1
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Freytes SN, Gobbini ML, Cerdán PD. The Plant Mediator Complex in the Initiation of Transcription by RNA Polymerase II. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:211-237. [PMID: 38277699 DOI: 10.1146/annurev-arplant-070623-114005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Thirty years have passed since the discovery of the Mediator complex in yeast. We are witnessing breakthroughs and advances that have led to high-resolution structural models of yeast and mammalian Mediators in the preinitiation complex, showing how it is assembled and how it positions the RNA polymerase II and its C-terminal domain (CTD) to facilitate the CTD phosphorylation that initiates transcription. This information may be also used to guide future plant research on the mechanisms of Mediator transcriptional control. Here, we review what we know about the subunit composition and structure of plant Mediators, the roles of the individual subunits and the genetic analyses that pioneered Mediator research, and how transcription factors recruit Mediators to regulatory regions adjoining promoters. What emerges from the research is a Mediator that regulates transcription activity and recruits hormonal signaling modules and histone-modifying activities to set up an off or on transcriptional state that recruits general transcription factors for preinitiation complex assembly.
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Affiliation(s)
| | | | - Pablo D Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina; , ,
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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2
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Liu L, Li C, Wu Z, Li Y, Yu H, Li T, Wang Y, Zhao W, Chen L. LCMR1 Promotes Large-Cell Lung Cancer Proliferation and Metastasis by Downregulating HLA-Encoding Genes. Cancers (Basel) 2023; 15:5445. [PMID: 38001705 PMCID: PMC10670470 DOI: 10.3390/cancers15225445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Lung cancer is notorious for its high global morbidity and mortality. Here, we examined whether the LCMR1 gene, which we previously cloned from a human large-cell lung carcinoma cell line, contributes to the proliferation and metastasis of large-cell lung carcinoma. To this end, we performed pan-cancer and non-small cell lung cancer (NSCLC) cell line-based LCMR1 expression profiling. Results revealed that LCMR1 was expressed at high levels in most solid tumors, including NSCLC. LCMR1 expression was the highest in the 95D large cell lung cancer cell line. Functional studies using lentivirus-based knockdown revealed that LCMR1 was critical for the proliferation, migration, and invasion of cultured large cell lung cancer cells. Moreover, blocking this gene significantly reduced tumor growth in a 95D cell xenograft mouse model. A multiple sequence-based assay revealed a mechanism by which LCMR1 diminished the RNA Pol II occupancy at the promoter of human leukocyte antigen (HLA)-encoding genes to prevent their transcription. The HLA genes play vital roles in cancer-specific antigen presentation and anticancer immunity. A correlation assay using TCGA database identified a negative relationship between the expression levels of LCMR1 and HLA coding genes. Taken together, our findings demonstrate that LCMR1 is required for large cell lung cancer cell growth and invasion and suggest its potential as a valid target in clinical treatment.
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Affiliation(s)
- Lu Liu
- Medical School of Chinese PLA, Beijing 100853, China; (L.L.); (H.Y.); (T.L.)
- Department of Nutrition, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Chunsun Li
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China; (C.L.); (Z.W.); (Y.L.); (Y.W.)
| | - Zhen Wu
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China; (C.L.); (Z.W.); (Y.L.); (Y.W.)
| | - Yanqin Li
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China; (C.L.); (Z.W.); (Y.L.); (Y.W.)
| | - Hang Yu
- Medical School of Chinese PLA, Beijing 100853, China; (L.L.); (H.Y.); (T.L.)
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China; (C.L.); (Z.W.); (Y.L.); (Y.W.)
| | - Tao Li
- Medical School of Chinese PLA, Beijing 100853, China; (L.L.); (H.Y.); (T.L.)
- Department of Oncology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Yueming Wang
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China; (C.L.); (Z.W.); (Y.L.); (Y.W.)
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Wei Zhao
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China; (C.L.); (Z.W.); (Y.L.); (Y.W.)
| | - Liangan Chen
- Medical School of Chinese PLA, Beijing 100853, China; (L.L.); (H.Y.); (T.L.)
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China; (C.L.); (Z.W.); (Y.L.); (Y.W.)
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3
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Jullien D, Guillou E, Bernat-Fabre S, Payet A, Bourbon HMG, Boube M. Inducible degradation of the Drosophila Mediator subunit Med19 reveals its role in regulating developmental but not constitutively-expressed genes. PLoS One 2022; 17:e0275613. [PMID: 36445897 PMCID: PMC9707739 DOI: 10.1371/journal.pone.0275613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
The multi-subunit Mediator complex plays a critical role in gene expression by bridging enhancer-bound transcription factors and the RNA polymerase II machinery. Although experimental case studies suggest differential roles of Mediator subunits, a comprehensive view of the specific set of genes regulated by individual subunits in a developing tissue is still missing. Here we address this fundamental question by focusing on the Med19 subunit and using the Drosophila wing imaginal disc as a developmental model. By coupling auxin-inducible degradation of endogenous Med19 in vivo with RNA-seq, we got access to the early consequences of Med19 elimination on gene expression. Differential gene expression analysis reveals that Med19 is not globally required for mRNA transcription but specifically regulates positively or negatively less than a quarter of the expressed genes. By crossing our transcriptomic data with those of Drosophila gene expression profile database, we found that Med19-dependent genes are highly enriched with spatially-regulated genes while the expression of most constitutively expressed genes is not affected upon Med19 loss. Whereas globally downregulation does not exceed upregulation, we identified a functional class of genes encoding spatially-regulated transcription factors, and more generally developmental regulators, responding unidirectionally to Med19 loss with an expression collapse. Moreover, we show in vivo that the Notch-responsive wingless and the E(spl)-C genes require Med19 for their expression. Combined with experimental evidences suggesting that Med19 could function as a direct transcriptional effector of Notch signaling, our data support a model in which Med19 plays a critical role in the transcriptional activation of developmental genes in response to cell signaling pathways.
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Affiliation(s)
- Denis Jullien
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
- * E-mail: (MB); (DJ)
| | - Emmanuelle Guillou
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Sandra Bernat-Fabre
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Adeline Payet
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Henri-Marc G. Bourbon
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Muriel Boube
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
- RESTORE Research Center, Université de Toulouse, INSERM 1301, CNRS 5070, EFS, ENVT, Toulouse, France
- * E-mail: (MB); (DJ)
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4
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Stellato M, Santini D, Cursano MC, Foderaro S, Tonini G, Procopio G. Bone metastases from urothelial carcinoma. The dark side of the moon. J Bone Oncol 2021; 31:100405. [PMID: 34934613 DOI: 10.1016/j.jbo.2021.100405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/01/2021] [Accepted: 11/24/2021] [Indexed: 10/19/2022] Open
Abstract
Bone metastases are common in genitourinary cancers, but they are underreported and not well researched. Synchronous bone metastases occur in 1.39-5.5% of bladder cancer patients, while 30-40% of cases are metachronous. Bone morphogenetic proteins (BMPs) play a key role in regulating proliferation, migration and invasion of tumor cells in bone microenvironment of bone metastases from metastatic urothelial carcinoma (mUC). Bone metastases represent a poor prognostic factor due to high morbidity and mortality correlated to skeletal-related events (SREs). The incidence rate of SREs in bladder, renal pelvis, and ureteral cancer varies from 39 to 68%. Radiotherapy is the most frequent treatment for SREs. The early use of bone targeted therapies (BTT), zoledronic acid and denosumab, improves SREs incidence and morbidity and it seems to improve overall survival (OS). To date, several new agents (immunotherapy and targeted drugs) demonstrated efficacy in mUC. However, subgroup analysis for bone metastases is often not available, due to difficulties in analysing bone samples, non-RECIST lesions and delay in systemic treatment due to SREs that limit the enrolment of bone mUC patients in clinical trials. Larger solid tumor studies that included UC patients are the main source of data for the management of mUC patients with bone metastases. For these patients, multidisciplinary approach should be preferred, involving orthopaedics, radiotherapists and rehabilitation to improve outcome and quality of life. New prospective trials should characterize clinical and molecular features of patients with bone metastases and the impact of new drugs on this poor prognostic metastatic site.
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Affiliation(s)
- Marco Stellato
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Rome, Italy.,Meet-URO: Italian Network For Research In Urologic-Oncology, Italy
| | - Daniele Santini
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Rome, Italy.,Meet-URO: Italian Network For Research In Urologic-Oncology, Italy
| | - Maria Concetta Cursano
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Rome, Italy.,Meet-URO: Italian Network For Research In Urologic-Oncology, Italy
| | - Simone Foderaro
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Rome, Italy.,Meet-URO: Italian Network For Research In Urologic-Oncology, Italy
| | - Giuseppe Tonini
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Rome, Italy.,Meet-URO: Italian Network For Research In Urologic-Oncology, Italy
| | - Giuseppe Procopio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Meet-URO: Italian Network For Research In Urologic-Oncology, Italy
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5
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Zhang Y, Qin P, Tian L, Yan J, Zhou Y. The role of mediator complex subunit 19 in human diseases. Exp Biol Med (Maywood) 2021; 246:1681-1687. [PMID: 34038190 PMCID: PMC8719036 DOI: 10.1177/15353702211011701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Mediator is an evolutionarily conserved multi-protein complex that mediates the interaction between different proteins as a basic linker in the transcription mechanism of eukaryotes. It interacts with RNA polymerase II and participates in the process of gene expression. Mediator complex subunit 19 or regulation by oxygen 3, or lung cancer metastasis-related protein 1 is located at the head of the mediator complex; it is a multi-protein co-activator that induces the transcription of RNA polymerase II by DNA transcription factors. It is a tumor-related gene that plays an important role in transcriptional regulation, cell proliferation, and apoptosis and is closely related to the occurrence and development of the cancers of the lung, bladder, skin, etc. Here, we used the structure of mediator complex subunit 19 to review its role in tumor progression, fat metabolism, drug therapy, as well as the novel coronavirus, which has attracted much attention at present, suggesting that mediator complex subunit 19 has broad application in the occurrence and development of clinical diseases. As a tumor-related gene, the role and mechanism of mediator complex subunit 19 in the regulation of tumor growth could be of great significance for the diagnosis, prognosis, and treatment of mediator complex subunit 19 -related tumors.
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Affiliation(s)
- Yuting Zhang
- Department of Microbiology, Guilin Medical University, Guilin 541004, China.,Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541004, China
| | - Peifang Qin
- Department of Microbiology, Guilin Medical University, Guilin 541004, China.,Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541004, China
| | - Linlin Tian
- Department of Microbiology, Guilin Medical University, Guilin 541004, China.,Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541004, China
| | - Jianguo Yan
- Department of Physiology, Guilin Medical University, Guilin 541004, China
| | - Yali Zhou
- Department of Microbiology, Guilin Medical University, Guilin 541004, China.,Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541004, China
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6
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Dean JM, He A, Tan M, Wang J, Lu D, Razani B, Lodhi IJ. MED19 Regulates Adipogenesis and Maintenance of White Adipose Tissue Mass by Mediating PPARγ-Dependent Gene Expression. Cell Rep 2020; 33:108228. [PMID: 33027649 PMCID: PMC7561447 DOI: 10.1016/j.celrep.2020.108228] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 08/11/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
The Mediator complex relays regulatory signals from gene-specific transcription factors to the basal transcriptional machinery. However, the role of individual Mediator subunits in different tissues remains unclear. Here, we demonstrate that MED19 is essential for adipogenesis and maintenance of white adipose tissue (WAT) by mediating peroxisome proliferator-activated receptor gamma (PPARγ) transcriptional activity. MED19 knockdown blocks white adipogenesis, but not brown adipogenesis or C2C12 myoblast differentiation. Adipose-specific MED19 knockout (KO) in mice results in a striking loss of WAT, whitening of brown fat, hepatic steatosis, and insulin resistance. Inducible adipose-specific MED19 KO in adult animals also results in lipodystrophy, demonstrating its requirement for WAT maintenance. Global gene expression analysis reveals induction of genes involved in apoptosis and inflammation and impaired expression of adipose-specific genes, resulting from decreased PPARγ residency on adipocyte gene promoters and reduced association of PPARγ with RNA polymerase II. These results identify MED19 as a crucial facilitator of PPARγ-mediated gene expression in adipose tissue.
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Affiliation(s)
- John M Dean
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anyuan He
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Min Tan
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jun Wang
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dongliang Lu
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Babak Razani
- Cardiology Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Veterans Affairs St. Louis Healthcare System, John Cochran Division, St. Louis, MO 63106, USA
| | - Irfan J Lodhi
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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7
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Immarigeon C, Bernat-Fabre S, Guillou E, Verger A, Prince E, Benmedjahed MA, Payet A, Couralet M, Monte D, Villeret V, Bourbon HM, Boube M. Mediator complex subunit Med19 binds directly GATA transcription factors and is required with Med1 for GATA-driven gene regulation in vivo. J Biol Chem 2020; 295:13617-13629. [PMID: 32737196 DOI: 10.1074/jbc.ra120.013728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/21/2020] [Indexed: 02/02/2023] Open
Abstract
The evolutionarily conserved multiprotein Mediator complex (MED) serves as an interface between DNA-bound transcription factors (TFs) and the RNA Pol II machinery. It has been proposed that each TF interacts with a dedicated MED subunit to induce specific transcriptional responses. But are these binary partnerships sufficient to mediate TF functions? We have previously established that the Med1 Mediator subunit serves as a cofactor of GATA TFs in Drosophila, as shown in mammals. Here, we observe mutant phenotype similarities between another subunit, Med19, and the Drosophila GATA TF Pannier (Pnr), suggesting functional interaction. We further show that Med19 physically interacts with the Drosophila GATA TFs, Pnr and Serpent (Srp), in vivo and in vitro through their conserved C-zinc finger domains. Moreover, Med19 loss of function experiments in vivo or in cellulo indicate that it is required for Pnr- and Srp-dependent gene expression, suggesting general GATA cofactor functions. Interestingly, Med19 but not Med1 is critical for the regulation of all tested GATA target genes, implying shared or differential use of MED subunits by GATAs depending on the target gene. Lastly, we show a direct interaction between Med19 and Med1 by GST pulldown experiments indicating privileged contacts between these two subunits of the MED middle module. Together, these findings identify Med19/Med1 as a composite GATA TF interface and suggest that binary MED subunit-TF partnerships are probably oversimplified models. We propose several mechanisms to account for the transcriptional regulation of GATA-targeted genes.
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Affiliation(s)
- Clément Immarigeon
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Sandra Bernat-Fabre
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Emmanuelle Guillou
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Alexis Verger
- Inserm, CHU Lille, Institut Pasteur de Lille, CNRS ERL 9002 Integrative Structural Biology, Université Lille, Lille, France
| | - Elodie Prince
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Mohamed A Benmedjahed
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Adeline Payet
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Marie Couralet
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Didier Monte
- Inserm, CHU Lille, Institut Pasteur de Lille, CNRS ERL 9002 Integrative Structural Biology, Université Lille, Lille, France
| | - Vincent Villeret
- Inserm, CHU Lille, Institut Pasteur de Lille, CNRS ERL 9002 Integrative Structural Biology, Université Lille, Lille, France
| | - Henri-Marc Bourbon
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France
| | - Muriel Boube
- Centre de Biologie Integrative CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse Cedex, France.
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8
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Twenty years of Mediator complex structural studies. Biochem Soc Trans 2019; 47:399-410. [PMID: 30733343 PMCID: PMC6393861 DOI: 10.1042/bst20180608] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/18/2022]
Abstract
Mediator is a large multiprotein complex conserved in all eukaryotes that plays an essential role in transcriptional regulation. Mediator comprises 25 subunits in yeast and 30 subunits in humans that form three main modules and a separable four-subunit kinase module. For nearly 20 years, because of its size and complexity, Mediator has posed a formidable challenge to structural biologists. The first two-dimensional electron microscopy (EM) projection map of Mediator leading to the canonical view of its division in three topological modules named Head, Middle and Tail, was published in 1999. Within the last few years, optimization of Mediator purification combined with technical and methodological advances in cryo-electron microscopy (cryo-EM) have revealed unprecedented details of Mediator subunit organization, interactions with RNA polymerase II and parts of its core structure at high resolution. To celebrate the twentieth anniversary of the first Mediator EM reconstruction, we look back on the structural studies of Mediator complex from a historical perspective and discuss them in the light of our current understanding of its role in transcriptional regulation.
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9
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Weber H, Garabedian MJ. The mediator complex in genomic and non-genomic signaling in cancer. Steroids 2018; 133:8-14. [PMID: 29157917 PMCID: PMC5864542 DOI: 10.1016/j.steroids.2017.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/04/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022]
Abstract
Mediator is a conserved, multi-subunit macromolecular machine divided structurally into head, middle, and tail modules, along with a transiently associating kinase module. Mediator functions as an integrator of transcriptional regulatory activity by interacting with DNA-bound transcription factors and with RNA polymerase II (Pol II) to both activate and repress gene expression. Mediator has been shown to affect multiple steps in transcription, including chromatin looping between enhancers and promoters, pre-initiation complex formation, transcriptional elongation, and mRNA splicing. Individual Mediator subunits participate in regulation of gene expression by the estrogen and androgen receptors and are altered in a number of endocrine cancers, including breast and prostate cancer. In addition to its role in genomic signaling, MED12 has been implicated in non-genomic signaling by interacting with and activating TGF-beta receptor 2 in the cytoplasm. Recent structural studies have revealed extensive inter-domain interactions and complex architecture of the Mediator-Pol II complex, suggesting that Mediator is capable of reorganizing its conformation and composition to fit cellular needs. We propose that alterations in Mediator subunit expression that occur in various cancers could impact the organization and function of Mediator, resulting in changes in gene expression that promote malignancy. A better understanding of the role of Mediator in cancer could reveal new approaches to the diagnosis and treatment of Mediator-dependent endocrine cancers, especially in settings of therapy resistance.
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Affiliation(s)
- Hannah Weber
- Departments of Microbiology and Urology, NYU School of Medicine, 550 First Ave, New York, NY 10012, United States
| | - Michael J Garabedian
- Departments of Microbiology and Urology, NYU School of Medicine, 550 First Ave, New York, NY 10012, United States.
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10
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Tsai KL, Yu X, Gopalan S, Chao TC, Zhang Y, Florens L, Washburn MP, Murakami K, Conaway RC, Conaway JW, Asturias FJ. Mediator structure and rearrangements required for holoenzyme formation. Nature 2017; 544:196-201. [PMID: 28241144 DOI: 10.1038/nature21393] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/28/2016] [Indexed: 12/12/2022]
Abstract
The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.
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Affiliation(s)
- Kuang-Lei Tsai
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla California, USA
| | - Xiaodi Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla California, USA
| | - Sneha Gopalan
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Ti-Chun Chao
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City Kansas, USA
| | - Kenji Murakami
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Biochemistry &Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Biochemistry &Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Francisco J Asturias
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla California, USA
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11
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Nagulapalli M, Maji S, Dwivedi N, Dahiya P, Thakur JK. Evolution of disorder in Mediator complex and its functional relevance. Nucleic Acids Res 2015; 44:1591-612. [PMID: 26590257 PMCID: PMC4770211 DOI: 10.1093/nar/gkv1135] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 10/18/2015] [Indexed: 12/27/2022] Open
Abstract
Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of ‘junction-MoRF’ has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein–protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms.
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Affiliation(s)
- Malini Nagulapalli
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pradeep Dahiya
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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12
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Crona F, Holmqvist PH, Tang M, Singla B, Vakifahmetoglu-Norberg H, Fantur K, Mannervik M. The Brakeless co-regulator can directly activate and repress transcription in early Drosophila embryos. Dev Biol 2015; 407:173-81. [PMID: 26260775 DOI: 10.1016/j.ydbio.2015.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/22/2015] [Accepted: 08/06/2015] [Indexed: 11/25/2022]
Abstract
The Brakeless protein performs many important functions during Drosophila development, but how it controls gene expression is poorly understood. We previously showed that Brakeless can function as a transcriptional co-repressor. In this work, we perform transcriptional profiling of brakeless mutant embryos. Unexpectedly, the majority of affected genes are down-regulated in brakeless mutants. We demonstrate that genomic regions in close proximity to some of these genes are occupied by Brakeless, that over-expression of Brakeless causes a reciprocal effect on expression of these genes, and that Brakeless remains an activator of the genes upon fusion to an activation domain. Together, our results show that Brakeless can both repress and activate gene expression. A yeast two-hybrid screen identified the Mediator complex subunit Med19 as interacting with an evolutionarily conserved part of Brakeless. Both down- and up-regulated Brakeless target genes are also affected in Med19-depleted embryos, but only down-regulated targets are influenced in embryos depleted of both Brakeless and Med19. Our data provide support for a Brakeless activator function that regulates transcription by interacting with Med19. We conclude that the transcriptional co-regulator Brakeless can either activate or repress transcription depending on context.
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Affiliation(s)
- Filip Crona
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Per-Henrik Holmqvist
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Min Tang
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Bhumica Singla
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Helin Vakifahmetoglu-Norberg
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Katrin Fantur
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Mattias Mannervik
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden.
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13
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Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. eLife 2015; 4. [PMID: 26402457 PMCID: PMC4631838 DOI: 10.7554/elife.08719] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/23/2015] [Indexed: 12/18/2022] Open
Abstract
The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI:http://dx.doi.org/10.7554/eLife.08719.001 Inside a cell, proteins are made from instructions encoded by DNA. To produce a particular protein, a section of DNA within a gene is copied into a molecule of messenger ribonucleic acid (or mRNA). This process is called transcription and is carried out by an enzyme known as RNA polymerase. Transcription begins in a region of DNA called a promoter, which is found at the start of the gene. RNA polymerase is brought to the DNA by many proteins, including the so-called Mediator complex. Mediator receives signals from within the cell and from the environment, processes the information, and instructs RNA polymerase whether to transcribe the gene or not. Mediator performs this important role in all organisms from yeast to humans, but it is not clear how it works. A crucial step towards the solution of this problem is to understand the three-dimensional structure of the complex. Previous research using a technique called ‘electron microscopy’ showed that Mediator is composed of three modules, referred to as Head, Middle and Tail. The images from electron microscopy were not sufficiently detailed to reveal the organization of the proteins within these modules. An open-source Integrative Modeling Platform (IMP for short) was recently developed to arrive at structural models of large protein complexes from a combination of experimental data and computer models. Now, Robinson, Trnka, Pellarin et al. have used this platform to study the Mediator complex. First, Robinson, Trnka, Pellarin et al. collected experimental data on the structure of the Mediator complex using two approaches called ‘chemical cross-linking’ and ‘mass spectrometry’. This data was combined with biochemical and structural information from previous studies to generate a three-dimensional model of the structure of the entire Mediator using IMP. The model is detailed enough to show the location and orientation of all the proteins in the complex. For example, a protein called Med17 connects the Head and Middle modules, while another subunit—known as Med14—spans the entire complex and makes extensive contacts with other proteins in all three modules. DOI:http://dx.doi.org/10.7554/eLife.08719.002
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Affiliation(s)
- Philip J Robinson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States.,Structural Bioinformatics Unit, Paris, France
| | - Charles H Greenberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Ralph Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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14
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Fungal mediator tail subunits contain classical transcriptional activation domains. Mol Cell Biol 2015; 35:1363-75. [PMID: 25645928 DOI: 10.1128/mcb.01508-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Classical activation domains within DNA-bound eukaryotic transcription factors make weak interactions with coactivator complexes, such as Mediator, to stimulate transcription. How these interactions stimulate transcription, however, is unknown. The activation of reporter genes by artificial fusion of Mediator subunits to DNA binding domains that bind to their promoters has been cited as evidence that the primary role of activators is simply to recruit Mediator. We have identified potent classical transcriptional activation domains in the C termini of several tail module subunits of Saccharomyces cerevisiae, Candida albicans, and Candida dubliniensis Mediator, while their N-terminal domains are necessary and sufficient for their incorporation into Mediator but do not possess the ability to activate transcription when fused to a DNA binding domain. This suggests that Mediator fusion proteins actually are functioning in a manner similar to that of a classical DNA-bound activator rather than just recruiting Mediator. Our finding that deletion of the activation domains of S. cerevisiae Med2 and Med3, as well as C. dubliniensis Tlo1 (a Med2 ortholog), impairs the induction of certain genes shows these domains function at native promoters. Activation domains within coactivators are likely an important feature of these complexes and one that may have been uniquely leveraged by a common fungal pathogen.
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15
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Tsai KL, Tomomori-Sato C, Sato S, Conaway RC, Conaway JW, Asturias FJ. Subunit architecture and functional modular rearrangements of the transcriptional mediator complex. Cell 2014; 157:1430-1444. [PMID: 24882805 DOI: 10.1016/j.cell.2014.05.015] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/18/2014] [Accepted: 05/10/2014] [Indexed: 11/16/2022]
Abstract
The multisubunit Mediator, comprising ∼30 distinct proteins, plays an essential role in gene expression regulation by acting as a bridge between DNA-binding transcription factors and the RNA polymerase II (RNAPII) transcription machinery. Efforts to uncover the Mediator mechanism have been hindered by a poor understanding of its structure, subunit organization, and conformational rearrangements. By overcoming biochemical and image analysis hurdles, we obtained accurate EM structures of yeast and human Mediators. Subunit localization experiments, docking of partial X-ray structures, and biochemical analyses resulted in comprehensive mapping of yeast Mediator subunits and a complete reinterpretation of our previous Mediator organization model. Large-scale Mediator rearrangements depend on changes at the interfaces between previously described Mediator modules, which appear to be facilitated by factors conducive to transcription initiation. Conservation across eukaryotes of Mediator structure, subunit organization, and RNA polymerase II interaction suggest conservation of fundamental aspects of the Mediator mechanism.
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Affiliation(s)
- Kuang-Lei Tsai
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Shigeo Sato
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Francisco J Asturias
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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16
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Wang X, Sun Q, Ding Z, Ji J, Wang J, Kong X, Yang J, Cai G. Redefining the modular organization of the core Mediator complex. Cell Res 2014; 24:796-808. [PMID: 24810298 PMCID: PMC4085763 DOI: 10.1038/cr.2014.64] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 02/13/2014] [Accepted: 03/13/2014] [Indexed: 01/24/2023] Open
Abstract
The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation.
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Affiliation(s)
- Xuejuan Wang
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Qianqian Sun
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Zhenrui Ding
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Jinhua Ji
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Jianye Wang
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Xiao Kong
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Jianghong Yang
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Gang Cai
- 1] School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China [2] Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, 443 Huang-Shan Road, Hefei, Anhui 230027, China [3] Center for Biomedical Engineering, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
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17
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Boube M, Hudry B, Immarigeon C, Carrier Y, Bernat-Fabre S, Merabet S, Graba Y, Bourbon HM, Cribbs DL. Drosophila melanogaster Hox transcription factors access the RNA polymerase II machinery through direct homeodomain binding to a conserved motif of mediator subunit Med19. PLoS Genet 2014; 10:e1004303. [PMID: 24786462 PMCID: PMC4006704 DOI: 10.1371/journal.pgen.1004303] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 02/28/2014] [Indexed: 11/18/2022] Open
Abstract
Hox genes in species across the metazoa encode transcription factors (TFs) containing highly-conserved homeodomains that bind target DNA sequences to regulate batteries of developmental target genes. DNA-bound Hox proteins, together with other TF partners, induce an appropriate transcriptional response by RNA Polymerase II (PolII) and its associated general transcription factors. How the evolutionarily conserved Hox TFs interface with this general machinery to generate finely regulated transcriptional responses remains obscure. One major component of the PolII machinery, the Mediator (MED) transcription complex, is composed of roughly 30 protein subunits organized in modules that bridge the PolII enzyme to DNA-bound TFs. Here, we investigate the physical and functional interplay between Drosophila melanogaster Hox developmental TFs and MED complex proteins. We find that the Med19 subunit directly binds Hox homeodomains, in vitro and in vivo. Loss-of-function Med19 mutations act as dose-sensitive genetic modifiers that synergistically modulate Hox-directed developmental outcomes. Using clonal analysis, we identify a role for Med19 in Hox-dependent target gene activation. We identify a conserved, animal-specific motif that is required for Med19 homeodomain binding, and for activation of a specific Ultrabithorax target. These results provide the first direct molecular link between Hox homeodomain proteins and the general PolII machinery. They support a role for Med19 as a PolII holoenzyme-embedded “co-factor” that acts together with Hox proteins through their homeodomains in regulated developmental transcription. Mutations of Hox developmental genes in the fruit fly Drosophila melanogaster may provoke spectacular changes in form: transformations of one body part into another, or loss of organs. This attribute identifies them as important developmental genes. Insect and vertebrate Hox proteins contain highly related homeodomain motifs used to bind to regulatory DNA and influence expression of developmental target genes. This occurs at the level of transcription of target gene DNA to messenger RNA by RNA polymerase II and its associated protein machinery (>50 proteins). How Hox homeodomain proteins induce fine-tuned transcription remains an open question. We provide an initial response, finding that Hox proteins also use their homeodomains to bind one machinery protein, Mediator complex subunit 19 (Med19) through a Med19 sequence that is highly conserved in animal phyla. Med19 mutants isolated in this work (the first animal mutants) show that Med19 assists Hox protein functions. Further, they indicate that homeodomain binding to the Med19 motif is required for normal expression of a Hox target gene. Our work provides new clues for understanding how the specific transcriptional inputs of the highly conserved Hox class of transcription factors are integrated at the level of the whole transcription machinery.
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Affiliation(s)
- Muriel Boube
- Centre de Biologie du Développement, CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse, France
- * E-mail: (MB); (HMB); (DLC)
| | - Bruno Hudry
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Université de la méditerranée, Marseille, France
| | - Clément Immarigeon
- Centre de Biologie du Développement, CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse, France
| | - Yannick Carrier
- Centre de Biologie du Développement, CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse, France
| | - Sandra Bernat-Fabre
- Centre de Biologie du Développement, CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse, France
| | - Samir Merabet
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Université de la méditerranée, Marseille, France
| | - Yacine Graba
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Université de la méditerranée, Marseille, France
| | - Henri-Marc Bourbon
- Centre de Biologie du Développement, CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse, France
- * E-mail: (MB); (HMB); (DLC)
| | - David L. Cribbs
- Centre de Biologie du Développement, CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse, France
- * E-mail: (MB); (HMB); (DLC)
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18
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Yu W, Zhang Z, Min D, Yang Q, Du X, Tang L, Lin F, Sun Y, Zhao H, Zheng S, He A, Li H, Yao Y, Shen Z. Mediator of RNA polymerase II transcription subunit 19 promotes osteosarcoma growth and metastasis and associates with prognosis. Eur J Cancer 2014; 50:1125-36. [PMID: 24565852 DOI: 10.1016/j.ejca.2014.01.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
Osteosarcoma (OS) is the most common primary malignant tumour of bone. Nearly 30-40% of OS patients have a poor prognosis despite multimodal treatments. Because the carcinogenesis of OS remains unclear, the identification of new oncogenes that control the tumourigenesis and progression of OS is crucial for developing new therapies. Here, we found that the expression of Mediator of RNA polymerase II transcription subunit 19 (Med19) was increased in OS samples from patients compared to normal bone tissues. Cyclin D1 and cyclin B1 are upregulated in Med19 positive OS tissues. Importantly, among 97 OS patients of Enneking stage IIB or IIIB, Med19 expression was correlated with metastasis (P<0.05) and poor prognosis (P<0.01). Med19 knockdown significantly induced growth inhibition, reduced colony-forming ability and suppressed migration in the OS cell lines Saos-2 and U2OS, along with the downregulated expression of cyclin D1 and cyclin B1. Med19 knockdown also induced apoptosis in Saos-2 cells via induction of caspase-3 and poly ADP-ribose polymerase (PARP). In addition, Med19 knockdown significantly suppressed tumour growth in an OS xenograft nude mouse model via suppression of cyclin D1 and cyclin B1. Simultaneously, Med19 downregulation decreased the expression of Ki67 and proliferating cell nuclear antigen (PCNA) in tumour samples from OS xenograft nude mice. Med19 depletion remarkably reduced tumour metastasis in a model of OS metastatic spreading. Taken together, our data suggest that Med19 acts as an oncogene in OS via a possible cyclin D1/cyclin B1 modulation pathway.
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Affiliation(s)
- Wenxi Yu
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Zhichang Zhang
- Department of Orthopedics, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Daliu Min
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Qingcheng Yang
- Department of Orthopedics, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Xuefei Du
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Lina Tang
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Feng Lin
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Yuanjue Sun
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Hui Zhao
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Shuier Zheng
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Aina He
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Hongtao Li
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Yang Yao
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China
| | - Zan Shen
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, 200233 Shanghai, People's Republic of China.
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19
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A downy mildew effector attenuates salicylic acid-triggered immunity in Arabidopsis by interacting with the host mediator complex. PLoS Biol 2013; 11:e1001732. [PMID: 24339748 PMCID: PMC3858237 DOI: 10.1371/journal.pbio.1001732] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/29/2013] [Indexed: 12/20/2022] Open
Abstract
HaRxL44, a secreted effector from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis, enhances disease susceptibility by interacting with and degrading Mediator subunit MED19a, thereby perturbing plant defense gene transcription. Plants are continually exposed to pathogen attack but usually remain healthy because they can activate defences upon perception of microbes. However, pathogens have evolved to overcome plant immunity by delivering effectors into the plant cell to attenuate defence, resulting in disease. Recent studies suggest that some effectors may manipulate host transcription, but the specific mechanisms by which such effectors promote susceptibility remain unclear. We study the oomycete downy mildew pathogen of Arabidopsis, Hyaloperonospora arabidopsidis (Hpa), and show here that the nuclear-localized effector HaRxL44 interacts with Mediator subunit 19a (MED19a), resulting in the degradation of MED19a in a proteasome-dependent manner. The Mediator complex of ∼25 proteins is broadly conserved in eukaryotes and mediates the interaction between transcriptional regulators and RNA polymerase II. We found MED19a to be a positive regulator of immunity against Hpa. Expression profiling experiments reveal transcriptional changes resembling jasmonic acid/ethylene (JA/ET) signalling in the presence of HaRxL44, and also 3 d after infection with Hpa. Elevated JA/ET signalling is associated with a decrease in salicylic acid (SA)–triggered immunity (SATI) in Arabidopsis plants expressing HaRxL44 and in med19a loss-of-function mutants, whereas SATI is elevated in plants overexpressing MED19a. Using a PR1::GUS reporter, we discovered that Hpa suppresses PR1 expression specifically in cells containing haustoria, into which RxLR effectors are delivered, but not in nonhaustoriated adjacent cells, which show high PR1::GUS expression levels. Thus, HaRxL44 interferes with Mediator function by degrading MED19, shifting the balance of defence transcription from SA-responsive defence to JA/ET-signalling, and enhancing susceptibility to biotrophs by attenuating SA-dependent gene expression. The highly conserved Mediator complex plays an essential role in transcriptional regulation by providing a molecular bridge between transcription factors and RNA polymerase II. Recent studies in Arabidopsis have revealed that it also performs an essential role in plant defence. However, it remains unknown how pathogens manipulate Mediator function in order to increase a plant's susceptibility to infection. In this article, we show that a secreted effector, HaRxL44, from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa), interacts with and degrades the Mediator subunit MED19a, resulting in the alteration of plant defence gene transcription. This effector-mediated interference with host transcriptional regulation perturbs the balance between jasmonic acid/ethylene (JA/ET) and salicylic acid (SA)–dependent defence. HaRxL44 interaction with MED19a results in reduced SA-regulated gene expression, indicating that this pathogen effector modulates host transcription to promote virulence. The resulting alteration in defence transcription patterns compromises the plant's ability to defend itself against pathogens, such as Hpa, that establish long-term parasitic interactions with living host cells via haustoria (a pathogen structure that creates an expanded host/parasite interface to extract nutrients) but not against necrotrophic pathogens that kill host cells. HaRxL44 is unlikely to be the sole effector that accomplishes this shift in hormonal balance, and other nuclear HaRxL proteins were reported by other researchers to interact with Mediator components, as well as with other regulators of the JA/ET signalling pathway. Functional analyses of these effectors should facilitate the discovery of new components of the plant immune system. These data show that pathogens can target fundamental mechanisms of host regulation in order to tip the balance of signalling pathways to suppress defence and favour parasitism.
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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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21
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Lee SK, Chen X, Huang L, Stargell LA. The head module of Mediator directs activation of preloaded RNAPII in vivo. Nucleic Acids Res 2013; 41:10124-34. [PMID: 24005039 PMCID: PMC3905900 DOI: 10.1093/nar/gkt796] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The successful synthesis of a transcript by RNA polymerase II (RNAPII) is a multistage process with distinct rate-limiting steps that can vary depending on the particular gene. A growing number of genes in a variety of organisms are regulated at steps after the recruitment of RNAPII. The best-characterized Saccharomyces cerevisiae gene regulated in this manner is CYC1. This gene has high occupancy of RNAPII under non-inducing conditions, defining it as a poised gene. Here, we find that subunits of the head module of Mediator, Med18 and Med20, and Med19 are required for activation of transcription at the CYC1 promoter in response to environmental cues. These subunits of Mediator are required at the preloaded promoter for normal levels of recruitment and activity of the general transcription factor TFIIH. Strikingly, these Mediator components are dispensable for activation by the same activator at a different gene, which lacks a preloaded polymerase in the promoter region. Based on these results and other studies, we speculate that Mediator plays an essential role in triggering an inactive polymerase at CYC1 into a productively elongating form.
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Affiliation(s)
- Sarah K Lee
- Department of Biochemistry and Molecular Biology, Colorado State University, CO 80523, USA
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Zhu LJ, Yan WX, Chen ZW, Chen Y, Chen D, Zhang TH, Liao GQ. Disruption of mediator complex subunit 19 (Med19) inhibits cell growth and migration in tongue cancer. World J Surg Oncol 2013; 11:116. [PMID: 23705783 PMCID: PMC3673833 DOI: 10.1186/1477-7819-11-116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 05/09/2013] [Indexed: 12/15/2022] Open
Abstract
Background Mediator complex subunit 19 (Med19) is a critical subunit of the mediator complex that forms a bridge between the transcription factors and RNA polymerase II. Although it has been reported that Med19 plays an important role in stabilizing the whole mediator complex, its biological importance in tongue cancer cell proliferation and migration has not been addressed. Methods By using MTT, BrdU incorporation, colony formation, flow cytometric, tumorigenesis and transwell assays, We tested the Med19 role on tongue cancer cell growth and migration. Results We demonstrated that lentivirus-mediated Med19 knockdown could arrest tongue cancer cells at G1 phase, inhibit tongue cancer cell proliferation and migration in vitro. The tumorigenicity of Med19 short hairpin RNA (shRNA)-expressing lentivirus infected tongue cancer cells were decreased after inoculating into nude mice. Conclusions These results indicate that Med19 plays an important role in tongue cancer proliferation and migration, and suggest possible applications for tongue cancer therapy.
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Affiliation(s)
- Li-Jun Zhu
- Department of Oral and Maxillofacial Surgery, Guanghua College of Stomatology, Sun Yat-Sen University, 56 Lingyuanxi Road, Guangzhou 510055, China
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Imberg-Kazdan K, Ha S, Greenfield A, Poultney CS, Bonneau R, Logan SK, Garabedian MJ. A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells. Genome Res 2013; 23:581-91. [PMID: 23403032 PMCID: PMC3613576 DOI: 10.1101/gr.144774.112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 01/31/2013] [Indexed: 01/22/2023]
Abstract
The androgen receptor (AR) is a mediator of both androgen-dependent and castration-resistant prostate cancers. Identification of cellular factors affecting AR transcriptional activity could in principle yield new targets that reduce AR activity and combat prostate cancer, yet a comprehensive analysis of the genes required for AR-dependent transcriptional activity has not been determined. Using an unbiased genetic approach that takes advantage of the evolutionary conservation of AR signaling, we have conducted a genome-wide RNAi screen in Drosophila cells for genes required for AR transcriptional activity and applied the results to human prostate cancer cells. We identified 45 AR-regulators, which include known pathway components and genes with functions not previously linked to AR regulation, such as HIPK2 (a protein kinase) and MED19 (a subunit of the Mediator complex). Depletion of HIPK2 and MED19 in human prostate cancer cells decreased AR target gene expression and, importantly, reduced the proliferation of androgen-dependent and castration-resistant prostate cancer cells. We also systematically analyzed additional Mediator subunits and uncovered a small subset of Mediator subunits that interpret AR signaling and affect AR-dependent transcription and prostate cancer cell proliferation. Importantly, targeting of HIPK2 by an FDA-approved kinase inhibitor phenocopied the effect of depletion by RNAi and reduced the growth of AR-positive, but not AR-negative, treatment-resistant prostate cancer cells. Thus, our screen has yielded new AR regulators including drugable targets that reduce the proliferation of castration-resistant prostate cancer cells.
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Affiliation(s)
- Keren Imberg-Kazdan
- Department of Biochemistry and Department of Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Susan Ha
- Department of Biochemistry and Department of Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Department of Urology, New York University School of Medicine, New York, New York 10016, USA
| | - Alex Greenfield
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | | | - Richard Bonneau
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Susan K. Logan
- Department of Biochemistry and Department of Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Department of Urology, New York University School of Medicine, New York, New York 10016, USA
- NYU Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Michael J. Garabedian
- Department of Urology, New York University School of Medicine, New York, New York 10016, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
- NYU Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
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24
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Kim S, Gross DS. Mediator recruitment to heat shock genes requires dual Hsf1 activation domains and mediator tail subunits Med15 and Med16. J Biol Chem 2013; 288:12197-213. [PMID: 23447536 DOI: 10.1074/jbc.m112.449553] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily conserved Mediator complex is central to the regulation of gene transcription in eukaryotes because it serves as a physical and functional interface between upstream regulators and the Pol II transcriptional machinery. Nonetheless, its role appears to be context-dependent, and the detailed mechanism by which it governs the expression of most genes remains unknown. Here we investigate Mediator involvement in HSP (heat shock protein) gene regulation in the yeast Saccharomyces cerevisiae. We find that in response to thermal upshift, subunits representative of each of the four Mediator modules (Head, Middle, Tail, and Kinase) are rapidly, robustly, and selectively recruited to the promoter regions of HSP genes. Their residence is transient, returning to near-background levels within 90 min. Hsf1 (heat shock factor 1) plays a central role in recruiting Mediator, as indicated by the fact that truncation of either its N- or C-terminal activation domain significantly reduces Mediator occupancy, whereas removal of both activation domains abolishes it. Likewise, ablation of either of two Mediator Tail subunits, Med15 or Med16, reduces Mediator recruitment to HSP promoters, whereas deletion of both abolishes it. Accompanying the loss of Mediator, recruitment of RNA polymerase II is substantially diminished. Interestingly, Mediator antagonizes Hsf1 occupancy of non-induced promoters yet facilitates enhanced Hsf1 association with activated ones. Collectively, our observations indicate that Hsf1, via its dual activation domains, recruits holo-Mediator to HSP promoters in response to acute heat stress through cooperative physical and/or functional interactions with the Tail module.
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Affiliation(s)
- Sunyoung Kim
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana 71130-3932, USA
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25
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Wen H, Feng CC, Ding GX, Meng DL, Ding Q, Fang ZJ, Xia GW, Xu G, Jiang HW. Med19 promotes bone metastasis and invasiveness of bladder urothelial carcinoma via bone morphogenetic protein 2. Ann Diagn Pathol 2012; 17:259-64. [PMID: 23276457 DOI: 10.1016/j.anndiagpath.2012.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 11/24/2012] [Indexed: 01/15/2023]
Abstract
Bladder cancer (BCa) remained a major health problem. Med19 was related to tumor growth of BCa. Bone morphogenetic proteins (BMPs) were reported to be critical in bone metastasis of cancer. We therefore investigated the relations between Med19 and BMPs in BCa and their effect on bone metastasis of BCa. Bladder cancer cell lines were cultured and interfered with Med19 shRNA and control. Expressions of BMP-1, BMP-2, BMP-4, BMP-5, BMP-6, BMP-7, BMP-9, and BMP-15 were studied between 2 groups. Fifty-two BCa samples were included for immunohistochemical staining of Med19 and BMP-2. Expressions were scored and studied statistically. Invasiveness was studied with Transwell assay. Silencing or Med19 in BCa cells induced altered expressions of BMPs. Increased expressions of BMP-1, BMP-4, BMP-6, BMP-7, and BMP-15 and decreased expressions of BMP-2, BMP-5, and BMP-9 were noticed, but only BMP-2 reached statistical significance. Expressions of Med19 and BMP-2 were significantly higher in cases with bone metastasis and were positively correlated in cases with bone metastasis and muscle invasion. Med19 is a critical factor involved in the invasiveness and promotion of bone metastasis of BCa, possibly via BMP-2.
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Affiliation(s)
- Hui Wen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, PR China
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26
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Chen Z, McCroskey S, Guo W, Li H, Gerton JL. A genetic screen to discover pathways affecting cohesin function in Schizosaccharomyces pombe identifies chromatin effectors. G3 (BETHESDA, MD.) 2012; 2:1161-8. [PMID: 23050226 PMCID: PMC3464108 DOI: 10.1534/g3.112.003327] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 07/23/2012] [Indexed: 11/23/2022]
Abstract
Cohesion, the force that holds sister chromatids together from the time of DNA replication until separation at the metaphase to anaphase transition, is mediated by the cohesin complex. This complex is also involved in DNA damage repair, chromosomes condensation, and gene regulation. To learn more about the cellular functions of cohesin, we conducted a genetic screen in Schizosaccharomyces pombe with two different cohesin mutants (eso1-G799D and mis4-242). We found synthetic negative interactions with deletions of genes involved in DNA replication and heterochromatin formation. We also found a few gene deletions that rescued the growth of eso1-G799D at the nonpermissive temperature, and these genes partially rescue the lagging chromosome phenotype. These genes are all chromatin effectors. Overall, our screen revealed an intimate association between cohesin and chromatin.
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Affiliation(s)
- Zhiming Chen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Scott McCroskey
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Weichao Guo
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
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Xu LL, Guo SL, Ma SR, Luo YA. Mammalian Mediator 19 Mediates H1299 Lung Adenocarcinoma Cell Clone Conformation, Growth, and Metastasis. Asian Pac J Cancer Prev 2012; 13:3695-700. [DOI: 10.7314/apjcp.2012.13.8.3695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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28
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Niederberger T, Etzold S, Lidschreiber M, Maier KC, Martin DE, Fröhlich H, Cramer P, Tresch A. MC EMiNEM maps the interaction landscape of the Mediator. PLoS Comput Biol 2012; 8:e1002568. [PMID: 22737066 PMCID: PMC3380870 DOI: 10.1371/journal.pcbi.1002568] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/04/2012] [Indexed: 11/18/2022] Open
Abstract
The Mediator is a highly conserved, large multiprotein complex that is involved essentially in the regulation of eukaryotic mRNA transcription. It acts as a general transcription factor by integrating regulatory signals from gene-specific activators or repressors to the RNA Polymerase II. The internal network of interactions between Mediator subunits that conveys these signals is largely unknown. Here, we introduce MC EMiNEM, a novel method for the retrieval of functional dependencies between proteins that have pleiotropic effects on mRNA transcription. MC EMiNEM is based on Nested Effects Models (NEMs), a class of probabilistic graphical models that extends the idea of hierarchical clustering. It combines mode-hopping Monte Carlo (MC) sampling with an Expectation-Maximization (EM) algorithm for NEMs to increase sensitivity compared to existing methods. A meta-analysis of four Mediator perturbation studies in Saccharomyces cerevisiae, three of which are unpublished, provides new insight into the Mediator signaling network. In addition to the known modular organization of the Mediator subunits, MC EMiNEM reveals a hierarchical ordering of its internal information flow, which is putatively transmitted through structural changes within the complex. We identify the N-terminus of Med7 as a peripheral entity, entailing only local structural changes upon perturbation, while the C-terminus of Med7 and Med19 appear to play a central role. MC EMiNEM associates Mediator subunits to most directly affected genes, which, in conjunction with gene set enrichment analysis, allows us to construct an interaction map of Mediator subunits and transcription factors.
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Affiliation(s)
- Theresa Niederberger
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Stefanie Etzold
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael Lidschreiber
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kerstin C. Maier
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Dietmar E. Martin
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Holger Fröhlich
- Bonn-Aachen International Center for IT (B-IT) Algorithmic Bioinformatics, Rheinische Friedrich-Wilhelms-University Bonn, Bonn, Germany
| | - Patrick Cramer
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Achim Tresch
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
- * E-mail:
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Liu Z, Myers LC. Med5(Nut1) and Med17(Srb4) are direct targets of mediator histone H4 tail interactions. PLoS One 2012; 7:e38416. [PMID: 22693636 PMCID: PMC3367926 DOI: 10.1371/journal.pone.0038416] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/09/2012] [Indexed: 11/18/2022] Open
Abstract
The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. In addition to its canonical role in transcriptional activation, recent studies have demonstrated that S. cerevisiae Mediator can interact directly with nucleosomes, and their histone tails. Mutations in Mediator subunits have shown that Mediator and certain chromatin structures mutually impact each other structurally and functionally in vivo. We have taken a UV photo cross-linking approach to further delineate the molecular basis of Mediator chromatin interactions and help determine whether the impact of certain Mediator mutants on chromatin is direct. Specifically, by using histone tail peptides substituted with an amino acid analog that is a UV activatible crosslinker, we have identified specific subunits within Mediator that participate in histone tail interactions. Using Mediator purified from mutant yeast strains we have evaluated the impact of these subunits on histone tail binding. This analysis has identified the Med5 subunit of Mediator as a target for histone tail interactions and suggests that the previously observed effect of med5 mutations on telomeric heterochromatin and silencing is direct.
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Affiliation(s)
- Zhongle Liu
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Lawrence C. Myers
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
- * E-mail:
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30
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The Tlo proteins are stoichiometric components of Candida albicans mediator anchored via the Med3 subunit. EUKARYOTIC CELL 2012; 11:874-84. [PMID: 22562472 DOI: 10.1128/ec.00095-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The amplification of the TLO (for telomere-associated) genes in Candida albicans, compared to its less pathogenic, close relative Candida dubliniensis, suggests a role in virulence. Little, however, is known about the function of the Tlo proteins. We have purified the Mediator coactivator complex from C. albicans (caMediator) and found that Tlo proteins are a stoichiometric component of caMediator. Many members of the Tlo family are expressed, and each is a unique member of caMediator. Protein expression analysis of individual Tlo proteins, as well as the purification of tagged Tlo proteins, demonstrate that there is a large free population of Tlo proteins in addition to the Mediator-associated population. Coexpression and copurification of Tloα12 and caMed3 in Escherichia coli established a direct physical interaction between the two proteins. We have also made a C. albicans med3Δ/Δ strain and purified an intact Mediator from this strain. The analysis of the composition of the med3Δ Mediator shows that it lacks a Tlo subunit. Regarding Mediator function, the med3Δ/Δ strain serves as a substitute for the difficult-to-make tloΔ/Δ C. albicans strain. A potential role of the TLO and MED3 genes in virulence is supported by the inability of the med3Δ/Δ strain to form normal germ tubes. This study of caMediator structure provides initial clues to the mechanism of action of the Tlo genes and a platform for further mechanistic studies of caMediator's involvement in gene regulatory patterns that underlie pathogenesis.
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Role of Mediator in regulating Pol II elongation and nucleosome displacement in Saccharomyces cerevisiae. Genetics 2012; 191:95-106. [PMID: 22377631 DOI: 10.1534/genetics.111.135806] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Mediator is a modular multisubunit complex that functions as a critical coregulator of RNA polymerase II (Pol II) transcription. While it is well accepted that Mediator plays important roles in the assembly and function of the preinitiation complex (PIC), less is known of its potential roles in regulating downstream steps of the transcription cycle. Here we use a combination of genetic and molecular approaches to investigate Mediator regulation of Pol II elongation in the model eukaryote, Saccharomyces cerevisiae. We find that ewe (expression without heat shock element) mutations in conserved Mediator subunits Med7, Med14, Med19, and Med21-all located within or adjacent to the middle module-severely diminish heat-shock-induced expression of the Hsf1-regulated HSP82 gene. Interestingly, these mutations do not impede Pol II recruitment to the gene's promoter but instead impair its transit through the coding region. This implies that a normal function of Mediator is to regulate a postinitiation step at HSP82. In addition, displacement of histones from promoter and coding regions, a hallmark of activated heat-shock genes, is significantly impaired in the med14 and med21 mutants. Suggestive of a more general role, ewe mutations confer hypersensitivity to the anti-elongation drug 6-azauracil (6-AU) and one of them-med21-impairs Pol II processivity on a GAL1-regulated reporter gene. Taken together, our results suggest that yeast Mediator, acting principally through its middle module, can regulate Pol II elongation at both heat-shock and non-heat-shock genes.
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32
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Li XH, Fang DN, Zeng CM. Knockdown of MED19 by short hairpin RNA-mediated gene silencing inhibits pancreatic cancer cell proliferation. Cancer Biother Radiopharm 2012; 26:495-501. [PMID: 21834715 DOI: 10.1089/cbr.2010.0863] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abnormal gene transcription plays an important role in oncogenesis. In cancer cells, the improper activation of specific genes is usually ascribed to aberrant transcription machinery including transcription factors, RNA polymerase II, and Mediator complex. This study reports on short hairpin RNA (shRNA)-mediated gene silencing of MED19, a subunit of Mediator complex, and its effect on the growth of pancreatic cancer cells. RNA interference was performed by lentivirus shRNA system to specifically knockdown MED19 expression in Aspc-1 and Panc-1 cells. The knockdown efficiency of MED19 was confirmed by quantitative RT-PCR and western blot. The effect of MED19 shRNA on Aspc-1 and Panc-1 cell proliferation was evaluated by methylthiazoletetrazolium assay, BrdU incorporation assay, colony formation assay, and flow cytometry assay. This study shows that downregulation of MED19 remarkably reduced cancer cell proliferation and colony formation capacity in two pancreatic cancer cell lines. In addition, downregulated MED19 induced G1-phase cell cycle arrest and apoptosis. This study provides a potent role of MED19 in promoting pancreatic cancer growth and a possible drug target for cancer therapy.
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Affiliation(s)
- Xing-Hua Li
- Department of Digestion Medicine, Shanghai Eighth People's Hospital, No. 8 Caobao Road, Shanghai, China.
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33
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Mathur S, Vyas S, Kapoor S, Tyagi AK. The Mediator complex in plants: structure, phylogeny, and expression profiling of representative genes in a dicot (Arabidopsis) and a monocot (rice) during reproduction and abiotic stress. PLANT PHYSIOLOGY 2011; 157:1609-27. [PMID: 22021418 PMCID: PMC3327187 DOI: 10.1104/pp.111.188300] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 10/20/2011] [Indexed: 05/20/2023]
Abstract
The Mediator (Med) complex relays regulatory information from DNA-bound transcription factors to the RNA polymerase II in eukaryotes. This macromolecular unit is composed of three core subcomplexes in addition to a separable kinase module. In this study, conservation of Meds has been investigated in 16 plant species representing seven diverse groups across the plant kingdom. Using Hidden Markov Model-based conserved motif searches, we have identified all the known yeast/metazoan Med components in one or more plant groups, including the Med26 subunits, which have not been reported so far for any plant species. We also detected orthologs for the Arabidopsis (Arabidopsis thaliana) Med32, -33, -34, -35, -36, and -37 in all the plant groups, and in silico analysis identified the Med32 and Med33 subunits as apparent orthologs of yeast/metazoan Med2/29 and Med5/24, respectively. Consequently, the plant Med complex appears to be composed of one or more members of 34 subunits, as opposed to 25 and 30 members in yeast and metazoans, respectively. Despite low similarity in primary Med sequences between the plants and their fungal/metazoan partners, secondary structure modeling of these proteins revealed a remarkable similarity between them, supporting the conservation of Med organization across kingdoms. Phylogenetic analysis between plant, human, and yeast revealed single clade relatedness for 29 Med genes families in plants, plant Meds being closer to human than to yeast counterparts. Expression profiling of rice (Oryza sativa) and Arabidopsis Med genes reveals that Meds not only act as a basal regulator of gene expression but may also have specific roles in plant development and under abiotic stress conditions.
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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: 3.2] [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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35
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Cui X, Xu D, Lv C, Qu F, He J, Chen M, Liu Y, Gao Y, Che J, Yao Y, Yu H. Suppression of MED19 expression by shRNA induces inhibition of cell proliferation and tumorigenesis in human prostate cancer cells. BMB Rep 2011; 44:547-52. [DOI: 10.5483/bmbrep.2011.44.8.547] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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36
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Zhu X, Zhang Y, Bjornsdottir G, Liu Z, Quan A, Costanzo M, Dávila López M, Westholm JO, Ronne H, Boone C, Gustafsson CM, Myers LC. Histone modifications influence mediator interactions with chromatin. Nucleic Acids Res 2011; 39:8342-54. [PMID: 21742760 PMCID: PMC3201872 DOI: 10.1093/nar/gkr551] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator-histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.
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Affiliation(s)
- Xuefeng Zhu
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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Ji-Fu E, Xing JJ, Hao LQ, Fu CG. Suppression of lung cancer metastasis-related protein 1 (LCMR1) inhibits the growth of colorectal cancer cells. Mol Biol Rep 2011; 39:3675-81. [DOI: 10.1007/s11033-011-1142-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 06/24/2011] [Indexed: 12/31/2022]
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38
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Sun M, Jiang R, Li JD, Luo SL, Gao HW, Jin CY, Shi DL, Wang CG, Wang B, Zhang XY. MED19 promotes proliferation and tumorigenesis of lung cancer. Mol Cell Biochem 2011; 355:27-33. [PMID: 21519921 DOI: 10.1007/s11010-011-0835-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 04/15/2011] [Indexed: 12/23/2022]
Abstract
MED19 is a subunit of Mediator that is an essential component of RNA polymerase II-mediated transcription machinery. High expression levels of MED19 were examined in human lung adenocarcinoma tissues by immunohistochemical assay. MED19-specific short hairpin RNA (shRNA) expressing lentivirus was constructed and infected lung cancer cell line A549. MED19 mRNA and protein expression levels were downregulated in A549 cells as evidenced by real-time PCR and western blot assays. Importantly, MED19 inhibition resulted in impaired proliferation and colony formation, and induced accumulation of G1-phase cells and mitigated invasiveness of cells. More importantly, downregulation of MED19 expression reduced the tumorigenicity of A549 cells in vivo. It was suggested that MED19 is a novel proliferation regulator that promotes growth of lung cancer cells, thereby indicating that MED19 may serve as a new molecular target for lung cancer therapy.
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Affiliation(s)
- Mei Sun
- Department of Pathology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun 130041, People's Republic of China
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Abstract
The Mediator complex is required for the regulated transcription of nearly all RNA polymerase II-dependent genes. Here we demonstrate a new role for Mediator which appears to be separate from its function as a transcriptional coactivator. Mediator associates directly with heterochromatin at telomeres and influences the exact boundary between active and inactive chromatin. Loss of the Mediator Med5 subunit or mutations in Med7 cause a depletion of the complex from regions located near subtelomeric X elements, which leads to a change in the balance between the Sir2 and Sas2 proteins. These changes in turn result in increased levels of H4K16 acetylation near telomeres and in desilencing of subtelomeric genes. Increases in H4K16 acetylation have been observed at telomeres in aging cells. In agreement with this observation, we found that the loss of MED5 leads to shortening of the Saccharomyces cerevisiae (budding yeast) replicative life span.
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Zhang H, Jiang H, Wang W, Gong J, Zhang L, Chen Z, Ding Q. Expression of Med19 in bladder cancer tissues and its role on bladder cancer cell growth. Urol Oncol 2011; 30:920-7. [PMID: 21478038 DOI: 10.1016/j.urolonc.2010.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Revised: 10/15/2010] [Accepted: 10/16/2010] [Indexed: 10/18/2022]
Abstract
OBJECTIVES The human Med19 gene encodes a critical subunit that stabilizes the whole mediator complex. To understand the role of Med19 in bladder cancer, we studied the effects of lentivirus-mediated suppression of Med19 expression on bladder cancer cells in vitro and in vivo. METHODS AND MATERIALS In this study, immunohistochemical analysis was used to demonstrate the expression of Med19 in human bladder cancer. The lentivirus vectors containing a small hairpin RNA (shRNA) to target Med19 were constructed. After bladder cancer cells (5637 and T24) were infected, RT-PCR and Western blotting were used to measure Med19 expression. The influence of Med19 on the proliferation of bladder cancer cells were assessed using MTT, BrdU, colony formation and tumorigenicity experiments. Cell cycle was analyzed with flow cytometric assay. RESULTS Med19 was up-regulated in human bladder cancers compared with adjacent benign tissues by immunohistochemical analysis, but was strongly inhibited in 5637 and T24 bladder cancer cells infected with lentiviruses delivering shRNA against Med19. The down-regulation of Med19 increased the proportion of cells in G0/G1 phases and attenuated the growth of 5637 and T24 cells in vitro. The tumorigenicity of Med19-suppressed T24 cells was decreased after inoculation into nude mice. CONCLUSIONS Our results suggested that lentiviruses delivering shRNA against Med19 may be a promising tool for bladder cancer therapy.
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Affiliation(s)
- Hu Zhang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
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The role of Med19 in the proliferation and tumorigenesis of human hepatocellular carcinoma cells. Acta Pharmacol Sin 2011; 32:354-60. [PMID: 21372827 DOI: 10.1038/aps.2010.223] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
AIM To explore the role of Med19, a component of the Mediator complex that coactivates DNA-binding transcription factors, in the proliferation and tumorigenesis of human hepatocellular carcinoma cells. METHODS The human hepatocellular carcinoma cell lines HepG2 and Hep3B were infected with lentiviral vectors encoding interfering RNA (RNAi) targeting the Med19 gene. To further confirm the inhibitory effects of RNAi vectors on Med19 gene expression, quantitative real-time RT-PCR and Western blotting assays were used. The proliferation of HepG2 and Hep3B cells after transduction with the Med19-RNAi-Lentivirus vector was evaluated by MTT conversion, BrdU incorporation, colony formation, and cell-cycle assays in vitro. In addition, the ability of the Med19-RNAi-Lentivirus vector-infected Hep3B cells to form tumors after inoculation into nude mice was determined. RESULTS Recombinant lentiviral vectors expressing small interfering RNA (siRNA) against Med19 were constructed and were found to efficiently downregulate Med19 mRNA and protein levels in HepG2 and Hep3B cells. Furthermore, the inhibition of Med19 by RNAi dramatically reduced hepatocellular carcinoma cell proliferation, induced cell-cycle arrest in the G(0)/G(1) phase, and suppressed tumor formation. CONCLUSION These results provide new evidence of an important role for Med19 in the development of hepatocellular carcinomas, suggesting that lentivirus-mediated RNAi to target Med19 is a potential tool for inhibiting cancer cell proliferation and tumorigenesis.
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Li LH, He J, Hua D, Guo ZJ, Gao Q. Lentivirus-mediated inhibition of Med19 suppresses growth of breast cancer cells in vitro. Cancer Chemother Pharmacol 2010; 68:207-15. [PMID: 20890603 DOI: 10.1007/s00280-010-1468-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Accepted: 09/10/2010] [Indexed: 12/20/2022]
Abstract
PURPOSE The mediator is a large multiprotein complex vital for transcription regulation. Human Med19 is a critical subunit of the mediator complex and plays an important role in stabilizing the whole mediator. To understand the role and mechanism of Med19 in breast cancer, we carried out studies on the impacts of lentivirus-mediated inhibition of Med19 on breast cancer cells in vitro. METHOD The expression of Med19 in breast cancer tissue was detected using immunohistochemical analysis. The impacts of lentivirus-mediated inhibition of Med19 on breast cancer cells were detected using flow cytometric, cell proliferation, BrdU incorporation, and colony formation assays. RESULTS The upregulated expression of Med19 was found in breast cancer tissues. Med19 expression was significantly associated with tumor grade (p = 0.026). The expression of Med19 was strongly suppressed in human breast cancer MDA-MB-231 and MCF-7 cells infected with lentiviruses delivering small hairpin RNA (shRNA) against Med19. The inhibition of Med19 elicited augmentation of G0/G1 phase proportion and significantly attenuated the growth of MDA-MB-231 and MCF-7 cells in vitro. CONCLUSION Med19 plays an important role in the proliferation of human breast cancer cells, which suggested that the lentiviruses delivering shRNA against Med19 could be a promising tool for breast cancer therapy.
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Affiliation(s)
- Li-Hua Li
- Oncology Institute, The Fourth Affiliated Hospital of Soochow University, 200 Huihe Road, Wuxi 214062, China.
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Koschubs T, Lorenzen K, Baumli S, Sandström S, Heck AJR, Cramer P. Preparation and topology of the Mediator middle module. Nucleic Acids Res 2010; 38:3186-95. [PMID: 20123732 PMCID: PMC2879511 DOI: 10.1093/nar/gkq029] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 11/18/2022] Open
Abstract
Mediator is the central coactivator complex required for regulated transcription by RNA polymerase (Pol) II. Mediator consists of 25 subunits arranged in the head, middle, tail and kinase modules. Structural and functional studies of Mediator are limited by the availability of protocols for the preparation of recombinant modules. Here, we describe protocols for obtaining pure endogenous and recombinant complete Mediator middle module from Saccharomyces cerevisiae that consists of seven subunits: Med1, 4, 7, 9, 10, 21 and 31. Native mass spectrometry reveals that all subunits are present in equimolar stoichiometry. Ion-mobility mass spectrometry, limited proteolysis, light scattering and small-angle X-ray scattering all indicate a high degree of intrinsic flexibility and an elongated shape of the middle module. Protein-protein interaction assays combined with previously published data suggest that the Med7 and Med4 subunits serve as a binding platform to form the three heterodimeric subcomplexes, Med7N/21, Med7C/31 and Med4/9. The subunits, Med1 and Med10, which bridge to the Mediator tail module, bind to both Med7 and Med4.
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Affiliation(s)
- Tobias Koschubs
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Kristina Lorenzen
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sonja Baumli
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Saana Sandström
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Albert J. R. Heck
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Patrick Cramer
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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Takahashi H, Kasahara K, Kokubo T. Saccharomyces cerevisiaeMed9 comprises two functionally distinct domains that play different roles in transcriptional regulation. Genes Cells 2009; 14:53-67. [DOI: 10.1111/j.1365-2443.2008.01250.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ding N, Tomomori-Sato C, Sato S, Conaway RC, Conaway JW, Boyer TG. MED19 and MED26 are synergistic functional targets of the RE1 silencing transcription factor in epigenetic silencing of neuronal gene expression. J Biol Chem 2008; 284:2648-2656. [PMID: 19049968 DOI: 10.1074/jbc.m806514200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A key hub for the orchestration of epigenetic modifications necessary to restrict neuronal gene expression to the nervous system is the RE1 silencing transcription factor (REST; also known as neuron restrictive silencer factor, NRSF). REST suppresses the nonspecific and premature expression of neuronal genes in non-neuronal and neural progenitor cells, respectively, via recruitment of enzymatically diverse corepressors, including G9a histone methyltransferase (HMTase) that catalyzes di-methylation of histone 3-lysine 9 (H3K9me2). Recently, we identified the RNA polymerase II transcriptional Mediator to be an essential link between RE1-bound REST and G9a in epigenetic suppression of neuronal genes in non-neuronal cells. However, the means by which REST recruits Mediator to facilitate G9a-dependent extra-neuronal gene silencing remains to be elucidated. Here, we identify the MED19 and MED26 subunits in Mediator as direct physical and synergistic functional targets of REST. We show that although REST independently binds to both MED19 and MED26 in isolation, combined depletion of both subunits is required to disrupt the association of REST with Mediator. Furthermore, combined, but not individual, depletion of MED19/MED26 impairs REST-directed recruitment to RE1 elements of Mediator and G9a, leading to a reversal of G9a-dependent H3K9me2 and de-repression of REST-target gene expression. Together, these findings identify MED19/MED26 as a probable composite REST interface in Mediator and further clarify the mechanistic basis by which Mediator facilitates REST-imposed epigenetic restrictions on neuronal gene expression.
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Affiliation(s)
- Ning Ding
- Institute of Biotechnology and Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245
| | - Chieri Tomomori-Sato
- Stowers Institute for Medical Research, Kansas City, Missouri 64110 and the Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160
| | - Shigeo Sato
- Stowers Institute for Medical Research, Kansas City, Missouri 64110 and the Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110 and the Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110 and the Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160
| | - Thomas G Boyer
- Institute of Biotechnology and Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245.
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Krycer JR, Pang CNI, Wilkins MR. High throughput protein-protein interaction data: clues for the architecture of protein complexes. Proteome Sci 2008; 6:32. [PMID: 19032795 PMCID: PMC2621150 DOI: 10.1186/1477-5956-6-32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 11/26/2008] [Indexed: 11/23/2022] Open
Abstract
Background High-throughput techniques are becoming widely used to study protein-protein interactions and protein complexes on a proteome-wide scale. Here we have explored the potential of these techniques to accurately determine the constituent proteins of complexes and their architecture within the complex. Results Two-dimensional representations of the 19S and 20S proteasome, mediator, and SAGA complexes were generated and overlaid with high quality pairwise interaction data, core-module-attachment classifications from affinity purifications of complexes and predicted domain-domain interactions. Pairwise interaction data could accurately determine the members of each complex, but was unexpectedly poor at deciphering the topology of proteins in complexes. Core and module data from affinity purification studies were less useful for accurately defining the member proteins of these complexes. However, these data gave strong information on the spatial proximity of many proteins. Predicted domain-domain interactions provided some insight into the topology of proteins within complexes, but was affected by a lack of available structural data for the co-activator complexes and the presence of shared domains in paralogous proteins. Conclusion The constituent proteins of complexes are likely to be determined with accuracy by combining data from high-throughput techniques. The topology of some proteins in the complexes will be able to be clearly inferred. We finally suggest strategies that can be employed to use high throughput interaction data to define the membership and understand the architecture of proteins in novel complexes.
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Carrera I, Treisman JE. Message in a nucleus: signaling to the transcriptional machinery. Curr Opin Genet Dev 2008; 18:397-403. [PMID: 18678250 DOI: 10.1016/j.gde.2008.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
Abstract
Tissue differentiation and signal transduction involve dramatic changes in gene expression. These changes can be brought about by the expression or activation of sequence-specific transcription factors. In order to regulate their target genes, such factors must navigate the intricate chromatin environment and engage the complex basal transcriptional machinery. We discuss three mechanisms through which signaling pathways can interact with complexes that alter chromatin structure or recruit RNA polymerase II. Signals that promote differentiation may alter the properties of such transcriptional regulatory complexes by incorporating tissue-specific subunits. Alternatively, adaptor subunits specialized to interact with specific transcription factors may allow a single complex to respond to multiple signals. Finally, individual regulatory proteins may integrate a variety of signals, allowing crosstalk between pathways.
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Affiliation(s)
- Inés Carrera
- Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, NYU School of Medicine, 540 First Avenue, New York, NY 10016, USA
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Bourbon HM. Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Res 2008; 36:3993-4008. [PMID: 18515835 PMCID: PMC2475620 DOI: 10.1093/nar/gkn349] [Citation(s) in RCA: 254] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The multisubunit Mediator (MED) complex bridges DNA-bound transcriptional regulators to the RNA polymerase II (PolII) initiation machinery. In yeast, the 25 MED subunits are distributed within three core subcomplexes and a separable kinase module composed of Med12, Med13 and the Cdk8-CycC pair thought to control the reversible interaction between MED and PolII by phosphorylating repeated heptapeptides within the Rpb1 carboxyl-terminal domain (CTD). Here, MED conservation has been investigated across the eukaryotic kingdom. Saccharomyces cerevisiae Med2, Med3/Pgd1 and Med5/Nut1 subunits are apparent homologs of metazoan Med29/Intersex, Med27/Crsp34 and Med24/Trap100, respectively, and these and other 30 identified human MED subunits have detectable counterparts in the amoeba Dictyostelium discoideum, indicating that none is specific to metazoans. Indeed, animal/fungal subunits are also conserved in plants, green and red algae, entamoebids, oomycetes, diatoms, apicomplexans, ciliates and the 'deep-branching' protists Trichomonas vaginalis and Giardia lamblia. Surprisingly, although lacking CTD heptads, T. vaginalis displays 44 MED subunit homologs, including several CycC, Med12 and Med13 paralogs. Such observations have allowed the identification of a conserved 17-subunit framework around which peripheral subunits may be assembled, and support a very ancient eukaryotic origin for a large, four-module MED. The implications of this comprehensive work for MED structure-function relationships are discussed.
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Affiliation(s)
- Henri-Marc Bourbon
- Centre de Biologie du Développement, UMR5547 CNRS/Toulouse III, IFR109, Université Paul Sabatier, 31062 Toulouse, France.
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Bjornsdottir G, Myers LC. Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box. Nucleic Acids Res 2008; 36:2906-16. [PMID: 18385157 PMCID: PMC2396422 DOI: 10.1093/nar/gkn130] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In Saccharomyces cerevisiae, multiple approaches have arrived at a consensus TATA box sequence of TATA(T/A)A(A/T)(A/G). TATA-binding protein (TBP) affinity alone does not determine TATA box function. To discover how a minimal set of factors required for basal and activated transcription contributed to the sequence requirements for a functional TATA box, we performed transcription reactions using highly purified proteins and CYC1 promoter TATA box mutants. The TATA box consensus sequence is a good predictor of promoter activity. However, several nonconsensus sequences are almost fully functional, indicating that mechanistic requirements are not the only selective pressure on the TATA box. We also found that the effect of a mutation at a certain position is often dependent on other bases within a particular TATA box. Although activators and coactivators strongly influence TBP recruitment and stability at promoters, neither Mediator, the activator Gal4-V16, nor TFIID specifically compensate for the low transcription levels of the weak TATA boxes. The addition of Mediator to purified transcription reactions did, however, increase the functional selectivity for certain consensus TATA sequences. Transcription in whole-cell extracts or in vivo with these TATA box mutants indicated that factors, other than those in our purified system, may help initiate transcription from weak TATA boxes.
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Affiliation(s)
- Gudrun Bjornsdottir
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA
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50
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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