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Rojas DA, Urbina F, Valenzuela-Pérez L, Leiva L, Miralles VJ, Maldonado E. Initiator-Directed Transcription: Fission Yeast Nmtl Initiator Directs Preinitiation Complex Formation and Transcriptional Initiation. Genes (Basel) 2022; 13:genes13020256. [PMID: 35205301 PMCID: PMC8871863 DOI: 10.3390/genes13020256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
The initiator element is a core promoter element encompassing the transcription start site, which is found in yeast, Drosophila, and human promoters. This element is observed in TATA-less promoters. Several studies have defined transcription factor requirements and additional cofactors that are needed for transcription initiation of initiator-containing promoters. However, those studies have been performed with additional core promoters in addition to the initiator. In this work, we have defined the pathway of preinitiation complex formation on the fission yeast nmt1 gene promoter, which contains a functional initiator with striking similarity to the initiator of the human dihydrofolate reductase (hDHFR) gene and to the factor requirement for transcription initiation of the nmt1 gene promoter. The results show that the nmt1 gene promoter possesses an initiator encompassing the transcription start site, and several conserved base positions are required for initiator function. A preinitiation complex formation on the nmt1 initiator can be started by TBP/TFIIA or TBP/TFIIB, but not TBP alone, and afterwards follows the same pathway as preinitiation complex formation on TATA-containing promoters. Transcription initiation is dependent on the general transcription factors TBP, TFIIB, TFIIE, TFIIF, TFIIH, RNA polymerase II, Mediator, and a cofactor identified as transcription cofactor for initiator function (TCIF), which is a high-molecular-weight protein complex of around 500 kDa. However, the TAF subunits of TFIID were not required for the nmt1 initiator transcription, as far as we tested. We also demonstrate that other initiators of the nmt1/hDHFR family can be transcribed in fission yeast whole-cell extracts.
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Affiliation(s)
- Diego A. Rojas
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910132, Chile
- Correspondence: address: (D.A.R.); (E.M.)
| | - Fabiola Urbina
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile; (F.U.); (L.V.-P.); (L.L.)
| | - Lucía Valenzuela-Pérez
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile; (F.U.); (L.V.-P.); (L.L.)
| | - Lorenzo Leiva
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile; (F.U.); (L.V.-P.); (L.L.)
| | - Vicente J. Miralles
- Departamento Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Valencia, 46010 Valencia, Spain;
| | - Edio Maldonado
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile; (F.U.); (L.V.-P.); (L.L.)
- Correspondence: address: (D.A.R.); (E.M.)
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2
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Lee WK, Cheng SY. Targeting transcriptional regulators for treatment of anaplastic thyroid cancer. JOURNAL OF CANCER METASTASIS AND TREATMENT 2021; 7. [PMID: 34761120 PMCID: PMC8577520 DOI: 10.20517/2394-4722.2021.58] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dysregulation of genes perpetuates cancer progression. During carcinogenesis, cancer cells acquire dependency of aberrant transcriptional programs (known as “transcription addiction”) to meet the high demands for uncontrolled proliferation. The needs for particular transcription programs for cancer growth could be cancer-type-selective. The dependencies of certain transcription regulators could be exploited for therapeutic benefits. Anaplastic thyroid cancer (ATC) is an extremely aggressive human cancer for which new treatment modalities are urgently needed. Its resistance to conventional treatments and the lack of therapeutic options for improving survival might have been attributed to extensive genetic heterogeneity due to subsequent evolving genetic alterations and clonal selections during carcinogenesis. Despite this genetic complexity, mounting evidence has revealed a characteristic transcriptional addiction of ATC cells resulting in evolving diverse oncogenic signaling for cancer cell survival. The transcriptional addiction has presented a huge challenge for effective targeting as shown by the failure of previous targeted therapies. However, an emerging notion is that many different oncogenic signaling pathways activated by multiple upstream driver mutations might ultimately converge on the transcriptional responses, which would provide an opportunity to target transcriptional regulators for treatment of ATC. Here, we review the current understanding of how genetic alterations in cancer distorted the transcription program, leading to acquisition of transcriptional addiction. We also highlight recent findings from studies aiming to exploit the opportunity for targeting transcription regulators as potential therapeutics for ATC.
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Affiliation(s)
- Woo Kyung Lee
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sheue-Yann Cheng
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Cevher MA. Reconstitution of Pol II (G) responsive form of the human Mediator complex. Turk J Biol 2021; 45:253-261. [PMID: 34377050 PMCID: PMC8313941 DOI: 10.3906/biy-2009-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/16/2021] [Indexed: 01/15/2023] Open
Abstract
RNA polymerase II (Pol II) is a 12 subunit protein complex from yeast to human that is required for gene expression. Gdown1 containing Pol II [Pol II (G)] is a special form of Pol II that is catalytically inactive and heavily depends on the 30-subunit Mediator complex for its activator and basal dependent function in vitro. Here we report for the first time, the identification and the generation of a 15-subunit human Mediator complex via the novel multibac baculovirus expression system that is fully responsive to Pol II (G). Our results show complete recovery of Pol II (G) dependent transcription both with full 30-subunit Mediator and also with 15-subunit recombinant Mediator that we synthesized. Moreover, we also show that the recombinant Mediator interacts with Pol II (G) as well. These results enlighten us towards understanding how a certain population of Pol II that is involved in selected gene regulation is activated by Mediator complex.
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Affiliation(s)
- Murat Alper Cevher
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara Turkey.,Visiting Assistant Professor, Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York USA
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4
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Chen X, Yin X, Li J, Wu Z, Qi Y, Wang X, Liu W, Xu Y. Structures of the human Mediator and Mediator-bound preinitiation complex. Science 2021; 372:science.abg0635. [DOI: 10.1126/science.abg0635] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/15/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022]
Abstract
The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)–mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)–mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module–extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xiaotong Yin
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jiabei Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zihan Wu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yilun Qi
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
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5
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Al-Husini N, Medler S, Ansari A. Crosstalk of promoter and terminator during RNA polymerase II transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194657. [PMID: 33246184 DOI: 10.1016/j.bbagrm.2020.194657] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
The transcription cycle of RNAPII is comprised of three consecutive steps; initiation, elongation and termination. It has been assumed that the initiation and termination steps occur in spatial isolation, essentially as independent events. A growing body of evidence, however, has challenged this dogma. First, factors involved in initiation and termination exhibit both a genetic and a physical interaction during transcription. Second, the initiation and termination factors have been found to occupy both ends of a transcribing gene. Third, physical interaction of initiation and termination factors occupying distal ends of a gene sometime results in the entire terminator region of a genes looping back and contact its cognate promoter, thereby forming a looped gene architecture during transcription. A logical interpretation of these findings is that the initiation and termination steps of transcription do not occur in isolation. There is extensive communication of factors occupying promoter and terminator ends of a gene during transcription cycle. This review entails a discussion of the promoter-terminator crosstalk and its implication in the context of transcription.
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Affiliation(s)
- Nadra Al-Husini
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Scott Medler
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America.
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6
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Legrand N, Bretscher CL, Zielke S, Wilke B, Daude M, Fritz B, Diederich WE, Adhikary T. PPARβ/δ recruits NCOR and regulates transcription reinitiation of ANGPTL4. Nucleic Acids Res 2019; 47:9573-9591. [PMID: 31428774 PMCID: PMC6765110 DOI: 10.1093/nar/gkz685] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/20/2019] [Accepted: 07/28/2019] [Indexed: 12/24/2022] Open
Abstract
In the absence of ligands, the nuclear receptor PPARβ/δ recruits the NCOR and SMRT corepressors, which form complexes with HDAC3, to canonical target genes. Agonistic ligands cause dissociation of corepressors and enable enhanced transcription. Vice versa, synthetic inverse agonists augment corepressor recruitment and repression. Both basal repression of the target gene ANGPTL4 and reinforced repression elicited by inverse agonists are partially insensitive to HDAC inhibition. This raises the question how PPARβ/δ represses transcription mechanistically. We show that the PPARβ/δ inverse agonist PT-S264 impairs transcription initiation by decreasing recruitment of activating Mediator subunits, RNA polymerase II, and TFIIB, but not of TFIIA, to the ANGPTL4 promoter. Mass spectrometry identifies NCOR as the main PT-S264-dependent interactor of PPARβ/δ. Reconstitution of knockout cells with PPARβ/δ mutants deficient in basal repression results in diminished recruitment of NCOR, SMRT, and HDAC3 to PPAR target genes, while occupancy by RNA polymerase II is increased. PT-S264 restores binding of NCOR, SMRT, and HDAC3 to the mutants, resulting in reduced polymerase II occupancy. Our findings corroborate deacetylase-dependent and -independent repressive functions of HDAC3-containing complexes, which act in parallel to downregulate transcription.
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Affiliation(s)
- Nathalie Legrand
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Clemens L Bretscher
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Svenja Zielke
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Bernhard Wilke
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Medicine, Institute for Medical Bioinformatics and Biostatistics, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Michael Daude
- Core Facility Medicinal Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Barbara Fritz
- Centre for Human Genetics, Universitätsklinikum Giessen und Marburg GmbH, Baldingerstrasse, 35043 Marburg, Germany
| | - Wibke E Diederich
- Core Facility Medicinal Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Pharmacy, Institute for Pharmaceutical Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Till Adhikary
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Medicine, Institute for Medical Bioinformatics and Biostatistics, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
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7
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Smad7:β-catenin complex regulates myogenic gene transcription. Cell Death Dis 2019; 10:387. [PMID: 31097718 PMCID: PMC6522533 DOI: 10.1038/s41419-019-1615-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/30/2019] [Accepted: 04/23/2019] [Indexed: 12/17/2022]
Abstract
Recent reports indicate that Smad7 promotes skeletal muscle differentiation and growth. We previously documented a non-canonical role of nuclear Smad7 during myogenesis, independent of its role in TGF-β signaling. Here further characterization of the myogenic function of Smad7 revealed β-catenin as a Smad7 interacting protein. Biochemical analysis identified a Smad7 interaction domain (SID) between aa575 and aa683 of β-catenin. Reporter gene analysis and chromatin immunoprecipitation demonstrated that Smad7 and β-catenin are cooperatively recruited to the extensively characterized ckm promoter proximal region to facilitate its muscle restricted transcriptional activation in myogenic cells. Depletion of endogenous Smad7 and β-catenin in muscle cells reduced ckm promoter activity indicating their role during myogenesis. Deletion of the β-catenin SID substantially reduced the effect of Smad7 on the ckm promoter and exogenous expression of SID abolished β-catenin function, indicating that SID functions as a trans dominant-negative regulator of β-catenin activity. β-catenin interaction with the Mediator kinase complex through its Med12 subunit led us to identify MED13 as an additional Smad7-binding partner. Collectively, these studies document a novel function of a Smad7-MED12/13-β-catenin complex at the ckm locus, indicating a key role of this complex in the program of myogenic gene expression underlying skeletal muscle development and regeneration.
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8
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Lee HJ. The Role of Tripartite Motif Family Proteins in TGF-β Signaling Pathway and Cancer. J Cancer Prev 2018; 23:162-169. [PMID: 30671398 PMCID: PMC6330992 DOI: 10.15430/jcp.2018.23.4.162] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 12/15/2022] Open
Abstract
TGF-β signaling plays a tumor suppressive role in normal and premalignant cells but promotes tumor progression during the late stages of tumor development. The TGF-β signaling pathway is tightly regulated at various levels, including transcriptional and post-translational mechanisms. Ubiquitination of signaling components, such as receptors and Smad proteins is one of the key regulatory mechanisms of TGF-β signaling. Tripartite motif (TRIM) family of proteins is a highly conserved group of E3 ubiquitin ligase proteins that have been implicated in a variety of cellular functions, including cell growth, differentiation, immune response, and carcinogenesis. Recent emerging studies have shown that some TRIM family proteins function as important regulators in tumor initiation and progression. This review summarizes current knowledge of TRIM family proteins regulating the TGF-β signaling pathway with relevance to cancer.
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Affiliation(s)
- Ho-Jae Lee
- Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon, Korea
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9
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Mediator, known as a coactivator, can act in transcription initiation in an activator-independent manner in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:687-696. [DOI: 10.1016/j.bbagrm.2018.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 01/20/2023]
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10
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Dimitrova E, Kondo T, Feldmann A, Nakayama M, Koseki Y, Konietzny R, Kessler BM, Koseki H, Klose RJ. FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment. eLife 2018; 7:e37084. [PMID: 29809150 PMCID: PMC5997449 DOI: 10.7554/elife.37084] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/26/2018] [Indexed: 01/05/2023] Open
Abstract
CpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to CpG island-associated promoters of non-transcribed developmental genes to prime these genes for activation during cell lineage commitment. We further show that recognition of CpG islands by FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment.
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Affiliation(s)
- Emilia Dimitrova
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Takashi Kondo
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | | | - Manabu Nakayama
- Department of Technology DevelopmentKazusa DNA Research InstituteKisarazuJapan
| | - Yoko Koseki
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Rebecca Konietzny
- Nuffield Department of MedicineTDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Benedikt M Kessler
- Nuffield Department of MedicineTDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Haruhiko Koseki
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
- CRESTJapan Science and Technology AgencyKawaguchiJapan
| | - Robert J Klose
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
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11
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Hayden MA, Ordulu Z, Gallagher CS, Quade BJ, Anchan RM, Middleton NR, Srouji SS, Stewart EA, Morton CC. Clinical, pathologic, cytogenetic, and molecular profiling in self-identified black women with uterine leiomyomata. Cancer Genet 2018; 222-223:1-8. [PMID: 29666002 DOI: 10.1016/j.cancergen.2018.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 11/16/2022]
Abstract
Black women are disproportionately affected by uterine leiomyomata (UL), or fibroids, compared to other racial groups, having a greater lifetime risk of developing UL and an earlier age of diagnosis. In order to elucidate molecular and genetic mechanisms responsible for the increased prevalence and morbidity associated with UL in black women, clinical, pathologic, cytogenetic, and select molecular profiling (MED12 mutation analysis) of 75 self-reported black women undergoing surgical treatment for UL was performed. Our observations are broadly representative of previous cytogenetic studies of UL: karyotypically abnormal tumors were detected in 30.7% of women and 17.4% of analyzed tumors. No notable association was observed between race and increased occurrence of cytogenetic abnormalities that might contribute to any population-specific morbidity or prevalence rate. Our data on MED12 mutation analyses (73.2% of tumors harbored a MED12 mutation) provide additional support for a significant role of MED12 in tumorigenesis. Although the effect of MED12-mediated tumorigenesis appears significant irrespective of race, other genetic events such as the distribution of karyotypic abnormalities appear differently in black women. This case series indicates that presently recognized genetic and molecular characteristics of UL do not appear to explain the increased prevalence and morbidity of UL in black women.
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Affiliation(s)
- Mark A Hayden
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Zehra Ordulu
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - C Scott Gallagher
- Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bradley J Quade
- Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Raymond M Anchan
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Nia Robinson Middleton
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Serene S Srouji
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth A Stewart
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN 55905, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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12
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Malik N, Agarwal P, Tyagi A. Emerging functions of multi-protein complex Mediator with special emphasis on plants. Crit Rev Biochem Mol Biol 2017; 52:475-502. [DOI: 10.1080/10409238.2017.1325830] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Akhilesh Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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13
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Spitler KM, Ponce JM, Oudit GY, Hall DD, Grueter CE. Cardiac Med1 deletion promotes early lethality, cardiac remodeling, and transcriptional reprogramming. Am J Physiol Heart Circ Physiol 2017; 312:H768-H780. [PMID: 28159809 PMCID: PMC5407164 DOI: 10.1152/ajpheart.00728.2016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/30/2017] [Accepted: 01/30/2017] [Indexed: 12/18/2022]
Abstract
The mediator complex, a multisubunit nuclear complex, plays an integral role in regulating gene expression by acting as a bridge between transcription factors and RNA polymerase II. Genetic deletion of mediator subunit 1 (Med1) results in embryonic lethality, due in large part to impaired cardiac development. We first established that Med1 is dynamically expressed in cardiac development and disease, with marked upregulation of Med1 in both human and murine failing hearts. To determine if Med1 deficiency protects against cardiac stress, we generated two cardiac-specific Med1 knockout mouse models in which Med1 is conditionally deleted (Med1cKO mice) or inducibly deleted in adult mice (Med1cKO-MCM mice). In both models, cardiac deletion of Med1 resulted in early lethality accompanied by pronounced changes in cardiac function, including left ventricular dilation, decreased ejection fraction, and pathological structural remodeling. We next defined how Med1 deficiency alters the cardiac transcriptional profile using RNA-sequencing analysis. Med1cKO mice demonstrated significant dysregulation of genes related to cardiac metabolism, in particular genes that are coordinated by the transcription factors Pgc1α, Pparα, and Errα. Consistent with the roles of these transcription factors in regulation of mitochondrial genes, we observed significant alterations in mitochondrial size, mitochondrial gene expression, complex activity, and electron transport chain expression under Med1 deficiency. Taken together, these data identify Med1 as an important regulator of vital cardiac gene expression and maintenance of normal heart function.NEW & NOTEWORTHY Disruption of transcriptional gene expression is a hallmark of dilated cardiomyopathy; however, its etiology is not well understood. Cardiac-specific deletion of the transcriptional coactivator mediator subunit 1 (Med1) results in dilated cardiomyopathy, decreased cardiac function, and lethality. Med1 deletion disrupted cardiac mitochondrial and metabolic gene expression patterns.
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Affiliation(s)
- Kathryn M Spitler
- Division of Cardiovascular Medicine, Department of Internal Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, Iowa; and
| | - Jessica M Ponce
- Division of Cardiovascular Medicine, Department of Internal Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, Iowa; and
| | - Gavin Y Oudit
- Mazankowski Alberta Heart Institute Canada Research Chair in Heart Failure, Division of Cardiology, Walter Mackenzie Health Sciences Centre, Edmonton, Alberta, Canada
| | - Duane D Hall
- Division of Cardiovascular Medicine, Department of Internal Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, Iowa; and
| | - Chad E Grueter
- Division of Cardiovascular Medicine, Department of Internal Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, Iowa; and
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14
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Montes M, Moreira-Ramos S, Rojas DA, Urbina F, Käufer NF, Maldonado E. RNA polymerase II components and Rrn7 form a preinitiation complex on the HomolD box to promote ribosomal protein gene expression in Schizosaccharomyces pombe. FEBS J 2017; 284:615-633. [PMID: 28060464 DOI: 10.1111/febs.14006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/02/2016] [Accepted: 01/05/2017] [Indexed: 01/29/2023]
Abstract
In Schizosaccharomyces pombe, ribosomal protein gene (RPG) promoters contain a TATA box analog, the HomolD box, which is bound by the Rrn7 protein. Despite the importance of ribosome biogenesis for cell survival, the mechanisms underlying RPG transcription remain unknown. In this study, we found that components of the RNA polymerase II (RNAPII) system, consisting of the initiation or general transcription factors (GTFs) TFIIA, IIB, IIE, TATA-binding protein (TBP) and the RNAPII holoenzyme, interacted directly with Rrn7 in vitro, and were able to form a preinitiation complex (PIC) on the HomolD box. PIC complex formation follows an ordered pathway on these promoters. The GTFs and RNAPII can also be cross-linked to HomolD-containing promoters in vivo. In an in vitro reconstituted transcription system, RNAPII components and Rrn7 were necessary for HomolD-directed transcription. The Mediator complex was required for basal transcription from those promoters in whole cell extract (WCE). The Med17 subunit of Mediator also can be cross-linked to the promoter region of HomolD-containing promoters in vivo, suggesting the presence of the Mediator complex on HomolD box-containing promoters. Together, these data show that components of the RNAPII machinery and Rrn7 participate in the PIC assembly on the HomolD box, thereby directing RPG transcription.
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Affiliation(s)
- Matías Montes
- Programa Biología Celular y Molecular, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Sandra Moreira-Ramos
- Programa Biología Celular y Molecular, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Diego A Rojas
- Microbiología y Micología, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Fabiola Urbina
- Programa Biología Celular y Molecular, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Norbert F Käufer
- Institute of Genetics, Technische Universität Braunschweig, Germany
| | - Edio Maldonado
- Programa Biología Celular y Molecular, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
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15
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Malik S, Molina H, Xue Z. PIC Activation through Functional Interplay between Mediator and TFIIH. J Mol Biol 2016; 429:48-63. [PMID: 27916598 DOI: 10.1016/j.jmb.2016.11.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/26/2016] [Accepted: 11/27/2016] [Indexed: 10/20/2022]
Abstract
The multiprotein Mediator coactivator complex functions in large part by controlling the formation and function of the promoter-bound preinitiation complex (PIC), which consists of RNA polymerase II and general transcription factors. However, precisely how Mediator impacts the PIC, especially post-recruitment, has remained unclear. Here, we have studied Mediator effects on basal transcription in an in vitro transcription system reconstituted from purified components. Our results reveal a close functional interplay between Mediator and TFIIH in the early stages of PIC development. We find that under conditions when TFIIH is not normally required for transcription, Mediator actually represses transcription. TFIIH, whose recruitment to the PIC is known to be facilitated by the Mediator, then acts to relieve Mediator-induced repression to generate an active form of the PIC. Gel mobility shift analyses of PICs and characterization of TFIIH preparations carrying mutant XPB translocase subunit further indicate that this relief of repression is achieved through expending energy via ATP hydrolysis, suggesting that it is coupled to TFIIH's established promoter melting activity. Our interpretation of these results is that Mediator functions as an assembly factor that facilitates PIC maturation through its various stages. Whereas the overall effect of the Mediator is to stimulate basal transcription, its initial engagement with the PIC generates a transcriptionally inert PIC intermediate, which necessitates energy expenditure to complete the process.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Zhu Xue
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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16
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Sato S, Tomomori-Sato C, Tsai KL, Yu X, Sardiu M, Saraf A, Washburn MP, Florens L, Asturias FJ, Conaway RC, Conaway JW. Role for the MED21-MED7 Hinge in Assembly of the Mediator-RNA Polymerase II Holoenzyme. J Biol Chem 2016; 291:26886-26898. [PMID: 27821593 DOI: 10.1074/jbc.m116.756098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/03/2016] [Indexed: 11/06/2022] Open
Abstract
Mediator plays an integral role in activation of RNA polymerase II (Pol II) transcription. A key step in activation is binding of Mediator to Pol II to form the Mediator-Pol II holoenzyme. Here, we exploit a combination of biochemistry and macromolecular EM to investigate holoenzyme assembly. We identify a subset of human Mediator head module subunits that bind Pol II independent of other subunits and thus probably contribute to a major Pol II binding site. In addition, we show that binding of human Mediator to Pol II depends on the integrity of a conserved "hinge" in the middle module MED21-MED7 heterodimer. Point mutations in the hinge region leave core Mediator intact but lead to increased disorder of the middle module and markedly reduced affinity for Pol II. These findings highlight the importance of Mediator conformation for holoenzyme assembly.
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Affiliation(s)
- Shigeo Sato
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | | | - Kuang-Lei Tsai
- the Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, and
| | - Xiaodi Yu
- the Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, and
| | - Mihaela Sardiu
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Anita Saraf
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Michael P Washburn
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110.,the Departments of Pathology and Laboratory Medicine and
| | - Laurence Florens
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Francisco J Asturias
- the Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, and
| | - Ronald C Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110.,Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160
| | - Joan W Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110, .,Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160
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17
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CDK8 Expression in Extrauterine Leiomyosarcoma Correlates With Tumor Stage and Progression. Appl Immunohistochem Mol Morphol 2016; 26:161-164. [PMID: 27389556 DOI: 10.1097/pai.0000000000000409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Mediator is a multiprotein complex that acts as a versatile transcription coactivator in eukaryotes. CDK8 kinase complex is a 4-protein subunit of the mediator complex that can act as a transcriptional repressor or coactivator, depending on the specific pathways involved. Although the role of MED12 exon 2 mutations is documented in the pathogenesis of uterine leiomyomas, its role in extrauterine smooth muscle tumorigenesis is less clear. Similarly, there is a paucity of data on the role of CDK8 in extrauterine smooth muscle tumorigenesis and progression. Our study correlates immunohistochemical expression of CDK8 and MED12 with clinical and pathologic parameters in extrauterine leiomyosarcomas. Immunohistochemical expression of CDK8 and MED12 in leiomyosarcomas was correlated with the tumor grade, stage, and the presence of local recurrence or metastasis. MED12 was expressed in the majority of leiomyosarcomas regardless of their stage or grade. CDK8 expression was lost in 1 of 6 pT1 tumors, compared with 9 of 10 pT2 tumors (P=0.0076). When the second group was expanded to include those tumors that did not have a recorded pathologic stage but had local recurrence and distant metastases, the difference in CDK8 expression was also statistically significant. Loss of CDK8 expression by immunohistochemistry is more prevalent in somatic leiomyosarcomas presenting at a higher histopathologic stage, as well as with local and distant recurrence, and can be used to enhance the current predictive parameters.
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18
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Wang C, Yao J, Du X, Zhang Y, Sun Y, Rollins JA, Mou Z. The Arabidopsis Mediator Complex Subunit16 Is a Key Component of Basal Resistance against the Necrotrophic Fungal Pathogen Sclerotinia sclerotiorum. PLANT PHYSIOLOGY 2015; 169:856-72. [PMID: 26143252 PMCID: PMC4577384 DOI: 10.1104/pp.15.00351] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/01/2015] [Indexed: 05/19/2023]
Abstract
Although Sclerotinia sclerotiorum is a devastating necrotrophic fungal plant pathogen in agriculture, the virulence mechanisms utilized by S. sclerotiorum and the host defense mechanisms against this pathogen have not been fully understood. Here, we report that the Arabidopsis (Arabidopsis thaliana) Mediator complex subunit MED16 is a key component of basal resistance against S. sclerotiorum. Mutants of MED16 are markedly more susceptible to S. sclerotiorum than mutants of 13 other Mediator subunits, and med16 has a much stronger effect on S. sclerotiorum-induced transcriptome changes compared with med8, a mutation not altering susceptibility to S. sclerotiorum. Interestingly, med16 is also more susceptible to S. sclerotiorum than coronatine-insensitive1-1 (coi1-1), which is the most susceptible mutant reported so far. Although the jasmonic acid (JA)/ethylene (ET) defense pathway marker gene PLANT DEFENSIN1.2 (PDF1.2) cannot be induced in either med16 or coi1-1, basal transcript levels of PDF1.2 in med16 are significantly lower than in coi1-1. Furthermore, ET-induced suppression of JA-activated wound responses is compromised in med16, suggesting a role for MED16 in JA-ET cross talk. Additionally, MED16 is required for the recruitment of RNA polymerase II to PDF1.2 and OCTADECANOID-RESPONSIVE ARABIDOPSIS ETHYLENE/ETHYLENE-RESPONSIVE FACTOR59 (ORA59), two target genes of both JA/ET-mediated and the transcription factor WRKY33-activated defense pathways. Finally, MED16 is physically associated with WRKY33 in yeast and in planta, and WRKY33-activated transcription of PDF1.2 and ORA59 as well as resistance to S. sclerotiorum depends on MED16. Taken together, these results indicate that MED16 regulates resistance to S. sclerotiorum by governing both JA/ET-mediated and WRKY33-activated defense signaling in Arabidopsis.
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Affiliation(s)
- Chenggang Wang
- Department of Microbiology and Cell Science (C.W., Z.M.) and Department of Plant Pathology (J.A.R.), University of Florida, Gainesville, Florida 32611;Department of Microbiology and Immunology, University of Buffalo, Buffalo, New York 14203 (J.Y., Y.S.);College of Life Science, Hubei University, Wuhan 430062, China (X.D.); andInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32601 (Y.Z.)
| | - Jin Yao
- Department of Microbiology and Cell Science (C.W., Z.M.) and Department of Plant Pathology (J.A.R.), University of Florida, Gainesville, Florida 32611;Department of Microbiology and Immunology, University of Buffalo, Buffalo, New York 14203 (J.Y., Y.S.);College of Life Science, Hubei University, Wuhan 430062, China (X.D.); andInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32601 (Y.Z.)
| | - Xuezhu Du
- Department of Microbiology and Cell Science (C.W., Z.M.) and Department of Plant Pathology (J.A.R.), University of Florida, Gainesville, Florida 32611;Department of Microbiology and Immunology, University of Buffalo, Buffalo, New York 14203 (J.Y., Y.S.);College of Life Science, Hubei University, Wuhan 430062, China (X.D.); andInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32601 (Y.Z.)
| | - Yanping Zhang
- Department of Microbiology and Cell Science (C.W., Z.M.) and Department of Plant Pathology (J.A.R.), University of Florida, Gainesville, Florida 32611;Department of Microbiology and Immunology, University of Buffalo, Buffalo, New York 14203 (J.Y., Y.S.);College of Life Science, Hubei University, Wuhan 430062, China (X.D.); andInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32601 (Y.Z.)
| | - Yijun Sun
- Department of Microbiology and Cell Science (C.W., Z.M.) and Department of Plant Pathology (J.A.R.), University of Florida, Gainesville, Florida 32611;Department of Microbiology and Immunology, University of Buffalo, Buffalo, New York 14203 (J.Y., Y.S.);College of Life Science, Hubei University, Wuhan 430062, China (X.D.); andInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32601 (Y.Z.)
| | - Jeffrey A Rollins
- Department of Microbiology and Cell Science (C.W., Z.M.) and Department of Plant Pathology (J.A.R.), University of Florida, Gainesville, Florida 32611;Department of Microbiology and Immunology, University of Buffalo, Buffalo, New York 14203 (J.Y., Y.S.);College of Life Science, Hubei University, Wuhan 430062, China (X.D.); andInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32601 (Y.Z.)
| | - Zhonglin Mou
- Department of Microbiology and Cell Science (C.W., Z.M.) and Department of Plant Pathology (J.A.R.), University of Florida, Gainesville, Florida 32611;Department of Microbiology and Immunology, University of Buffalo, Buffalo, New York 14203 (J.Y., Y.S.);College of Life Science, Hubei University, Wuhan 430062, China (X.D.); andInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32601 (Y.Z.)
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19
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Croce S, Chibon F. MED12 and uterine smooth muscle oncogenesis: State of the art and perspectives. Eur J Cancer 2015; 51:1603-10. [DOI: 10.1016/j.ejca.2015.04.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 10/23/2022]
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20
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Samanta S, Thakur JK. Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:757. [PMID: 26442070 PMCID: PMC4584954 DOI: 10.3389/fpls.2015.00757] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/04/2015] [Indexed: 05/19/2023]
Abstract
Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either increase or decrease the rate of transcription. Mediator complex is one such cofactor, and recently has drawn a lot of interest because of its integrative power to converge different signaling pathways before channeling the transcription instructions to the RNA polymerase II machinery. Like yeast and metazoans, plants do possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Genetic, and molecular analyses have unraveled important regulatory roles of Mediator subunits at every stage of plant life cycle starting from flowering to embryo and organ development, to even size determination. It also contributes immensely to the survival of plants against different environmental vagaries by the timely activation of its resistance mechanisms. Here, we have provided an overview of plant Mediator complex starting from its discovery to regulation of stoichiometry of its subunits. We have also reviewed involvement of different Mediator subunits in different processes and pathways including defense response pathways evoked by diverse biotic cues. Wherever possible, attempts have been made to provide mechanistic insight of Mediator's involvement in these processes.
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Affiliation(s)
| | - Jitendra K. Thakur
- *Correspondence: Jitendra K. Thakur, Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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21
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Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat Struct Mol Biol 2014; 21:1028-34. [PMID: 25383669 PMCID: PMC4259101 DOI: 10.1038/nsmb.2914] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/09/2014] [Indexed: 01/01/2023]
Abstract
The evolutionarily conserved Mediator complex is a critical coactivator for RNA polymerase II (Pol II)-mediated transcription. Here, we report the reconstitution of a functional 15-subunit human core Mediator complex and its characterization by functional assays and chemical cross-linking coupled to mass spectrometry (CX-MS). Whereas the reconstituted head and middle modules can stably associate, only with incorporation of MED14 into the bi-modular complex does it acquire basal and coactivator functions. This results from a dramatically enhanced ability of MED14-containing complexes to associate with Pol II. Altogether, our analyses identify MED14 as both an architectural and a functional backbone of the Mediator complex. We further establish a conditional requirement for metazoan-specific MED26 that becomes evident in the presence of heterologous nuclear factors. This general approach paves the way for systematically dissecting the multiple layers of functionalities associated with the Mediator complex.
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22
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A functional portrait of Med7 and the mediator complex in Candida albicans. PLoS Genet 2014; 10:e1004770. [PMID: 25375174 PMCID: PMC4222720 DOI: 10.1371/journal.pgen.1004770] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/22/2014] [Indexed: 11/19/2022] Open
Abstract
Mediator is a multi-subunit protein complex that regulates gene expression in eukaryotes by integrating physiological and developmental signals and transmitting them to the general RNA polymerase II machinery. We examined, in the fungal pathogen Candida albicans, a set of conditional alleles of genes encoding Mediator subunits of the head, middle, and tail modules that were found to be essential in the related ascomycete Saccharomyces cerevisiae. Intriguingly, while the Med4, 8, 10, 11, 14, 17, 21 and 22 subunits were essential in both fungi, the structurally highly conserved Med7 subunit was apparently non-essential in C. albicans. While loss of CaMed7 did not lead to loss of viability under normal growth conditions, it dramatically influenced the pathogen's ability to grow in different carbon sources, to form hyphae and biofilms, and to colonize the gastrointestinal tracts of mice. We used epitope tagging and location profiling of the Med7 subunit to examine the distribution of the DNA sites bound by Mediator during growth in either the yeast or the hyphal form, two distinct morphologies characterized by different transcription profiles. We observed a core set of 200 genes bound by Med7 under both conditions; this core set is expanded moderately during yeast growth, but is expanded considerably during hyphal growth, supporting the idea that Mediator binding correlates with changes in transcriptional activity and that this binding is condition specific. Med7 bound not only in the promoter regions of active genes but also within coding regions and at the 3′ ends of genes. By combining genome-wide location profiling, expression analyses and phenotyping, we have identified different Med7p-influenced regulons including genes related to glycolysis and the Filamentous Growth Regulator family. In the absence of Med7, the ribosomal regulon is de-repressed, suggesting Med7 is involved in central aspects of growth control. In this study, we have investigated Mediator function in the human fungal pathogen C. albicans. An initial screening of conditionally regulated Mediator subunits showed that the Med7 of C. albicans was not essential, in contrast to the situation noted for S. cerevisiae. While loss of CaMed7 did not lead to loss of viability under normal growth conditions, it dramatically influenced the pathogen's ability to grow in different carbon sources, to form hyphae and biofilms, and to colonize the gastrointestinal tracts of mice. We used location profiling to determine Mediator binding under yeast and hyphal morphologies characterized by different transcription profiles. We observed a core set of specific and common genes bound by Med7 under both conditions; this specific core set is expanded considerably during hyphal growth, supporting the idea that Mediator binding correlates with changes in transcriptional activity and that this binding is condition specific. Med7 bound not only in the promoter regions of active genes but also of inactive genes and within coding regions and at the 3′ ends of genes. By combining genome-wide location profiling, expression analyses and phenotyping, we have identified different Med7 regulons including genes related to glycolysis and the Filamentous Growth Regulator family.
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23
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Genomics of uterine leiomyomas: insights from high-throughput sequencing. Fertil Steril 2014; 102:621-9. [PMID: 25106763 DOI: 10.1016/j.fertnstert.2014.06.050] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/27/2014] [Accepted: 06/27/2014] [Indexed: 02/07/2023]
Abstract
Uterine leiomyomas are benign smooth-muscle tumors of extremely low malignant potential. Early work utilizing classical cytogenetics revealed that a subset of uterine leiomyomas harbor recurrent chromosomal rearrangements, such as translocations affecting the HMGA2 gene. Our understanding of the genetics of many tumor types has deepened remarkably with the emergence of next-generation sequencing technologies. Exome sequencing identified that the majority of leiomyomas display highly specific MED12 mutations. Further studies suggest that these MED12 hotspot mutations are also frequent in breast fibroadenomas, but not in other human tumors. Whole-genome sequencing showed that a subset of leiomyomas display complex chromosomal rearrangements resembling chromothripsis. These were formed in a single event of chromosomal breakage and random reassembly involving one or a limited number of chromosomes. Although most leiomyomas have been shown to arise independently, these studies also revealed that distinct nodules within a uterus may display identical genetic changes indicating a common clonal origin. A minority of leiomyomas were also found to display deletions within the COL4A5-COL4A6 genes, leading to upregulation of the adjacent gene IRS4. The findings derived from high-throughput sequencing combined with previous knowledge have led to an emerging molecular classification of leiomyomas, suggesting that there are several distinct pathogenic pathways involved in leiomyoma formation. The evidence points to at least 4 molecular subclasses: leiomyomas with MED12 mutation, FH inactivation, HMGA2 overexpression, and COL4A6-COL4A5 deletion. Elucidating the molecular pathogenesis of leiomyomas should be relevant for developing treatments for this very common disease.
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24
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Fuxreiter M, Tóth-Petróczy Á, Kraut DA, Matouschek AT, Lim RYH, Xue B, Kurgan L, Uversky VN. Disordered proteinaceous machines. Chem Rev 2014; 114:6806-43. [PMID: 24702702 PMCID: PMC4350607 DOI: 10.1021/cr4007329] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Ágnes Tóth-Petróczy
- Department
of Biological Chemistry, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Daniel A. Kraut
- Department
of Chemistry, Villanova University, 800 East Lancaster Avenue, Villanova, Pennsylvania 19085, United States
| | - Andreas T. Matouschek
- Section
of Molecular Genetics and Microbiology, Institute for Cellular &
Molecular Biology, The University of Texas
at Austin, 2506 Speedway, Austin, Texas 78712, United States
| | - Roderick Y. H. Lim
- Biozentrum
and the Swiss Nanoscience Institute, University
of Basel, Klingelbergstrasse
70, CH-4056 Basel, Switzerland
| | - Bin Xue
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Lukasz Kurgan
- Department
of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Vladimir N. Uversky
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute
for Biological Instrumentation, Russian
Academy of Sciences, 142290 Pushchino, Moscow Region 119991, Russia
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25
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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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26
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Xu W, Amire-Brahimi B, Xie XJ, Huang L, Ji JY. All-atomic molecular dynamic studies of human CDK8: insight into the A-loop, point mutations and binding with its partner CycC. Comput Biol Chem 2014; 51:1-11. [PMID: 24754906 DOI: 10.1016/j.compbiolchem.2014.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/23/2014] [Accepted: 03/24/2014] [Indexed: 12/31/2022]
Abstract
The Mediator, a conserved multisubunit protein complex in eukaryotic organisms, regulates gene expression by bridging sequence-specific DNA-binding transcription factors to the general RNA polymerase II machinery. In yeast, Mediator complex is organized in three core modules (head, middle and tail) and a separable 'CDK8 submodule' consisting of four subunits including Cyclin-dependent kinase CDK8 (CDK8), Cyclin C (CycC), MED12, and MED13. The 3-D structure of human CDK8-CycC complex has been recently experimentally determined. To take advantage of this structure and the improved theoretical calculation methods, we have performed molecular dynamic simulations to study dynamics of CDK8 and two CDK8 point mutations (D173A and D189N), which have been identified in human cancers, with and without full length of the A-loop, as well as the binding between CDK8 and CycC. We found that CDK8 structure gradually loses two helical structures during the 50-ns molecular dynamic simulation, likely due to the presence of the full-length A-loop. In addition, our studies showed the hydrogen bond occupation of the CDK8 A-loop increases during the first 20-ns MD simulation and stays stable during the later 30-ns MD simulation. Four residues in the A-loop of CDK8 have high hydrogen bond occupation, while the rest residues have low or no hydrogen bond occupation. The hydrogen bond dynamic study of the A-loop residues exhibits three types of changes: increasing, decreasing, and stable. Furthermore, the 3-D structures of CDK8 point mutations D173A, D189N, T196A and T196D have been built by molecular modeling and further investigated by 50-ns molecular dynamic simulations. D173A has the highest average potential energy, while T196D has the lowest average potential energy, indicating that T196D is the most stable structure. Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex. Taken together, these analyses will improve our understanding of the exact functions of CDK8 and the interaction with its partner CycC.
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Affiliation(s)
- Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
| | - Benjamin Amire-Brahimi
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Xiao-Jun Xie
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Liying Huang
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA.
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27
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Mäkinen N, Heinonen HR, Sjöberg J, Taipale J, Vahteristo P, Aaltonen LA. Mutation analysis of components of the Mediator kinase module in MED12 mutation-negative uterine leiomyomas. Br J Cancer 2014; 110:2246-9. [PMID: 24642626 PMCID: PMC4007231 DOI: 10.1038/bjc.2014.138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/14/2014] [Accepted: 02/21/2014] [Indexed: 02/06/2023] Open
Abstract
Background: Kinase module of Mediator complex (‘CDK8 submodule') consists of four subunits: CDK8, Cyclin C, MED12, and MED13. Recently, we reported recurrent MED12 mutations in 70% of uterine leiomyomas. The aim of this study was to analyse whether mutations in other components of the module contribute to the development of these lesions. Methods: Mutation screening of altogether 70 MED12 mutation-negative uterine leiomyomas was carried out by direct sequencing. Results: None of the tumours displayed somatic mutations in the coding regions of CDK8/CDK19, CCNC, or MED13. Conclusions: Mutations in CDK8/CDK19, CCNC, and MED13 do not frequently contribute to genesis of uterine leiomyomas.
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Affiliation(s)
- N Mäkinen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - H-R Heinonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - J Sjöberg
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, PO Box 140, 00029 Helsinki, Finland
| | - J Taipale
- 1] Genome-Scale Biology Research Program and Department of Pathology, Haartman Institute, University of Helsinki, PO Box 63, 00014 Helsinki, Finland [2] Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - P Vahteristo
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
| | - L A Aaltonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, PO Box 63, 00014 Helsinki, Finland
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Villicaña C, Cruz G, Zurita M. The basal transcription machinery as a target for cancer therapy. Cancer Cell Int 2014; 14:18. [PMID: 24576043 PMCID: PMC3942515 DOI: 10.1186/1475-2867-14-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/21/2014] [Indexed: 01/11/2023] Open
Abstract
General transcription is required for the growth and survival of all living cells. However, tumor cells require extraordinary levels of transcription, including the transcription of ribosomal RNA genes by RNA polymerase I (RNPI) and mRNA by RNA polymerase II (RNPII). In fact, cancer cells have mutations that directly enhance transcription and are frequently required for cancer transformation. For example, the recent discovery that MYC enhances the transcription of the majority genes in the genome correlates with the fact that several transcription interfering drugs preferentially kill cancer cells. In recent years, advances in the mechanistic studies of the basal transcription machinery and the discovery of drugs that interfere with multiple components of transcription are being used to combat cancer. For example, drugs such as triptolide that targets the general transcription factors TFIIH and JQ1 to inhibit BRD4 are administered to target the high proliferative rate of cancer cells. Given the importance of finding new strategies to preferentially sensitize tumor cells, this review primarily focuses on several transcription inhibitory drugs to demonstrate that the basal transcription machinery constitutes a potential target for the design of novel cancer drugs. We highlight the drugs’ mechanisms for interfering with tumor cell survival, their importance in cancer treatment and the challenges of clinical application.
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Affiliation(s)
| | | | - Mario Zurita
- Departament of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico, Mexico.
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29
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Mahajan MA, Stanley FM. Insulin-activated Elk-1 recruits the TIP60/NuA4 complex to increase prolactin gene transcription. Mol Cell Endocrinol 2014; 382:159-169. [PMID: 24075908 DOI: 10.1016/j.mce.2013.09.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 11/17/2022]
Abstract
Insulin increases prolactin gene expression in GH4 cells through phosphorylation of Elk-1 (Jacob and Stanley, 2001). We preformed a reverse two-hybrid screen using Elk-1-B42 as bait to identify proteins from GH4 cells that might serve as co-activators or co-repressors for insulin-increased prolactin gene expression. A number of the components of the TIP60/NuA4 complex interacted with Elk-1 suggesting that Elk-1 might activate transcription by recruiting the TIP60 chromatin-remodeling complex to the prolactin promoter. Inhibition of insulin-increased prolactin-luciferase expression by wild type and mutant adenovirus E1A protein provided physiological context for these yeast studies. Inhibition of histone deacetylases dramatically increased both basal and insulin-increased prolactin gene transcription. Co-immune precipitation experiments demonstrated Elk-1 and TIP60 associate in vitro. Transient or stable expression of TIP60 activated insulin-increased prolactin gene expression while a mutated TIP60 blocked insulin-increased prolactin gene expression. Analysis of the prolactin mRNA by quantitative RT-PCR showed that insulin-increased prolactin mRNA accumulation and that this was inhibited in GH4 cells that stably expressed mutant TIP60. Finally, ChIP experiments demonstrate the insulin-dependent occupancy of the prolactin promoter by Elk-1 and TIP60. Our studies suggest that insulin activates prolactin gene transcription by activating Elk-1 that recruits the NuA4 complex to the promoter.
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Affiliation(s)
- Muktar A Mahajan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, United States
| | - Frederick M Stanley
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, United States; NYU Cancer Institute, New York University School of Medicine, New York, NY 10016, United States.
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30
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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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31
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Lacombe T, Poh SL, Barbey R, Kuras L. Mediator is an intrinsic component of the basal RNA polymerase II machinery in vivo. Nucleic Acids Res 2013; 41:9651-62. [PMID: 23963697 PMCID: PMC3834807 DOI: 10.1093/nar/gkt701] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mediator is a prominent multisubunit coactivator that functions as a bridge between gene-specific activators and the basal RNA polymerase (Pol) II initiation machinery. Here, we study the poorly documented role of Mediator in basal, or activator-independent, transcription in vivo. We show that Mediator is still present at the promoter when the Pol II machinery is recruited in the absence of an activator, in this case through a direct fusion between a basal transcription factor and a heterologous DNA binding protein bound to the promoter. Moreover, transcription resulting from activator-independent recruitment of the Pol II machinery is impaired by inactivation of the essential Mediator subunit Med17 due to the loss of Pol II from the promoter. Our results strongly support that Mediator is an integral component of the minimal machinery essential in vivo for stable Pol II association with the promoter.
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Affiliation(s)
- Thierry Lacombe
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, affiliated with Université Paris-Sud, Gif-sur-Yvette 91198, France
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32
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Zhang X, Yao J, Zhang Y, Sun Y, Mou Z. The Arabidopsis Mediator complex subunits MED14/SWP and MED16/SFR6/IEN1 differentially regulate defense gene expression in plant immune responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:484-97. [PMID: 23607369 DOI: 10.1111/tpj.12216] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 05/20/2023]
Abstract
Pathogen infection in plants triggers large-scale transcriptional changes, both locally and systemically. Emerging evidence suggests that the Arabidopsis Mediator complex plays a crucial role in these transcriptional changes. Mediator is highly conserved in eukaryotes, and its core comprises more than 20 subunits organized into three modules named head, middle and tail. The head and middle modules interact with general transcription factors and RNA polymerase II, whereas the tail module associates with activators, and signals through the head and middle modules to the basal transcription machinery. In Arabidopsis, three tail module subunits, MED14, MED15 and MED16, have been identified. Both MED15 and MED16 have been implicated in plant immunity, but the role of MED14 has not been established. Here, we report the characterization of an Arabidopsis T-DNA insertion mutant of the MED14 gene. Similarly to the med15 and/or med16 mutations, the med14 mutation significantly suppresses salicylic acid-induced defense responses, alters transcriptional changes induced by the avirulent bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000/avrRpt2, and renders plants susceptible to both Pst DC3000/avrRpt2 and Pst DC3000. The med14 mutation also completely compromises biological induction of systemic acquired resistance (SAR), indicating that the tail module as a whole is essential for SAR. Interestingly, unlike the med16 mutation, which differentially affects expression of several SAR positive and negative regulators, med14 inhibits induction of a large group of defense genes, including both SAR positive and negative regulators, suggesting that individual subunits of the Mediator tail module employ distinct mechanisms to regulate plant immune responses.
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Affiliation(s)
- Xudong Zhang
- Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611, USA
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33
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Ansari SA, Morse RH. Mechanisms of Mediator complex action in transcriptional activation. Cell Mol Life Sci 2013; 70:2743-56. [PMID: 23361037 PMCID: PMC11113466 DOI: 10.1007/s00018-013-1265-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 12/14/2022]
Abstract
Mediator is a large multisubunit complex that plays a central role in the regulation of RNA Pol II transcribed genes. Conserved in overall structure and function among eukaryotes, Mediator comprises 25-30 protein subunits that reside in four distinct modules, termed head, middle, tail, and CDK8/kinase. Different subunits of Mediator contact other transcriptional regulators including activators, co-activators, general transcription factors, subunits of RNA Pol II, and specifically modified histones, leading to the regulated expression of target genes. This review is focused on the interactions of specific Mediator subunits with diverse transcription regulators and how those interactions contribute to Mediator function in transcriptional activation.
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Affiliation(s)
- Suraiya A. Ansari
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
| | - Randall H. Morse
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
- Department of Biomedical Science, University at Albany School of Public Health, Albany, NY USA
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34
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Steimel A, Suh J, Hussainkhel A, Deheshi S, Grants JM, Zapf R, Moerman DG, Taubert S, Hutter H. The C. elegans CDK8 Mediator module regulates axon guidance decisions in the ventral nerve cord and during dorsal axon navigation. Dev Biol 2013; 377:385-98. [PMID: 23458898 DOI: 10.1016/j.ydbio.2013.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 01/21/2013] [Accepted: 02/14/2013] [Indexed: 11/30/2022]
Abstract
Receptors expressed on the growth cone of outgrowing axons detect cues required for proper navigation. The pathway choices available to an axon are in part defined by the set of guidance receptors present on the growth cone. Regulated expression of receptors and genes controlling the localization and activity of receptors ensures that axons respond only to guidance cues relevant for reaching their targets. In genetic screens for axon guidance mutants, we isolated an allele of let-19/mdt-13, a component of the Mediator, a large ~30 subunit protein complex essential for gene transcription by RNA polymerase II. LET-19/MDT-13 is part of the CDK8 module of the Mediator. By testing other Mediator components, we found that all subunits of the CDK8 module as well as some other Mediator components are required for specific axon navigation decisions in a subset of neurons. Expression profiling demonstrated that let-19/mdt-13 regulates the expression of a large number of genes in interneurons. A mutation in the sax-3 gene, encoding a receptor for the repulsive guidance cue SLT-1, suppresses the commissure navigation defects found in cdk-8 mutants. This suggests that the CDK8 module specifically represses the SAX-3/ROBO pathway to ensure proper commissure navigation.
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Affiliation(s)
- Andreas Steimel
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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35
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Mukundan B, Ansari A. Srb5/Med18-mediated termination of transcription is dependent on gene looping. J Biol Chem 2013; 288:11384-94. [PMID: 23476016 PMCID: PMC3630880 DOI: 10.1074/jbc.m112.446773] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/21/2013] [Indexed: 11/06/2022] Open
Abstract
We have earlier demonstrated the involvement of Mediator subunit Srb5/Med18 in the termination of transcription for a subset of genes in yeast. Srb5/Med18 could affect termination either indirectly by modulating CTD-Ser(2) phosphorylation near the 3' end of a gene or directly by physically interacting with the cleavage and polyadenylation factor or cleavage factor 1 (CF1) complex and facilitating their recruitment to the terminator region. Here, we show that the CTD-Ser(2) phosphorylation pattern on Srb5/Med18-dependent genes remains unchanged in the absence of Srb5 in cells. Coimmunoprecipitation analysis revealed the physical interaction of Srb5/Med18 with the CF1 complex. No such interaction of Srb5/Med18 with the cleavage and polyadenylation factor complex, however, could be detected. The Srb5/Med18-CF1 interaction was not observed in the looping defective sua7-1 strain. Srb5/Med18 cross-linking to the 3' end of genes was also abolished in the sua7-1 strain. Chromosome conformation capture analysis revealed that the looped architecture of Srb5/Med18-dependent genes was abrogated in srb5(-) cells. Furthermore, Srb5-dependent termination of transcription was compromised in the looping defective sua7-1 cells. The overall conclusion of these results is that gene looping plays a crucial role in Srb5/Med18 facilitated termination of transcription, and the looped gene architecture may have a general role in termination of transcription in budding yeast.
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Affiliation(s)
- Banupriya Mukundan
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Athar Ansari
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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36
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Barrero MJ, Malik S. The RNA polymerase II transcriptional machinery and its epigenetic context. Subcell Biochem 2013; 61:237-259. [PMID: 23150254 DOI: 10.1007/978-94-007-4525-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RNA polymerase II (Pol II) is the main engine that drives transcription of protein-encoding genes in eukaryotes. Despite its intrinsic subunit complexity, Pol II is subject to a host of factors that regulate the multistep transcription process. Indeed, the hallmark of the transcription cycle is the dynamic association of Pol II with initiation, elongation and other factors. In addition, Pol II transcription is regulated by a series of cofactors (coactivators and corepressors). Among these, the Mediator has emerged as one of the key regulatory factors for Pol II. Transcription by Pol II takes place in the context of chromatin, which is subject to numerous epigenetic modifications. This chapter mainly summarizes the various biochemical mechanisms that determine formation and function of a Pol II preinitiation complex (PIC) and those that affect its progress along the gene body (elongation). It further examines the various epigenetic modifications that the Pol II machinery encounters, especially in certain developmental contexts, and highlights newer evidence pointing to a likely close interplay between this machinery and factors responsible for the chromatin modifications.
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Affiliation(s)
- Maria J Barrero
- Center for Regenerative Medicine, Dr Aiguader 88, Barcelona, Spain,
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37
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Zhang X, Wang C, Zhang Y, Sun Y, Mou Z. The Arabidopsis mediator complex subunit16 positively regulates salicylate-mediated systemic acquired resistance and jasmonate/ethylene-induced defense pathways. THE PLANT CELL 2012; 24:4294-309. [PMID: 23064320 PMCID: PMC3517251 DOI: 10.1105/tpc.112.103317] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 09/14/2012] [Accepted: 09/26/2012] [Indexed: 05/18/2023]
Abstract
Systemic acquired resistance (SAR) is a long-lasting plant immunity against a broad spectrum of pathogens. Biological induction of SAR requires the signal molecule salicylic acid (SA) and involves profound transcriptional changes that are largely controlled by the transcription coactivator nonexpressor of pathogenesis-related genes1 (NPR1). However, it is unclear how SAR signals are transduced from the NPR1 signaling node to the general transcription machinery. Here, we report that the Arabidopsis thaliana Mediator subunit16 (MED16) is an essential positive regulator of SAR. Mutations in MED16 reduced NPR1 protein levels and completely compromised biological induction of SAR. These mutations also significantly suppressed SA-induced defense responses, altered the transcriptional changes induced by the avirulent bacterial pathogen Pseudomonas syringae pv tomato (Pst) DC3000/avrRpt2, and rendered plants susceptible to both Pst DC3000/avrRpt2 and Pst DC3000. In addition, mutations in MED16 blocked the induction of several jasmonic acid (JA)/ethylene (ET)-responsive genes and compromised resistance to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola. The Mediator complex acts as a bridge between specific transcriptional activators and the RNA polymerase II transcription machinery; therefore, our data suggest that MED16 may be a signaling component in the gap between the NPR1 signaling node and the general transcription machinery and may relay signals from both the SA and the JA/ET pathways.
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Affiliation(s)
- Xudong Zhang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Chenggang Wang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32610
| | - Yijun Sun
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32610
| | - Zhonglin Mou
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
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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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Sikorski TW, Joo YJ, Ficarro SB, Askenazi M, Buratowski S, Marto JA. Proteomic analysis demonstrates activator- and chromatin-specific recruitment to promoters. J Biol Chem 2012; 287:35397-35408. [PMID: 22902623 DOI: 10.1074/jbc.m112.391581] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In-depth characterization of RNA polymerase II preinitiation complexes remains an important and challenging goal. We used quantitative mass spectrometry to explore context-dependent Saccharomyces cerevisiae preinitiation complex formation at the HIS4 promoter reconstituted on naked and chromatinized DNA templates. The transcription activators Gal4-VP16 and Gal4-Gcn4 recruited a limited set of chromatin-related coactivator complexes, namely the chromatin remodeler Swi/Snf and histone acetyltransferases SAGA and NuA4, suggesting that transcription stimulation is mediated through these factors. Moreover, the two activators differentially recruited the coactivator complexes, consistent with specific activator-coactivator interactions. Chromatinized templates suppressed recruitment of basal transcription factors, thereby amplifying the effect of activators, compared with naked DNA templates. This system is sensitive, highly reproducible, and easily applicable to mapping the repertoire of proteins found at any promoter.
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Affiliation(s)
- Timothy W Sikorski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Yoo Jin Joo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Scott B Ficarro
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115; Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Manor Askenazi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115; Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
| | - Jarrod A Marto
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115; Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115.
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40
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Uwamahoro N, Qu Y, Jelicic B, Lo TL, Beaurepaire C, Bantun F, Quenault T, Boag PR, Ramm G, Callaghan J, Beilharz TH, Nantel A, Peleg AY, Traven A. The functions of Mediator in Candida albicans support a role in shaping species-specific gene expression. PLoS Genet 2012; 8:e1002613. [PMID: 22496666 PMCID: PMC3320594 DOI: 10.1371/journal.pgen.1002613] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 02/07/2012] [Indexed: 01/01/2023] Open
Abstract
The Mediator complex is an essential co-regulator of RNA polymerase II that is conserved throughout eukaryotes. Here we present the first study of Mediator in the pathogenic fungus Candida albicans. We focused on the Middle domain subunit Med31, the Head domain subunit Med20, and Srb9/Med13 from the Kinase domain. The C. albicans Mediator shares some roles with model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, such as functions in the response to certain stresses and the role of Med31 in the expression of genes regulated by the activator Ace2. The C. albicans Mediator also has additional roles in the transcription of genes associated with virulence, for example genes related to morphogenesis and gene families enriched in pathogens, such as the ALS adhesins. Consistently, Med31, Med20, and Srb9/Med13 contribute to key virulence attributes of C. albicans, filamentation, and biofilm formation; and ALS1 is a biologically relevant target of Med31 for development of biofilms. Furthermore, Med31 affects virulence of C. albicans in the worm infection model. We present evidence that the roles of Med31 and Srb9/Med13 in the expression of the genes encoding cell wall adhesins are different between S. cerevisiae and C. albicans: they are repressors of the FLO genes in S. cerevisiae and are activators of the ALS genes in C. albicans. This suggests that Mediator subunits regulate adhesion in a distinct manner between these two distantly related fungal species.
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Affiliation(s)
- Nathalie Uwamahoro
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Yue Qu
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Branka Jelicic
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Tricia L. Lo
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Cecile Beaurepaire
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada
| | - Farkad Bantun
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Tara Quenault
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Peter R. Boag
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Georg Ramm
- Monash Micro Imaging, Monash University, Clayton, Australia
| | - Judy Callaghan
- Monash Micro Imaging, Monash University, Clayton, Australia
| | - Traude H. Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - André Nantel
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada
- * E-mail: (AT); (AN)
| | - Anton Y. Peleg
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail: (AT); (AN)
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41
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Bernecky C, Taatjes DJ. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. J Mol Biol 2012; 417:387-94. [PMID: 22343046 DOI: 10.1016/j.jmb.2012.02.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 02/07/2012] [Indexed: 01/07/2023]
Abstract
The human Mediator complex controls RNA polymerase II (pol II) function in ways that remain incompletely understood. Activator-Mediator binding alters Mediator structure, and these activator-induced structural shifts appear to play key roles in regulating transcription. A recent cryo-electron microscopy (EM) analysis revealed that pol II adopted a stable orientation within a Mediator-pol II-TFIIF assembly in which Mediator was bound to the activation domain of viral protein 16 (VP16). Whereas TFIIF was shown to be important for orienting pol II within this assembly, the potential role of the activator was not assessed. To determine how activator binding might affect pol II orientation, we isolated human Mediator-pol II-TFIIF complexes in which Mediator was not bound to an activator. Cryo-EM analysis of this assembly, coupled with pol II crystal structure docking, revealed that pol II binds Mediator at the same general location; however, in contrast to VP16-bound Mediator, pol II does not appear to stably orient in the absence of an activator. Variability in pol II orientation might be important mechanistically, perhaps to enable sense and antisense transcription at human promoters. Because Mediator interacts extensively with pol II, these results suggest that Mediator structural shifts induced by activator binding help stably orient pol II prior to transcription initiation.
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Affiliation(s)
- Carrie Bernecky
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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42
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Xu M, Sharma P, Pan S, Malik S, Roeder RG, Martinez E. Core promoter-selective function of HMGA1 and Mediator in Initiator-dependent transcription. Genes Dev 2012; 25:2513-24. [PMID: 22156211 DOI: 10.1101/gad.177360.111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The factors and mechanisms underlying the differential activity and regulation of eukaryotic RNA polymerase II on different types of core promoters have remained elusive. Here we show that the architectural factor HMGA1 and the Mediator coregulator complex cooperate to enhance basal transcription from core promoters containing both a TATA box and an Initiator (INR) element but not from "TATA-only" core promoters. INR-dependent activation by HMGA1 and Mediator requires the TATA-binding protein (TBP)-associated factors (TAFs) within the TFIID complex and counteracts negative regulators of TBP/TATA-dependent transcription such as NC2 and Topoisomerase I. HMGA1 interacts with TFIID and Mediator and is required for the synergy of TATA and INR elements in mammalian cells. Accordingly, natural HMGA1-activated genes in embryonic stem cells tend to have both TATA and INR elements in a synergistic configuration. Our results suggest a core promoter-specific regulation of Mediator and the basal transcription machinery by HMGA1.
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Affiliation(s)
- Muyu Xu
- Department of Biochemistry, University of California at Riverside, Riverside, California 92521, USA
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43
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Abstract
The sterol regulatory element-binding proteins (SREBPs) play an important role in regulating lipid homeostasis. Translated as inactive precursors that are localized in the endoplasmic reticulum (ER) membrane, SREBPs are activated through a proteolytic process in response to intracellular demands for lipids. The cleaved amino-terminal fragments of SREBPs then translocate into the nucleus as homodimers and stimulate the transcription of target genes by binding to the sterol response elements (SREs) in their promoters. Numerous studies using cell culture or genetically modified mouse models have demonstrated that the major target genes of SREBPs include rate-limiting enzymes in the pathways of fatty acid and cholesterol biosynthesis as well as the low-density lipoprotein (LDL) receptor. The proteolytic maturation of SREBPs has been well studied in the past. However, recent studies have also improved our understanding on the regulation of nuclear SREBPs. In the nucleus, SREBPs interact with specific transcriptional cofactors, such as CBP/p300 and the Mediator complex, resulting in stimulation or inhibition of their transcriptional activities. In addition, nuclear SREBP protein stability is dynamically regulated by phosphorylation and acetylation. Such protein-protein interactions and post-translational modifications elegantly link the extracellular signals, such as insulin, or intracellular signals, such as oxidative stress, to lipid biosynthesis by modulating the transcriptional activity of SREBPs. Under normal physiological states, lipid homeostasis is strictly maintained. However, the SREBP pathways are often dysregulated in pathophysiological conditions, such as obesity, type 2 diabetes, and fatty liver diseases. Thus, the novel regulatory mechanisms of SREBPs may provide new opportunities for fighting these metabolic diseases.
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44
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Mukundan B, Ansari A. Novel role for mediator complex subunit Srb5/Med18 in termination of transcription. J Biol Chem 2011; 286:37053-7. [PMID: 21921038 PMCID: PMC3199451 DOI: 10.1074/jbc.c111.295915] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 09/13/2011] [Indexed: 11/06/2022] Open
Abstract
Mediator complex functions at the recruitment as well as the post-recruitment steps of transcription. Here we provide evidence for a novel role of Mediator in termination of transcription. Mediator subunit Srb5/Med18 cross-links to the 5' and 3' ends of INO1 and CHA1. In srb5(-) cells, recruitment of TATA-binding protein (TBP) and transcription factor IIB (TFIIB) onto the promoter of these genes remained unaffected, but cross-linking of the cleavage-polyadenylation factors Rna15 and Pta1 toward the 3' end of genes was compromised. In these cells, RNA polymerase II accumulated near the 3' end of genes and beyond. Transcription run-on analysis confirmed a transcription readthrough phenotype in the absence of Srb5/Med18. These results strongly suggest that Mediator subunit Srb5/Med18 is required for proper termination of transcription of a subset of genes in budding yeast.
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Affiliation(s)
- Banupriya Mukundan
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Athar Ansari
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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45
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Xu W, Ji JY. Dysregulation of CDK8 and Cyclin C in tumorigenesis. J Genet Genomics 2011; 38:439-52. [PMID: 22035865 PMCID: PMC9792140 DOI: 10.1016/j.jgg.2011.09.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 01/23/2023]
Abstract
Appropriately controlled gene expression is fundamental for normal growth and survival of all living organisms. In eukaryotes, the transcription of protein-coding mRNAs is dependent on RNA polymerase II (Pol II). The multi-subunit transcription cofactor Mediator complex is proposed to regulate most, if not all, of the Pol II-dependent transcription. Here we focus our discussion on two subunits of the Mediator complex, cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC), because they are either mutated or amplified in a variety of human cancers. CDK8 functions as an oncoprotein in melanoma and colorectal cancers, thus there are considerable interests in developing drugs specifically targeting the CDK8 kinase activity. However, to evaluate the feasibility of targeting CDK8 for cancer therapy and to understand how their dysregulation contributes to tumorigenesis, it is essential to elucidate the in vivo function and regulation of CDK8-CycC, which are still poorly understood in multi-cellular organisms. We summarize the evidence linking their dysregulation to various cancers and present our bioinformatics and computational analyses on the structure and evolution of CDK8. We also discuss the implications of these observations in tumorigenesis. Because most of the Mediator subunits, including CDK8 and CycC, are highly conserved during eukaryotic evolution, we expect that investigations using model organisms such as Drosophila will provide important insights into the function and regulation of CDK8 and CycC in different cellular and developmental contexts.
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Affiliation(s)
- Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
- Corresponding author: Tel: +1 979 845 6389, fax: +1 979 847 9481. (J.-Y. Ji)
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46
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Takahashi H, Parmely TJ, Sato S, Tomomori-Sato C, Banks CAS, Kong SE, Szutorisz H, Swanson SK, Martin-Brown S, Washburn MP, Florens L, Seidel CW, Lin C, Smith ER, Shilatifard A, Conaway RC, Conaway JW. Human mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell 2011; 146:92-104. [PMID: 21729782 DOI: 10.1016/j.cell.2011.06.005] [Citation(s) in RCA: 261] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 04/15/2011] [Accepted: 06/03/2011] [Indexed: 01/13/2023]
Abstract
Promoter-proximal pausing by initiated RNA polymerase II (Pol II) and regulated release of paused polymerase into productive elongation has emerged as a major mechanism of transcription activation. Reactivation of paused Pol II correlates with recruitment of super-elongation complexes (SECs) containing ELL/EAF family members, P-TEFb, and other proteins, but the mechanism of their recruitment is an unanswered question. Here, we present evidence for a role of human Mediator subunit MED26 in this process. We identify in the conserved N-terminal domain of MED26 overlapping docking sites for SEC and a second ELL/EAF-containing complex, as well as general initiation factor TFIID. In addition, we present evidence consistent with the model that MED26 can function as a molecular switch that interacts first with TFIID in the Pol II initiation complex and then exchanges TFIID for complexes containing ELL/EAF and P-TEFb to facilitate transition of Pol II into the elongation stage of transcription.
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47
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Ries D, Meisterernst M. Control of gene transcription by Mediator in chromatin. Semin Cell Dev Biol 2011; 22:735-40. [PMID: 21864698 DOI: 10.1016/j.semcdb.2011.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 08/02/2011] [Accepted: 08/08/2011] [Indexed: 01/07/2023]
Abstract
The Mediator complex serves as an adaptor for regulatory factors, recruits and controls RNA polymerase II promotes preinitiation complex formation and functions post initiation. There is increasing evidence for further coordinating roles of the Mediator complex in chromatin. Here we summarize interactions with regulatory, general and accessory factors that function in transcription and chromatin.
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Affiliation(s)
- David Ries
- Institute of Molecular Tumor Biology, Westfalian Wilhelms University, Münster, Germany, Robert-Koch Strasse 43, 48149 Münster, Germany
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48
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Chen W, Roeder RG. Mediator-dependent nuclear receptor function. Semin Cell Dev Biol 2011; 22:749-58. [PMID: 21854863 DOI: 10.1016/j.semcdb.2011.07.026] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 12/24/2022]
Abstract
As gene-specific transcription factors, nuclear receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss our current understanding of (i) pathways involved in Mediator recruitment and function through nuclear receptor target gene enhancers and promoters, (ii) conditional requirements for the strong nuclear receptor-Mediator interactions mediated by NR AF2 domains and the MED1 LXXLL motifs, (iii) Mediator functions, through different nuclear receptor-interacting subunits, in different metabolic pathways, (iv) emerging functions of Mediator as a corepressor in addition to its major role as a coactivator and (v) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. As a nuclear receptor coregulator with increasingly diverse functions, Mediator may thus modulate nuclear receptor signaling through several different mechanisms.
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Affiliation(s)
- Wei Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
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49
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Conaway RC, Conaway JW. Origins and activity of the Mediator complex. Semin Cell Dev Biol 2011; 22:729-34. [PMID: 21821140 DOI: 10.1016/j.semcdb.2011.07.021] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 11/16/2022]
Abstract
The Mediator is a large, multisubunit RNA polymerase II transcriptional regulator that was first identified in Saccharomyces cerevisiae as a factor required for responsiveness of Pol II and the general initiation factors to DNA binding transactivators. Since its discovery in yeast, Mediator has been shown to be an integral and highly evolutionarily conserved component of the Pol II transcriptional machinery with critical roles in multiple stages of transcription, from regulation of assembly of the Pol II initiation complex to regulation of Pol II elongation. Here we provide a brief overview of the evolutionary origins of Mediator, its subunit composition, and its remarkably diverse collection of activities in Pol II transcription.
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Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA.
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50
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Abstract
Mediator, a conserved multiprotein complex in animals, plants, and fungi, is a cofactor of RNA Polymerase II (Pol II). It is known to promote basal Pol II-mediated transcription as well as bridge sequence-specific transcriptional regulators and Pol II to integrate regulatory information. Pol II transcribes not only protein-coding genes but also intergenic regions to generate noncoding RNAs such as small RNAs (microRNAs and small interfering RNAs) and long noncoding RNAs. Intriguingly, two plant-specific polymerases, Pol IV and Pol V, have evolved from Pol II and play a role in the production of small interfering RNAs and long noncoding RNAs at heterochromatic regions to maintain genome stability through transcriptional gene silencing (TGS). Recent studies have defined the composition of the plant Mediator and evaluated its role in noncoding RNA production in relationship to Pol II, Pol IV and Pol V. Here, we review the functions of Mediator and that of noncoding RNAs generated by Pol II, Pol IV and Pol V in plants, and discuss a role of Mediator in epigenetic regulation via noncoding RNA production.
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Affiliation(s)
- Yun Ju Kim
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
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