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Yu X, He Y, Kamenecka TM, Kojetin DJ. Towards a unified molecular mechanism for liganddependent activation of NR4A-RXR heterodimers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.19.642122. [PMID: 40166180 PMCID: PMC11956975 DOI: 10.1101/2025.03.19.642122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
A subset of nuclear receptors (NRs) function as permissive heterodimers with retinoid X receptor (RXR), defined by transcriptional activation in response to binding RXR agonist ligands. Permissive NR-RXR activation operates via a classical pharmacological mechanism, where binding of an RXR agonist increases coactivator recruitment to the heterodimer. However, we previously demonstrated that transcriptional activation of permissive Nurr1-RXRα (NR4A2-NR2B1) heterodimers by an RXR ligand set, which included pharmacological RXR agonists and selective Nurr1-RXRα agonists that function as antagonists of RXRα homodimers, occurs via a non-classical mechanism: ligand-binding domain (LBD) heterodimer dissociation (Yu et al., 2023). Here, we extend mechanistic ligand profiling of the same RXR ligand set to Nur77-RXRγ (NR4A1-NR2B3), which is evolutionarily related to Nurr1-RXRα. Biochemical and NMR protein-protein interaction profiling along with cellular transcription studies indicate that the RXR ligand set, which lacks selective Nur77-RXRγ agonists, may influence Nur77-RXRγ transcriptional activation through both classical pharmacological activation and LBD heterodimer dissociation. However, upon reanalyzing our previously published data for Nurr1-RXRα, we found that the inclusion of selective Nurr1-RXRα agonists was essential for elucidating the LBD heterodimer dissociation mechanism. Our findings underscore the need for a more functionally diverse RXR ligand set to explore Nur77-RXRγ activation and unify LBD heterodimer dissociation as a potential targeting mechanism for NR4A-RXR heterodimers in neurodegenerative and inflammatory diseases.
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Affiliation(s)
- Xiaoyu Yu
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States
- Department of Integrative Structural and Computational Biology, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, United States
| | - Yuanjun He
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
| | - Theodore M. Kamenecka
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
| | - Douglas J. Kojetin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States
- Department of Integrative Structural and Computational Biology, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, United States
- Center for Applied AI in Protein Dynamics, Vanderbilt University, Nashville, Tennessee, United States
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Sinha RA, Bruinstroop E, Yen PM. Actions of thyroid hormones and thyromimetics on the liver. Nat Rev Gastroenterol Hepatol 2025; 22:9-22. [PMID: 39420154 PMCID: PMC7616774 DOI: 10.1038/s41575-024-00991-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2024] [Indexed: 10/19/2024]
Abstract
Thyroid hormones (triiodothyronine and thyroxine) are pivotal for metabolic balance in the liver and entire body. Dysregulation of the hypothalamus-pituitary-thyroid axis can contribute to hepatic metabolic disturbances, affecting lipid metabolism, glucose regulation and protein synthesis. In addition, reductions in circulating and intrahepatic thyroid hormone concentrations increase the risk of metabolic dysfunction-associated steatotic liver disease by inducing lipotoxicity, inflammation and fibrosis. Amelioration of hepatic metabolic disease by thyroid hormones in preclinical and clinical studies has spurred the development of thyromimetics that target THRB (the predominant thyroid hormone receptor isoform in the liver) and/or the liver itself to provide more selective activation of hepatic thyroid hormone-regulated metabolic pathways while reducing thyrotoxic side effects in tissues that predominantly express THRA such as the heart and bone. Resmetirom, a liver and THRB-selective thyromimetic, recently became the first FDA-approved drug for metabolic dysfunction-associated steatohepatitis (MASH). Thus, a better understanding of the metabolic actions of thyroid hormones and thyromimetics in the liver is timely and clinically relevant. Here, we describe the roles of thyroid hormones in normal liver function and pathogenesis of MASH, as well as some potential clinical issues that might arise when treating patients with MASH with thyroid hormone supplementation or thyromimetics.
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Affiliation(s)
- Rohit A Sinha
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Eveline Bruinstroop
- Department of Endocrinology and Metabolism, Amsterdam UMC, Location University of Amsterdam, Amsterdam, Netherlands
| | - Paul M Yen
- Laboratory of Hormonal Regulation, Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore.
- Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA.
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Zhu S, Chen Z, Liu C, Duong J, Tran T, Liang Z, Fang X, Ouyang K. The essential role of MED27 in stabilizing the mediator complex for cardiac development and function. Life Sci 2024; 356:123020. [PMID: 39209248 DOI: 10.1016/j.lfs.2024.123020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/15/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
AIM Transcriptional regulation of gene expression plays a crucial role in orchestrating complex morphogenetic and molecular events during heart development and function. Mediator complex is an essential multi-subunit protein complex that governs gene expression in eukaryotic cells. Although Mediator subunits (MEDs) work integrally in the complex, individual MED component displays specialized functions. MED27, categorized as an Upper Tail subunit, possesses an as-yet-uncharacterized function. In this study, we aimed to investigate the physiological role of MED27 in cardiomyocytes. MATERIALS AND METHODS we generated a Med27 floxed mouse line, which was further used to generate constitutive (cKO) and inducible (icKO) cardiomyocyte-specific Med27 knockout mouse models. Morphological, histological analysis and cardiac physiological studies were performed in Med27 cKO and icKO mutants. Transcriptional profiles were determined by RNA sequencing (RNAseq) analysis. KEY FUNDINGS Ablation of MED27 in developing mouse cardiomyocytes results in embryonic lethality, while its deletion in adult cardiomyocytes leads to heart failure and mortality. Similar to the ablation of another Upper Tail subunit, MED30 in cardiomyocytes, deletion of MED27 leads to decreased protein levels of most MEDs in cardiomyocytes. Interestingly, overexpression of MED30 fails to restore the protein levels of Mediator subunits in MED27-deficient cardiomyocytes, demonstrating that the role of MED27 in maintaining the integrity and stability of the Mediator complex is independent of MED30. SIGNIFICANCE Our results revealed an essential role of MED27 in cardiac development and function by maintaining the stability of the Mediator core.
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Affiliation(s)
- Siting Zhu
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China; Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Ze'e Chen
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China; Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Canzhao Liu
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Department of Cardiovascular Medicine, Translational Medicine Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Janelle Duong
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Tiana Tran
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Zhengyu Liang
- Department of Systems Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xi Fang
- Department of Medicine, University of California San Diego, La Jolla, California, USA.
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China.
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4
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Su D, Zhu S, Xu K, Hou Z, Hao F, Xu F, Lin Y, Zhu Y, Liu D, Duan Q, Zhang X, Yuan Y, Xu J, Tao J. Phosphoproteomic analysis reveals changes in A-Raf-related protein phosphorylation in response to Toxoplasma gondii infection in porcine macrophages. Parasit Vectors 2024; 17:191. [PMID: 38643189 PMCID: PMC11031963 DOI: 10.1186/s13071-024-06273-x] [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: 02/09/2024] [Accepted: 04/07/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Toxoplasma gondii is an obligate intracellular protozoan parasite that causes severe threats to humans and livestock. Macrophages are the cell type preferentially infected by T. gondii in vivo. Protein phosphorylation is an important posttranslational modification involved in diverse cellular functions. A rapidly accelerated fibrosarcoma kinase (A-Raf) is a member of the Raf family of serine/threonine protein kinases that is necessary for MAPK activation. Our previous research found that knockout of A-Raf could reduce T. gondii-induced apoptosis in porcine alveolar macrophages (3D4/21 cells). However, limited information is available on protein phosphorylation variations and the role of A-Raf in macrophages infected with T. gondii. METHODS We used immobilized metal affinity chromatography (IMAC) in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS) to profile changes in phosphorylation in T. gondii-infected 3D4/21 and 3D4/21-ΔAraf cells. RESULTS A total of 1647 differentially expressed phosphorylated proteins (DEPPs) with 3876 differentially phosphorylated sites (DPSs) were identified in T. gondii-infected 3D4/21 cells (p3T group) when compared with uninfected 3D4/21 cells (pho3 group), and 959 DEPPs with 1540 DPSs were identified in the p3T group compared with infected 3D4/21-ΔAraf cells (p3KT group). Venn analysis revealed 552 DPSs corresponding to 406 DEPPs with the same phosphorylated sites when comparing p3T/pho3 versus p3T/p3KT, which were identified as DPSs and DEPPs that were directly or indirectly related to A-Raf. CONCLUSIONS Our results revealed distinct responses of macrophages to T. gondii infection and the potential roles of A-Raf in fighting infection via phosphorylation of crucial proteins.
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Affiliation(s)
- Dingzeyang Su
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Shifan Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Kangzhi Xu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Zhaofeng Hou
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China.
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China.
| | - Fuxing Hao
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, 225300, People's Republic of China
| | - Fan Xu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Yifan Lin
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Yuyang Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Dandan Liu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Qiangde Duan
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Xinjun Zhang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Yuguo Yuan
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jinjun Xu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jianping Tao
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, People's Republic of China.
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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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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Nakadai T, Shimada M, Ito K, Cevher MA, Chu CS, Kumegawa K, Maruyama R, Malik S, Roeder RG. Two target gene activation pathways for orphan ERR nuclear receptors. Cell Res 2023; 33:165-183. [PMID: 36646760 PMCID: PMC9892517 DOI: 10.1038/s41422-022-00774-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/02/2022] [Indexed: 01/18/2023] Open
Abstract
Estrogen-related receptors (ERRα/β/γ) are orphan nuclear receptors that function in energy-demanding physiological processes, as well as in development and stem cell maintenance, but mechanisms underlying target gene activation by ERRs are largely unknown. Here, reconstituted biochemical assays that manifest ERR-dependent transcription have revealed two complementary mechanisms. On DNA templates, ERRs activate transcription with just the normal complement of general initiation factors through an interaction of the ERR DNA-binding domain with the p52 subunit of initiation factor TFIIH. On chromatin templates, activation by ERRs is dependent on AF2 domain interactions with the cell-specific coactivator PGC-1α, which in turn recruits the ubiquitous p300 and MED1/Mediator coactivators. This role of PGC-1α may also be fulfilled by other AF2-interacting coactivators like NCOA3, which is shown to recruit Mediator selectively to ERRβ and ERRγ. Importantly, combined genetic and RNA-seq analyses establish that both the TFIIH and the AF2 interaction-dependent pathways are essential for ERRβ/γ-selective gene expression and pluripotency maintenance in embryonic stem cells in which NCOA3 is a critical coactivator.
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Affiliation(s)
- Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Japan
| | - Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Murat Alper Cevher
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Kohei Kumegawa
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.
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Lyons H, Veettil RT, Pradhan P, Fornero C, De La Cruz N, Ito K, Eppert M, Roeder RG, Sabari BR. Functional partitioning of transcriptional regulators by patterned charge blocks. Cell 2023; 186:327-345.e28. [PMID: 36603581 PMCID: PMC9910284 DOI: 10.1016/j.cell.2022.12.013] [Citation(s) in RCA: 141] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/15/2022] [Accepted: 12/07/2022] [Indexed: 01/05/2023]
Abstract
Components of transcriptional machinery are selectively partitioned into specific condensates, often mediated by protein disorder, yet we know little about how this specificity is achieved. Here, we show that condensates composed of the intrinsically disordered region (IDR) of MED1 selectively partition RNA polymerase II together with its positive allosteric regulators while excluding negative regulators. This selective compartmentalization is sufficient to activate transcription and is required for gene activation during a cell-state transition. The IDRs of partitioned proteins are necessary and sufficient for selective compartmentalization and require alternating blocks of charged amino acids. Disrupting this charge pattern prevents partitioning, whereas adding the pattern to proteins promotes partitioning with functional consequences for gene activation. IDRs with similar patterned charge blocks show similar partitioning and function. These findings demonstrate that disorder-mediated interactions can selectively compartmentalize specific functionally related proteins from a complex mixture of biomolecules, leading to regulation of a biochemical pathway.
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Affiliation(s)
- Heankel Lyons
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reshma T Veettil
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Pradhan
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christy Fornero
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nancy De La Cruz
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, the Rockefeller University, New York, NY 10065, USA
| | - Mikayla Eppert
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, the Rockefeller University, New York, NY 10065, USA
| | - Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Cdk8 Kinase Module: A Mediator of Life and Death Decisions in Times of Stress. Microorganisms 2021; 9:microorganisms9102152. [PMID: 34683473 PMCID: PMC8540245 DOI: 10.3390/microorganisms9102152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/18/2023] Open
Abstract
The Cdk8 kinase module (CKM) of the multi-subunit mediator complex plays an essential role in cell fate decisions in response to different environmental cues. In the budding yeast S. cerevisiae, the CKM consists of four conserved subunits (cyclin C and its cognate cyclin-dependent kinase Cdk8, Med13, and Med12) and predominantly negatively regulates a subset of stress responsive genes (SRG’s). Derepression of these SRG’s is accomplished by disassociating the CKM from the mediator, thus allowing RNA polymerase II-directed transcription. In response to cell death stimuli, cyclin C translocates to the mitochondria where it induces mitochondrial hyper-fission and promotes regulated cell death (RCD). The nuclear release of cyclin C requires Med13 destruction by the ubiquitin-proteasome system (UPS). In contrast, to protect the cell from RCD following SRG induction induced by nutrient deprivation, cyclin C is rapidly destroyed by the UPS before it reaches the cytoplasm. This enables a survival response by two mechanisms: increased ATP production by retaining reticular mitochondrial morphology and relieving CKM-mediated repression on autophagy genes. Intriguingly, nitrogen starvation also stimulates Med13 destruction but through a different mechanism. Rather than destruction via the UPS, Med13 proteolysis occurs in the vacuole (yeast lysosome) via a newly identified Snx4-assisted autophagy pathway. Taken together, these findings reveal that the CKM regulates cell fate decisions by both transcriptional and non-transcriptional mechanisms, placing it at a convergence point between cell death and cell survival pathways.
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Mediator subunit MED1 is required for E2A-PBX1-mediated oncogenic transcription and leukemic cell growth. Proc Natl Acad Sci U S A 2021; 118:1922864118. [PMID: 33542097 DOI: 10.1073/pnas.1922864118] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The chimeric transcription factor E2A-PBX1, containing the N-terminal activation domains of E2A fused to the C-terminal DNA-binding domain of PBX1, results in 5% of pediatric acute lymphoblastic leukemias (ALL). We recently have reported a mechanism for RUNX1-dependent recruitment of E2A-PBX1 to chromatin in pre-B leukemic cells; but the subsequent E2A-PBX1 functions through various coactivators and the general transcriptional machinery remain unclear. The Mediator complex plays a critical role in cell-specific gene activation by serving as a key coactivator for gene-specific transcription factors that facilitates their function through the RNA polymerase II transcriptional machinery, but whether Mediator contributes to aberrant expression of E2A-PBX1 target genes remains largely unexplored. Here we show that Mediator interacts directly with E2A-PBX1 through an interaction of the MED1 subunit with an E2A activation domain. Results of MED1 depletion by CRISPR/Cas9 further indicate that MED1 is specifically required for E2A-PBX1-dependent gene activation and leukemic cell growth. Integrated transcriptome and cistrome analyses identify pre-B cell receptor and cell cycle regulatory genes as direct cotargets of MED1 and E2A-PBX1. Notably, complementary biochemical analyses also demonstrate that recruitment of E2A-PBX1 to a target DNA template involves a direct interaction with DNA-bound RUNX1 that can be further stabilized by EBF1. These findings suggest that E2A-PBX1 interactions with RUNX1 and MED1/Mediator are of functional importance for both gene-specific transcriptional activation and maintenance of E2A-PBX1-driven leukemia. The MED1 dependency for E2A-PBX1-mediated gene activation and leukemogenesis may provide a potential therapeutic opportunity by targeting MED1 in E2A-PBX1+ pre-B leukemia.
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10
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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: 0.5] [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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11
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Chu CS, Hellmuth JC, Singh R, Ying HY, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG. Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage. Mol Cell 2020; 80:845-861.e10. [PMID: 33232656 DOI: 10.1016/j.molcel.2020.10.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/09/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022]
Abstract
Locus control region (LCR) functions define cellular identity and have critical roles in diseases such as cancer, although the hierarchy of structural components and associated factors that drive functionality are incompletely understood. Here we show that OCA-B, a B cell-specific coactivator essential for germinal center (GC) formation, forms a ternary complex with the lymphoid-enriched OCT2 and GC-specific MEF2B transcription factors and that this complex occupies and activates an LCR that regulates the BCL6 proto-oncogene and is uniquely required by normal and malignant GC B cells. Mechanistically, through OCA-B-MED1 interactions, this complex is required for Mediator association with the BCL6 promoter. Densely tiled CRISPRi screening indicates that only LCR segments heavily bound by this ternary complex are essential for its function. Our results demonstrate how an intimately linked complex of lineage- and stage-specific factors converges on specific and highly essential enhancer elements to drive the function of a cell-type-defining LCR.
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Affiliation(s)
- Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Johannes C Hellmuth
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rajat Singh
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hsia-Yuan Ying
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lucy Skrabanek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA
| | - Matthew R Teater
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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12
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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: 2.2] [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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13
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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: 0.8] [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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14
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Drosophila Mediator Subunit Med1 Is Required for GATA-Dependent Developmental Processes: Divergent Binding Interfaces for Conserved Coactivator Functions. Mol Cell Biol 2019; 39:MCB.00477-18. [PMID: 30670567 DOI: 10.1128/mcb.00477-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/13/2019] [Indexed: 01/26/2023] Open
Abstract
DNA-bound transcription factors (TFs) governing developmental gene regulation have been proposed to recruit polymerase II machinery at gene promoters through specific interactions with dedicated subunits of the evolutionarily conserved Mediator (MED) complex. However, whether such MED subunit-specific functions and partnerships have been conserved during evolution has been poorly investigated. To address this issue, we generated the first Drosophila melanogaster loss-of-function mutants for Med1, known as a specific cofactor for GATA TFs and hormone nuclear receptors in mammals. We show that Med1 is required for cell proliferation and hematopoietic differentiation depending on the GATA TF Serpent (Srp). Med1 physically binds Srp in cultured cells and in vitro through its conserved GATA zinc finger DNA-binding domain and the divergent Med1 C terminus. Interestingly, GATA-Srp interaction occurs through the longest Med1 isoform, suggesting a functional diversity of MED complex populations. Furthermore, we show that Med1 acts as a coactivator for the GATA factor Pannier during thoracic development. In conclusion, the Med1 requirement for GATA-dependent regulatory processes is a common feature in insects and mammals, although binding interfaces have diverged. Further work in Drosophila should bring valuable insights to fully understand GATA-MED functional partnerships, which probably involve other MED subunits depending on the cellular context.
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15
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Parrini M, Meissl K, Ola MJ, Lederer T, Puga A, Wienerroither S, Kovarik P, Decker T, Müller M, Strobl B. The C-Terminal Transactivation Domain of STAT1 Has a Gene-Specific Role in Transactivation and Cofactor Recruitment. Front Immunol 2018; 9:2879. [PMID: 30574148 PMCID: PMC6291510 DOI: 10.3389/fimmu.2018.02879] [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: 09/28/2018] [Accepted: 11/23/2018] [Indexed: 01/12/2023] Open
Abstract
STAT1 has a key role in the regulation of innate and adaptive immunity by inducing transcriptional changes in response to cytokines, such as all types of interferons (IFN). STAT1 exist as two splice isoforms, which differ in regard to the C-terminal transactivation domain (TAD). STAT1β lacks the C-terminal TAD and has been previously reported to be a weaker transcriptional activator than STAT1α, although this was strongly dependent on the target gene. The mechanism of this context-dependent effects remained unclear. By using macrophages from mice that only express STAT1β, we investigated the role of the C-terminal TAD during the distinct steps of transcriptional activation of selected target genes in response to IFNγ. We show that the STAT1 C-terminal TAD is absolutely required for the recruitment of RNA polymerase II (Pol II) and for the establishment of active histone marks at the class II major histocompatibility complex transactivator (CIIta) promoter IV, whereas it is dispensable for histone acetylation at the guanylate binding protein 2 (Gbp2) promoter but required for an efficient recruitment of Pol II, which correlated with a strongly reduced, but not absent, transcriptional activity. IFNγ-induced expression of Irf7, which is mediated by STAT1 in complex with STAT2 and IRF9, did not rely on the presence of the C-terminal TAD of STAT1. Moreover, we show for the first time that the STAT1 C-terminal TAD is required for an efficient recruitment of components of the core Mediator complex to the IFN regulatory factor (Irf) 1 and Irf8 promoters, which both harbor an open chromatin state under basal conditions. Our study identified novel functions of the STAT1 C-terminal TAD in transcriptional activation and provides mechanistic explanations for the gene-specific transcriptional activity of STAT1β.
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Affiliation(s)
- Matthias Parrini
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Katrin Meissl
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mojoyinola Joanna Ola
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Therese Lederer
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ana Puga
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Pavel Kovarik
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Thomas Decker
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Mathias Müller
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.,University Center Biomodels Austria, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Birgit Strobl
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
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16
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Nagpal N, Sharma S, Maji S, Durante G, Ferracin M, Thakur JK, Kulshreshtha R. Essential role of MED1 in the transcriptional regulation of ER-dependent oncogenic miRNAs in breast cancer. Sci Rep 2018; 8:11805. [PMID: 30087366 PMCID: PMC6081450 DOI: 10.1038/s41598-018-29546-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 07/12/2018] [Indexed: 01/24/2023] Open
Abstract
Mediator complex has been extensively shown to regulate the levels of several protein-coding genes; however, its role in the regulation of miRNAs in humans remains unstudied so far. Here we show that MED1, a Mediator subunit in the Middle module of Mediator complex, is overexpressed in breast cancer and is a negative prognostic factor. The levels of several miRNAs (miR-100-5p, -191-5p, -193b-3p, -205-5p, -326, -422a and -425-5p) were found to be regulated by MED1. MED1 induces miR-191/425 cluster in an estrogen receptor-alpha (ER-α) dependent manner. Occupancy of MED1 on estrogen response elements (EREs) upstream of miR-191/425 cluster is estrogen and ER-α-dependent and ER-α-induced expression of these miRNAs is MED1-dependent. MED1 mediates induction of cell proliferation and migration and the genes associated with it (JUN, FOS, EGFR, VEGF, MMP1, and ERBB4) in breast cancer, which is abrogated when used together with miR-191-inhibition. Additionally, we show that MED1 also regulates the levels of direct miR-191 target genes such as SATB1, CDK6 and BDNF. Overall, the results show that MED1/ER-α/miR-191 axis promotes breast cancer cell proliferation and migration and may serve as a novel target for therapy.
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Affiliation(s)
- Neha Nagpal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.,Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shivani Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Sourobh Maji
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Giorgio Durante
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126, Bologna, Italy
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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17
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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: 1.7] [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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18
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Jusu S, Presley JF, Williams C, Das SK, Jean-Claude B, Kremer R. Examination of VDR/RXR/DRIP205 Interaction, Intranuclear Localization, and DNA Binding in Ras-Transformed Keratinocytes and Its Implication for Designing Optimal Vitamin D Therapy in Cancer. Endocrinology 2018; 159:1303-1327. [PMID: 29300860 DOI: 10.1210/en.2017-03098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/19/2017] [Indexed: 11/19/2022]
Abstract
Retinoid X receptor (RXR) occupies a central position within the nuclear receptor superfamily, serving as an obligatory partner to numerous other nuclear receptors, including vitamin D receptor (VDR). In the current study, we examined whether phosphorylation of RXRα at serine 260 affects VDR/RXR and VDR interacting protein (DRIP) 205 coactivator recruitment, interactions, and binding of the VDR/human RXRα (hRXRα)/DRIP205 complex to chromatin. Serine 260 is a critical amino acid on the hRXRα that is located in close spatial proximity to regions of coactivator and corepressor interactions. Using fluorescence resonance energy transfer and immunofluorescence studies, we showed that the physical interaction between hRXRα and DRIP205 coactivator was impaired in human keratinocytes with the ras oncogene (HPK1Aras) or transfected with the wild-type hRXRα. Furthermore, the nuclear colocalization of VDR/DRIP205, hRXRα/DRIP205, and VDR/hRXRα/DRIP205 complex binding to chromatin is impaired in the HPK1Aras cells when compared with the normal human keratinocytes (HPK1A cells). However, transfection with the nonphosphorylatable hRXRα (S260A) mutant or treatment with the mitogen-activated protein kinase (MAPK) inhibitor UO126 rescued their nuclear localization, interaction, and binding of the complex to chromatin in the HPK1Aras cells. In summary, we have demonstrated, using highly specific intracellular tagging methods in live and fixed cells, important alterations of the vitamin D signaling system in cancer cells in which the ras-raf-MAPK system is activated, suggesting that specific inhibition of this commonly activated pathway could be targeted therapeutically to enhance vitamin D efficacy.
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Affiliation(s)
- Sylvester Jusu
- Department of Medicine and Calcium Research Laboratory, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada
- Metabolic Diseases and Complications Program, Research institute-McGill University Health Centre, Montreal, Quebec, Canada
| | - John F Presley
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | | | - Sanjoy Kumar Das
- Drug Discovery Core, Research Institute-McGill University Health Centre, Montreal, Quebec H3A 3J1, Canada
| | - Bertrand Jean-Claude
- Metabolic Diseases and Complications Program, Research institute-McGill University Health Centre, Montreal, Quebec, Canada
- Drug Discovery Core, Research Institute-McGill University Health Centre, Montreal, Quebec H3A 3J1, Canada
| | - Richard Kremer
- Department of Medicine and Calcium Research Laboratory, Royal Victoria Hospital, McGill University Health Centre, Montreal, Quebec, Canada
- Metabolic Diseases and Complications Program, Research institute-McGill University Health Centre, Montreal, Quebec, Canada
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19
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Chereji RV, Bharatula V, Elfving N, Blomberg J, Larsson M, Morozov AV, Broach JR, Björklund S. Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly. Nucleic Acids Res 2017; 45:8806-8821. [PMID: 28575439 PMCID: PMC5587782 DOI: 10.1093/nar/gkx491] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 05/23/2017] [Indexed: 01/24/2023] Open
Abstract
Mediator is a multi-unit molecular complex that plays a key role in transferring signals from transcriptional regulators to RNA polymerase II in eukaryotes. We have combined biochemical purification of the Saccharomyces cerevisiae Mediator from chromatin with chromatin immunoprecipitation in order to reveal Mediator occupancy on DNA genome-wide, and to identify proteins interacting specifically with Mediator on the chromatin template. Tandem mass spectrometry of proteins in immunoprecipitates of mediator complexes revealed specific interactions between Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin. These factors are primarily involved in chromatin remodeling, actin assembly, mRNA 3′-end processing, gene looping and mRNA decay, but they have also been shown to enter the nucleus and participate in Pol II transcription. Moreover, we have found that Mediator, in addition to binding Pol II promoters, occupies chromosomal interacting domain (CID) boundaries and that Mediator in chromatin associates with proteins that have been shown to interact with CID boundaries, such as Sth1, Ssu72 and histone H4. This suggests that Mediator plays a significant role in higher-order genome organization.
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Affiliation(s)
- Razvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vasudha Bharatula
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Nils Elfving
- Department of Medical Biochemistry and Biophysics Umeå University, 901 87 Umeå, Sweden
| | - Jeanette Blomberg
- Department of Medical Biochemistry and Biophysics Umeå University, 901 87 Umeå, Sweden
| | - Miriam Larsson
- Department of Medical Biochemistry and Biophysics Umeå University, 901 87 Umeå, Sweden
| | - Alexandre V Morozov
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA.,Center for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics Umeå University, 901 87 Umeå, Sweden
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20
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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: 0.6] [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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21
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Eychenne T, Werner M, Soutourina J. Toward understanding of the mechanisms of Mediator function in vivo: Focus on the preinitiation complex assembly. Transcription 2017; 8:328-342. [PMID: 28841352 DOI: 10.1080/21541264.2017.1329000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mediator is a multisubunit complex conserved in eukaryotes that plays an essential coregulator role in RNA polymerase (Pol) II transcription. Despite intensive studies of the Mediator complex, the molecular mechanisms of its function in vivo remain to be fully defined. In this review, we will discuss the different aspects of Mediator function starting with its interactions with specific transcription factors, its recruitment to chromatin and how, as a coregulator, it contributes to the assembly of transcription machinery components within the preinitiation complex (PIC) in vivo and beyond the PIC formation.
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Affiliation(s)
- Thomas Eychenne
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France.,b Institut Pasteur, (Epi)genomics of Animal Development Unit , Development and Stem Cell Biology Department, CNRS UMR3778 , Paris , France
| | - Michel Werner
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
| | - Julie Soutourina
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
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22
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Taatjes DJ. Transcription Factor-Mediator Interfaces: Multiple and Multi-Valent. J Mol Biol 2017; 429:2996-2998. [PMID: 28716626 DOI: 10.1016/j.jmb.2017.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA.
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23
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Kostrouchová M, Kostrouch D, Chughtai AA, Kaššák F, Novotný JP, Kostrouchová V, Benda A, Krause MW, Saudek V, Kostrouchová M, Kostrouch Z. The nematode homologue of Mediator complex subunit 28, F28F8.5, is a critical regulator of C. elegans development. PeerJ 2017; 5:e3390. [PMID: 28603670 PMCID: PMC5464003 DOI: 10.7717/peerj.3390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/08/2017] [Indexed: 11/20/2022] Open
Abstract
The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, the Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, modulate the influence of Mediator on RNA Polymerase II activity. One Mediator subunit, MED28, is known to interact with cytoplasmic structural proteins, providing a potential direct link between cytoplasmic dynamics and the control of gene transcription. Although identified in many animals and plants, MED28 is not present in yeast; no bona fide MED28 has been described previously in Caenorhabditis elegans. Here, we identify bioinformatically F28F8.5, an uncharacterized predicted protein, as the nematode homologue of MED28. As in other Metazoa, F28F8.5 has dual nuclear and cytoplasmic localization and plays critical roles in the regulation of development. F28F8.5 is a vital gene and its null mutants have severely malformed gonads and do not reproduce. F28F8.5 interacts on the protein level with the Mediator subunits MDT-6 and MDT-30. Our results indicate that F28F8.5 is an orthologue of MED28 and suggest that the potential to link cytoplasmic and nuclear events is conserved between MED28 vertebrate and nematode orthologues.
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Affiliation(s)
- Markéta Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Kostrouch
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ahmed A Chughtai
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Filip Kaššák
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan P Novotný
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Aleš Benda
- Imaging Methods Core Facility, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael W Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vladimír Saudek
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Marta Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Zdeněk Kostrouch
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
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24
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Kim HJ, Yun J. Checkpoint-dependent phosphorylation of Med1/TRAP220 in response to DNA damage. Acta Biochim Biophys Sin (Shanghai) 2017; 49:496-502. [PMID: 28430840 DOI: 10.1093/abbs/gmx036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Indexed: 12/11/2022] Open
Abstract
Mediator complex subunit 1 (Med1)/Thyroid hormone receptor-associated protein 220 (TRAP220), an essential component of thyroid hormone receptor-associated proteins (TRAP)/mediator, plays important roles in hormone responses and tumorigenesis. However, the role of Med1 in the DNA damage response has not been studied. In this study, we found that DNA damage, resulted from γ-irradiation, ultraviolet (UV)-irradiation, or hydroxyurea, induced phosphorylation of Med1 in vivo. Phosphorylation of Med1 was abrogated by either caffeine or wortmannin treatment, suggesting that Med1 is phosphorylated through the DNA damage checkpoint pathway. A checkpoint kinase 1 (Chk1)/checkpoint kinase 2 (Chk2) consensus phosphorylation motif was identified at Serine 671 of Med1 and Ser671 motif was primarily phosphorylated by Chk2 in vitro. Moreover, the in vivo phosphorylation of Med1 was abrogated by a Chk2 inhibitor, and physical interaction between Chk2 and Med1 was observed, confirming that Chk2 is responsible for Med1 phosphorylation upon DNA damage. These results suggest that Med1 is a novel target for the DNA damage checkpoint pathway and may participate in the DNA damage response. Consistent with this notion, knockdown of Med1 expression caused a significant increase in cellular sensitivity to UV irradiation. Moreover, microarray analysis revealed that the UV-induced activation of the transcription of important regulators of cell cycle control and DNA repair, including p21, Gadd45, Rad50, DnaJ, and RecQL, was impaired upon Med1 knockdown. Taken together, our data suggest that Med1 is a novel target for Chk2-mediated phosphorylation and may play a role in cellular DNA damage responses by mediating proper induction of gene transcription upon DNA damage.
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Affiliation(s)
- Hyun-Ju Kim
- Peripheral Neuropathy Research Center, College of Medicine, Dong-A University, Busan 49201, Korea
- Department of Biochemistry, College of Medicine, Dong-A University, Busan 49201, Korea
| | - Jeanho Yun
- Peripheral Neuropathy Research Center, College of Medicine, Dong-A University, Busan 49201, Korea
- Department of Biochemistry, College of Medicine, Dong-A University, Busan 49201, Korea
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25
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Malik S, Molina H, Xue Z. PIC Activation through Functional Interplay between Mediator and TFIIH. J Mol Biol 2016; 429:48-63. [PMID: 27916598 DOI: 10.1016/j.jmb.2016.11.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/26/2016] [Accepted: 11/27/2016] [Indexed: 10/20/2022]
Abstract
The multiprotein Mediator coactivator complex functions in large part by controlling the formation and function of the promoter-bound preinitiation complex (PIC), which consists of RNA polymerase II and general transcription factors. However, precisely how Mediator impacts the PIC, especially post-recruitment, has remained unclear. Here, we have studied Mediator effects on basal transcription in an in vitro transcription system reconstituted from purified components. Our results reveal a close functional interplay between Mediator and TFIIH in the early stages of PIC development. We find that under conditions when TFIIH is not normally required for transcription, Mediator actually represses transcription. TFIIH, whose recruitment to the PIC is known to be facilitated by the Mediator, then acts to relieve Mediator-induced repression to generate an active form of the PIC. Gel mobility shift analyses of PICs and characterization of TFIIH preparations carrying mutant XPB translocase subunit further indicate that this relief of repression is achieved through expending energy via ATP hydrolysis, suggesting that it is coupled to TFIIH's established promoter melting activity. Our interpretation of these results is that Mediator functions as an assembly factor that facilitates PIC maturation through its various stages. Whereas the overall effect of the Mediator is to stimulate basal transcription, its initial engagement with the PIC generates a transcriptionally inert PIC intermediate, which necessitates energy expenditure to complete the process.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Zhu Xue
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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26
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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: 3.0] [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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27
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Yang Y, Li L, Qu LJ. Plant Mediator complex and its critical functions in transcription regulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:106-18. [PMID: 26172375 DOI: 10.1111/jipb.12377] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 07/07/2015] [Indexed: 05/08/2023]
Abstract
The Mediator complex is an important component of the eukaryotic transcriptional machinery. As an essential link between transcription factors and RNA polymerase II, the Mediator complex transduces diverse signals to genes involved in different pathways. The plant Mediator complex was recently purified and comprises conserved and specific subunits. It functions in concert with transcription factors to modulate various responses. In this review, we summarize the recent advances in understanding the plant Mediator complex and its diverse roles in plant growth, development, defense, non-coding RNA production, response to abiotic stresses, flowering, genomic stability and metabolic homeostasis. In addition, the transcription factors interacting with the Mediator complex are also highlighted.
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Affiliation(s)
- Yan Yang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Ling Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
- The National Plant Gene Research Center (Beijing), Beijing 100101, China
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28
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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: 4.5] [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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29
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Liu C, Feng T, Zhu N, Liu P, Han X, Chen M, Wang X, Li N, Li Y, Xu Y, Si S. Identification of a novel selective agonist of PPARγ with no promotion of adipogenesis and less inhibition of osteoblastogenesis. Sci Rep 2015; 5:9530. [PMID: 25827822 PMCID: PMC4381330 DOI: 10.1038/srep09530] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/05/2015] [Indexed: 12/31/2022] Open
Abstract
Nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) plays an important role in the regulation of glucose homeostasis and lipid metabolism. However, current PPARγ-targeting drugs such as thiazolidinediones (TZDs) are associated with undesirable side effects. We identified a small molecular compound, F12016, as a selective PPARγ agonist by virtual screening, which showed moderate PPARγ agonistic activity and binding ability for PPARγ. F12016 did not activate other PPAR subtypes at 30 μM and selectively modulated PPARγ target gene expression. In diabetic KKAy mice, F12016 had insulin-sensitizing and glucose-lowering properties, and suppressed weight gain. In vitro, F12016 effectively increased glucose uptake and blocked cyclin-dependent kinase 5-mediated phosphorylation of PPARγ at Ser273, but slightly triggered adipogenesis and less inhibited osteoblastogenesis than rosiglitazone. Moreover, compared with the full agonist rosiglitazone, F12016 had a distinct group of coregulators and a different predicted binding mode for the PPARγ ligand-binding domain. A site mutation assay confirmed the key epitopes, especially Tyr473 in AF-2. In summary, our study shows that F12016 is a non-TZD, novel selective PPARγ agonist without the classical lipogenic side effects, which may provide a new structural strategy for designing PPARγ ligands with advantages over TZDs.
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Affiliation(s)
- Chang Liu
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Tingting Feng
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Ningyu Zhu
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Peng Liu
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Xiaowan Han
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Minghua Chen
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Xiao Wang
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Ni Li
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Yongzhen Li
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Yanni Xu
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
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30
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Iida S, Chen W, Nakadai T, Ohkuma Y, Roeder RG. PRDM16 enhances nuclear receptor-dependent transcription of the brown fat-specific Ucp1 gene through interactions with Mediator subunit MED1. Genes Dev 2015; 29:308-21. [PMID: 25644605 PMCID: PMC4318147 DOI: 10.1101/gad.252809.114] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
PRDM16 induces expression of brown fat-specific genes in brown and beige adipocytes. Here, Iida et al. show that PRDM16, through its zinc finger domains, directly interacts with the MED1 subunit of the Mediator complex and is recruited to the enhancer of the brown fat-specific Ucp1 gene through this interaction. This enhances thyroid hormone receptor-driven transcription in a biochemically defined system in a Mediator-dependent manner, thus providing a direct link to the general transcription machinery. PR domain-containing 16 (PRDM16) induces expression of brown fat-specific genes in brown and beige adipocytes, although the underlying transcription-related mechanisms remain largely unknown. Here, in vitro studies show that PRDM16, through its zinc finger domains, directly interacts with the MED1 subunit of the Mediator complex, is recruited to the enhancer of the brown fat-specific uncoupling protein 1 (Ucp1) gene through this interaction, and enhances thyroid hormone receptor (TR)-driven transcription in a biochemically defined system in a Mediator-dependent manner, thus providing a direct link to the general transcription machinery. Complementary cell-based studies show that upon forskolin treatment, PRDM16 induces Ucp1 expression in undifferentiated murine embryonic fibroblasts, that this induction depends on MED1 and TR, and, consistent with a direct effect, that PRDM16 is recruited to the Ucp1 enhancer. Related studies have defined MED1 and PRDM16 interaction domains important for Ucp1 versus Ppargc1a induction by PRDM16. These results reveal novel mechanisms for PRDM16 function through the Mediator complex.
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Affiliation(s)
- Satoshi Iida
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Wei Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Yoshiaki Ohkuma
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Science, University of Toyama, Toyama 930-0194, Japan
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA;
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31
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Allen BL, Taatjes DJ. The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol 2015; 16:155-66. [PMID: 25693131 DOI: 10.1038/nrm3951] [Citation(s) in RCA: 657] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The RNA polymerase II (Pol II) enzyme transcribes all protein-coding and most non-coding RNA genes and is globally regulated by Mediator - a large, conformationally flexible protein complex with a variable subunit composition (for example, a four-subunit cyclin-dependent kinase 8 module can reversibly associate with it). These biochemical characteristics are fundamentally important for Mediator's ability to control various processes that are important for transcription, including the organization of chromatin architecture and the regulation of Pol II pre-initiation, initiation, re-initiation, pausing and elongation. Although Mediator exists in all eukaryotes, a variety of Mediator functions seem to be specific to metazoans, which is indicative of more diverse regulatory requirements.
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Affiliation(s)
- Benjamin L Allen
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
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32
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Manavathi B, Samanthapudi VSK, Gajulapalli VNR. Estrogen receptor coregulators and pioneer factors: the orchestrators of mammary gland cell fate and development. Front Cell Dev Biol 2014; 2:34. [PMID: 25364741 PMCID: PMC4207046 DOI: 10.3389/fcell.2014.00034] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/21/2014] [Indexed: 12/14/2022] Open
Abstract
The steroid hormone, 17β-estradiol (E2), plays critical role in various cellular processes such as cell proliferation, differentiation, migration and apoptosis, and is essential for reproduction and mammary gland development. E2 actions are mediated by two classical nuclear hormone receptors, estrogen receptor α and β (ERs). The activity of ERs depends on the coordinated activity of ligand binding, post-translational modifications (PTMs), and importantly the interaction with their partner proteins called “coregulators.” Because coregulators are proved to be crucial for ER transcriptional activity, and majority of breast cancers are ERα positive, an increased interest in the field has led to the identification of a large number of coregulators. In the last decade, gene knockout studies using mouse models provided impetus to our further understanding of the role of these coregulators in mammary gland development. Several coregulators appear to be critical for terminal end bud (TEB) formation, ductal branching and alveologenesis during mammary gland development. The emerging studies support that, coregulators along with the other ER partner proteins called “pioneer factors” together contribute significantly to E2 signaling and mammary cell fate. This review discusses emerging themes in coregulator and pioneer factor mediated action on ER functions, in particular their role in mammary gland cell fate and development.
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Affiliation(s)
- Bramanandam Manavathi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad Hyderabad, India
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Abstract
Crystal structures represent the static picture in the life of a molecule giving a sneak preview what it might be in reality. Hence, it is very hard to extrapolate from these photos toward dynamic processes such as transcriptional regulation. Mechanistically VDR may be considered as molecular machine able to perform ligand-, DNA- and protein recognition, and interaction in a multi-task manner. Taking this into account the functional net effect will be the combination of all these processes. The long awaited answer to explain the differences in physiological effects for various ligands was one of the biggest disappointment that crystal structures provided since no substantial distinction could be made for the conformation of the active VDR-ligand complexes. This may have come from the limitation on the complexity of the available ligand-VDR structures. The recent studies with full length VDR-RXRα showed somewhat more comprehensive perspective for the 3D organization and possible function of the VDR-RXRα-cofactor complex. In addition to in vitro approaches, also computational tools had been introduced with the aim to get understanding on the mechanic and dynamic properties of the VDR complexes with some success. Using these methods and based on measurable descriptors such as pocket size and positions of side chains it is possible to note subtle differences between the structures. The meaning of these differences has not been fully understood yet but the possibility of a “butterfly effect” may have more extreme consequences in terms of VDR signaling. In this review, the three functional aspects (ligand-, DNA- and protein recognition, and binding) will be discussed with respect to available data as well as possible implication and questions that may be important to address in the future.
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Affiliation(s)
- Ferdinand Molnár
- Faculty of Health Sciences, School of Pharmacy, Institute of Biopharmacy, University of Eastern Finland Kuopio, Finland
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Yu J, Xiao Y, Liu J, Ji Y, Liu H, Xu J, Jin X, Liu L, Guan MX, Jiang P. Loss of MED1 triggers mitochondrial biogenesis in C2C12 cells. Mitochondrion 2013; 14:18-25. [PMID: 24368311 DOI: 10.1016/j.mito.2013.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 10/31/2013] [Accepted: 12/12/2013] [Indexed: 01/09/2023]
Abstract
Under stress conditions transcription factors, including their coactivators, play major roles in mitochondrial biogenesis and oxidative phosphorylation. MED1 (Mediator complex subunit 1) functions as a coactivator of several transcription factors and is implicated in adipogenesis of the lipid and glucose metabolism. This suggests that MED1 may play a role in mitochondrial function. In this study, we found that both the mtDNA content and mitochondrial mass were markedly increased and cell proliferation markedly suppressed in MED1-deficient cells. Upon MED1 loss, Nrf1 and its downstream target genes involved in mitochondrial biogenesis (Tfam, Plormt, Tfb1m), were up-regulated as were those genes in the OXPHOS pathway. Moreover, the knockdown of MED1 resulted in significant changes in the profile of mitochondrial respiration, accompanied by a prominent decrease in the generation of ATP. Collectively, these observations strongly suggest that MED1 has an important affect on mitochondrial function. This further elucidates the role of MED1, particularly its role in the energy metabolism.
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Affiliation(s)
- Jialing Yu
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yun Xiao
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junxia Liu
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yanchun Ji
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Liu
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Xu
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaofen Jin
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Li Liu
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min-Xin Guan
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pingping Jiang
- Department of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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35
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Abstract
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
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Affiliation(s)
- Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA
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Ansari SA, Morse RH. Mechanisms of Mediator complex action in transcriptional activation. Cell Mol Life Sci 2013; 70:2743-56. [PMID: 23361037 PMCID: PMC11113466 DOI: 10.1007/s00018-013-1265-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 12/14/2022]
Abstract
Mediator is a large multisubunit complex that plays a central role in the regulation of RNA Pol II transcribed genes. Conserved in overall structure and function among eukaryotes, Mediator comprises 25-30 protein subunits that reside in four distinct modules, termed head, middle, tail, and CDK8/kinase. Different subunits of Mediator contact other transcriptional regulators including activators, co-activators, general transcription factors, subunits of RNA Pol II, and specifically modified histones, leading to the regulated expression of target genes. This review is focused on the interactions of specific Mediator subunits with diverse transcription regulators and how those interactions contribute to Mediator function in transcriptional activation.
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Affiliation(s)
- Suraiya A. Ansari
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
| | - Randall H. Morse
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
- Department of Biomedical Science, University at Albany School of Public Health, Albany, NY USA
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37
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Sela D, Conkright JJ, Chen L, Gilmore J, Washburn MP, Florens L, Conaway RC, Conaway JW. Role for human mediator subunit MED25 in recruitment of mediator to promoters by endoplasmic reticulum stress-responsive transcription factor ATF6α. J Biol Chem 2013; 288:26179-26187. [PMID: 23864652 DOI: 10.1074/jbc.m113.496968] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription factor ATF6α functions as a master regulator of endoplasmic reticulum (ER) stress response genes. In response to ER stress, ATF6α translocates from its site of latency in the ER membrane to the nucleus, where it activates RNA polymerase II transcription of ER stress response genes upon binding sequence-specifically to ER stress response enhancer elements (ERSEs) in their promoter-regulatory regions. In a recent study, we demonstrated that ATF6α activates transcription of ER stress response genes by a mechanism involving recruitment to ERSEs of the multisubunit Mediator and several histone acetyltransferase (HAT) complexes, including Spt-Ada-Gcn5 (SAGA) and Ada-Two-A-containing (ATAC) (Sela, D., Chen, L., Martin-Brown, S., Washburn, M.P., Florens, L., Conaway, J.W., and Conaway, R.C. (2012) J. Biol. Chem. 287, 23035-23045). In this study, we extend our investigation of the mechanism by which ATF6α supports recruitment of Mediator to ER stress response genes. We present findings arguing that Mediator subunit MED25 plays a critical role in this process and identify a MED25 domain that serves as a docking site on Mediator for the ATF6α transcription activation domain.
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Affiliation(s)
- Dotan Sela
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Juliana J Conkright
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Lu Chen
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, and
| | - Joshua Gilmore
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Michael P Washburn
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,; Departments of Pathology & Laboratory Medicine, Kansas University Medical Center, Kansas City, Kansas 66160
| | - Laurence Florens
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Ronald C Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, and
| | - Joan Weliky Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, and.
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Grueter CE. Mediator complex dependent regulation of cardiac development and disease. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:151-7. [PMID: 23727265 PMCID: PMC4357813 DOI: 10.1016/j.gpb.2013.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/09/2013] [Accepted: 05/18/2013] [Indexed: 11/22/2022]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality. The risk factors for CVD include environmental and genetic components. Human mutations in genes involved in most aspects of cardiovascular function have been identified, many of which are involved in transcriptional regulation. The Mediator complex serves as a pivotal transcriptional regulator that functions to integrate diverse cellular signals by multiple mechanisms including recruiting RNA polymerase II, chromatin modifying proteins and non-coding RNAs to promoters in a context dependent manner. This review discusses components of the Mediator complex and the contribution of the Mediator complex to normal and pathological cardiac development and function. Enhanced understanding of the role of this core transcriptional regulatory complex in the heart will help us gain further insights into CVD.
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Affiliation(s)
- Chad E Grueter
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
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Jin F, Irshad S, Yu W, Belakavadi M, Chekmareva M, Ittmann MM, Abate-Shen C, Fondell JD. ERK and AKT signaling drive MED1 overexpression in prostate cancer in association with elevated proliferation and tumorigenicity. Mol Cancer Res 2013; 11:736-47. [PMID: 23538858 DOI: 10.1158/1541-7786.mcr-12-0618] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
MED1 is a key coactivator of the androgen receptor (AR) and other signal-activated transcription factors. Whereas MED1 is overexpressed in prostate cancer cell lines and is thought to coactivate distinct target genes involved in cell-cycle progression and castration-resistant growth, the underlying mechanisms by which MED1 becomes overexpressed and its oncogenic role in clinical prostate cancer have remained unclear. Here, we report that MED1 is overexpressed in the epithelium of clinically localized human prostate cancer patients, which correlated with elevated cellular proliferation. In a Nkx3.1:Pten mutant mouse model of prostate cancer that recapitulates the human disease, MED1 protein levels were markedly elevated in the epithelium of both invasive and castration-resistant adenocarcinoma prostate tissues. Mechanistic evidence showed that hyperactivated ERK and/or AKT signaling pathways promoted MED1 overexpression in prostate cancer cells. Notably, ectopic MED1 overexpression in prostate cancer xenografts significantly promoted tumor growth in nude mice. Furthermore, MED1 expression in prostate cancer cells promoted the expression of a number of novel genes involved in inflammation, cell proliferation, and survival. Together, these findings suggest that elevated MED1 is a critical molecular event associated with prostate oncogenesis.
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Affiliation(s)
- Feng Jin
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, UMDNJ, 683 Hoes Lane, Piscataway, New Jersey 08854, USA
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Control of mitochondrial metabolism and systemic energy homeostasis by microRNAs 378 and 378*. Proc Natl Acad Sci U S A 2012; 109:15330-5. [PMID: 22949648 DOI: 10.1073/pnas.1207605109] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Obesity and metabolic syndrome are associated with mitochondrial dysfunction and deranged regulation of metabolic genes. Peroxisome proliferator-activated receptor γ coactivator 1β (PGC-1β) is a transcriptional coactivator that regulates metabolism and mitochondrial biogenesis through stimulation of nuclear hormone receptors and other transcription factors. We report that the PGC-1β gene encodes two microRNAs (miRNAs), miR-378 and miR-378*, which counterbalance the metabolic actions of PGC-1β. Mice genetically lacking miR-378 and miR-378* are resistant to high-fat diet-induced obesity and exhibit enhanced mitochondrial fatty acid metabolism and elevated oxidative capacity of insulin-target tissues. Among the many targets of these miRNAs, carnitine O-acetyltransferase, a mitochondrial enzyme involved in fatty acid metabolism, and MED13, a component of the Mediator complex that controls nuclear hormone receptor activity, are repressed by miR-378 and miR-378*, respectively, and are elevated in the livers of miR-378/378* KO mice. Consistent with these targets as contributors to the metabolic actions of miR-378 and miR-378*, previous studies have implicated carnitine O-acetyltransferase and MED13 in metabolic syndrome and obesity. Our findings identify miR-378 and miR-378* as integral components of a regulatory circuit that functions under conditions of metabolic stress to control systemic energy homeostasis and the overall oxidative capacity of insulin target tissues. Thus, these miRNAs provide potential targets for pharmacologic intervention in obesity and metabolic syndrome.
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Kim HJ, Roh MS, Son CH, Kim AJ, Jee HJ, Song N, Kim M, Seo SY, Yoo YH, Yun J. Loss of Med1/TRAP220 promotes the invasion and metastasis of human non-small-cell lung cancer cells by modulating the expression of metastasis-related genes. Cancer Lett 2012; 321:195-202. [DOI: 10.1016/j.canlet.2012.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 11/29/2022]
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Grueter CE, van Rooij E, Johnson BA, DeLeon SM, Sutherland LB, Qi X, Gautron L, Elmquist JK, Bassel-Duby R, Olson EN. A cardiac microRNA governs systemic energy homeostasis by regulation of MED13. Cell 2012; 149:671-83. [PMID: 22541436 DOI: 10.1016/j.cell.2012.03.029] [Citation(s) in RCA: 285] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/06/2012] [Accepted: 03/19/2012] [Indexed: 12/31/2022]
Abstract
Obesity, type 2 diabetes, and heart failure are associated with aberrant cardiac metabolism. We show that the heart regulates systemic energy homeostasis via MED13, a subunit of the Mediator complex, which controls transcription by thyroid hormone and other nuclear hormone receptors. MED13, in turn, is negatively regulated by a heart-specific microRNA, miR-208a. Cardiac-specific overexpression of MED13 or pharmacologic inhibition of miR-208a in mice confers resistance to high-fat diet-induced obesity and improves systemic insulin sensitivity and glucose tolerance. Conversely, genetic deletion of MED13 specifically in cardiomyocytes enhances obesity in response to high-fat diet and exacerbates metabolic syndrome. The metabolic actions of MED13 result from increased energy expenditure and regulation of numerous genes involved in energy balance in the heart. These findings reveal a role of the heart in systemic metabolic control and point to MED13 and miR-208a as potential therapeutic targets for metabolic disorders.
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Affiliation(s)
- Chad E Grueter
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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43
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The Mediator complex in thyroid hormone receptor action. Biochim Biophys Acta Gen Subj 2012; 1830:3867-75. [PMID: 22402254 DOI: 10.1016/j.bbagen.2012.02.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/16/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND Mediator is an evolutionarily conserved multisubunit complex that plays an essential regulatory role in eukaryotic transcription of protein-encoding genes. The human complex was first isolated as a transcriptional coactivator bound to the thyroid hormone receptor (TR) and has since been shown to play a key coregulatory role for a broad range of nuclear hormone receptors (NRs) as well as other signal-activated transcription factors. SCOPE OF REVIEW We provide a general overview of Mediator structure and function, summarize the mechanisms by which Mediator is targeted to NRs, and outline recent evidence revealing Mediator as a regulatory axis for other distinct coregulatory factors, chromatin modifying enzymes and cellular signal transduction pathways. MAJOR CONCLUSIONS Besides serving as a functional interface with the RNA polymerase II basal transcription machinery, Mediator plays a more versatile role in regulating transcription including the ability to: a) facilitate gene-specific chromatin looping events; b) coordinate chromatin modification events with preinitiation complex assembly; and c) regulate critical steps that occur during transcriptional elongation. The variably associated MED1 subunit continues to emerge as a pivotal player in Mediator function, not only as the primary interaction site for NRs, but also as a crucial interaction hub for other coregulatory factors, and as an important regulatory target for signal-activated kinases. GENERAL SIGNIFICANCE Mediator plays an integral coregulatory role at NR target genes by functionally interacting with the basal transcription apparatus and by coordinating the action of chromatin modifying enzymes and transcription elongation factors. This article is part of a Special Issue entitled Thyroid hormone signalling.
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Nagalingam A, Tighiouart M, Ryden L, Joseph L, Landberg G, Saxena NK, Sharma D. Med1 plays a critical role in the development of tamoxifen resistance. Carcinogenesis 2012; 33:918-30. [PMID: 22345290 DOI: 10.1093/carcin/bgs105] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the molecular pathways that contribute to the development of tamoxifen resistance is a critical research priority as acquired tamoxifen resistance is the principal cause of poor prognosis and death of patients with originally good prognosis hormone-responsive breast tumors. In this report, we provide evidence that Med1, an important subunit of mediator coactivator complex, is spontaneously upregulated during acquired tamoxifen-resistance development potentiating agonist activities of tamoxifen. Phosphorylated Med1 and estrogen receptor (ER) are abundant in tamoxifen-resistant breast cancer cells due to persistent activation of extracellular signal-regulated kinases. Mechanistically, phosphorylated Med1 exhibits nuclear accumulation, increased interaction with ER and higher tamoxifen-induced recruitment to ER-responsive promoters, which is abrogated by inhibition of Med1 phosphorylation. Stable knockdown of Med1 in tamoxifen-resistant cells not only reverses tamoxifen resistance in vitro but also in vivo. Finally, higher expression levels of Med1 in the tumor significantly correlated with tamoxifen resistance in ER-positive breast cancer patients on adjuvant tamoxifen monotherapy. In silico analysis of breast cancer, utilizing published profiling studies showed that Med1 is overexpressed in aggressive subsets. These findings provide what we believe is the first evidence for a critical role for Med1 in tamoxifen resistance and identify this coactivator protein as an essential effector of the tamoxifen-induced breast cancer growth.
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Affiliation(s)
- Arumugam Nagalingam
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, 1650 Orleans Street, CRB 1, Room 145, Baltimore, MD 21231, USA
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Xu W, Ji JY. Dysregulation of CDK8 and Cyclin C in tumorigenesis. J Genet Genomics 2011; 38:439-52. [PMID: 22035865 PMCID: PMC9792140 DOI: 10.1016/j.jgg.2011.09.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 01/23/2023]
Abstract
Appropriately controlled gene expression is fundamental for normal growth and survival of all living organisms. In eukaryotes, the transcription of protein-coding mRNAs is dependent on RNA polymerase II (Pol II). The multi-subunit transcription cofactor Mediator complex is proposed to regulate most, if not all, of the Pol II-dependent transcription. Here we focus our discussion on two subunits of the Mediator complex, cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC), because they are either mutated or amplified in a variety of human cancers. CDK8 functions as an oncoprotein in melanoma and colorectal cancers, thus there are considerable interests in developing drugs specifically targeting the CDK8 kinase activity. However, to evaluate the feasibility of targeting CDK8 for cancer therapy and to understand how their dysregulation contributes to tumorigenesis, it is essential to elucidate the in vivo function and regulation of CDK8-CycC, which are still poorly understood in multi-cellular organisms. We summarize the evidence linking their dysregulation to various cancers and present our bioinformatics and computational analyses on the structure and evolution of CDK8. We also discuss the implications of these observations in tumorigenesis. Because most of the Mediator subunits, including CDK8 and CycC, are highly conserved during eukaryotic evolution, we expect that investigations using model organisms such as Drosophila will provide important insights into the function and regulation of CDK8 and CycC in different cellular and developmental contexts.
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Affiliation(s)
- Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
- Corresponding author: Tel: +1 979 845 6389, fax: +1 979 847 9481. (J.-Y. Ji)
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46
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Abstract
How is specificity transmitted over long distances at the molecular level? REs (regulatory elements) are often far from transcription start sites. In the present review we discuss possible mechanisms to explain how information from specific REs is conveyed to the basal transcription machinery through TFs (transcription factors) and the Mediator complex. We hypothesize that this occurs through allosteric pathways: binding of a TF to a RE results in changes in the AD (activation domain) of the TF, which binds to Mediator and alters the distribution of the Mediator conformations, thereby affecting transcription initiation/activation. We argue that Mediator is formed by highly disordered proteins with large densely packed interfaces that make efficient long-range signal propagation possible. We suggest two possible general mechanisms for Mediator action: one in which Mediator influences PIC (pre-initiation complex) assembly and transcription initiation, and another in which Mediator exerts its effect on the already assembled but stalled transcription complex. We summarize (i) relevant information from the literature about Mediator composition, organization and structure; (ii) Mediator interaction partners and their effect on Mediator conformation, function and correlation to the RNA Pol II (polymerase II) CTD (C-terminal domain) phosphorylation; and (iii) propose that different allosteric signal propagation pathways in Mediator relate to PIC assembly and polymerase activation of the stalled transcription complex. The emerging picture provides for the first time a mechanistic view of allosteric signalling from the RE sequence to transcription activation, and an insight into how gene specificity and signal transmission can take place in transcription initiation.
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Affiliation(s)
- Chung-Jung Tsai
- Basic Science Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702, U.S.A
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702, U.S.A
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Unraveling framework of the ancestral Mediator complex in human diseases. Biochimie 2011; 94:579-87. [PMID: 21983542 DOI: 10.1016/j.biochi.2011.09.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 09/15/2011] [Indexed: 01/13/2023]
Abstract
Mediator (MED) is a fundamental component of the RNA polymerase II-mediated transcription machinery. This multiprotein complex plays a pivotal role in the regulation of eukaryotic mRNA synthesis. The yeast Mediator complex consists of 26 different subunits. Recent studies indicate additional pathogenic roles for Mediator, for example during transcription elongation and non-coding RNA production. Mediator subunits have been emerging also to have pathophysiological roles suggesting MED-dependent therapeutic targets involving in several diseases, such as cancer, cardiovascular disease (CVD), metabolic and neurological disorders.
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48
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Chen W, Roeder RG. Mediator-dependent nuclear receptor function. Semin Cell Dev Biol 2011; 22:749-58. [PMID: 21854863 DOI: 10.1016/j.semcdb.2011.07.026] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 12/24/2022]
Abstract
As gene-specific transcription factors, nuclear receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss our current understanding of (i) pathways involved in Mediator recruitment and function through nuclear receptor target gene enhancers and promoters, (ii) conditional requirements for the strong nuclear receptor-Mediator interactions mediated by NR AF2 domains and the MED1 LXXLL motifs, (iii) Mediator functions, through different nuclear receptor-interacting subunits, in different metabolic pathways, (iv) emerging functions of Mediator as a corepressor in addition to its major role as a coactivator and (v) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. As a nuclear receptor coregulator with increasingly diverse functions, Mediator may thus modulate nuclear receptor signaling through several different mechanisms.
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Affiliation(s)
- Wei Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
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49
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Interactions between subunits of the Mediator complex with gene-specific transcription factors. Semin Cell Dev Biol 2011; 22:759-68. [PMID: 21839847 DOI: 10.1016/j.semcdb.2011.07.022] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 07/26/2011] [Accepted: 07/28/2011] [Indexed: 11/24/2022]
Abstract
The Mediator complex forms the bridge between gene-specific transcription factors and the RNA polymerase II (RNAP II) machinery. Mediator is a large polypetide complex consisting of about thirty polypeptides that are mostly conserved from yeast to human. Mediator coordinates RNAP II recruitment, phosphorylation of the C-terminal domain of RNAP II, enhancer-loop formation and post-initiation events. The focus of the review is to summarize the current knowledge of transcription factor/Mediator interactions in higher eukaryotes and illuminate the physiological and gene-selective roles of Mediator.
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50
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Ma B, Tsai CJ, Haliloğlu T, Nussinov R. Dynamic allostery: linkers are not merely flexible. Structure 2011; 19:907-17. [PMID: 21742258 PMCID: PMC6361528 DOI: 10.1016/j.str.2011.06.002] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/05/2011] [Accepted: 06/07/2011] [Indexed: 12/19/2022]
Abstract
Most proteins consist of multiple domains. How do linkers efficiently transfer information between sites that are on different domains to activate the protein? Mere flexibility only implies that the conformations would be sampled. For fast timescales between triggering events and cellular response, which often involves large conformational change, flexibility on its own may not constitute a good solution. We posit that successive conformational states along major allosteric propagation pathways are pre-encoded in linker sequences where each state is encoded by the previous one. The barriers between these states that are hierarchically populated are lower, achieving faster timescales even for large conformational changes. We further propose that evolution has optimized the linker sequences and lengths for efficiency, which explains why mutations in linkers may affect protein function and review the literature in this light.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
| | - Türkan Haliloğlu
- Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek-Istanbul 34342, Turkey
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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