1
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Simsek YK, Tofil HP, Rosenthal MI, Evans RM, Danielski CL, Beasley KE, Alsayed H, Shapira ME, Strauss RI, Wang M, Roggero VR, Allison LA. Nuclear receptor corepressor 1 levels differentially impact the intracellular dynamics of mutant thyroid hormone receptors associated with resistance to thyroid hormone syndrome. Mol Cell Endocrinol 2024; 594:112373. [PMID: 39299378 DOI: 10.1016/j.mce.2024.112373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 09/05/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Thyroid hormone receptor α1 (TRα1) undergoes nucleocytoplasmic shuttling and mediates gene expression in response to thyroid hormone (T3). In Resistance to Thyroid Hormone Syndrome α (RTHα), certain TRα1 mutants have higher affinity for nuclear corepressor 1 (NCoR1) and may form stable complexes that are not released in the presence of T3. Here, we examined whether NCoR1 modulates intranuclear mobility and nuclear retention of TRα1 or RTHα-associated mutants in transfected human cells, as a way of analyzing critical structural components of TRα1 and to further explore the correlation between mutations in TRα1 and aberrant intracellular trafficking. We found no significant difference in intranuclear mobility, as measured by fluorescence recovery after photobleaching, between TRα1 and select RTHα mutants, irrespective of NCoR1 expression. Nuclear-to-cytoplasmic fluorescence ratios of RTHα mutants, however, varied from TRα1 when NCoR1 was overexpressed, with a significant increase in nuclear retention for A263V and a significant decrease for A263S and R384H. In NCoR1-knockout cells, nuclear retention of A263S, A263V, P389R, A382P, C392X, and F397fs406X was significantly decreased compared to control (wild-type) cells. Luciferase reporter gene transcription mediated by TRα1 was significantly repressed by both NCoR1 overexpression and NCoR1 knockout. Most RTHα mutants showed minimal induction regardless of NCoR1 levels, but T3-mediated transcriptional activity was decreased for R384C and F397fs406X when NCoR1 was overexpressed, and also decreased for N359Y in NCoR1-knockout cells. Our results suggest a complex interaction between NCoR1 and RTHα mutants characterized by aberrant intracellular localization patterns and transcriptional activity that potentially arise from variable repressor complex stability, and may provide insight into RTHα pathogenesis on a molecular and cellular level.
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Affiliation(s)
- Yigit K Simsek
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - H Page Tofil
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Matthew I Rosenthal
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Rochelle M Evans
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Caroline L Danielski
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Katelyn E Beasley
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Haytham Alsayed
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Molly E Shapira
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Rebecca I Strauss
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Moyao Wang
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Vincent R Roggero
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Lizabeth A Allison
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA.
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2
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Zhao H, Li J, Xiang Y, Malik S, Vartak SV, Veronezi GMB, Young N, Riney M, Kalchschmidt J, Conte A, Jung SK, Ramachandran S, Roeder RG, Shi Y, Casellas R, Asturias FJ. An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Mol Cell 2024; 84:2648-2664.e10. [PMID: 38955181 PMCID: PMC11283359 DOI: 10.1016/j.molcel.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 02/29/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction.
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Affiliation(s)
- Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Jiaqin Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Yufei Xiang
- Center of Protein Engineering and Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | | | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - McKayla Riney
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | | | - Andrea Conte
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Seol Kyoung Jung
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Center of Protein Engineering and Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA.
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3
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Chaudhuri SM, Weinberg SE, Wang D, Yalom LK, Montauti E, Iyer R, Tang AY, Torres Acosta MA, Shen J, Mani NL, Wang S, Liu K, Lu W, Bui TM, Manzanares LD, Dehghani Z, Wai CM, Gao B, Wei J, Yue F, Cui W, Singer BD, Sumagin R, Zhang Y, Fang D. Mediator complex subunit 1 architects a tumorigenic Treg cell program independent of inflammation. Cell Rep Med 2024; 5:101441. [PMID: 38428427 PMCID: PMC10983042 DOI: 10.1016/j.xcrm.2024.101441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/18/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
While immunotherapy has revolutionized cancer treatment, its safety has been hampered by immunotherapy-related adverse events. Unexpectedly, we show that Mediator complex subunit 1 (MED1) is required for T regulatory (Treg) cell function specifically in the tumor microenvironment. Treg cell-specific MED1 deletion does not predispose mice to autoimmunity or excessive inflammation. In contrast, MED1 is required for Treg cell promotion of tumor growth because MED1 is required for the terminal differentiation of effector Treg cells in the tumor. Suppression of these terminally differentiated Treg cells is sufficient for eliciting antitumor immunity. Both human and murine Treg cells experience divergent paths of differentiation in tumors and matched tissues with non-malignant inflammation. Collectively, we identify a pathway promoting the differentiation of a Treg cell effector subset specific to tumors and demonstrate that suppression of a subset of Treg cells is sufficient for promoting antitumor immunity in the absence of autoimmune consequences.
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Affiliation(s)
- Shuvam M Chaudhuri
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Samuel E Weinberg
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Dongmei Wang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lenore K Yalom
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elena Montauti
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Radhika Iyer
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Amy Y Tang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Manuel A Torres Acosta
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jian Shen
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nikita L Mani
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shengnan Wang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kun Liu
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Weiyuan Lu
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Triet M Bui
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Laura D Manzanares
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Zeinab Dehghani
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ching Man Wai
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Beixue Gao
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Juncheng Wei
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Feng Yue
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Weiguo Cui
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ronen Sumagin
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yana Zhang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Deyu Fang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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4
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Russo M, Gualdrini F, Vallelonga V, Prosperini E, Noberini R, Pedretti S, Borriero C, Di Chiaro P, Polletti S, Imperato G, Marenda M, Ghirardi C, Bedin F, Cuomo A, Rodighiero S, Bonaldi T, Mitro N, Ghisletti S, Natoli G. Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide. Mol Cell 2024; 84:967-980.e10. [PMID: 38242130 PMCID: PMC7615796 DOI: 10.1016/j.molcel.2023.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
Histone-modifying enzymes depend on the availability of cofactors, with acetyl-coenzyme A (CoA) being required for histone acetyltransferase (HAT) activity. The discovery that mitochondrial acyl-CoA-producing enzymes translocate to the nucleus suggests that high concentrations of locally synthesized metabolites may impact acylation of histones and other nuclear substrates, thereby controlling gene expression. Here, we show that 2-ketoacid dehydrogenases are stably associated with the Mediator complex, thus providing a local supply of acetyl-CoA and increasing the generation of hyper-acetylated histone tails. Nitric oxide (NO), which is produced in large amounts in lipopolysaccharide-stimulated macrophages, inhibited the activity of Mediator-associated 2-ketoacid dehydrogenases. Elevation of NO levels and the disruption of Mediator complex integrity both affected de novo histone acetylation within a shared set of genomic regions. Our findings indicate that the local supply of acetyl-CoA generated by 2-ketoacid dehydrogenases bound to Mediator is required to maximize acetylation of histone tails at sites of elevated HAT activity.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Francesco Gualdrini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Pierluigi Di Chiaro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Gabriele Imperato
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; Department of Hematology and Hematology-Oncology (DIPO), Università degli Studi di Milano, Milano 20122, Italy
| | - Nico Mitro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
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5
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Zhou Z, Liu J, Zhang J, Yan H, Yi T, Shim WB. Characterization of Fusarium verticillioides Med1 LxxLL Motif Involved in Fumonisin Biosynthesis. Toxins (Basel) 2023; 15:652. [PMID: 37999515 PMCID: PMC10675092 DOI: 10.3390/toxins15110652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
The Med1 transcriptional coactivator is a crucial component of the Mediator middle complex, which regulates the expression of specific genes involved in cell development, differentiation, reproduction, and homeostasis. The Med1 LxxLL motif, a five-amino-acid peptide sequence, is essential for Med1-mediated gene expression. Our previous study revealed that the disruption of the Med1 subunit leads to a significant increase in fumonisin B1 (FB1) production in the maize pathogen Fusarium verticillioides. However, our understanding of how Med1 regulates FB1 biosynthesis in F. verticillioides, particularly through the Med1 LxxLL motifs, remains limited. To characterize the role of LxxLL motifs, we generated a series of Med1 LxxLL deletion and amino acid substitution mutants. These mutants exhibited impaired mycelial growth and conidia germination while demonstrating enhanced conidia production and virulence. Similar to the Med1 deletion mutant, Med1 LxxLL motif mutants also exhibited increased FB1 biosynthesis in F. verticillioides. Proteomic profiling revealed that the Med1 LxxLL motif regulated the biosynthesis of several key substances that affected FB1 production, including starch and carotenoid. Subsequent studies demonstrated that the production of amylopectin, which is strongly linked to FB1 biosynthesis, was significantly increased in Med1 LxxLL motif mutants. In addition, the disruption of carotenoid metabolic genes decreased carotenoid content, thus stimulating FB1 biosynthesis in F. verticillioides. Taken together, our results provide valuable insights into how the Med1 LxxLL motif regulates FB1 biosynthesis in the mycotoxigenic fungus F. verticillioides.
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Affiliation(s)
- Zehua Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, Hunan Agricultural University, Changsha 410128, China; (Z.Z.); (J.L.)
| | - Jie Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, Hunan Agricultural University, Changsha 410128, China; (Z.Z.); (J.L.)
| | - Jie Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Huijuan Yan
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Tuyong Yi
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, Hunan Agricultural University, Changsha 410128, China; (Z.Z.); (J.L.)
| | - Won Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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6
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Wang M, Roggero VR, Allison LA. Mediator subunit MED1 differentially modulates mutant thyroid hormone receptor intracellular dynamics in Resistance to Thyroid Hormone syndrome. Mol Cell Endocrinol 2023; 559:111781. [PMID: 36191835 PMCID: PMC9985138 DOI: 10.1016/j.mce.2022.111781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 02/03/2023]
Abstract
Thyroid hormone receptor (TR) controls the expression of thyroid hormone (T3)-responsive genes, while undergoing rapid nucleocytoplasmic shuttling. In Resistance to Thyroid Hormone syndrome (RTH), mutant TR fails to activate T3-dependent transcription. Previously, we showed that Mediator subunit 1 (MED1) plays a role in TR nuclear retention. Here, we investigated MED1's effect on RTH mutants using nucleocytoplasmic scoring and fluorescence recovery after photobleaching in transfected cells. MED1 overexpression and knockout did not change the nucleocytoplasmic distribution or intranuclear mobility of C392X and P398R TRα1 at physiological T3 levels. At elevated T3 levels, however, overexpression increased P398R's nuclear retention and MED1 knockout decreased P398R's and A263V's intranuclear mobility, while not impacting C392X. Although A263V TRα1-transfected cells had a high percentage of aggregates, MED1 rescued A263V's impaired intranuclear mobility, suggesting that MED1 ameliorates nonfunctional aggregates. Results correlate with clinical severity, suggesting that altered interaction between MED1 and TRα1 mutants contributes to RTH pathology.
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Affiliation(s)
- Moyao Wang
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Vincent R Roggero
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA
| | - Lizabeth A Allison
- Department of Biology, William & Mary, 540 Landrum Drive, Integrated Science Center 3030, Williamsburg, VA, 23185, USA.
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7
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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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8
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Akter R, Afrose A, Sharmin S, Rezwan R, Rahman MR, Neelotpol S. A comprehensive look into the association of vitamin D levels and vitamin D receptor gene polymorphism with obesity in children. Biomed Pharmacother 2022; 153:113285. [PMID: 35728355 DOI: 10.1016/j.biopha.2022.113285] [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: 04/26/2022] [Revised: 05/27/2022] [Accepted: 06/09/2022] [Indexed: 11/02/2022] Open
Abstract
Childhood obesity accounts for several psychosocial and clinical consequences. Psychosocial consequences include lower self-esteem, social isolation, poor academic achievement, peer problems, and depression, whereas clinical consequences are cardiovascular diseases, type 2 diabetes, dyslipidemia, cancer, autoimmune diseases, girls early polycystic ovarian syndrome (PCOS), asthma, bone deformities, etc. A growing number of studies have uncovered the association of childhood obesity and its consequences with vitamin-D (vit-D) deficiency and vitamin-D receptor (VDR) gene polymorphisms such as single nucleotide polymorphisms (SNPs), e.g., TaqI, BsmI, ApaI, FokI, and Cdx2. Considering the impact of vit-D deficiency and VDR gene polymorphisms, identifying associated factors and risk groups linked to lower serum vit-D levels and prevention of obesity-related syndromes in children is of utmost importance. Previously published review articles mainly focused on the association of vit-D deficiency with obesity or other non-communicable diseases in children. The nature of the correlation between vit-D deficiency and VDR gene polymorphisms with obesity in children is yet to be clarified. Therefore, this review attempts to delineate the association of obesity with these two factors by identifying the molecular mechanism of the relationship.
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Affiliation(s)
- Raushanara Akter
- School of Pharmacy, Brac University, 66 Mohakhali, Dhaka, Bangladesh
| | - Afrina Afrose
- School of Pharmacy, Brac University, 66 Mohakhali, Dhaka, Bangladesh
| | - Shahana Sharmin
- School of Pharmacy, Brac University, 66 Mohakhali, Dhaka, Bangladesh
| | - Rifat Rezwan
- School of Pharmacy, Brac University, 66 Mohakhali, Dhaka, Bangladesh
| | - Md Rashidur Rahman
- Department of Pharmacy, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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9
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Vitamin D and Its Target Genes. Nutrients 2022; 14:nu14071354. [PMID: 35405966 PMCID: PMC9003440 DOI: 10.3390/nu14071354] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 12/22/2022] Open
Abstract
The vitamin D metabolite 1α,25-dihydroxyvitamin D3 is the natural, high-affinity ligand of the transcription factor vitamin D receptor (VDR). In many tissues and cell types, VDR binds in a ligand-dependent fashion to thousands of genomic loci and modulates, via local chromatin changes, the expression of hundreds of primary target genes. Thus, the epigenome and transcriptome of VDR-expressing cells is directly affected by vitamin D. Vitamin D target genes encode for proteins with a large variety of physiological functions, ranging from the control of calcium homeostasis, innate and adaptive immunity, to cellular differentiation. This review will discuss VDR’s binding to genomic DNA, as well as its genome-wide locations and interaction with partner proteins, in the context of chromatin. This information will be integrated into a model of vitamin D signaling, explaining the regulation of vitamin D target genes.
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10
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Zhou L, Li H, Sun S, Zhang T, Yu Y, Xu L, Wang M. Thrap3 promotes osteogenesis by inhibiting the degradation of Runx2. FASEB J 2022; 36:e22231. [PMID: 35230719 DOI: 10.1096/fj.202101706r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/23/2022] [Accepted: 02/14/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Lei Zhou
- Department of Orthopedics Shanghai Fifth People’s Hospital Fudan University Shanghai China
- Department of Orthopedic Surgery Zhongshan Hospital Fudan University Shanghai China
| | - Haoran Li
- Department of Orthopedics Shanghai Fifth People’s Hospital Fudan University Shanghai China
| | - Shiwei Sun
- Department of Orthopedics Shanghai Fifth People’s Hospital Fudan University Shanghai China
| | - Tieqi Zhang
- Department of Orthopedics Shanghai Fifth People’s Hospital Fudan University Shanghai China
| | - Yueming Yu
- Department of Orthopedics Shanghai Fifth People’s Hospital Fudan University Shanghai China
| | - Liang Xu
- Department of Orthopedics Shanghai Fifth People’s Hospital Fudan University Shanghai China
| | - Minghai Wang
- Department of Orthopedics Shanghai Fifth People’s Hospital Fudan University Shanghai China
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11
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Structure-guided approach to relieving transcriptional repression inResistance to Thyroid Hormone α. Mol Cell Biol 2021; 42:e0036321. [PMID: 34871063 PMCID: PMC8852717 DOI: 10.1128/mcb.00363-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in thyroid hormone receptor α (TRα), a ligand-inducible transcription factor, cause Resistance to Thyroid Hormone α (RTHα). This disorder is characterised by tissue-specific hormone refractoriness and hypothyroidism, due to inhibition of target gene expression by mutant TRα-corepressor complexes. Using biophysical approaches, we show that RTHα-associated TRα mutants devoid of ligand-dependent transcription activation function, unexpectedly retain the ability to bind thyroid hormone. Visualisation of ligand (T3) within the crystal structure of a prototypic TRα mutant, validates this notion. This finding prompted synthesis of different thyroid hormone analogues, identifying a lead compound (ES08) which dissociates corepressor from mutant human TRα more efficaciously than T3. ES08 rescues developmental anomalies in a zebrafish model of RTHα and induces target gene expression in TRα mutation-containing cells from an RTHα patient, more effectively than T3. Our observations provide proof-of-principle for developing synthetic ligands that can relieve transcriptional repression by the mutant TRα-corepressor complex, for treatment of RTHα.
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12
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Bhardwaj R, Thakur JK, Kumar S. MedProDB: A database of Mediator proteins. Comput Struct Biotechnol J 2021; 19:4165-4176. [PMID: 34527190 PMCID: PMC8342855 DOI: 10.1016/j.csbj.2021.07.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/08/2021] [Accepted: 07/24/2021] [Indexed: 12/03/2022] Open
Abstract
Mediator complex is a key component of transcriptional regulation in eukaryotes. Identification of Mediator subunits was done by using computational approaches. Different physicochemical properties, and functions of Mediators were discussed. We have developed first database of Mediator proteins e.g. MedProDB. MedProDB contains different types of search and browse options, and various tools.
In the last three decades, the multi-subunit Mediator complex has emerged as the key component of transcriptional regulation of eukaryotic gene expression. Although there were initial hiccups, recent advancements in bioinformatics tools contributed significantly to in-silico prediction and characterization of Mediator subunits from several organisms belonging to different eukaryotic kingdoms. In this study, we have developed the first database of Mediator proteins named MedProDB with 33,971 Mediator protein entries. Out of those, 12531, 11545, and 9895 sequences belong to metazoans, plants, and fungi, respectively. Apart from the core information consisting of sequence, length, position, organism, molecular weight, and taxonomic lineage, additional information of each Mediator sequence like aromaticity, hydropathy, instability index, isoelectric point, functions, interactions, repeat regions, diseases, sequence alignment to Mediator subunit family, Intrinsically Disordered Regions (IDRs), Post-translation modifications (PTMs), and Molecular Recognition Features (MoRFs) may be of high utility to the users. Furthermore, different types of search and browse options with four different tools namely BLAST, Smith-Waterman Align, IUPred, and MoRF-Chibi_Light are provided at MedProDB to perform different types of analysis. Being a critical component of the transcriptional machinery and regulating almost all the aspects of transcription, it generated lots of interest in structural and functional studies of Mediator functioning. So, we think that the MedProDB database will be very useful for researchers studying the process of transcription. This database is freely available at www.nipgr.ac.in/MedProDB.
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Affiliation(s)
- Rohan Bhardwaj
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.,Plant Mediator Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra Kumar Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.,Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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13
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Ito K, Schneeberger M, Gerber A, Jishage M, Marchildon F, Maganti AV, Cohen P, Friedman JM, Roeder RG. Critical roles of transcriptional coactivator MED1 in the formation and function of mouse adipose tissues. Genes Dev 2021; 35:729-748. [PMID: 33888560 PMCID: PMC8091968 DOI: 10.1101/gad.346791.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/16/2021] [Indexed: 01/12/2023]
Abstract
In this study, Ito et al. sought to understand the precise roles of MED1, and its various domains, at various stages of adipogenesis and in adipose tissue. Using multiple genetic approaches to assess requirements for MED1 in adipocyte formation and function in mice, they show that MED1 is indeed essential for the differentiation and/or function of both brown and white adipocytes, as its absence in these cells leads to, respectively, defective brown fat function and lipodystrophy. The MED1 subunit has been shown to mediate ligand-dependent binding of the Mediator coactivator complex to multiple nuclear receptors, including the adipogenic PPARγ, and to play an essential role in ectopic PPARγ-induced adipogenesis of mouse embryonic fibroblasts. However, the precise roles of MED1, and its various domains, at various stages of adipogenesis and in adipose tissue have been unclear. Here, after establishing requirements for MED1, including specific domains, for differentiation of 3T3L1 cells and both primary white and brown preadipocytes, we used multiple genetic approaches to assess requirements for MED1 in adipocyte formation, maintenance, and function in mice. We show that MED1 is indeed essential for the differentiation and/or function of both brown and white adipocytes, as its absence in these cells leads to, respectively, defective brown fat function and lipodystrophy. This work establishes MED1 as an essential transcriptional coactivator that ensures homeostatic functions of adipocytes.
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Affiliation(s)
- Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Marc Schneeberger
- Laboratory of Molecular Genetics, The Rockefeller University, New York, New York 10065, USA
| | - Alan Gerber
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Miki Jishage
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Francois Marchildon
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Aarthi V Maganti
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Jeffrey M Friedman
- Laboratory of Molecular Genetics, The Rockefeller University, New York, New York 10065, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
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14
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Zhou J, Singh BK, Ho JP, Lim A, Bruinstroop E, Ohba K, Sinha RA, Yen PM. MED1 mediator subunit is a key regulator of hepatic autophagy and lipid metabolism. Autophagy 2021; 17:4043-4061. [PMID: 33734012 DOI: 10.1080/15548627.2021.1899691] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hepatic macroautophagy/autophagy and fatty acid metabolism are transcriptionally regulated by nuclear receptors (NRs); however, it is not known whether their transcriptional co-activators are involved in autophagy. We thus examined MED1 (mediator complex subunit 1), a key component of the Mediator Complex that directly interacts with NRs, on these processes. We found that MED1 knockdown (KD) in cultured hepatic cells decreased autophagy and mitochondrial activity that was accompanied by decreased transcription of genes involved in these processes. Lipophagy and fatty acid β-oxidation also were impaired. These effects also occurred after thyroid hormone stimulation, nutrient-replete or -deplete conditions, and in liver-specific Med1 KD (Med1 LKD) mice under fed and fasting conditions. Together, these findings showed that Med1 played a key role in hepatic autophagy, mitochondria function, and lipid metabolism under these conditions. Additionally, we identified downregulated hepatic genes in Med1 LKD mice, and subjected them to ChIP Enrichment Analysis. Our findings showed that the transcriptional activity of several NRs and transcription factors (TFs), including PPARA and FOXO1, likely were affected by Med1 LKD. Finally, Med1 expression and autophagy also were decreased in two mouse models of nonalcoholic fatty liver disease (NAFLD) suggesting that decreased Med1 may contribute to hepatosteatosis. In summary, MED1 plays an essential role in regulating hepatic autophagy and lipid oxidation during different hormonal and nutrient conditions. Thus, MED1 may serve as an integrator of multiple transcriptional pathways involved in these metabolic processes.Abbreviations: BAF: bafilomycin A1; db/db mice; Leprdb/db mice; ECAR: extracellular acidification rate; KD: knockdown; MED1: mediator complex subunit 1; NAFLD: nonalcoholic fatty liver disease; OCR: oxygen consumption rate; PPARA/PPARα: peroxisomal proliferator activated receptor alpha; TF: transcription factor; TFEB: transcription factor EB; tf-LC3: tandem fluorescence RFP-GFP-LC3; TG: triglyceride; TH: Thyroid hormone; TR: thyroid hormone receptors; V-ATPase: vacuolar-type H+-ATPase; WDF: Western diet with 15% fructose in drinking water.
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Affiliation(s)
- Jin Zhou
- Program of Cardiovascular & Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore
| | - Brijesh K Singh
- Program of Cardiovascular & Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore
| | - Jia Pei Ho
- Program of Cardiovascular & Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore
| | - Andrea Lim
- Program of Cardiovascular & Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore
| | - Eveline Bruinstroop
- Department of Endocrinology and Metabolism, Amsterdam UMC, Amsterdam, The Netherlands
| | - Kenji Ohba
- Program of Cardiovascular & Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore
| | - Rohit A Sinha
- Program of Cardiovascular & Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore.,Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow India
| | - Paul M Yen
- Program of Cardiovascular & Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore.,Duke Molecular Physiology Institute and Department of Medicine, Duke University Medical Center, Durham, NC USA
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15
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What do Transcription Factors Interact With? J Mol Biol 2021; 433:166883. [PMID: 33621520 DOI: 10.1016/j.jmb.2021.166883] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022]
Abstract
Although we have made significant progress, we still possess a limited understanding of how genomic and epigenomic information directs gene expression programs through sequence-specific transcription factors (TFs). Extensive research has settled on three general classes of TF targets in metazoans: promoter accessibility via chromatin regulation (e.g., SAGA), assembly of the general transcription factors on promoter DNA (e.g., TFIID), and recruitment of RNA polymerase (Pol) II (e.g., Mediator) to establish a transcription pre-initiation complex (PIC). Here we discuss TFs and their targets. We also place this in the context of our current work with Saccharomyces (yeast), where we find that promoters typically lack an architecture that supports TF function. Moreover, yeast promoters that support TF binding also display interactions with cofactors like SAGA and Mediator, but not TFIID. It is unknown to what extent all genes in metazoans require TFs and their cofactors.
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16
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Zhang H, Chen DH, Mattoo RUH, Bushnell DA, Wang Y, Yuan C, Wang L, Wang C, Davis RE, Nie Y, Kornberg RD. Mediator structure and conformation change. Mol Cell 2021; 81:1781-1788.e4. [PMID: 33571424 DOI: 10.1016/j.molcel.2021.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 01/22/2023]
Abstract
Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription machinery. Previous structural studies revealed a relatively small part of Mediator and none of the gene activator-binding regions. We have determined the cryo-EM structure of the Mediator at near-atomic resolution. The structure reveals almost all amino acid residues in ordered regions, including the major targets of activator proteins, the Tail module, and the Med1 subunit of the Middle module. Comparison of Mediator structures with and without pol II reveals conformational changes that propagate across the entire Mediator, from Head to Tail, coupling activator- and pol II-interacting regions.
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Affiliation(s)
- Heqiao Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dong-Hua Chen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rayees U H Mattoo
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yannan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Chao Yuan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Chunnian Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Ralph E Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yan Nie
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China.
| | - Roger D Kornberg
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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17
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MED19 alters AR occupancy and gene expression in prostate cancer cells, driving MAOA expression and growth under low androgen. PLoS Genet 2021; 17:e1008540. [PMID: 33513133 PMCID: PMC7875385 DOI: 10.1371/journal.pgen.1008540] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/10/2021] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Androgen deprivation therapy (ADT) is a mainstay of prostate cancer treatment, given the dependence of prostate cells on androgen and the androgen receptor (AR). However, tumors become ADT-resistant, and there is a need to understand the mechanism. One possible mechanism is the upregulation of AR co-regulators, although only a handful have been definitively linked to disease. We previously identified the Mediator subunit MED19 as an AR co-regulator, and reported that MED19 depletion inhibits AR transcriptional activity and growth of androgen-insensitive LNCaP-abl cells. Therefore, we proposed that MED19 upregulation would promote AR activity and drive androgen-independent growth. Here, we show that stable overexpression of MED19 in androgen-dependent LNCaP cells promotes growth under conditions of androgen deprivation. To delineate the mechanism, we determined the MED19 and AR transcriptomes and cistromes in control and MED19-overexpressing LNCaP cells. We also examined genome-wide H3K27 acetylation. MED19 overexpression selectively alters AR occupancy, H3K27 acetylation, and gene expression. Under conditions of androgen deprivation, genes regulated by MED19 correspond to genes regulated by ELK1, a transcription factor that binds the AR N-terminus to induce select AR target gene expression and proliferation, and genomic sites occupied by MED19 and AR are enriched for motifs associated with ELK1. Strikingly, MED19 upregulates expression of monoamine oxidase A (MAOA), a factor that promotes prostate cancer growth. MAOA depletion reduces androgen-independent growth. MED19 and AR occupy the MAOA promoter, with MED19 overexpression enhancing AR occupancy and H3K27 acetylation. Furthermore, MED19 overexpression increases ELK1 occupancy at the MAOA promoter, and ELK1 depletion reduces MAOA expression and androgen-independent growth. This suggests that MED19 cooperates with ELK1 to regulate AR occupancy and H3K27 acetylation at MAOA, upregulating its expression and driving androgen independence in prostate cancer cells. This study provides important insight into the mechanisms of prostate cancer cell growth under low androgen, and underscores the importance of the MED19-MAOA axis in this process.
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18
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Belorusova AY, Bourguet M, Hessmann S, Chalhoub S, Kieffer B, Cianférani S, Rochel N. Molecular determinants of MED1 interaction with the DNA bound VDR-RXR heterodimer. Nucleic Acids Res 2020; 48:11199-11213. [PMID: 32990725 PMCID: PMC7641746 DOI: 10.1093/nar/gkaa775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
The MED1 subunit of the Mediator complex is an essential coactivator of nuclear receptor-mediated transcriptional activation. While structural requirements for ligand-dependent binding of classical coactivator motifs of MED1 to numerous nuclear receptor ligand-binding domains have been fully elucidated, the recognition of the full-length or truncated coactivator by full nuclear receptor complexes remain unknown. Here we present structural details of the interaction between a large part of MED1 comprising its structured N-terminal and the flexible receptor-interacting domains and the mutual heterodimer of the vitamin D receptor (VDR) and the retinoid X receptor (RXR) bound to their cognate DNA response element. Using a combination of structural and biophysical methods we show that the ligand-dependent interaction between VDR and the second coactivator motif of MED1 is crucial for complex formation and we identify additional, previously unseen, interaction details. In particular, we identified RXR regions involved in the interaction with the structured N-terminal domain of MED1, as well as VDR regions outside the classical coactivator binding cleft affected by coactivator recruitment. These findings highlight important roles of each receptor within the heterodimer in selective recognition of MED1 and contribute to our understanding of the nuclear receptor-coregulator complexes.
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Affiliation(s)
- Anna Y Belorusova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Sandra Chalhoub
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
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19
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Jumonji domain containing 1C (JMJD1C) sequence variants in seven patients with autism spectrum disorder, intellectual disability and seizures. Eur J Med Genet 2020; 63:103850. [DOI: 10.1016/j.ejmg.2020.103850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 11/26/2019] [Accepted: 01/12/2020] [Indexed: 12/25/2022]
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20
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Femia MR, Evans RM, Zhang J, Sun X, Lebegue CJ, Roggero VR, Allison LA. Mediator subunit MED1 modulates intranuclear dynamics of the thyroid hormone receptor. J Cell Biochem 2019; 121:2909-2926. [PMID: 31692077 DOI: 10.1002/jcb.29532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022]
Abstract
The thyroid hormone receptors (TRs) mediate thyroid hormone (T3 )-dependent gene expression. The nuclear import and export signals that direct TR shuttling are well characterized, but little is known about factors modulating nuclear retention. We used fluorescence-based nucleocytoplasmic scoring and fluorescence recovery after photobleaching in transfected cells to investigate whether Mediator subunits MED1 and MED13 play a role in nuclear retention of TR. When MED1 was overexpressed, there was a striking shift towards a greater nuclear localization of TRβ1 and the oncoprotein v-ErbA, subtypes with cytosolic populations at steady-state, and TRβ1 intranuclear mobility was reduced. For TRα1, there was no observable change in its predominantly nuclear distribution pattern or mobility. Consistent with a role for MED1 in nuclear retention, the cytosolic TRα1 and TRβ1 population were significantly greater in MED1-/- cells, compared with MED1+/+ cells. Exposure to T3 and epidermal growth factor, which induces MED1 phosphorylation, also altered TR intranuclear dynamics. Overexpression of miR-208a, which downregulates MED13, led to a more cytosolic distribution of nuclear-localized TRα1; however, overexpression of MED13 had no effect on TRβ1 localization. The known binding site of MED1 overlaps with a transactivation domain and nuclear export signal in helix 12 of TR's ligand-binding domain (LBD). Coimmunoprecipitation assays demonstrated that TR's LBD interacts directly with exportins 5 and 7, suggesting that binding of exportins and MED1 to TR may be mutually exclusive. Collectively, our data provide evidence that MED1 promotes nuclear retention of TR, and highlight the dual functionality of helix 12 in TR transactivation and nuclear export.
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Affiliation(s)
- Matthew R Femia
- Department of Biology, William and Mary, Williamsburg, Viginia
| | | | - Jibo Zhang
- Department of Biology, William and Mary, Williamsburg, Viginia
| | - Xiaopeng Sun
- Department of Biology, William and Mary, Williamsburg, Viginia
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21
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Quevedo M, Meert L, Dekker MR, Dekkers DHW, Brandsma JH, van den Berg DLC, Ozgür Z, van IJcken WFJ, Demmers J, Fornerod M, Poot RA. Mediator complex interaction partners organize the transcriptional network that defines neural stem cells. Nat Commun 2019; 10:2669. [PMID: 31209209 PMCID: PMC6573065 DOI: 10.1038/s41467-019-10502-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/10/2019] [Indexed: 01/13/2023] Open
Abstract
The Mediator complex regulates transcription by connecting enhancers to promoters. High Mediator binding density defines super enhancers, which regulate cell-identity genes and oncogenes. Protein interactions of Mediator may explain its role in these processes but have not been identified comprehensively. Here, we purify Mediator from neural stem cells (NSCs) and identify 75 protein-protein interaction partners. We identify super enhancers in NSCs and show that Mediator-interacting chromatin modifiers colocalize with Mediator at enhancers and super enhancers. Transcription factor families with high affinity for Mediator dominate enhancers and super enhancers and can explain genome-wide Mediator localization. We identify E-box transcription factor Tcf4 as a key regulator of NSCs. Tcf4 interacts with Mediator, colocalizes with Mediator at super enhancers and regulates neurogenic transcription factor genes with super enhancers and broad H3K4me3 domains. Our data suggest that high binding-affinity for Mediator is an important organizing feature in the transcriptional network that determines NSC identity. The Mediator complex regulates transcription by connecting enhancers to promoters. Here, the authors purify Mediator from neural stem cells (NSCs), identify 75 novel protein-protein interaction partners and characterize the Mediator-interacting network that regulates transcription and establishes NSC identity.
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Affiliation(s)
- Marti Quevedo
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Lize Meert
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Mike R Dekker
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Dick H W Dekkers
- Center for Proteomics, Erasmus MC, 3015 CN, Rotterdam, Netherlands
| | - Johannes H Brandsma
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | | | - Zeliha Ozgür
- Center for Biomics, Erasmus MC, 3015 CN, Rotterdam, Netherlands
| | | | - Jeroen Demmers
- Center for Proteomics, Erasmus MC, 3015 CN, Rotterdam, Netherlands
| | - Maarten Fornerod
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands.
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22
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Minerath RA, Dewey CM, Hall DD, Grueter CE. Regulation of cardiac transcription by thyroid hormone and Med13. J Mol Cell Cardiol 2019; 129:27-38. [PMID: 30769017 DOI: 10.1016/j.yjmcc.2019.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/19/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022]
Abstract
Thyroid hormone (TH) is a key regulator of transcriptional homeostasis in the heart. While hypothyroidism is known to result in adverse cardiac effects, the molecular mechanisms that modulate TH signaling are not completely understood. Mediator is a multiprotein complex that coordinates signal-dependent transcription factors with the basal transcriptional machinery to regulate gene expression. Mediator complex protein, Med13, represses numerous thyroid receptor (TR) response genes in the heart. Further, cardiac-specific overexpression of Med13 in mice that were treated with propylthiouracil (PTU), an inhibitor of the biosynthesis of the active TH, triiodothyronine (T3), resulted in resistance to PTU-dependent decreases in cardiac contractility. Therefore, these studies aimed to determine if Med13 is necessary for the cardiac response to hypothyroidism. Here we demonstrate that Med13 expression is induced in the hearts of mice with hypothyroidism. To elucidate the role of Med13 in regulating gene transcription in response to TH signaling in cardiac tissue, we utilized an unbiased RNA sequencing approach to define the TH-dependent alterations in gene expression in wild-type mice or those with a cardiac-specific deletion in Med13 (Med13cKO). Mice were fed a diet of PTU to induce a hypothyroid state or normal chow for either 4 or 16 weeks, and an additional group of mice on a PTU diet were treated acutely with T3 to re-establish a euthyroid state. Echocardiography revealed that wild-type mice had a decreased heart rate in response to PTU with a trend toward a reduced cardiac ejection fraction. Notably, cardiomyocyte-specific deletion of Med13 exacerbated cardiac dysfunction. Collectively, these studies reveal cardiac transcriptional pathways regulated in response to hypothyroidism and re-establishment of a euthyroid state and define molecular pathways that are regulated by Med13 in response to TH signaling.
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Affiliation(s)
- Rachel A Minerath
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; Department of Pharmacology, University of Iowa, Iowa City 52242, IA, USA
| | - Colleen M Dewey
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Duane D Hall
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Chad E Grueter
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA.
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23
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Sedgeman LR, Beysen C, Allen RM, Ramirez Solano MA, Turner SM, Vickers KC. Intestinal bile acid sequestration improves glucose control by stimulating hepatic miR-182-5p in type 2 diabetes. Am J Physiol Gastrointest Liver Physiol 2018; 315:G810-G823. [PMID: 30160993 PMCID: PMC6415711 DOI: 10.1152/ajpgi.00238.2018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Colesevelam is a bile acid sequestrant approved to treat both hyperlipidemia and type 2 diabetes, but the mechanism for its glucose-lowering effects is not fully understood. The aim of this study was to investigate the role of hepatic microRNAs (miRNAs) as regulators of metabolic disease and to investigate the link between the cholesterol and glucose-lowering effects of colesevelam. To quantify the impact of colesevelam treatment in rodent models of diabetes, metabolic studies were performed in Zucker diabetic fatty (ZDF) rats and db/db mice. Colesevelam treatments significantly decreased plasma glucose levels and increased glycolysis in the absence of changes to insulin levels in ZDF rats and db/db mice. High-throughput sequencing and real-time PCR were used to quantify hepatic miRNA and mRNA changes, and the cholesterol-sensitive miR-96/182/183 cluster was found to be significantly increased in livers from ZDF rats treated with colesevelam compared with vehicle controls. Inhibition of miR-182 in vivo attenuated colesevelam-mediated improvements to glycemic control in db/db mice. Hepatic expression of mediator complex subunit 1 (MED1), a nuclear receptor coactivator, was significantly decreased with colesevelam treatments in db/db mice, and MED1 was experimentally validated to be a direct target of miR-96/182/183 in humans and mice. In summary, these results support that colesevelam likely improves glycemic control through hepatic miR-182-5p, a mechanism that directly links cholesterol and glucose metabolism. NEW & NOTEWORTHY Colesevelam lowers systemic glucose levels in Zucker diabetic fatty rats and db/db mice and increases hepatic levels of the sterol response element binding protein 2-responsive microRNA cluster miR-96/182/183. Inhibition of miR-182 in vivo reverses the glucose-lowering effects of colesevelam in db/db mice. Mediator complex subunit 1 (MED1) is a novel, direct target of the miR-96/182/183 cluster in mice and humans.
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Affiliation(s)
- Leslie R. Sedgeman
- 1Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | | | - Ryan M. Allen
- 3Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - Kasey C. Vickers
- 1Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee,3Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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24
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The E3 ubiquitin ligase TRIM25 regulates adipocyte differentiation via proteasome-mediated degradation of PPARγ. Exp Mol Med 2018; 50:1-11. [PMID: 30323259 PMCID: PMC6189217 DOI: 10.1038/s12276-018-0162-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/29/2018] [Accepted: 07/04/2018] [Indexed: 01/04/2023] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a ligand-dependent transcription factor that regulates adipocyte differentiation and glucose homeostasis. The transcriptional activity of PPARγ is regulated not only by ligands but also by post-translational modifications (PTMs). In this study, we demonstrate that a novel E3 ligase of PPARγ, tripartite motif-containing 25 (TRIM25), directly induced the ubiquitination of PPARγ, leading to its proteasome-dependent degradation. During adipocyte differentiation, both TRIM25 mRNA and protein expression significantly decreased and negatively correlated with the expression of PPARγ. The stable expression of TRIM25 reduced PPARγ protein levels and suppressed adipocyte differentiation in 3T3-L1 cells. In contrast, the specific knockdown of TRIM25 increased PPARγ protein levels and stimulated adipocyte differentiation. Furthermore, TRIM25-knockout mouse embryonic fibroblasts (MEFs) exhibited an increased adipocyte differentiation capability compared with wild-type MEFs. Taken together, these data indicate that TRIM25 is a novel E3 ubiquitin ligase of PPARγ and that TRIM25 is a novel target for PPARγ-associated metabolic diseases.
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25
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Broekema MF, Hollman DAA, Koppen A, van den Ham HJ, Melchers D, Pijnenburg D, Ruijtenbeek R, van Mil SWC, Houtman R, Kalkhoven E. Profiling of 3696 Nuclear Receptor-Coregulator Interactions: A Resource for Biological and Clinical Discovery. Endocrinology 2018; 159:2397-2407. [PMID: 29718163 DOI: 10.1210/en.2018-00149] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022]
Abstract
Nuclear receptors (NRs) are ligand-inducible transcription factors that play critical roles in metazoan development, reproduction, and physiology and therefore are implicated in a broad range of pathologies. The transcriptional activity of NRs critically depends on their interaction(s) with transcriptional coregulator proteins, including coactivators and corepressors. Short leucine-rich peptide motifs in these proteins (LxxLL in coactivators and LxxxIxxxL in corepressors) are essential and sufficient for NR binding. With 350 different coregulator proteins identified to date and with many coregulators containing multiple interaction motifs, an enormous combinatorial potential is present for selective NR-mediated gene regulation. However, NR-coregulator interactions have often been determined experimentally on a one-to-one basis across diverse experimental conditions. In addition, NR-coregulator interactions are difficult to predict because the molecular determinants that govern specificity are not well established. Therefore, many biologically and clinically relevant NR-coregulator interactions may remain to be discovered. Here, we present a comprehensive overview of 3696 NR-coregulator interactions by systematically characterizing the binding of 24 nuclear receptors with 154 coregulator peptides. We identified unique ligand-dependent NR-coregulator interaction profiles for each NR, confirming many well-established NR-coregulator interactions. Hierarchical clustering based on the NR-coregulator interaction profiles largely recapitulates the classification of NR subfamilies based on the primary amino acid sequences of the ligand-binding domains, indicating that amino acid sequence is an important, although not the only, molecular determinant in directing and fine-tuning NR-coregulator interactions. This NR-coregulator peptide interactome provides an open data resource for future biological and clinical discovery as well as NR-based drug design.
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Affiliation(s)
- Marjoleine F Broekema
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - Danielle A A Hollman
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - Arjen Koppen
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | | | - Diana Melchers
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Dirk Pijnenburg
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Rob Ruijtenbeek
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Saskia W C van Mil
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - René Houtman
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Eric Kalkhoven
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
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26
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Weber H, Garabedian MJ. The mediator complex in genomic and non-genomic signaling in cancer. Steroids 2018; 133:8-14. [PMID: 29157917 PMCID: PMC5864542 DOI: 10.1016/j.steroids.2017.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/04/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022]
Abstract
Mediator is a conserved, multi-subunit macromolecular machine divided structurally into head, middle, and tail modules, along with a transiently associating kinase module. Mediator functions as an integrator of transcriptional regulatory activity by interacting with DNA-bound transcription factors and with RNA polymerase II (Pol II) to both activate and repress gene expression. Mediator has been shown to affect multiple steps in transcription, including chromatin looping between enhancers and promoters, pre-initiation complex formation, transcriptional elongation, and mRNA splicing. Individual Mediator subunits participate in regulation of gene expression by the estrogen and androgen receptors and are altered in a number of endocrine cancers, including breast and prostate cancer. In addition to its role in genomic signaling, MED12 has been implicated in non-genomic signaling by interacting with and activating TGF-beta receptor 2 in the cytoplasm. Recent structural studies have revealed extensive inter-domain interactions and complex architecture of the Mediator-Pol II complex, suggesting that Mediator is capable of reorganizing its conformation and composition to fit cellular needs. We propose that alterations in Mediator subunit expression that occur in various cancers could impact the organization and function of Mediator, resulting in changes in gene expression that promote malignancy. A better understanding of the role of Mediator in cancer could reveal new approaches to the diagnosis and treatment of Mediator-dependent endocrine cancers, especially in settings of therapy resistance.
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Affiliation(s)
- Hannah Weber
- Departments of Microbiology and Urology, NYU School of Medicine, 550 First Ave, New York, NY 10012, United States
| | - Michael J Garabedian
- Departments of Microbiology and Urology, NYU School of Medicine, 550 First Ave, New York, NY 10012, United States.
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27
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Khabou H, Garita-Hernandez M, Chaffiol A, Reichman S, Jaillard C, Brazhnikova E, Bertin S, Forster V, Desrosiers M, Winckler C, Goureau O, Picaud S, Duebel J, Sahel JA, Dalkara D. Noninvasive gene delivery to foveal cones for vision restoration. JCI Insight 2018; 3:96029. [PMID: 29367457 DOI: 10.1172/jci.insight.96029] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/12/2017] [Indexed: 01/02/2023] Open
Abstract
Intraocular injection of adeno-associated viral (AAV) vectors has been an evident route for delivering gene drugs into the retina. However, gaps in our understanding of AAV transduction patterns within the anatomically unique environments of the subretinal and intravitreal space of the primate eye impeded the establishment of noninvasive and efficient gene delivery to foveal cones in the clinic. Here, we establish new vector-promoter combinations to overcome the limitations associated with AAV-mediated cone transduction in the fovea with supporting studies in mouse models, human induced pluripotent stem cell-derived organoids, postmortem human retinal explants, and living macaques. We show that an AAV9 variant provides efficient foveal cone transduction when injected into the subretinal space several millimeters away from the fovea, without detaching this delicate region. An engineered AAV2 variant provides gene delivery to foveal cones with a well-tolerated dose administered intravitreally. Both delivery modalities rely on a cone-specific promoter and result in high-level transgene expression compatible with optogenetic vision restoration. The model systems described here provide insight into the behavior of AAV vectors across species to obtain safety and efficacy needed for gene therapy in neurodegenerative disorders.
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Affiliation(s)
- Hanen Khabou
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Antoine Chaffiol
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Sacha Reichman
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Céline Jaillard
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Elena Brazhnikova
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Stéphane Bertin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Valérie Forster
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Mélissa Desrosiers
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Céline Winckler
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Olivier Goureau
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Serge Picaud
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Jens Duebel
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - José-Alain Sahel
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Fondation Ophtalmologique Rothschild, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Deniz Dalkara
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
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28
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Anttonen AK, Laari A, Kousi M, Yang YJ, Jääskeläinen T, Somer M, Siintola E, Jakkula E, Muona M, Tegelberg S, Lönnqvist T, Pihko H, Valanne L, Paetau A, Lun MP, Hästbacka J, Kopra O, Joensuu T, Katsanis N, Lehtinen MK, Palvimo JJ, Lehesjoki AE. ZNHIT3 is defective in PEHO syndrome, a severe encephalopathy with cerebellar granule neuron loss. Brain 2017; 140:1267-1279. [PMID: 28335020 DOI: 10.1093/brain/awx040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 01/06/2017] [Indexed: 11/12/2022] Open
Abstract
Progressive encephalopathy with oedema, hypsarrhythmia, and optic atrophy (PEHO) syndrome is an early childhood onset, severe autosomal recessive encephalopathy characterized by extreme cerebellar atrophy due to almost total granule neuron loss. By combining homozygosity mapping in Finnish families with Sanger sequencing of positional candidate genes and with exome sequencing a homozygous missense substitution of leucine for serine at codon 31 in ZNHIT3 was identified as the primary cause of PEHO syndrome. ZNHIT3 encodes a nuclear zinc finger protein previously implicated in transcriptional regulation and in small nucleolar ribonucleoprotein particle assembly and thus possibly to pre-ribosomal RNA processing. The identified mutation affects a highly conserved amino acid residue in the zinc finger domain of ZNHIT3. Both knockdown and genome editing of znhit3 in zebrafish embryos recapitulate the patients' cerebellar defects, microcephaly and oedema. These phenotypes are rescued by wild-type, but not mutant human ZNHIT3 mRNA, suggesting that the patient missense substitution causes disease through a loss-of-function mechanism. Transfection of cell lines with ZNHIT3 expression vectors showed that the PEHO syndrome mutant protein is unstable. Immunohistochemical analysis of mouse cerebellar tissue demonstrated ZNHIT3 to be expressed in proliferating granule cell precursors, in proliferating and post-mitotic granule cells, and in Purkinje cells. Knockdown of Znhit3 in cultured mouse granule neurons and ex vivo cerebellar slices indicate that ZNHIT3 is indispensable for granule neuron survival and migration, consistent with the zebrafish findings and patient neuropathology. These results suggest that loss-of-function of a nuclear regulator protein underlies PEHO syndrome and imply that establishment of its spatiotemporal interaction targets will be the basis for developing therapeutic approaches and for improved understanding of cerebellar development.
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Affiliation(s)
- Anna-Kaisa Anttonen
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, Viikinkaari 4, 00790 Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland.,Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Anni Laari
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, Viikinkaari 4, 00790 Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Maria Kousi
- Center for Human Disease Modeling, Duke University Medical Center, Carmichael Building, 300 North Duke Street, Suite 48-118, Durham, NC 27701, USA
| | - Yawei J Yang
- Division of Genetics, Howard Hughes Medical Institute.,Institute for Molecular Medicine Finland, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland.,Department of Pediatric Neurology, Children's Hospital, University of Helsinki and Helsinki University Hospital, Lastenlinnantie 2, 00290 Helsinki, Finland
| | - Tiina Jääskeläinen
- Institute of Biomedicine, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland.,Institute of Dentistry, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Mirja Somer
- The Norio Centre, The Rinnekoti Foundation, Kornetintie 8, 00380 Helsinki, Finland
| | - Eija Siintola
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, Viikinkaari 4, 00790 Helsinki, Finland
| | - Eveliina Jakkula
- Institute for Molecular Medicine Finland, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Mikko Muona
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, Viikinkaari 4, 00790 Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Saara Tegelberg
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, Viikinkaari 4, 00790 Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Tuula Lönnqvist
- Department of Pediatric Neurology, Children's Hospital, University of Helsinki and Helsinki University Hospital, Lastenlinnantie 2, 00290 Helsinki, Finland
| | - Helena Pihko
- Department of Pediatric Neurology, Children's Hospital, University of Helsinki and Helsinki University Hospital, Lastenlinnantie 2, 00290 Helsinki, Finland
| | - Leena Valanne
- Department of Radiology, HUS Medical Imaging Center, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Anders Paetau
- Department of Pathology, Helsinki University Hospital, Haartmaninkatu 3, 00290 Helsinki, Finland
| | - Melody P Lun
- Department of Pathology, Boston Children's Hospital, BCH 3108, 300 Longwood Ave., Boston, MA 02115, USA.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - Johanna Hästbacka
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Department of Pediatrics, Children's Hospital, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 11, 00290 Helsinki, Finland
| | - Outi Kopra
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, Viikinkaari 4, 00790 Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Tarja Joensuu
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, Viikinkaari 4, 00790 Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Carmichael Building, 300 North Duke Street, Suite 48-118, Durham, NC 27701, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital, BCH 3108, 300 Longwood Ave., Boston, MA 02115, USA
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Anna-Elina Lehesjoki
- The Folkhälsan Institute of Genetics, Haartmaninkatu 8, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, Viikinkaari 4, 00790 Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
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29
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Ranjan A, Ansari SA. Therapeutic potential of Mediator complex subunits in metabolic diseases. Biochimie 2017; 144:41-49. [PMID: 29061530 DOI: 10.1016/j.biochi.2017.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/16/2017] [Indexed: 01/16/2023]
Abstract
The multisubunit Mediator is an evolutionary conserved transcriptional coregulatory complex in eukaryotes. It is needed for the transcriptional regulation of gene expression in general as well as in a gene specific manner. Mediator complex subunits interact with different transcription factors as well as components of RNA Pol II transcription initiation complex and in doing so act as a bridge between gene specific transcription factors and general Pol II transcription machinery. Specific interaction of various Mediator subunits with nuclear receptors (NRs) and other transcription factors involved in metabolism has been reported in different studies. Evidences indicate that ligand-activated NRs recruit Mediator complex for RNA Pol II-dependent gene transcription. These NRs have been explored as therapeutic targets in different metabolic diseases; however, they show side-effects as targets due to their overlapping involvement in different signaling pathways. Here we discuss the interaction of various Mediator subunits with transcription factors involved in metabolism and whether specific interaction of these transcription factors with Mediator subunits could be potentially utilized as therapeutic strategy in a variety of metabolic diseases.
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Affiliation(s)
- Amol Ranjan
- Stowers Institute for Medical Research, 1000 E, 50th Street, Kansas City, MO, 64110, USA
| | - Suraiya A Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, UAE University, AlAin, Abu Dhabi, United Arab Emirates.
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30
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Vignali PDA, Barbi J, Pan F. Metabolic Regulation of T Cell Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1011:87-130. [DOI: 10.1007/978-94-024-1170-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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31
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Abstract
A growing epidemic of nonalcoholic fatty liver disease (NAFLD) is paralleling the increase in the incidence of obesity and diabetes mellitus in countries that consume a Western diet. As NAFLD can lead to life-threatening conditions such as cirrhosis and hepatocellular carcinoma, an understanding of the factors that trigger its development and pathological progression is needed. Although by definition this disease is not associated with alcohol consumption, exposure to environmental agents that have been linked to other diseases might have a role in the development of NAFLD. Here, we focus on one class of these agents, endocrine-disrupting chemicals (EDCs), and their potential to influence the initiation and progression of a cascade of pathological conditions associated with hepatic steatosis (fatty liver). Experimental studies have revealed several potential mechanisms by which EDC exposure might contribute to disease pathogenesis, including the modulation of nuclear hormone receptor function and the alteration of the epigenome. However, many questions remain to be addressed about the causal link between acute and chronic EDC exposure and the development of NAFLD in humans. Future studies that address these questions hold promise not only for understanding the linkage between EDC exposure and liver disease but also for elucidating the molecular mechanisms that underpin NAFLD, which in turn could facilitate the development of new prevention and treatment opportunities.
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Affiliation(s)
- Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine
- Center for Precision Environmental Health, Baylor College of Medicine
| | - Lindsey S Treviño
- Department of Molecular and Cellular Biology, Baylor College of Medicine
- Center for Precision Environmental Health, Baylor College of Medicine
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine
- Dan L. Duncan Cancer Center, Baylor College of Medicine
| | - Cheryl L Walker
- Department of Molecular and Cellular Biology, Baylor College of Medicine
- Center for Precision Environmental Health, Baylor College of Medicine
- Dan L. Duncan Cancer Center, Baylor College of Medicine
- Department of Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
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32
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Bai L, Li Z, Li Q, Guan H, Zhao S, Liu R, Wang R, Zhang J, Jia Y, Fan J, Wang N, Reddy JK, Shyy JYJ, Liu E. Mediator 1 Is Atherosclerosis Protective by Regulating Macrophage Polarization. Arterioscler Thromb Vasc Biol 2017. [PMID: 28642237 DOI: 10.1161/atvbaha.117.309672] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE MED1 (mediator 1) interacts with transcription factors to regulate transcriptional machinery. The role of MED1 in macrophage biology and the relevant disease state remains to be investigated. APPROACH AND RESULTS To study the molecular mechanism by which MED1 regulates the M1/M2 phenotype switch of macrophage and the effect on atherosclerosis, we generated MED1/apolipoprotein E (ApoE) double-deficient (MED1ΔMac/ApoE-/-) mice and found that atherosclerosis was greater in MED1ΔMac/ApoE-/- mice than in MED1fl/fl/ApoE-/- littermates. The gene expression of M1 markers was increased and that of M2 markers decreased in both aortic wall and peritoneal macrophages from MED1ΔMac/ApoE-/- mice, whereas MED1 overexpression rectified the changes in M1/M2 expression. Moreover, LDLR (low-density lipoprotein receptor)-deficient mice received bone marrow from MED1ΔMac mice showed greater atherosclerosis. Mechanistically, MED1 ablation decreased the binding of PPARγ (peroxisome proliferator-activated receptor γ) and enrichment of H3K4me1 and H3K27ac to upstream region of M2 marker genes. Furthermore, interleukin 4 induction of PPARγ and MED1 increased the binding of PPARγ or MED1 to the PPAR response elements of M2 marker genes. CONCLUSIONS Our data suggest that MED1 is required for the PPARγ-mediated M2 phenotype switch, with M2 marker genes induced but M1 marker genes suppressed. MED1 in macrophages has an antiatherosclerotic role via PPARγ-regulated transactivation.
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Affiliation(s)
- Liang Bai
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Zhao Li
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Qianwei Li
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Hua Guan
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Sihai Zhao
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Ruihan Liu
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Rong Wang
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Jin Zhang
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Yuzhi Jia
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Jianglin Fan
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Nanping Wang
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Janardan K Reddy
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - John Y-J Shyy
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.).
| | - Enqi Liu
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.).
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Song Z, Xiaoli AM, Zhang Q, Zhang Y, Yang EST, Wang S, Chang R, Zhang ZD, Yang G, Strich R, Pessin JE, Yang F. Cyclin C regulates adipogenesis by stimulating transcriptional activity of CCAAT/enhancer-binding protein α. J Biol Chem 2017; 292:8918-8932. [PMID: 28351837 DOI: 10.1074/jbc.m117.776229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/27/2017] [Indexed: 11/06/2022] Open
Abstract
Brown adipose tissue is important for maintaining energy homeostasis and adaptive thermogenesis in rodents and humans. As disorders arising from dysregulated energy metabolism, such as obesity and metabolic diseases, have increased, so has interest in the molecular mechanisms of adipocyte biology. Using a functional screen, we identified cyclin C (CycC), a conserved subunit of the Mediator complex, as a novel regulator for brown adipocyte formation. siRNA-mediated CycC knockdown (KD) in brown preadipocytes impaired the early transcriptional program of differentiation, and genetic KO of CycC completely blocked the differentiation process. RNA sequencing analyses of CycC-KD revealed a critical role of CycC in activating genes co-regulated by peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα). Overexpression of PPARγ2 or addition of the PPARγ ligand rosiglitazone rescued the defects in CycC-KO brown preadipocytes and efficiently activated the PPARγ-responsive promoters in both WT and CycC-KO cells, suggesting that CycC is not essential for PPARγ transcriptional activity. In contrast, CycC-KO significantly reduced C/EBPα-dependent gene expression. Unlike for PPARγ, overexpression of C/EBPα could not induce C/EBPα target gene expression in CycC-KO cells or rescue the CycC-KO defects in brown adipogenesis, suggesting that CycC is essential for C/EBPα-mediated gene activation. CycC physically interacted with C/EBPα, and this interaction was required for C/EBPα transactivation domain activity. Consistent with the role of C/EBPα in white adipogenesis, CycC-KD also inhibited differentiation of 3T3-L1 cells into white adipocytes. Together, these data indicate that CycC activates adipogenesis in part by stimulating the transcriptional activity of C/EBPα.
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Affiliation(s)
- Ziyi Song
- From the Laboratory of Animal Fat Deposition and Muscle Development, Department of Animal Sciences, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.,the Department of Medicine, Division of Endocrinology and Diabetes Research Center, and
| | - Alus M Xiaoli
- the Department of Medicine, Division of Endocrinology and Diabetes Research Center, and.,Departments of Developmental and Molecular Biology
| | | | - Yi Zhang
- the Department of Medicine, Division of Endocrinology and Diabetes Research Center, and.,Departments of Developmental and Molecular Biology
| | - Ellen S T Yang
- the Department of Medicine, Division of Endocrinology and Diabetes Research Center, and.,Departments of Developmental and Molecular Biology
| | - Sven Wang
- the Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, and
| | - Rui Chang
- the Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, and
| | | | - Gongshe Yang
- From the Laboratory of Animal Fat Deposition and Muscle Development, Department of Animal Sciences, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China,
| | - Randy Strich
- the Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08055
| | - Jeffrey E Pessin
- the Department of Medicine, Division of Endocrinology and Diabetes Research Center, and.,Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Fajun Yang
- the Department of Medicine, Division of Endocrinology and Diabetes Research Center, and .,Departments of Developmental and Molecular Biology
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34
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Klümper N, Syring I, Vogel W, Schmidt D, Müller SC, Ellinger J, Shaikhibrahim Z, Brägelmann J, Perner S. Mediator Complex Subunit MED1 Protein Expression Is Decreased during Bladder Cancer Progression. Front Med (Lausanne) 2017; 4:30. [PMID: 28367434 PMCID: PMC5355444 DOI: 10.3389/fmed.2017.00030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/03/2017] [Indexed: 01/03/2023] Open
Abstract
Introduction Bladder cancer (BCa) is among the most frequent cancer entities and relevantly contributes to cancer-associated deaths worldwide. The multi-protein Mediator complex is a central regulator of the transcriptional machinery of protein-coding genes and has been described to be altered in several malignancies. MED1, a subunit of the tail module, was described to negatively modulate expression of metastasis-related genes and to be downregulated in melanoma and lung cancer. In contrast, MED1 hyperactivity was described in breast and prostate cancer, likely due its function as a hub for nuclear hormone receptors. So far, only little is known about the function of the Mediator complex in BCa. The aim of this study was therefore to investigate the role of MED1 in BCa as a prognostic biomarker and a biomarker of disease progression. Methods The protein expression of MED1 was assessed by immunohistochemistry (IHC) on tissue microarrays from 224 patients: benign urothelium n = 31, non-muscle invasive BCa (pTis, pT1) n = 72, and muscle invasive BCa (pT2–T4) n = 121. Comprehensive clinicopathological information including follow-up were available. Quantification of MED1 protein expression was evaluated by the semiquantitative image analysis program Definiens. Results MED1 expression significantly decreased during BCa progression from benign urothelium to advanced BCa. Muscle invasion, the crucial step in BCa progression, was associated with low MED1 protein expression. Accordingly, decreased MED1 expression was found in primary BCa samples with positive lymphonodal status and distant metastases. Furthermore, cancer-specific survival was significantly worse in the group of low MED1 expression. Conclusion Our findings show that the downregulation of MED1 is associated with muscle invasion, metastatic spread, and shorter overall survival in BCa.
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Affiliation(s)
- Niklas Klümper
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences , Luebeck , Germany
| | - Isabella Syring
- Clinic for Urology and Pediatric Urology, University Hospital of Bonn , Bonn , Germany
| | - Wenzel Vogel
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences , Luebeck , Germany
| | - Doris Schmidt
- Clinic for Urology and Pediatric Urology, University Hospital of Bonn , Bonn , Germany
| | - Stefan C Müller
- Clinic for Urology and Pediatric Urology, University Hospital of Bonn , Bonn , Germany
| | - Jörg Ellinger
- Clinic for Urology and Pediatric Urology, University Hospital of Bonn , Bonn , Germany
| | - Zaki Shaikhibrahim
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences , Luebeck , Germany
| | - Johannes Brägelmann
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences, Luebeck, Germany; Department of Hematology, Oncology and Rheumatology, University Hospital of Bonn, Bonn, Germany
| | - Sven Perner
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences , Luebeck , Germany
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35
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Regulation of metabolism by the Mediator complex. BIOPHYSICS REPORTS 2016; 2:69-77. [PMID: 28018965 PMCID: PMC5138257 DOI: 10.1007/s41048-016-0031-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/15/2016] [Indexed: 01/11/2023] Open
Abstract
The Mediator complex was originally discovered in yeast, but it is conserved in all eukaryotes. Its best-known function is to regulate RNA polymerase II-dependent gene transcription. Although the mechanisms by which the Mediator complex regulates transcription are often complicated by the context-dependent regulation, this transcription cofactor complex plays a pivotal role in numerous biological pathways. Biochemical, molecular, and physiological studies using cancer cell lines or model organisms have established the current paradigm of the Mediator functions. However, the physiological roles of the mammalian Mediator complex remain poorly defined, but have attracted a great interest in recent years. In this short review, we will summarize some of the reported functions of selective Mediator subunits in the regulation of metabolism. These intriguing findings suggest that the Mediator complex may be an important player in nutrient sensing and energy balance in mammals.
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36
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Lee B, Wu CY, Lin YW, Park SW, Wei LN. Synergistic activation of Arg1 gene by retinoic acid and IL-4 involves chromatin remodeling for transcription initiation and elongation coupling. Nucleic Acids Res 2016; 44:7568-79. [PMID: 27166374 PMCID: PMC5027474 DOI: 10.1093/nar/gkw392] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 04/28/2016] [Indexed: 01/15/2023] Open
Abstract
All-trans Retinoic acid (RA) and its derivatives are potent therapeutics for immunological functions including wound repair. However, the molecular mechanism of RA modulation in innate immunity is poorly understood, especially in macrophages. We found that topical application of RA significantly improves wound healing and that RA and IL-4 synergistically activate Arg1, a critical gene for tissue repair, in M2 polarized macrophages. This involves feed forward regulation of Raldh2, a rate-limiting enzyme for RA biosynthesis, and requires Med25 to coordinate RAR, STAT6 and chromatin remodeler, Brg1 to remodel the +1 nucleosome of Arg1 for transcription initiation. By recruiting elongation factor TFIIS, Med25 also facilitates transcriptional initiation-elongation coupling. This study uncovers synergistic activation of Arg1 by RA and IL-4 in M2 macrophages that involves feed forward regulation of RA synthesis and dual functions of Med25 in nucleosome remodeling and transcription initiation-elongation coupling that underlies robust modulatory activity of RA in innate immunity.
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Affiliation(s)
- Bomi Lee
- Department of Pharmacology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cheng-Ying Wu
- Department of Pharmacology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yi-Wei Lin
- Department of Pharmacology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sung Wook Park
- Department of Pharmacology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Li-Na Wei
- Department of Pharmacology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
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Olivares AM, Moreno-Ramos OA, Haider NB. Role of Nuclear Receptors in Central Nervous System Development and Associated Diseases. J Exp Neurosci 2016; 9:93-121. [PMID: 27168725 PMCID: PMC4859451 DOI: 10.4137/jen.s25480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/13/2022] Open
Abstract
The nuclear hormone receptor (NHR) superfamily is composed of a wide range of receptors involved in a myriad of important biological processes, including development, growth, metabolism, and maintenance. Regulation of such wide variety of functions requires a complex system of gene regulation that includes interaction with transcription factors, chromatin-modifying complex, and the proper recognition of ligands. NHRs are able to coordinate the expression of genes in numerous pathways simultaneously. This review focuses on the role of nuclear receptors in the central nervous system and, in particular, their role in regulating the proper development and function of the brain and the eye. In addition, the review highlights the impact of mutations in NHRs on a spectrum of human diseases from autism to retinal degeneration.
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Affiliation(s)
- Ana Maria Olivares
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Oscar Andrés Moreno-Ramos
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Neena B Haider
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
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Nichol JN, Galbraith MD, Kleinman CL, Espinosa JM, Miller WH. NPM and BRG1 Mediate Transcriptional Resistance to Retinoic Acid in Acute Promyelocytic Leukemia. Cell Rep 2016; 14:2938-49. [PMID: 26997274 DOI: 10.1016/j.celrep.2016.02.074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/16/2015] [Accepted: 02/17/2016] [Indexed: 11/19/2022] Open
Abstract
Perturbation in the transcriptional control of genes driving differentiation is an established paradigm whereby oncogenic fusion proteins promote leukemia. From a retinoic acid (RA)-sensitive acute promyelocytic leukemia (APL) cell line, we derived an RA-resistant clone characterized by a block in transcription initiation, despite maintaining wild-type PML/RARA expression. We uncovered an aberrant interaction among PML/RARA, nucleophosmin (NPM), and topoisomerase II beta (TOP2B). Surprisingly, RA stimulation in these cells results in enhanced chromatin association of the nucleosome remodeler BRG1. Inhibition of NPM or TOP2B abrogated BRG1 recruitment. Furthermore, NPM inhibition and targeting BRG1 restored differentiation when combined with RA. Here, we demonstrate a role for NPM and BRG1 in obstructing RA differentiation and implicate chromatin remodeling in mediating therapeutic resistance in malignancies. NPM mutations are the most common genetic change in patients with acute leukemia (AML); therefore, our model may be applicable to other more common leukemias driven by NPM.
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Affiliation(s)
- Jessica N Nichol
- Division of Experimental Medicine, Department of Oncology, Segal Cancer Centre and Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Matthew D Galbraith
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Claudia L Kleinman
- Department of Human Genetics, Segal Cancer Centre and Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Joaquín M Espinosa
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Wilson H Miller
- Division of Experimental Medicine, Department of Oncology, Segal Cancer Centre and Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada.
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Kaya Okur HS, Das A, Taylor RN, Bagchi IC, Bagchi MK. Roles of Estrogen Receptor-α and the Coactivator MED1 During Human Endometrial Decidualization. Mol Endocrinol 2016; 30:302-13. [PMID: 26849466 DOI: 10.1210/me.2015-1274] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The steroid hormones 17β-estradiol and progesterone are critical regulators of endometrial stromal cell differentiation, known as decidualization, which is a prerequisite for successful establishment of pregnancy. The present study using primary human endometrial stromal cells (HESCs) addressed the role of estrogen receptor-α (ESR1) in decidualization. Knockdown of ESR1 transcripts by RNA interference led to a marked reduction in decidualization of HESCs. Gene expression profiling at an early stage of decidualization indicated that ESR1 negatively regulates several cell cycle regulatory factors, thereby suppressing the proliferation of HESCs as these cells enter the differentiation program. ESR1 also controls the expression of WNT4, FOXO1, and progesterone receptor (PGR), well-known mediators of decidualization. Whereas ESR1 knockdown strongly inhibited the expression of FOXO1 and WNT4 transcripts within 24 hours of the initiation of decidualization, PGR expression remained unaffected at this early time point. Our study also revealed a major role of cAMP signaling in influencing the function of ESR1 during decidualization. Using a proteomic approach, we discovered that the cAMP-dependent protein kinase A (PKA) phosphorylates Mediator 1 (MED1), a subunit of the mediator coactivator complex, during HESC differentiation. Using immunoprecipitation, we demonstrated that PKA-phosphorylated MED1 interacts with ESR1. The PKA-dependent phosphorylation of MED1 was also correlated with its enhanced recruitment to estrogen-responsive elements in the WNT4 gene. Knockdown of MED1 transcripts impaired the expression of ESR1-induced WNT4 and FOXO1 transcripts and blocked decidualization. Based on these findings, we conclude that modulation of ESR1-MED1 interactions by cAMP signaling plays a critical role in human decidualization.
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Affiliation(s)
- Hatice S Kaya Okur
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Amrita Das
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Robert N Taylor
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Indrani C Bagchi
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Milan K Bagchi
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
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Nagulapalli M, Maji S, Dwivedi N, Dahiya P, Thakur JK. Evolution of disorder in Mediator complex and its functional relevance. Nucleic Acids Res 2015; 44:1591-612. [PMID: 26590257 PMCID: PMC4770211 DOI: 10.1093/nar/gkv1135] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 10/18/2015] [Indexed: 12/27/2022] Open
Abstract
Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of ‘junction-MoRF’ has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein–protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms.
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Affiliation(s)
- Malini Nagulapalli
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pradeep Dahiya
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Kwon KA, Yun J, Oh SY, Seo BG, Lee S, Lee JH, Kim SH, Choi HJ, Roh MS, Kim HJ. Clinical Significance of Peroxisome Proliferator-Activated Receptor γ and TRAP220 in Patients with Operable Colorectal Cancer. Cancer Res Treat 2015; 48:198-207. [PMID: 26130665 PMCID: PMC4720060 DOI: 10.4143/crt.2015.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/30/2015] [Indexed: 11/21/2022] Open
Abstract
Purpose The peroxisome proliferator-activated receptor γ (PPARγ) is a nuclear receptor that regulates expression of mediators of lipid metabolism and the inflammatory response. Thyroid hormone receptor-associated proteins 220 (TRAP220) is an essential component of the TRAP/Mediator complex. The objective of this study was to clarify whether PPARγ or TRAP220 are significant prognostic markers in resectable colorectal cancer (CRC). Materials and Methods A total of 399 patients who underwent curative resection for CRC were enrolled. We investigated the presence of PPARγ and TARP220 in CRC tissues and adjacent normal tissues by immunohistochemistry. Correlation between the expression of these factors and clinicopathologic features and survival was investigated. Results Median age of the patients was 63 years (range, 22 to 87 years), and median follow-up duration 61.1 months (range, 2 to 114 months). PPARγ and TRAP220 expression showed significant correlation with depth of invasion (p=0.013 and p=0.001, respectively). Expression of TRAP220 also showed association with lymph node metastasis and TNM stage (p=0.001). Compared with patients with TRAP220 negative tumors, patients with TRAP220 positive tumors had longer 5-year disease-free survival (DFS) tendency (p=0.051). Patients who were PPARγ positive combined with TRAP220 positive had a better 5-year DFS (64.8% vs. 79.3%, p=0.013). In multivariate analysis expression of both PPARγ and TRAP220 significantly affected DFS (hazard ratio, 0.620; 95% confidence interval, 0.379 to 0.997; p=0.048). Conclusion TRAP220 may be a valuable marker for nodal metastasis and TNM stage. Tumor co-expression of PPARγ and TRAP220 represents a biomarker for good prognosis in CRC patients.
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Affiliation(s)
- Kyung A Kwon
- Division of Hematology-Oncology, Department of Internal Medicine, Dongnam Institute of Radiological and Medical Sciences, Busan, Korea
| | - Jeanho Yun
- Department of Biochemistry, Dong-A University College of Medicine, Busan, Korea
| | - Sung Yong Oh
- Department of Internal Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Bong-Gun Seo
- Division of Hematology-Oncology, Department of Internal Medicine, Dongnam Institute of Radiological and Medical Sciences, Busan, Korea
| | - Suee Lee
- Department of Internal Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Ji-Hyun Lee
- Department of Internal Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Sung-Hyun Kim
- Department of Internal Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Hong Jo Choi
- Department of Surgery, Dong-A University College of Medicine, Busan, Korea
| | - Mee Sook Roh
- Department of Pathology, Dong-A University College of Medicine, Busan, Korea
| | - Hyo-Jin Kim
- Department of Internal Medicine, Dong-A University College of Medicine, Busan, Korea
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Diiodothyropropionic acid in the management of cardiovascular disease. Cardiovasc Endocrinol 2015. [DOI: 10.1097/xce.0000000000000046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Huszar JM, Jia Y, Reddy JK, Payne CJ. Med1 regulates meiotic progression during spermatogenesis in mice. Reproduction 2015; 149:597-604. [PMID: 25778538 PMCID: PMC4417004 DOI: 10.1530/rep-14-0483] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 03/16/2015] [Indexed: 12/30/2022]
Abstract
Spermatogenesis is a highly coordinated process. Signaling from nuclear hormone receptors, like those for retinoic acid (RA), is important for normal spermatogenesis. However, the mechanisms regulating these signals are poorly understood. Mediator complex subunit 1 (MED1) is a transcriptional enhancer that directly modulates transcription from nuclear hormone receptors. MED1 is present in male germ cells throughout mammalian development, but its function during spermatogenesis is unknown. To determine its role, we generated mice lacking Med1 specifically in their germ cells beginning just before birth. Conditional Med1 knockout males are fertile, exhibiting normal testis weights and siring ordinary numbers of offspring. RA-responsive gene products stimulated by RA gene 8 (Stra8) and synaptonemal complex protein 3 (Sycp3) are first detected in knockout spermatogonia at the expected time points during the first wave of spermatogenesis, and persist with normal patterns of cellular distribution in adult knockout testes. Meiotic progression, however, is altered in the absence of Med1. At postnatal day 7 (P7), zygotene-stage knockout spermatocytes are already detected, unlike in control testes, with fewer pre-leptotene-stage cells and more leptotene spermatocytes observed in the knockouts. At P9, Med1 knockout spermatocytes prematurely enter pachynema. Once formed, greater numbers of knockout spermatocytes remain in pachynema relative to the other stages of meiosis throughout testis development and its maintenance in the adult. Meiotic exit is not inhibited. We conclude that MED1 regulates the temporal progression of primary spermatocytes through meiosis, with its absence resulting in abbreviated pre-leptotene, leptotene, and zygotene stages, and a prolonged pachytene stage.
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Affiliation(s)
- Jessica M Huszar
- Driskill Graduate ProgramDepartment of PathologyDepartments of Pediatrics and Obstetrics and GynecologyNorthwestern University Feinberg School of Medicine and Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, PO Box 211, Chicago, Illinois 60611, USA
| | - Yuzhi Jia
- Driskill Graduate ProgramDepartment of PathologyDepartments of Pediatrics and Obstetrics and GynecologyNorthwestern University Feinberg School of Medicine and Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, PO Box 211, Chicago, Illinois 60611, USA
| | - Janardan K Reddy
- Driskill Graduate ProgramDepartment of PathologyDepartments of Pediatrics and Obstetrics and GynecologyNorthwestern University Feinberg School of Medicine and Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, PO Box 211, Chicago, Illinois 60611, USA
| | - Christopher J Payne
- Driskill Graduate ProgramDepartment of PathologyDepartments of Pediatrics and Obstetrics and GynecologyNorthwestern University Feinberg School of Medicine and Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, PO Box 211, Chicago, Illinois 60611, USA Driskill Graduate ProgramDepartment of PathologyDepartments of Pediatrics and Obstetrics and GynecologyNorthwestern University Feinberg School of Medicine and Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, PO Box 211, Chicago, Illinois 60611, USA
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Harms MJ, Lim HW, Ho Y, Shapira SN, Ishibashi J, Rajakumari S, Steger DJ, Lazar MA, Won KJ, Seale P. PRDM16 binds MED1 and controls chromatin architecture to determine a brown fat transcriptional program. Genes Dev 2015; 29:298-307. [PMID: 25644604 PMCID: PMC4318146 DOI: 10.1101/gad.252734.114] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PR (PRD1-BF1-RIZ1 homologous) domain-containing 16 (PRDM16) drives a brown fat differentiation program, but the mechanisms by which PRDM16 activates brown fat-selective genes have been unclear. Through chromatin immunoprecipitation (ChIP) followed by deep sequencing (ChIP-seq) analyses in brown adipose tissue (BAT), we reveal that PRDM16 binding is highly enriched at a broad set of brown fat-selective genes. Importantly, we found that PRDM16 physically binds to MED1, a component of the Mediator complex, and recruits it to superenhancers at brown fat-selective genes. PRDM16 deficiency in BAT reduces MED1 binding at PRDM16 target sites and causes a fundamental change in chromatin architecture at key brown fat-selective genes. Together, these data indicate that PRDM16 controls chromatin architecture and superenhancer activity in BAT.
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Affiliation(s)
- Matthew J Harms
- Institute for Diabetes, Obesity, and Metabolism, Department of Cell and Developmental Biology
| | - Hee-Woong Lim
- Institute for Diabetes, Obesity, and Metabolism, Genetics Department, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yugong Ho
- Genetics Department, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Suzanne N Shapira
- Institute for Diabetes, Obesity, and Metabolism, Department of Cell and Developmental Biology
| | - Jeff Ishibashi
- Institute for Diabetes, Obesity, and Metabolism, Department of Cell and Developmental Biology
| | - Sona Rajakumari
- Institute for Diabetes, Obesity, and Metabolism, Department of Cell and Developmental Biology
| | | | | | - Kyoung-Jae Won
- Institute for Diabetes, Obesity, and Metabolism, Genetics Department, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Patrick Seale
- Institute for Diabetes, Obesity, and Metabolism, Department of Cell and Developmental Biology,
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45
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Kim GH, Oh GS, Yoon J, Lee GG, Lee KU, Kim SW. Hepatic TRAP80 selectively regulates lipogenic activity of liver X receptor. J Clin Invest 2014; 125:183-93. [PMID: 25437875 DOI: 10.1172/jci73615] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 10/30/2014] [Indexed: 01/08/2023] Open
Abstract
Inflammation in response to excess low-density lipoproteins in the blood is an important driver of atherosclerosis development. Due to its ability to enhance ATP-binding cassette A1-dependent (ABCA1-dependent) reverse cholesterol transport (RCT), liver X receptor (LXR) is an attractive target for the treatment of atherosclerosis. However, LXR also upregulates the expression of sterol regulatory element-binding protein 1c (SREBP-1c), leading to increased hepatic triglyceride synthesis, an independent risk factor for atherosclerosis. Here, we developed a strategy to separate the favorable and unfavorable effects of LXR by exploiting the specificity of the coactivator thyroid hormone receptor-associated protein 80 (TRAP80). Using human hepatic cell lines, we determined that TRAP80 selectively promotes the transcription of SREBP-1c but not ABCA1. Adenovirus-mediated expression of shTRAP80 inhibited LXR-dependent SREBP-1c expression and RNA polymerase II recruitment to the LXR responsive element (LXRE) of SREBP-1c, but not to the LXRE of ABCA1. In murine models, liver-specific knockdown of TRAP80 ameliorated liver steatosis and hypertriglyceridemia induced by LXR activation and maintained RCT stimulation by the LXR ligand. Together, these data indicate that TRAP80 is a selective regulator of hepatic lipogenesis and is required for LXR-dependent SREBP-1c activation. Moreover, targeting the interaction between TRAP80 and LXR should facilitate the development of potential LXR agonists that effectively prevent atherosclerosis.
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46
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Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat Struct Mol Biol 2014; 21:1028-34. [PMID: 25383669 PMCID: PMC4259101 DOI: 10.1038/nsmb.2914] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/09/2014] [Indexed: 01/01/2023]
Abstract
The evolutionarily conserved Mediator complex is a critical coactivator for RNA polymerase II (Pol II)-mediated transcription. Here, we report the reconstitution of a functional 15-subunit human core Mediator complex and its characterization by functional assays and chemical cross-linking coupled to mass spectrometry (CX-MS). Whereas the reconstituted head and middle modules can stably associate, only with incorporation of MED14 into the bi-modular complex does it acquire basal and coactivator functions. This results from a dramatically enhanced ability of MED14-containing complexes to associate with Pol II. Altogether, our analyses identify MED14 as both an architectural and a functional backbone of the Mediator complex. We further establish a conditional requirement for metazoan-specific MED26 that becomes evident in the presence of heterologous nuclear factors. This general approach paves the way for systematically dissecting the multiple layers of functionalities associated with the Mediator complex.
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47
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Choi JH, Choi SS, Kim ES, Jedrychowski MP, Yang YR, Jang HJ, Suh PG, Banks AS, Gygi SP, Spiegelman BM. Thrap3 docks on phosphoserine 273 of PPARγ and controls diabetic gene programming. Genes Dev 2014; 28:2361-9. [PMID: 25316675 PMCID: PMC4215181 DOI: 10.1101/gad.249367.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphorylation of peroxisome proliferator-activated receptor γ (PPARγ) at Ser273 by cyclin-dependent kinase 5 (CDK5) in adipose tissue stimulates insulin resistance, but the underlying molecular mechanisms are unclear. We show here that Thrap3 (thyroid hormone receptor-associated protein 3) can directly interact with PPARγ when it is phosphorylated at Ser273, and this interaction controls the diabetic gene programming mediated by the phosphorylation of PPARγ. Knockdown of Thrap3 restores most of the genes dysregulated by CDK5 action on PPARγ in cultured adipocytes. Importantly, reduced expression of Thrap3 in fat tissue by antisense oligonucleotides (ASOs) regulates a specific set of genes, including the key adipokines adiponectin and adipsin, and effectively improves hyperglycemia and insulin resistance in high-fat-fed mice without affecting body weight. These data indicate that Thrap3 plays a crucial role in controlling diabetic gene programming and may provide opportunities for the development of new therapeutics for obesity and type 2 diabetes.
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Affiliation(s)
- Jang Hyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea;
| | - Sun-Sil Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea;
| | - Eun Sun Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
| | - Mark P Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yong Ryoul Yang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
| | - Hyun-Jun Jang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea;
| | - Pann-Ghill Suh
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
| | - Alexander S Banks
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Bruce M Spiegelman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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48
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Gou LT, Dai P, Liu MF. Small noncoding RNAs and male infertility. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:733-45. [PMID: 25044449 DOI: 10.1002/wrna.1252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 11/07/2022]
Abstract
Small noncoding RNAs (ncRNAs) are a novel class of gene regulators that modulate gene expression at transcriptional, post-transcriptional, and epigenetic levels, and they play crucial roles in almost all cellular processes in eukaryotes. Recent studies have indicated that several types of small noncoding RNAs, including microRNAs (miRNAs), endo-small interference RNAs (endo-siRNAs), and Piwi-interacting RNAs (piRNAs), are expressed in the male germline and are required for spermatogenesis in animals. In this review, we summarize the recent knowledge of these small noncoding RNAs in male germ cells and their biological functions and mechanisms of action in animal spermatogenesis.
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Affiliation(s)
- Lan-Tao Gou
- Center for RNA Research, State Key Laboratory of Molecular Biology-University of Chinese Academy of Sciences, Shanghai, China; Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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49
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Campbell MJ. Vitamin D and the RNA transcriptome: more than mRNA regulation. Front Physiol 2014; 5:181. [PMID: 24860511 PMCID: PMC4030167 DOI: 10.3389/fphys.2014.00181] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 04/21/2014] [Indexed: 12/23/2022] Open
Abstract
The GRCh37.p13 primary assembly of the human genome contains 20805 protein coding mRNA, and 37147 non-protein coding genes and pseudogenes that as a result of RNA processing and editing generate 196501 gene transcripts. Given the size and diversity of the human transcriptome, it is timely to revisit what is known of VDR function in the regulation and targeting of transcription. Early transcriptomic studies using microarray approaches focused on the protein coding mRNA that were regulated by the VDR, usually following treatment with ligand. These studies quickly established the approximate size, and surprising diversity of the VDR transcriptome, revealing it to be highly heterogenous and cell type and time dependent. With the discovery of microRNA, investigators also considered VDR regulation of these non-protein coding RNA. Again, cell and time dependency has emerged. Attempts to integrate mRNA and miRNA regulation patterns are beginning to reveal patterns of co-regulation and interaction that allow for greater control of mRNA expression, and the capacity to govern more complex cellular events. As the awareness of the diversity of non-coding RNA increases, it is increasingly likely it will be revealed that VDR actions are mediated through these molecules also. Key knowledge gaps remain over the VDR transcriptome. The causes for the cell and type dependent transcriptional heterogenetiy remain enigmatic. ChIP-Seq approaches have confirmed that VDR binding choices differ very significantly by cell type, but as yet the underlying causes distilling VDR binding choices are unclear. Similarly, it is clear that many of the VDR binding sites are non-canonical in nature but again the mechanisms underlying these interactions are unclear. Finally, although alternative splicing is clearly a very significant process in cellular transcriptional control, the lack of RNA-Seq data centered on VDR function are currently limiting the global assessment of the VDR transcriptome. VDR focused research that complements publically available data (e.g., ENCODE Birney et al., 2007; Birney, 2012), TCGA (Strausberg et al., 2002), GTEx (Consortium, 2013) will enable these questions to be addressed through large-scale data integration efforts.
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Affiliation(s)
- Moray J Campbell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute Buffalo, NY, USA
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50
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Yin JW, Wang G. The Mediator complex: a master coordinator of transcription and cell lineage development. Development 2014; 141:977-87. [PMID: 24550107 DOI: 10.1242/dev.098392] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mediator is a multiprotein complex that is required for gene transcription by RNA polymerase II. Multiple subunits of the complex show specificity in relaying information from signals and transcription factors to the RNA polymerase II machinery, thus enabling control of the expression of specific genes. Recent studies have also provided novel mechanistic insights into the roles of Mediator in epigenetic regulation, transcriptional elongation, termination, mRNA processing, noncoding RNA activation and super enhancer formation. Based on these specific roles in gene regulation, Mediator has emerged as a master coordinator of development and cell lineage determination. Here, we describe the most recent advances in understanding the mechanisms of Mediator function, with an emphasis on its role during development and disease.
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Affiliation(s)
- Jing-wen Yin
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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