mediator of lipid metabolism and inflammation. Activation of PPARA in rodents causes hepatocyte proliferation, but the underlying mechanism is poorly understood. This study focused on genes repressed by PPARA and analyzed the mechanism by which PPARA promotes hepatocyte proliferation in mice. Activation of PPARA by agonist treatment was autoregulated, and induced expression of the epigenetic regulator UHRF1 via activation of the newly described PPARA target gene E2f8, which, in turn, regulates Uhrf1. UHRF1 strongly repressed the expression of CDH1 via methylation of the Cdh1 promoter marked with H3K9me3. Repression of CDH1 by PPARA activation was reversed by PPARA deficiency or knockdown of E2F8 or UHRF1. Furthermore, a forced expression of CDH1 inhibited expression of the Wnt signaling target genes such as Myc after PPARA activation, and suppressed hepatocyte hyperproliferation. These results demonstrate that the PPARA-E2F8-UHRF1-CDH1 axis causes epigenetic regulation of hepatocyte proliferation. PPARA activation induces the UHRF1 expression via novel PPARA target gene E2f8 Induction of UHRF1 by PPARA activation represses Cdh1 gene marked with H3K9me3 CDH1 suppresses hepatocyte proliferation after PPARA activation Autoinduction of PPARA by agonist enhances cell proliferation via E2F8-UHRF1-CDH1
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Affiliation(s)
- Daisuke Aibara
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Faculty of Pharmaceutical Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shogo Takahashi
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC 20057, USA
- Corresponding author
| | - Tomoki Yagai
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Donghwan Kim
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chad N. Brocker
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Moshe Levi
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - Kimihiko Matsusue
- Faculty of Pharmaceutical Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Corresponding author
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Yagai T, Nakamura T. Mechanistic insights into the peroxisome proliferator-activated receptor alpha as a transcriptional suppressor. Front Med (Lausanne) 2022; 9:1060244. [PMID: 36507526 PMCID: PMC9732035 DOI: 10.3389/fmed.2022.1060244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/08/2022] [Indexed: 11/27/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is one of the most prevalent hepatic disorders that 20-30% of the world population suffers from. The feature of NAFLD is excess lipid accumulation in the liver, exacerbating multiple metabolic syndromes such as hyperlipidemia, hypercholesterolemia, hypertension, and type 2 diabetes. Approximately 20-30% of NAFLD cases progress to more severe chronic hepatitis, known as non-alcoholic steatohepatitis (NASH), showing deterioration of hepatic functions and liver fibrosis followed by cirrhosis and cancer. Previous studies uncovered that several metabolic regulators had roles in disease progression as key factors. Peroxisome proliferator-activated receptor alpha (PPARα) has been identified as one of the main players in hepatic lipid homeostasis. PPARα is abundantly expressed in hepatocytes, and is a ligand-dependent nuclear receptor belonging to the NR1C nuclear receptor subfamily, orchestrating lipid/glucose metabolism, inflammation, cell proliferation, and carcinogenesis. PPARα agonists are expected to be novel prescription drugs for NASH treatment, and some of them (e.g., Lanifibranor) are currently under clinical trials. These potential novel drugs are developed based on the knowledge of PPARα-activating target genes related to NAFLD and NASH. Intriguingly, PPARα is known to suppress the expression of subsets of target genes under agonist treatment; however, the mechanisms of PPARα-mediated gene suppression and functions of these genes are not well understood. In this review, we summarize and discuss the mechanisms of target gene repression by PPARα and the roles of repressed target genes on hepatic lipid metabolism, fibrosis and carcinogenesis related to NALFD and NASH, and provide future perspectives for PPARα pharmaceutical potentials.
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Affiliation(s)
- Tomoki Yagai
- Department of Metabolic Bioregulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Takahisa Nakamura
- Department of Metabolic Bioregulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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10
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Shang J, Kojetin DJ. Structural mechanism underlying ligand binding and activation of PPARγ. Structure 2021; 29:940-950.e4. [PMID: 33713599 DOI: 10.1016/j.str.2021.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022]
Abstract
Ligands bind to an occluded orthosteric ligand-binding pocket within the nuclear receptor ligand-binding domain. Molecular simulations have revealed theoretical ligand entry/exit pathways to the orthosteric pocket; however, it remains unclear whether ligand binding proceeds through induced fit or conformational selection mechanisms. Here, using nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, and surface plasmon resonance analysis, we provide evidence that structurally distinct agonists bind peroxisome proliferator-activated receptor γ (PPARγ) via a two-step induced fit mechanism involving an initial fast kinetic step followed by a slow conformational change. The agonist encounter complex binding pose is suggested in crystal structures where ligands bind to a surface pore suggested as a ligand entry site in molecular simulations. Our findings suggest an activation mechanism for PPARγ whereby agonist binding occurs through an initial encounter complex followed by a transition of the ligand into the final binding pose within the orthosteric pocket, inducing a transcriptionally active conformation.
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Affiliation(s)
- Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA.
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11
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Lamorte S, Shinde R, McGaha TL. Nuclear receptors, the aryl hydrocarbon receptor, and macrophage function. Mol Aspects Med 2021; 78:100942. [PMID: 33451803 DOI: 10.1016/j.mam.2021.100942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Nuclear receptors (NRs) are key regulators of innate immune responses and tissue homeostasis. Evidence indicates that NRs significantly impact steady-state immune regulation, uptake and processing of apoptotic cells, tolerance induction, and control of inflammatory immunity. In this review, we describe our current understanding of the NR activity for balancing inflammation and tolerance, the signaling cascade inducing the NR activation and functional responses, and different mechanisms of the NR-driven immune effects in the context of autoimmune diseases. We further describe the ligand-activated transcription factor the aryl hydrocarbon receptor (AhR) that exhibits analogous functionality. Moreover, we will discuss the putative role of NRs and AhR in immune regulation and disease pathogenesis providing a rationale for therapeutic targeting as a unique opportunities in the clinical management of autoimmune diseases.
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Affiliation(s)
- Sara Lamorte
- Tumor Immunotherapy Program, The Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rahul Shinde
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute Cancer Center, Philadelphia, PA, USA
| | - Tracy L McGaha
- Tumor Immunotherapy Program, The Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; The Department of Immunology, The University of Toronto, Toronto, ON, Canada.
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12
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Sissaoui S, Yu J, Yan A, Li R, Yukselen O, Kucukural A, Zhu LJ, Lawson ND. Genomic Characterization of Endothelial Enhancers Reveals a Multifunctional Role for NR2F2 in Regulation of Arteriovenous Gene Expression. Circ Res 2020; 126:875-888. [PMID: 32065070 PMCID: PMC7212523 DOI: 10.1161/circresaha.119.316075] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RATIONALE Significant progress has revealed transcriptional inputs that underlie regulation of artery and vein endothelial cell fates. However, little is known concerning genome-wide regulation of this process. Therefore, such studies are warranted to address this gap. OBJECTIVE To identify and characterize artery- and vein-specific endothelial enhancers in the human genome, thereby gaining insights into mechanisms by which blood vessel identity is regulated. METHODS AND RESULTS Using chromatin immunoprecipitation and deep sequencing for markers of active chromatin in human arterial and venous endothelial cells, we identified several thousand artery- and vein-specific regulatory elements. Computational analysis revealed that NR2F2 (nuclear receptor subfamily 2, group F, member 2) sites were overrepresented in vein-specific enhancers, suggesting a direct role in promoting vein identity. Subsequent integration of chromatin immunoprecipitation and deep sequencing data sets with RNA sequencing revealed that NR2F2 regulated 3 distinct aspects related to arteriovenous identity. First, consistent with previous genetic observations, NR2F2 directly activated enhancer elements flanking cell cycle genes to drive their expression. Second, NR2F2 was essential to directly activate vein-specific enhancers and their associated genes. Our genomic approach further revealed that NR2F2 acts with ERG (ETS-related gene) at many of these sites to drive vein-specific gene expression. Finally, NR2F2 directly repressed only a small number of artery enhancers in venous cells to prevent their activation, including a distal element upstream of the artery-specific transcription factor, HEY2 (hes related family bHLH transcription factor with YRPW motif 2). In arterial endothelial cells, this enhancer was normally bound by ERG, which was also required for arterial HEY2 expression. By contrast, in venous endothelial cells, NR2F2 was bound to this site, together with ERG, and prevented its activation. CONCLUSIONS By leveraging a genome-wide approach, we revealed mechanistic insights into how NR2F2 functions in multiple roles to maintain venous identity. Importantly, characterization of its role at a crucial artery enhancer upstream of HEY2 established a novel mechanism by which artery-specific expression can be achieved.
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Affiliation(s)
- Samir Sissaoui
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - Aimin Yan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - Onur Yukselen
- Department of Bioinformatics Core, University of Massachusetts Medical School, Worcester, MA, 01605
| | - Alper Kucukural
- Department of Bioinformatics Core, University of Massachusetts Medical School, Worcester, MA, 01605
- Department of Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605
- Department of Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605
- Department of Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - Nathan D. Lawson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605
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13
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Bianco S, Bellefleur AM, Beaulieu É, Beauparlant CJ, Bertolin K, Droit A, Schoonjans K, Murphy BD, Gévry N. The Ovulatory Signal Precipitates LRH-1 Transcriptional Switching Mediated by Differential Chromatin Accessibility. Cell Rep 2019; 28:2443-2454.e4. [DOI: 10.1016/j.celrep.2019.07.088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/01/2019] [Accepted: 07/24/2019] [Indexed: 12/23/2022] Open
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14
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Kim YK, Maquat LE. UPFront and center in RNA decay: UPF1 in nonsense-mediated mRNA decay and beyond. RNA (NEW YORK, N.Y.) 2019; 25:407-422. [PMID: 30655309 PMCID: PMC6426291 DOI: 10.1261/rna.070136.118] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nonsense-mediated mRNA decay (NMD), which is arguably the best-characterized translation-dependent regulatory pathway in mammals, selectively degrades mRNAs as a means of post-transcriptional gene control. Control can be for the purpose of ensuring the quality of gene expression. Alternatively, control can facilitate the adaptation of cells to changes in their environment. The key to NMD, no matter what its purpose, is the ATP-dependent RNA helicase upstream frameshift 1 (UPF1), without which NMD fails to occur. However, UPF1 does much more than regulate NMD. As examples, UPF1 is engaged in functionally diverse mRNA decay pathways mediated by a variety of RNA-binding proteins that include staufen, stem-loop-binding protein, glucocorticoid receptor, and regnase 1. Moreover, UPF1 promotes tudor-staphylococcal/micrococcal-like nuclease-mediated microRNA decay. In this review, we first focus on how the NMD machinery recognizes an NMD target and triggers mRNA degradation. Next, we compare and contrast the mechanisms by which UPF1 functions in the decay of other mRNAs and also in microRNA decay. UPF1, as a protein polymath, engenders cells with the ability to shape their transcriptome in response to diverse biological and physiological needs.
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Affiliation(s)
- Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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15
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Proietti CJ, Cenciarini ME, Elizalde PV. Revisiting progesterone receptor (PR) actions in breast cancer: Insights into PR repressive functions. Steroids 2018; 133:75-81. [PMID: 29317254 DOI: 10.1016/j.steroids.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/08/2017] [Accepted: 12/23/2017] [Indexed: 12/18/2022]
Abstract
Progesterone receptor (PR) is a master regulator in female reproductive tissues that controls developmental processes and proliferation and differentiation during the reproductive cycle and pregnancy. PR also plays a role in progression of endocrine-dependent breast cancer. As a member of the nuclear receptor family of ligand-dependent transcription factors, the main action of PR is to regulate networks of target gene expression in response to binding its cognate steroid hormone, progesterone. Liganded-PR transcriptional activation has been thoroughly studied and associated mechanisms have been described while progesterone-mediated repression has remained less explored. The present work summarizes recent advances in the understanding of how PR-mediated repression is accomplished in breast cancer cells and highlights the significance of fully understanding the determinants of context-dependent PR action.
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Affiliation(s)
- Cecilia J Proietti
- Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, Buenos Aires C1428ADN, Argentina.
| | - Mauro E Cenciarini
- Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, Buenos Aires C1428ADN, Argentina
| | - Patricia V Elizalde
- Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, Buenos Aires C1428ADN, Argentina
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16
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Fernandes V, Teles K, Ribeiro C, Treptow W, Santos G. Fat nucleosome: Role of lipids on chromatin. Prog Lipid Res 2018; 70:29-34. [PMID: 29678609 DOI: 10.1016/j.plipres.2018.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/18/2018] [Accepted: 04/16/2018] [Indexed: 01/01/2023]
Abstract
Structural changes in chromatin regulate gene expression and define phenotypic outcomes. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Most recently, the formation of condensed chromatin regions based on phase-separation in the cell, a basic physical mechanism, was proposed. Increased understanding of the mechanisms of interaction between chromatin and lipids suggest that small lipid molecules, such as cholesterol and short-chain fatty acids, can regulate important nuclear functions. New biophysical data has suggested that cholesterol interacts with nucleosome through multiple binding sites and affects chromatin structure in vitro. Regardless of the mechanism of how lipids bind to chromatin, there is currently little awareness that lipids may be stored in chromatin and influence its state. Focusing on lipids that bind to nuclear receptors, clinically relevant transcription factors, we discuss the potential interactions of the nucleosome with steroid hormones, bile acids and fatty acids, which suggest that other lipid chemotypes may also impact chromatin structure through binding to common sites on the nucleosome. Herein, we review the main impacts of lipids on the nuclear environment, emphasizing its role on chromatin architecture. We postulate that lipids that bind to nucleosomes and affect chromatin states are likely to be worth investigating as tools to modify disease phenotypes at a molecular level.
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Affiliation(s)
- Vinicius Fernandes
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil; Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF 70910-900, Brasília, Brazil
| | - Kaian Teles
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil
| | - Camyla Ribeiro
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF 70910-900, Brasília, Brazil
| | - Guilherme Santos
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil.
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17
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Mathew SP, Thakur K, Kumar S, Yende AS, Singh SK, Dash AK, Tyagi RK. A Comprehensive Analysis and Prediction of Sub-Cellular Localization of Human Nuclear Receptors. NUCLEAR RECEPTOR RESEARCH 2018. [DOI: 10.11131/2018/101324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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McDowell IC, Manandhar D, Vockley CM, Schmid AK, Reddy TE, Engelhardt BE. Clustering gene expression time series data using an infinite Gaussian process mixture model. PLoS Comput Biol 2018; 14:e1005896. [PMID: 29337990 PMCID: PMC5786324 DOI: 10.1371/journal.pcbi.1005896] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 01/26/2018] [Accepted: 11/25/2017] [Indexed: 12/24/2022] Open
Abstract
Transcriptome-wide time series expression profiling is used to characterize the cellular response to environmental perturbations. The first step to analyzing transcriptional response data is often to cluster genes with similar responses. Here, we present a nonparametric model-based method, Dirichlet process Gaussian process mixture model (DPGP), which jointly models data clusters with a Dirichlet process and temporal dependencies with Gaussian processes. We demonstrate the accuracy of DPGP in comparison to state-of-the-art approaches using hundreds of simulated data sets. To further test our method, we apply DPGP to published microarray data from a microbial model organism exposed to stress and to novel RNA-seq data from a human cell line exposed to the glucocorticoid dexamethasone. We validate our clusters by examining local transcription factor binding and histone modifications. Our results demonstrate that jointly modeling cluster number and temporal dependencies can reveal shared regulatory mechanisms. DPGP software is freely available online at https://github.com/PrincetonUniversity/DP_GP_cluster.
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Affiliation(s)
- Ian C. McDowell
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina, United States of America
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Dinesh Manandhar
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina, United States of America
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Christopher M. Vockley
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics & Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Amy K. Schmid
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Timothy E. Reddy
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina, United States of America
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics & Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Barbara E. Engelhardt
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey, United States of America
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19
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Little AG. Local Regulation of Thyroid Hormone Signaling. VITAMINS AND HORMONES 2018; 106:1-17. [DOI: 10.1016/bs.vh.2017.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Campos JLO, Doratioto TR, Videira NB, Ribeiro Filho HV, Batista FAH, Fattori J, Indolfo NDC, Nakahira M, Bajgelman MC, Cvoro A, Laurindo FRM, Webb P, Figueira ACM. Protein Disulfide Isomerase Modulates the Activation of Thyroid Hormone Receptors. Front Endocrinol (Lausanne) 2018; 9:784. [PMID: 30671024 PMCID: PMC6331412 DOI: 10.3389/fendo.2018.00784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 12/12/2018] [Indexed: 12/30/2022] Open
Abstract
Thyroid hormone receptors (TRs) are responsible for mediating thyroid hormone (T3 and T4) actions at a cellular level. They belong to the nuclear receptor (NR) superfamily and execute their main functions inside the cell nuclei as hormone-regulated transcription factors. These receptors also exhibit so-called "non-classic" actions, for which other cellular proteins, apart from coregulators inside nuclei, regulate their activity. Aiming to find alternative pathways of TR modulation, we searched for interacting proteins and found that PDIA1 interacts with TRβ in a yeast two-hybrid screening assay. The functional implications of PDIA1-TR interactions are still unclear; however, our co-immunoprecipitation (co-IP) and fluorescence assay results showed that PDI was able to bind both TR isoforms in vitro. Moreover, T3 appears to have no important role in these interactions in cellular assays, where PDIA1 was able to regulate transcription of TRα and TRβ-mediated genes in different ways depending on the promoter region and on the TR isoform involved. Although PDIA1 appears to act as a coregulator, it binds to a TR surface that does not interfere with coactivator binding. However, the TR:PDIA1 complex affinity and activation are different depending on the TR isoform. Such differences may reflect the structural organization of the PDIA1:TR complex, as shown by models depicting an interaction interface with exposed cysteines from both proteins, suggesting that PDIA1 might modulate TR by its thiol reductase/isomerase activity.
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Affiliation(s)
- Jessica L. O. Campos
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
- Graduation Program of Biosciences and Bioactive Products Technology, Institute of Biology, State University of Campinas (Unicamp), São Paulo, Brazil
| | - Tabata R. Doratioto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
- Graduation Program of Biosciences and Bioactive Products Technology, Institute of Biology, State University of Campinas (Unicamp), São Paulo, Brazil
| | - Natalia B. Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
- Graduation Program of Biosciences and Bioactive Products Technology, Institute of Biology, State University of Campinas (Unicamp), São Paulo, Brazil
| | - Helder V. Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
- Graduation Program of Biosciences and Bioactive Products Technology, Institute of Biology, State University of Campinas (Unicamp), São Paulo, Brazil
| | - Fernanda A. H. Batista
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
| | - Juliana Fattori
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
| | - Nathalia de C. Indolfo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
- Graduation Program of Biosciences and Bioactive Products Technology, Institute of Biology, State University of Campinas (Unicamp), São Paulo, Brazil
| | - Marcel Nakahira
- Institute of Chemistry (IQ), State University of Campinas (Unicamp), São Paulo, Brazil
| | - Marcio C. Bajgelman
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
| | - Aleksandra Cvoro
- Genomic Medicine, The Methodist Hospital Research Institute, Houston, TX, United States
| | - Francisco R. M. Laurindo
- Vascular Biology Laboratory, Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Paul Webb
- California Institute for Regenerative Medicine, Oakland, CA, United States
| | - Ana Carolina M. Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research Energy and Materials (CNPEM), São Paulo, Brazil
- *Correspondence: Ana Carolina M. Figueira
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Abstract
As one of the most basal living vertebrates, lampreys represent an excellent model system to study the evolution of thyroid hormone (TH) signaling. The lamprey hypothalamic-pituitary-thyroid and reproductive axes overlap functionally. Lampreys have 3 gonadotropin-releasing hormones and a single glycoprotein hormone from the hypothalamus and pituitary, respectively, that regulate both the reproductive and thyroid axes. TH synthesis in larval lampreys takes place in an endostyle that transforms into typical vertebrate thyroid tissue during metamorphosis; both the endostyle and follicular tissue have all the typical TH synthetic components found in other vertebrates. Furthermore, lampreys also have the vertebrate suite of peripheral regulators including TH distributor proteins (THDPs), deiodinases and TH receptors (TRs). Although at the molecular level the components of the lamprey thyroid system are ancestral to other vertebrates, their functions have been largely conserved. TH signaling as it relates to lamprey metamorphosis represents a particularly interesting phenomenon. Unlike other metamorphosing vertebrates, lamprey THs increase throughout the larval period, peak prior to metamorphosis and decline rapidly at the onset of metamorphosis; patterns of deiodinase activity are consistent with these increases and declines. Moreover, goitrogens (which suppress TH levels) initiate precocious metamorphosis, and exogenous TH treatment blocks goitrogen-induced metamorphosis and disrupts natural metamorphosis. Despite this clear physiological difference, TH action via TRs is consistent with higher vertebrates. Based on observations that TRs are upregulated in a tissue-specific fashion during morphogenesis and the finding that lamprey TRs upregulate genes via THs in a fashion similar to higher vertebrates, we propose the following hypothesis for further testing. THs have a dual role in lampreys where high TH levels promote larval feeding and growth and then at the onset of metamorphosis TH levels decrease rapidly; at this time the relatively low TH levels function via TRs in a fashion similar to that of other metamorphosing vertebrates.
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Affiliation(s)
- Richard G Manzon
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada.
| | - Lori A Manzon
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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Carleton JB, Berrett KC, Gertz J. Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers. Cell Syst 2017; 5:333-344.e5. [PMID: 28964699 DOI: 10.1016/j.cels.2017.08.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/13/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022]
Abstract
Multiple regulatory regions have the potential to regulate a single gene, yet how these elements combine to affect gene expression remains unclear. To uncover the combinatorial relationships between enhancers, we developed Enhancer-interference (Enhancer-i), a CRISPR interference-based approach that uses 2 different repressive domains, KRAB and SID, to prevent enhancer activation simultaneously at multiple regulatory regions. We applied Enhancer-i to promoter-distal estrogen receptor α binding sites (ERBS), which cluster around estradiol-responsive genes and therefore may collaborate to regulate gene expression. Targeting individual sites revealed predominant ERBS that are completely required for the transcriptional response, indicating a lack of redundancy. Simultaneous interference of different ERBS combinations identified supportive ERBS that contribute only when predominant sites are active. Using mathematical modeling, we find strong evidence for collaboration between predominant and supportive ERBS. Overall, our findings expose a complex functional hierarchy of enhancers, where multiple loci bound by the same transcription factor combine to fine-tune the expression of target genes.
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Affiliation(s)
- Julia B Carleton
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Kristofer C Berrett
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
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Sasaki S, Matsushita A, Kuroda G, Nakamura HM, Oki Y, Suda T. The Mechanism of Negative Transcriptional Regulation by Thyroid Hormone: Lessons From the Thyrotropin β Subunit Gene. VITAMINS AND HORMONES 2017; 106:97-127. [PMID: 29407449 DOI: 10.1016/bs.vh.2017.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Thyroid hormone (T3) activates (positive regulation) or represses (negative regulation) target genes at the transcriptional level. The molecular mechanism of the former has been elucidated in detail; however, the mechanism for negative regulation has not been established. The best example of the gene that is negatively regulated by T3 is the thyrotropin (thyroid-stimulating hormone) β subunit (TSHβ) gene. Analogous to the T3-responsive element (TRE) in positive regulation, a negative TRE (nTRE) has been postulated in the TSHβ gene. However, TSHβ promoter analysis, performed in the presence of transcription factors Pit1 and GATA2, which are determinants of thyrotroph differentiation in the pituitary, revealed that the nTRE is dispensable for inhibition by T3. We propose a tethering model in which the T3 receptor is tethered to GATA2 via protein-protein interaction and inhibits GATA2-dependent transactivation of the TSHβ gene in a T3-dependent manner.
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Affiliation(s)
| | | | - Go Kuroda
- Hamamatsu University School of Medicine, Shizuoka, Japan
| | | | - Yutaka Oki
- Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Takafumi Suda
- Hamamatsu University School of Medicine, Shizuoka, Japan
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24
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Gil-Ibáñez P, Belinchón MM, Morte B, Obregón MJ, Bernal J. Is the Intrinsic Genomic Activity of Thyroxine Relevant In Vivo? Effects on Gene Expression in Primary Cerebrocortical and Neuroblastoma Cells. Thyroid 2017; 27:1092-1098. [PMID: 28605984 DOI: 10.1089/thy.2017.0024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND The possibility that the intrinsic genomic activity of thyroxine (T4) is of physiological relevance has been frequently hypothesized. It might explain gene expression patterns in the brain found in type 2-deiodinase (Dio2)-deficient mice. These mice display normal expression of most thyroid hormone-dependent genes, despite decreased brain triiodothyronine (T3). METHODS The relative effects of T4 and T3 on gene expression were analyzed in mouse neuro-2a (N2a) cells stably expressing the thyroid hormone receptor α1, and in primary mouse cerebrocortical cells enriched in astrocytes or in neurons. Cortical cells were derived from Dio2-deficient mice to prevent conversion of T4 to T3. T4 and T3 were measured in the media at the beginning and end of incubation, and T4 and T3 antibodies were used to block T4 and T3 action. RESULTS In all cell types, T4 had intrinsic genomic activity. In N2a cells, T4 activity was higher on negative regulation (1/5th of T3 activity) than on positive regulation (1/40th of T3 activity). T4 activity on positive regulation was dependent on the cell context, and was higher in primary cells than in N2a cells. CONCLUSION T4 has intrinsic genomic activity. Positive regulation depends on the cell context, and primary cells appear much more sensitive than neuroblastoma cells. In all cells, negative regulation is more sensitive to T4 than positive regulation. These properties may explain the mostly normal gene expression in the brain of Dio2-deficient mice.
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Affiliation(s)
- Pilar Gil-Ibáñez
- 1 Instituto de Investigaciones Biomédicas , Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
- 2 Center for Biomedical Research on Rare Diseases, Instituto de Salud Carlos III , Madrid, Spain
| | - Mónica M Belinchón
- 1 Instituto de Investigaciones Biomédicas , Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
- 2 Center for Biomedical Research on Rare Diseases, Instituto de Salud Carlos III , Madrid, Spain
| | - Beatriz Morte
- 2 Center for Biomedical Research on Rare Diseases, Instituto de Salud Carlos III , Madrid, Spain
| | - Maria Jesus Obregón
- 1 Instituto de Investigaciones Biomédicas , Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Bernal
- 1 Instituto de Investigaciones Biomédicas , Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
- 2 Center for Biomedical Research on Rare Diseases, Instituto de Salud Carlos III , Madrid, Spain
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25
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Walter KR, Goodman ML, Singhal H, Hall JA, Li T, Holloran SM, Trinca GM, Gibson KA, Jin VX, Greene GL, Hagan CR. Interferon-Stimulated Genes Are Transcriptionally Repressed by PR in Breast Cancer. Mol Cancer Res 2017; 15:1331-1340. [PMID: 28684637 DOI: 10.1158/1541-7786.mcr-17-0180] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/20/2017] [Accepted: 07/03/2017] [Indexed: 12/21/2022]
Abstract
The progesterone receptor (PR) regulates transcriptional programs that drive proliferation, survival, and stem cell phenotypes. Although the role of native progesterone in the development of breast cancer remains controversial, PR clearly alters the transcriptome in breast tumors. This study identifies a class of genes, Interferon (IFN)-stimulated genes (ISGs), potently downregulated by ligand-activated PR which have not been previously shown to be regulated by PR. Progestin-dependent transcriptional repression of ISGs was observed in breast cancer cell line models and human breast tumors. Ligand-independent regulation of ISGs was also observed, as basal transcript levels were markedly higher in cells with PR knockdown. PR repressed ISG transcription in response to IFN treatment, the canonical mechanism through which these genes are activated. Liganded PR is robustly recruited to enhancer regions of ISGs, and ISG transcriptional repression is dependent upon PR's ability to bind DNA. In response to PR activation, key regulatory transcription factors that are required for IFN-activated ISG transcription, STAT2 and IRF9, exhibit impaired recruitment to ISG promoter regions, correlating with PR/ligand-dependent ISG transcriptional repression. IFN activation is a critical early step in nascent tumor recognition and destruction through immunosurveillance. As the large majority of breast tumors are PR positive at the time of diagnosis, PR-dependent downregulation of IFN signaling may be a mechanism through which early PR-positive breast tumors evade the immune system and develop into clinically relevant tumors.Implications: This study highlights a novel transcriptional mechanism through which PR drives breast cancer development and potentially evades the immune system. Mol Cancer Res; 15(10); 1331-40. ©2017 AACR.
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Affiliation(s)
- Katherine R Walter
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Merit L Goodman
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Hari Singhal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jade A Hall
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Tianbao Li
- Department of Molecular Medicine, University of Texas Health San Antonio (UTHSA), San Antonio, Texas
| | - Sean M Holloran
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Gloria M Trinca
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Katelin A Gibson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health San Antonio (UTHSA), San Antonio, Texas
| | - Geoffrey L Greene
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois
| | - Christy R Hagan
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas. .,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
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Park OH, Park J, Yu M, An HT, Ko J, Kim YK. Identification and molecular characterization of cellular factors required for glucocorticoid receptor-mediated mRNA decay. Genes Dev 2017; 30:2093-2105. [PMID: 27798850 PMCID: PMC5066615 DOI: 10.1101/gad.286484.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/08/2016] [Indexed: 11/24/2022]
Abstract
In this study, Park et al. investigated the molecular mechanisms regulating glucocorticoid receptor-mediated mRNA decay (GMD). The authors characterize the molecular details of GMD, identify specific factors required for efficient GMD, and perform RNA sequencing, identifying many endogenous GMD substrates. Glucocorticoid (GC) receptor (GR) has been shown recently to bind a subset of mRNAs and elicit rapid mRNA degradation. However, the molecular details of GR-mediated mRNA decay (GMD) remain unclear. Here, we demonstrate that GMD triggers rapid degradation of target mRNAs in a translation-independent and exon junction complex-independent manner, confirming that GMD is mechanistically distinct from nonsense-mediated mRNA decay (NMD). Efficient GMD requires PNRC2 (proline-rich nuclear receptor coregulatory protein 2) binding, helicase ability, and ATM-mediated phosphorylation of UPF1 (upstream frameshift 1). We also identify two GMD-specific factors: an RNA-binding protein, YBX1 (Y-box-binding protein 1), and an endoribonuclease, HRSP12 (heat-responsive protein 12). In particular, using HRSP12 variants, which are known to disrupt trimerization of HRSP12, we show that HRSP12 plays an essential role in the formation of a functionally active GMD complex. Moreover, we determine the hierarchical recruitment of GMD factors to target mRNAs. Finally, our genome-wide analysis shows that GMD targets a variety of transcripts, implicating roles in a wide range of cellular processes, including immune responses.
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Affiliation(s)
- Ok Hyun Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Mira Yu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyoung-Tae An
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jesang Ko
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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Zhang F, Qin H, Zhao Y, Wei Y, Xi L, Rao Z, Zhang J, Ma Y, Duan Y, Wu X. Effect of cholecystectomy on bile acids as well as relevant enzymes and transporters in mice: Implication for pharmacokinetic changes of rifampicin. Eur J Pharm Sci 2017; 96:141-153. [DOI: 10.1016/j.ejps.2016.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/06/2016] [Accepted: 09/06/2016] [Indexed: 12/19/2022]
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Nacht AS, Beato M, Vicent GP. Steroid hormone receptors silence genes by a chromatin-targeted mechanism similar to those used for gene activation. Transcription 2016; 8:15-20. [PMID: 27700223 DOI: 10.1080/21541264.2016.1242456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
How genes are repressed by steroid hormones remains a matter of debate, and several indirect mechanisms have been proposed. We found that the ligand-activated progesterone receptor recruits to the promoter of downregulated genes a repressor complex composed of HP1γ, the lysine demethylase LSD1, histone deacetylases, coREST, the RNA SRA, and the ATPase BRG1. BRG1 is needed for chromatin remodeling and facilitates the deposition of linker histone variant H1.2, which compacts chromatin and hinders RNA polymerase loading and transcription. Thus, steroid hormone receptors can repress genes in ways reminiscent of those used for gene induction, namely by directly targeting factors that remodel chromatin. But while PR-dependent gene induction in T47D cells is mainly achieved by potentiating enhancer activity, repression acts at the level of gene promoters.
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Affiliation(s)
- A Silvina Nacht
- a Centre de Regulació Genòmica (CRG) , The Barcelona Institute for Science and Technology (BIST) , Barcelona , Spain.,b Gene Regulation , Stem Cells and Cancer Program, Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Miguel Beato
- a Centre de Regulació Genòmica (CRG) , The Barcelona Institute for Science and Technology (BIST) , Barcelona , Spain.,b Gene Regulation , Stem Cells and Cancer Program, Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Guillermo P Vicent
- a Centre de Regulació Genòmica (CRG) , The Barcelona Institute for Science and Technology (BIST) , Barcelona , Spain.,b Gene Regulation , Stem Cells and Cancer Program, Universitat Pompeu Fabra (UPF) , Barcelona , Spain
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Weitzel JM. Impaired Repressor Function in SUMOylation-Defective Thyroid Hormone Receptor Isoforms. Eur Thyroid J 2016; 5:152-163. [PMID: 27843805 PMCID: PMC5091228 DOI: 10.1159/000447232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/27/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Many nuclear receptors are modified by posttranslational modifications. OBJECTIVES The transcriptional activity of thyroid hormone receptors (TRs) is modified by the influence of its ligand (thyroid hormones T3 and T4), but is also affected by posttranslational modifications. This study focuses on the SUMOylation of TR isoforms and the consequences on transcriptional activity and promoter occupancy. METHODS SUMOylation of TR wild-type as well as isoform-specific point mutations have been studied in vitro. The promoter occupancy of TR (wild-type and double- or triple-mutated versions) and transcriptional cofactors have been investigated in chromatin immunoprecipitation (ChIP) and Re-ChIP analysis. RESULTS TR is modified by SUMO proteins at defined residues: the isoform TRα is mainly modified at lysines 281 and 387, whereas lysines 50 and 443 are major SUMOylation sites of isoform TRβ. Lysine residues K281 (TRα) and K50 (TRβ) are isoform-specific SUMOylation sites influencing differing TR domains, whereas K387 (TRα) and K443 (TRβ) are orthologous residues. TRs are targets of all three SUMO variants (SUMO-1, -2, and -3). The transcriptional activity of SUMOylation-defective mutants of TR alters gene transcription from positively and negatively regulated T3 target genes. CONCLUSIONS The most pronounced effect is an impaired repressor function of SUMOylation-deficient TR in the absence of T3. The transcriptional properties of SUMOylation-defective TRs can be at least in part ascribed to altered interaction with transcriptional cofactors such as SRC-1 and NCoR. Thus, these data indicate that posttranslational modification of TR by SUMOylation contribute to the fine tuning of its transcriptional response maintaining effects on cellular and physiological homeostasis.
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Affiliation(s)
- Joachim M. Weitzel
- *Joachim M. Weitzel, Institute of Reproductive Biology, Leibniz Institute for Farm, Animal Biology (FBN), FBN Dummerstorf, Wilhelm-Stahl-Allee 2, DE-18196 Dummerstorf (Germany), E-Mail
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Nacht AS, Pohl A, Zaurin R, Soronellas D, Quilez J, Sharma P, Wright RH, Beato M, Vicent GP. Hormone-induced repression of genes requires BRG1-mediated H1.2 deposition at target promoters. EMBO J 2016; 35:1822-43. [PMID: 27390128 DOI: 10.15252/embj.201593260] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 06/07/2016] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic gene regulation is associated with changes in chromatin compaction that modulate access to DNA regulatory sequences relevant for transcriptional activation or repression. Although much is known about the mechanism of chromatin remodeling in hormonal gene activation, how repression is accomplished is much less understood. Here we report that in breast cancer cells, ligand-activated progesterone receptor (PR) is directly recruited to transcriptionally repressed genes involved in cell proliferation along with the kinases ERK1/2 and MSK1. PR recruits BRG1 associated with the HP1γ-LSD1 complex repressor complex, which is further anchored via binding of HP1γ to the H3K9me3 signal deposited by SUV39H2. In contrast to what is observed during gene activation, only BRG1 and not the BAF complex is recruited to repressed promoters, likely due to local enrichment of the pioneer factor FOXA1. BRG1 participates in gene repression by interacting with H1.2, facilitating its deposition and stabilizing nucleosome positioning around the transcription start site. Our results uncover a mechanism of hormone-dependent transcriptional repression and a novel role for BRG1 in progestin regulation of breast cancer cell growth.
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Affiliation(s)
- Ana Silvina Nacht
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andy Pohl
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roser Zaurin
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Daniel Soronellas
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Javier Quilez
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Priyanka Sharma
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roni H Wright
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miguel Beato
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillermo P Vicent
- Centre de Regulació Genòmica (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
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31
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Little AG. A review of the peripheral levels of regulation by thyroid hormone. J Comp Physiol B 2016; 186:677-88. [DOI: 10.1007/s00360-016-0984-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
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Rana M, Devi S, Gourinath S, Goswami R, Tyagi RK. A comprehensive analysis and functional characterization of naturally occurring non-synonymous variants of nuclear receptor PXR. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1183-1197. [PMID: 26962022 DOI: 10.1016/j.bbagrm.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 01/17/2023]
Abstract
Pregnane & Xenobiotic Receptor (PXR) acts as a xenosensing transcriptional regulator of many drug metabolizing enzymes and transporters of the 'detoxification machinery' that coordinate in elimination of xenobiotics and endobiotics from the cellular milieu. It is an accepted view that some individuals or specific populations display considerable differences in their ability to metabolize different drugs, dietary constituents, herbals etc. In this context we speculated that polymorphisms in PXR gene might contribute to variability in cytochrome P450 (CYP450) metabolizing enzymes of phase I, drug metabolizing components of phase II and efflux components of the detoxification machinery. Therefore, in this study, we have undertaken a comprehensive functional analysis of seventeen naturally occurring non-synonymous variants of human PXR. When compared, we observed that some of the PXR SNP variants exhibit distinct functional and dynamic responses on parameters which included transcriptional function, sub-cellular localization, mitotic chromatin binding, DNA-binding properties and other molecular interactions. One of the unique SNP located within the DNA-binding domain of PXR was found to be functionally null and distinct on other parameters. Similarly, some of the non-synonymous SNPs in PXR imparted reduced transactivation function as compared to wild type PXR. Interestingly, PXR is reported to be a mitotic chromatin binding protein and such an association has been correlated to an emerging concept of 'transcription memory' and altered transcription output. In view of the observations made herein our data suggest that some of the natural PXR variants may have adverse physiological consequences owing to its influence on the expression levels and functional output of drug-metabolizing enzymes and transporters. The present study is expected to explain not only the observed inter-individual responses to different drugs but may also highlight the mechanistic details and importance of PXR in drug clearance, drug-drug interactions and diverse metabolic disorders. This article is part of a Special Issue entitled: Xenobiotic nuclear receptors: New Tricks for An Old Dog, edited by Dr. Wen Xie.
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Affiliation(s)
- Manjul Rana
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneeta Devi
- School of Life-Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Samudrala Gourinath
- School of Life-Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ravinder Goswami
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India.
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In Vivo Screening Using Transgenic Zebrafish Embryos Reveals New Effects of HDAC Inhibitors Trichostatin A and Valproic Acid on Organogenesis. PLoS One 2016; 11:e0149497. [PMID: 26900852 PMCID: PMC4763017 DOI: 10.1371/journal.pone.0149497] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 02/02/2016] [Indexed: 01/04/2023] Open
Abstract
The effects of endocrine disrupting chemicals (EDCs) on reproduction are well known, whereas their developmental effects are much less characterized. However, exposure to endocrine disruptors during organogenesis may lead to deleterious and permanent problems later in life. Zebrafish (Danio rerio) transgenic lines expressing the green fluorescent protein (GFP) in specific organs and tissues are powerful tools to uncover developmental defects elicited by EDCs. Here, we used seven transgenic lines to visualize in vivo whether a series of EDCs and other pharmaceutical compounds can alter organogenesis in zebrafish. We used transgenic lines expressing GFP in pancreas, liver, blood vessels, inner ear, nervous system, pharyngeal tooth and pectoral fins. This screen revealed that four of the tested chemicals have detectable effects on different organs, which shows that the range of effects elicited by EDCs is wider than anticipated. The endocrine disruptor tetrabromobisphenol-A (TBBPA), as well as the three drugs diclofenac, trichostatin A (TSA) and valproic acid (VPA) induced abnormalities in the embryonic vascular system of zebrafish. Moreover, TSA and VPA induced specific alterations during the development of pancreas, an observation that was confirmed by in situ hybridization with specific markers. Developmental delays were also induced by TSA and VPA in the liver and in pharyngeal teeth, resulting in smaller organ size. Our results show that EDCs can induce a large range of developmental alterations during embryogenesis of zebrafish and establish GFP transgenic lines as powerful tools to screen for EDCs effects in vivo.
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Schoenmakers N, Alatzoglou KS, Chatterjee VK, Dattani MT. Recent advances in central congenital hypothyroidism. J Endocrinol 2015; 227:R51-71. [PMID: 26416826 PMCID: PMC4629398 DOI: 10.1530/joe-15-0341] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 09/17/2015] [Accepted: 09/28/2015] [Indexed: 01/23/2023]
Abstract
Central congenital hypothyroidism (CCH) may occur in isolation, or more frequently in combination with additional pituitary hormone deficits with or without associated extrapituitary abnormalities. Although uncommon, it may be more prevalent than previously thought, affecting up to 1:16 000 neonates in the Netherlands. Since TSH is not elevated, CCH will evade diagnosis in primary, TSH-based, CH screening programs and delayed detection may result in neurodevelopmental delay due to untreated neonatal hypothyroidism. Alternatively, coexisting growth hormones or ACTH deficiency may pose additional risks, such as life threatening hypoglycaemia. Genetic ascertainment is possible in a minority of cases and reveals mutations in genes controlling the TSH biosynthetic pathway (TSHB, TRHR, IGSF1) in isolated TSH deficiency, or early (HESX1, LHX3, LHX4, SOX3, OTX2) or late (PROP1, POU1F1) pituitary transcription factors in combined hormone deficits. Since TSH cannot be used as an indicator of euthyroidism, adequacy of treatment can be difficult to monitor due to a paucity of alternative biomarkers. This review will summarize the normal physiology of pituitary development and the hypothalamic-pituitary-thyroid axis, then describe known genetic causes of isolated central hypothyroidism and combined pituitary hormone deficits associated with TSH deficiency. Difficulties in diagnosis and management of these conditions will then be discussed.
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Affiliation(s)
- Nadia Schoenmakers
- University of Cambridge Metabolic Research LaboratoriesWellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, Level 4, PO Box 289, Hills Road, Cambridge CB2 0QQ, UKDevelopmental Endocrinology Research GroupSection of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Kyriaki S Alatzoglou
- University of Cambridge Metabolic Research LaboratoriesWellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, Level 4, PO Box 289, Hills Road, Cambridge CB2 0QQ, UKDevelopmental Endocrinology Research GroupSection of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - V Krishna Chatterjee
- University of Cambridge Metabolic Research LaboratoriesWellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, Level 4, PO Box 289, Hills Road, Cambridge CB2 0QQ, UKDevelopmental Endocrinology Research GroupSection of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Mehul T Dattani
- University of Cambridge Metabolic Research LaboratoriesWellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, Level 4, PO Box 289, Hills Road, Cambridge CB2 0QQ, UKDevelopmental Endocrinology Research GroupSection of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
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Matsunaga H, Sasaki S, Suzuki S, Matsushita A, Nakamura H, Nakamura HM, Hirahara N, Kuroda G, Iwaki H, Ohba K, Morita H, Oki Y, Suda T. Essential Role of GATA2 in the Negative Regulation of Type 2 Deiodinase Gene by Liganded Thyroid Hormone Receptor β2 in Thyrotroph. PLoS One 2015; 10:e0142400. [PMID: 26571013 PMCID: PMC4646574 DOI: 10.1371/journal.pone.0142400] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/21/2015] [Indexed: 12/30/2022] Open
Abstract
The inhibition of thyrotropin (thyroid stimulating hormone; TSH) by thyroid hormone (T3) and its receptor (TR) is the central mechanism of the hypothalamus-pituitary-thyroid axis. Two transcription factors, GATA2 and Pit-1, determine thyrotroph differentiation and maintain the expression of the β subunit of TSH (TSHβ). We previously reported that T3-dependent repression of the TSHβ gene is mediated by GATA2 but not by the reported negative T3-responsive element (nTRE). In thyrotrophs, T3 also represses mRNA of the type-2 deiodinase (D2) gene, where no nTRE has been identified. Here, the human D2 promoter fused to the CAT or modified Renilla luciferase gene was co-transfected with Pit-1 and/or GATA2 expression plasmids into cell lines including CV1 and thyrotroph-derived TαT1. GATA2 but not Pit-1 activated the D2 promoter. Two GATA responsive elements (GATA-REs) were identified close to cAMP responsive element. The protein kinase A activator, forskolin, synergistically enhanced GATA2-dependent activity. Gel-shift and chromatin immunoprecipitation assays with TαT1 cells indicated that GATA2 binds to these GATA-REs. T3 repressed the GATA2-induced activity of the D2 promoter in the presence of the pituitary-specific TR, TRβ2. The inhibition by T3-bound TRβ2 was dominant over the synergism between GATA2 and forskolin. The D2 promoter is also stimulated by GATA4, the major GATA in cardiomyocytes, and this activity was repressed by T3 in the presence of TRα1. These data indicate that the GATA-induced activity of the D2 promoter is suppressed by T3-bound TRs via a tethering mechanism, as in the case of the TSHβ gene.
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Affiliation(s)
- Hideyuki Matsunaga
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Shigekazu Sasaki
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Shingo Suzuki
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Akio Matsushita
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Hirotoshi Nakamura
- Kuma Hospital, 8-2-35 Shimoyamate-dori, Chuo-ku, Kobe, Hyogo, 650–0011, Japan
| | - Hiroko Misawa Nakamura
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Naoko Hirahara
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Go Kuroda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Hiroyuki Iwaki
- Division of Endocrinology, Seirei Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, Hamamatsu, Shizuoka, 430–0906, Japan
| | - Kenji Ohba
- Duke-NUS Graduate Medical School Singapore, No 8 College Road, Level 8th, 169857, Singapore
| | - Hiroshi Morita
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Yutaka Oki
- Department of Family and Community Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan
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Vicent GP, Wright RHG, Beato M. Linker histones in hormonal gene regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:520-5. [PMID: 26518266 DOI: 10.1016/j.bbagrm.2015.10.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 12/20/2022]
Abstract
In the present review, we summarize advances in our knowledge on the role of the histone H1 family of proteins in breast cancer cells, focusing on their response to progestins. Histone H1 plays a dual role in gene regulation by hormones, both as a structural component of chromatin and as a dynamic modulator of transcription. It contributes to hormonal regulation of the MMTV promoter by stabilizing a homogeneous nucleosome positioning, which reduces basal transcription whereas at the same time promoting progesterone receptor binding and nucleosome remodeling. These combined effects enhance hormone dependent gene transcription, which eventually requires H1 phosphorylation and displacement. Various isoforms of histone H1 have specific functions in differentiated breast cancer cells and compact nucleosomal arrays to different extents in vitro. Genome-wide studies show that histone H1 has a key role in chromatin dynamics of hormone regulated genes. A complex sequence of enzymatic events, including phosphorylation by CDK2, PARylation by PARP1 and the ATP-dependent activity of NURF, are required for H1 displacement and gene de-repression, as a prerequisite for further nucleosome remodeling. Similarly, during hormone-dependent gene repression a dedicated enzymatic mechanism controls H1 deposition at promoters by a complex containing HP1γ, LSD1 and BRG1, the ATPase of the BAF complex. Thus, a broader vision of the histone code should include histone H1, as the linker histone variants actively participate in the regulation of the chromatin structure. How modifications of the core histones tails affect H1 modifications and vice versa is one of the many questions that remains to be addressed to provide a more comprehensive view of the histone cross-talk mechanisms.
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Affiliation(s)
- G P Vicent
- Centre de Regulació Genòmica (CRG), Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, E-08003, Barcelona, Spain
| | - R H G Wright
- Centre de Regulació Genòmica (CRG), Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, E-08003, Barcelona, Spain
| | - M Beato
- Centre de Regulació Genòmica (CRG), Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, E-08003, Barcelona, Spain
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37
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Hoffmann JM, Partridge L. Nuclear hormone receptors: Roles of xenobiotic detoxification and sterol homeostasis in healthy aging. Crit Rev Biochem Mol Biol 2015; 50:380-92. [PMID: 26383043 DOI: 10.3109/10409238.2015.1067186] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Health during aging can be improved by genetic, dietary and pharmacological interventions. Many of these increase resistance to various stressors, including xenobiotics. Up-regulation of xenobiotic detoxification genes is a transcriptomic signature shared by long-lived nematodes, flies and mice, suggesting that protection of cells from toxicity of xenobiotics may contribute to longevity. Expression of genes involved in xenobiotic detoxification is controlled by evolutionarily conserved transcriptional regulators. Three closely related subgroups of nuclear hormone receptors (NHRs) have a major role, and these include DAF-12 and NHR-8 in C. elegans, DHR96 in Drosophila and FXR, LXRs, PXR, CAR and VDR in mammals. In the invertebrates, these NHRs have been experimentally demonstrated to play a role in extension of lifespan by genetic and environmental interventions. NHRs represent critical hubs in that they regulate detoxification enzymes with broad substrate specificities, metabolizing both endo- and xeno-biotics. They also modulate homeostasis of steroid hormones and other endogenous cholesterol derivatives and lipid metabolism, and these roles, as well as xenobiotic detoxification, may contribute to the effects of NHRs on lifespan and health during aging, an issue that is being increasingly addressed in C. elegans and Drosophila. Disentangling the contribution of these processes to longevity will require more precise understanding of the molecular mechanisms by which each is effected, including identification of ligands and co-regulators of NHRs, patterns of tissue-specificity and mechanisms of interaction between tissues. The roles of vertebrate NHRs in determination of health during aging and lifespan have yet to be investigated.
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Affiliation(s)
| | - Linda Partridge
- a Max Planck Institute for Biology of Ageing , Cologne , Germany and.,b Institute of Healthy Ageing, and GEE (Genetics, Evolution and Environment), University College , London , UK
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Yen PM. Classical nuclear hormone receptor activity as a mediator of complex biological responses: a look at health and disease. Best Pract Res Clin Endocrinol Metab 2015; 29:517-28. [PMID: 26303080 DOI: 10.1016/j.beem.2015.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nuclear hormone receptors are a large family of receptors that bind a wide range of lipolic hormones and intracellular ligands. They act as ligand-inducible transcription factors to regulate the expression of target genes and play important roles in normal development, reproduction, and metabolism. NRs bind to hormones steroids, thyroid hormone, and vitamin D as well as metabolites of fatty acids, cholesterol, and bild acids. Orphan receptors are another group of NRs for which no known ligands have been identified yet but appear to have major roles in regulating intracellular metabolism. Targeting NRs has been a major source for the development of new drugs, particularly selective agonists and antagonists for cancer and metabolic diseases. Additionally, hormone resistance syndromes in man have enlarged our understanding of the functions of specific NRs and their isoforms as well as genetic mechanisms for phenotype expression.
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Affiliation(s)
- Paul Michael Yen
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore.
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Wu SM, Cheng WL, Liao CJ, Chi HC, Lin YH, Tseng YH, Tsai CY, Chen CY, Lin SL, Chen WJ, Yeh YH, Huang CYF, Chen MH, Yeh YC, Lin KH. Negative modulation of the epigenetic regulator, UHRF1, by thyroid hormone receptors suppresses liver cancer cell growth. Int J Cancer 2015; 137:37-49. [PMID: 25430639 DOI: 10.1002/ijc.29368] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 11/12/2014] [Indexed: 12/16/2022]
Abstract
The thyroid hormone, 3,3',5-triiodo-l-thyronine (T3 ), mediates several physiological processes, including embryonic development, cellular differentiation, metabolism and regulation of cell proliferation. Thyroid hormone (T3 ) and its receptor (TR) are involved in metabolism and growth. In addition to their developmental and metabolic functions, TRs play a tumor suppressor role, and therefore, their aberrant expression can lead to tumor transformation. Aberrant epigenetic silencing of tumor suppressor genes promotes cancer progression. The epigenetic regulator, Ubiquitin-like with PHD and ring finger domains 1 (UHRF1), is overexpressed in various cancers. In our study, we demonstrated that T3 negatively regulates UHRF1 expression, both in vitro and in vivo. Our results further indicate that UHRF1 regulation by T3 is indirect and mediated by Sp1. Sp1-binding elements of UHRF1 were identified at positions -664/-505 of the promoter region using the luciferase and chromatin immunoprecipitation assays. Notably, UHRF1 and Sp1 levels were elevated in subgroups of hepatocellular carcinoma patients and inversely correlated with TRα1 expression. Knockdown of UHRF1 expression should therefore provide a means to inhibit hepatoma cell proliferation. Expression of UHRF1 was downregulated by TRs, in turn, relieving silencing of the UHRF1 target gene, p21. Based on the collective findings, we propose that T3 /TR signaling induces hepatoma cell growth inhibition via UHRF1 repression.
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Affiliation(s)
- Sheng-Ming Wu
- Department of Biochemistry, School of Medicine, Chang-Gung University, Taoyuan, Taiwan
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Glucocorticoid receptor interacts with PNRC2 in a ligand-dependent manner to recruit UPF1 for rapid mRNA degradation. Proc Natl Acad Sci U S A 2015; 112:E1540-9. [PMID: 25775514 DOI: 10.1073/pnas.1409612112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glucocorticoid receptor (GR), which was originally known to function as a nuclear receptor, plays a role in rapid mRNA degradation by acting as an RNA-binding protein. The mechanism by which this process occurs remains unknown. Here, we demonstrate that GR, preloaded onto the 5'UTR of a target mRNA, recruits UPF1 through proline-rich nuclear receptor coregulatory protein 2 (PNRC2) in a ligand-dependent manner, so as to elicit rapid mRNA degradation. We call this process GR-mediated mRNA decay (GMD). Although GMD, nonsense-mediated mRNA decay (NMD), and staufen-mediated mRNA decay (SMD) share upstream frameshift 1 (UPF1) and PNRC2, we find that GMD is mechanistically distinct from NMD and SMD. We also identify de novo cellular GMD substrates using microarray analysis. Intriguingly, GMD functions in the chemotaxis of human monocytes by targeting chemokine (C-C motif) ligand 2 (CCL2) mRNA. Thus, our data provide molecular evidence of a posttranscriptional role of the well-studied nuclear hormone receptor, GR, which is traditionally considered a transcription factor.
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Fattori J, Campos JLO, Doratioto TR, Assis LM, Vitorino MT, Polikarpov I, Xavier-Neto J, Figueira ACM. RXR agonist modulates TR: corepressor dissociation upon 9-cis retinoic acid treatment. Mol Endocrinol 2014; 29:258-73. [PMID: 25541638 DOI: 10.1210/me.2014-1251] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transcriptional regulation controlled by thyroid hormone receptor (TR) drives events such as development, differentiation, and metabolism. TRs may act either as homodimers or as heterodimers with retinoid X receptor (RXR). Thyroid hormone T3 preferentially binds TR-RXR heterodimers, which activate transcription through coactivator recruitment. However, it is unclear whether TR-RXR heterodimers may also be responsive to the canonical RXR agonist 9-cis retinoic acid (9C) in the context of physiological gene regulation. New structural studies suggest that 9C promotes the displacement of bound coactivators from the heterodimer, modifying TR-RXR activity. To shed light on the molecular mechanisms that control TR-RXR function, we used biophysical approaches to characterize coregulator recruitment to TR-TR or to TR-RXR in the presence of T3 and/or 9C as well as cell-based assays to establish the functional significance of biophysical findings. Using cell-based and fluorescence assays with mutant and wild-type TR, we show that 9C does indeed have a function in the TR-RXR heterodimer context, in which it induces the release of corepressors. Furthermore, we show that 9C does not promote detectable conformational changes in the structure of the TR-RXR heterodimer and does not affect coactivator recruitment. Finally, our data support the view that DNA binding domain and Hinge regions are important to set up NR-coactivator binding interfaces. In summary, we showed that the RXR agonist 9C can regulate TR function through its modulation of corepressor dissociation.
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Affiliation(s)
- Juliana Fattori
- Centro Nacional de Pesquisa em Energia e Materiais (J.F., J.L.O.C., T.R.D., L.M.A., M.T.V., J.X.-N., A.C.M.F.), Laboratório Nacional de Biociências, Campinas SP, 13083-970, Brazil; and Instituto de Física de São Carlos (I.P.), Universidade de São Paulo, São Carlos SP, 13560-970, Brazil
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Zhang D, Wang X, Li Y, Zhao L, Lu M, Yao X, Xia H, Wang YC, Liu MF, Jiang J, Li X, Ying H. Thyroid hormone regulates muscle fiber type conversion via miR-133a1. ACTA ACUST UNITED AC 2014; 207:753-66. [PMID: 25512392 PMCID: PMC4274265 DOI: 10.1083/jcb.201406068] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Thyroid hormone promotes slow-to-fast muscle fiber type conversion by inducing miR-133a1 and thereby repressing the expression of the slow muscle determinant TEAD1. It is known that thyroid hormone (TH) is a major determinant of muscle fiber composition, but the molecular mechanism by which it does so remains unclear. Here, we demonstrated that miR-133a1 is a direct target gene of TH in muscle. Intriguingly, miR-133a, which is enriched in fast-twitch muscle, regulates slow-to-fast muscle fiber type conversion by targeting TEA domain family member 1 (TEAD1), a key regulator of slow muscle gene expression. Inhibition of miR-133a in vivo abrogated TH action on muscle fiber type conversion. Moreover, TEAD1 overexpression antagonized the effect of miR-133a as well as TH on muscle fiber type switch. Additionally, we demonstrate that TH negatively regulates the transcription of myosin heavy chain I indirectly via miR-133a/TEAD1. Collectively, we propose that TH inhibits the slow muscle phenotype through a novel epigenetic mechanism involving repression of TEAD1 expression via targeting by miR-133a1. This identification of a TH-regulated microRNA therefore sheds new light on how TH achieves its diverse biological activities.
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Affiliation(s)
- Duo Zhang
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; and Center for RNA Research, State Key Laboratory of Molecular Biology; University of Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China
| | - Xiaoyun Wang
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; and Center for RNA Research, State Key Laboratory of Molecular Biology; University of Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China
| | - Yuying Li
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; and Center for RNA Research, State Key Laboratory of Molecular Biology; University of Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China
| | - Lei Zhao
- Department of Neuromuscular Disease, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Minghua Lu
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; and Center for RNA Research, State Key Laboratory of Molecular Biology; University of Chinese Academy of Sciences, Shanghai 200031, China Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, and Clinical Research Center of Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xuan Yao
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; and Center for RNA Research, State Key Laboratory of Molecular Biology; University of Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China
| | - Hongfeng Xia
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; and Center for RNA Research, State Key Laboratory of Molecular Biology; University of Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China
| | - Yu-Cheng Wang
- Department of Nutrition, Shanghai Xuhui Central Hospital, Shanghai 200031, China
| | - Mo-Fang Liu
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; and Center for RNA Research, State Key Laboratory of Molecular Biology; University of Chinese Academy of Sciences, Shanghai 200031, China Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, and Clinical Research Center of Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jingjing Jiang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xihua Li
- Department of Neuromuscular Disease, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Hao Ying
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; and Center for RNA Research, State Key Laboratory of Molecular Biology; University of Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, and Clinical Research Center of Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Fattori J, Indolfo NDC, Campos JCLDO, Videira NB, Bridi AV, Doratioto TR, Assis MAD, Figueira ACM. Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Juliana Fattori
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Nathalia de Carvalho Indolfo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | | | - Natália Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Aline Villanova Bridi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Tábata Renée Doratioto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Michelle Alexandrino de Assis
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
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Feed-forward transcriptional programming by nuclear receptors: regulatory principles and therapeutic implications. Pharmacol Ther 2014; 145:85-91. [PMID: 25168919 DOI: 10.1016/j.pharmthera.2014.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 01/22/2023]
Abstract
Nuclear receptors (NRs) are widely targeted to treat a range of human diseases. Feed-forward loops are an ancient mechanism through which single cell organisms organize transcriptional programming and modulate gene expression dynamics, but they have not been systematically studied as a regulatory paradigm for NR-mediated transcriptional responses. Here, we provide an overview of the basic properties of feed-forward loops as predicted by mathematical models and validated experimentally in single cell organisms. We review existing evidence implicating feed-forward loops as important in controlling clinically relevant transcriptional responses to estrogens, progestins, and glucocorticoids, among other NR ligands. We propose that feed-forward transcriptional circuits are a major mechanism through which NRs integrate signals, exert temporal control over gene regulation, and compartmentalize client transcriptomes into discrete subunits. Implications for the design and function of novel selective NR ligands are discussed.
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45
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Graeppi-Dulac J, Vlaeminck-Guillem V, Perier-Muzet M, Dalle S, Orgiazzi J. Endocrine side-effects of anti-cancer drugs: the impact of retinoids on the thyroid axis. Eur J Endocrinol 2014; 170:R253-62. [PMID: 24616413 DOI: 10.1530/eje-13-0920] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bexarotene (Targretin), approved since 1999 as a second-line treatment for late stage cutaneous T-cell lymphomas, has been shown to induce significant hypothyroidism through TSH suppression. This review revisits, through a case report, mechanisms by which rexinoids repress the expression of TSHB gene as well as αTSH and TRH genes. It appears that rexinoids suppress TSH independently from tri-iodothyronine. Bexarotene also differently affects the gene expression of deiodinases 1 and 2 as well as the peripheral clearance of thyroxine. These data might open new ways of research on the potential interaction between thyroid axis and endogenous rexinoids.
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Affiliation(s)
- Julia Graeppi-Dulac
- Service d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceService d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Virginie Vlaeminck-Guillem
- Service d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceService d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceService d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Marie Perier-Muzet
- Service d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceService d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Stéphane Dalle
- Service d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceService d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceService d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Jacques Orgiazzi
- Service d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceService d'EndocrinologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Chemin du grand Revoyet, F 69495 Pierre Bénite, FranceUniversité Claude Bernard Lyon1 - Université de LyonLyon, FranceUnité d'Oncologie Moléculaire et TransfertService de Biochimie et biologie moléculaire sud, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, FranceInserm U1052CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, FranceService de DermatologieCentre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre Bénite, France
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Abstract
Retinoid X Receptors (RXR) were initially identified as nuclear receptors binding with stereo-selectivity the vitamin A derivative 9-cis retinoic acid, although the relevance of this molecule as endogenous activator of RXRs is still elusive. Importantly, within the nuclear receptor superfamily, RXRs occupy a peculiar place, as they are obligatory partners for a number of other nuclear receptors, thus integrating the corresponding signaling pathways. In this chapter, we describe the structural features allowing RXR to form homo- and heterodimers, and the functional consequences of this unique ability. Furthermore, we discuss the importance of studying RXR activity at a genome-wide level in order to comprehensively address the biological implications of their action that is fundamental to understand to what extent RXRs could be exploited as new therapeutic targets.
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Affiliation(s)
- Federica Gilardi
- Center for Integrative Genomics, University of Lausanne, Genopode Building, 1015, Lausanne, Switzerland,
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Abstract
Nuclear Retinoic Acid receptors (RARs) consist of three subtypes, α, β, and γ, encoded by separate genes. They function as ligand-dependent transcriptional regulators, forming heterodimers with Retinoid X receptors (RXRs). RARs mediate the effects of retinoic acid (RA), the active metabolite of Vitamin A, and regulate many biological functions such as embryonic development, organogenesis, homeostasis, vision, immune functions, and reproduction. During the two last decades, a number of in-depth structure-function relationship studies have been performed, in particular with drug design perspectives in the therapeutics for cancer, dermatology, metabolic disease, and other human diseases. Recent structural results concerning integral receptors in diverse functional states, obtained using a combination of different methods, allow a better understanding of the mechanisms involved in molecular regulation. The structural data highlight the importance of DNA sequences for binding selectivity and the role of promoter response elements in the spatial organization of the protein domains into functional complexes.
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Affiliation(s)
- Natacha Rochel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM), U964, Centre National de Recherche Scientifique (CNRS), UMR7104, Université de Strasbourg, 67404, Illkirch, France,
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48
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Decherf S, Seugnet I, Becker N, Demeneix BA, Clerget-Froidevaux MS. Retinoic X receptor subtypes exert differential effects on the regulation of Trh transcription. Mol Cell Endocrinol 2013; 381:115-23. [PMID: 23896434 DOI: 10.1016/j.mce.2013.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 07/19/2013] [Accepted: 07/19/2013] [Indexed: 02/07/2023]
Abstract
How Retinoid X receptors (RXR) and thyroid hormone receptors (TR) interact on negative TREs and whether RXR subtype specificity is determinant in such regulations is unknown. In a set of functional studies, we analyzed RXR subtype effects in T3-dependent repression of hypothalamic thyrotropin-releasing hormone (Trh). Two-hybrid screening of a hypothalamic paraventricular nucleus cDNA bank revealed specific, T3-dependent interaction of TRs with RXRβ. In vivo chromatin immuno-precipitation showed recruitment of RXRs to the TRE-site 4 region of the Trh promoter in the absence of T3. In vivo overexpression of RXRα in the mouse hypothalamus heightened T3-independent Trh transcription, whereas RXRβ overexpression abrogated this activity. Loss of function of RXRα and β by shRNAs induced inverse regulations. Thus, RXRα and RXRβ display specific roles in modulating T3-dependent regulation of Trh. These results provide insight into the actions of these different TR heterodimerization partners within the context of a negatively regulated gene.
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Affiliation(s)
- Stéphanie Decherf
- CNRS UMR 7221-USM 501, «Evolution of Endocrine Regulations», «Regulations, Development and Molecular Diversity» Department, Muséum National d'Histoire Naturelle, 57 rue Cuvier, CP 32, 75231 Paris Cedex 5, France
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49
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Shchelkunova TA, Morozov IA, Rubtsov PM, Samokhodskaya LM, Sobenin IA, Orekhov AN, Smirnov AN. Coordination in gene expression during atherogenesis. BIOCHEMISTRY (MOSCOW) 2013; 78:933-45. [PMID: 24228883 DOI: 10.1134/s0006297913080117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
General tendencies in the regulation of gene expression during atherogenesis were investigated using correlation analysis for 34 mRNA species of several functional groups. The contents of mRNA were measured by quantitative PCR in samples of human aortal intima containing no lesions or atherosclerotic lesions of types I (initial lesions), II (fatty streaks), and Va (fibroatheromas). The coupling between mRNA contents in lesions and the same mRNAs in intact tissue was found to descend in the course of the disease progression. The data are in accordance with the opinion that successive morphologic types of atherosclerotic lesions correspond to steps of atherogenesis. In addition, the contents of individual mRNA species could correlate with each other within the given sample type, the extent of this coupling rising along with the disease progression. The exception from this rule was a collapse in coupling for several functional groups of mRNA in lesions of type I. This collapse could indicate special position of these lesions in pathogenesis. Statistically significant correlations between mRNAs found in samples of all four types comprised in total about 50% of all possible correlations. 66% of these correlations were conservative, i.e. observed in at least two sample types. By coupling-strength, the studied mRNAs could be divided into four clusters whose composition significantly varied along with the disease progression. The disease progression was also associated with decline in number of regulatory factors that determine coordination in expression of the analyzed genes.
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Affiliation(s)
- T A Shchelkunova
- Biological Faculty, Lomonosov Moscow State University, Moscow, 119899, Russia.
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50
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Mannervik M. Control of Drosophila embryo patterning by transcriptional co-regulators. Exp Cell Res 2013; 321:47-57. [PMID: 24157250 DOI: 10.1016/j.yexcr.2013.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
A combination of broadly expressed transcriptional activators and spatially restricted repressors are used to pattern embryos into cells of different fate. Transcriptional co-regulators are essential mediators of transcription factor function, and contribute to selective transcriptional responses in embryo development. A two step mechanism of transcriptional regulation is discussed, where remodeling of chromatin is initially required, followed by stimulation of recruitment or release of RNA polymerase from the promoter. Transcriptional co-regulators are essential for both of these steps. In particular, most co-activators are associated with histone acetylation and co-repressors with histone deacetylation. In the early Drosophila embryo, genome-wide studies have shown that the CBP co-activator has a preference for associating with some transcription factors and regulatory regions. The Groucho, CtBP, Ebi, Atrophin and Brakeless co-repressors are selectively used to limit zygotic gene expression. New findings are summarized which show that different co-repressors are often utilized by a single repressor, that the context in which a co-repressor is recruited to DNA can affect its activity, and that co-regulators may switch from co-repressors to co-activators and vice versa. The possibility that co-regulator activity is regulated and plays an instructive role in development is discussed as well. This review highlights how findings in Drosophila embryos have contributed to the understanding of transcriptional regulation in eukaryotes as well as to mechanisms of animal embryo patterning.
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Affiliation(s)
- Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Arrheniuslaboratories E3, SE-106 91 Stockholm, Sweden.
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