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Freytes SN, Gobbini ML, Cerdán PD. The Plant Mediator Complex in the Initiation of Transcription by RNA Polymerase II. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:211-237. [PMID: 38277699 DOI: 10.1146/annurev-arplant-070623-114005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Thirty years have passed since the discovery of the Mediator complex in yeast. We are witnessing breakthroughs and advances that have led to high-resolution structural models of yeast and mammalian Mediators in the preinitiation complex, showing how it is assembled and how it positions the RNA polymerase II and its C-terminal domain (CTD) to facilitate the CTD phosphorylation that initiates transcription. This information may be also used to guide future plant research on the mechanisms of Mediator transcriptional control. Here, we review what we know about the subunit composition and structure of plant Mediators, the roles of the individual subunits and the genetic analyses that pioneered Mediator research, and how transcription factors recruit Mediators to regulatory regions adjoining promoters. What emerges from the research is a Mediator that regulates transcription activity and recruits hormonal signaling modules and histone-modifying activities to set up an off or on transcriptional state that recruits general transcription factors for preinitiation complex assembly.
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Affiliation(s)
| | | | - Pablo D Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina; , ,
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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2
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Abdel-Fattah WR, Carlsson M, Hu GZ, Singh A, Vergara A, Aslam R, Ronne H, Björklund S. Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes. Nucleic Acids Res 2024; 52:6220-6233. [PMID: 38613396 PMCID: PMC11194063 DOI: 10.1093/nar/gkae266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2-8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3'-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3'-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron-exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.
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Affiliation(s)
- Wael R Abdel-Fattah
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Mattias Carlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - Guo-Zhen Hu
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - Ajeet Singh
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Alexander Vergara
- Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Rameen Aslam
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Hans Ronne
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
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3
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Kolonay DW, Sattler KM, Strawser C, Rafael-Fortney J, Mihaylova MM, Miller KE, Lepper C, Baskin KK. Temporal regulation of the Mediator complex during muscle proliferation, differentiation, regeneration, aging, and disease. Front Cell Dev Biol 2024; 12:1331563. [PMID: 38690566 PMCID: PMC11058648 DOI: 10.3389/fcell.2024.1331563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024] Open
Abstract
Genesis of skeletal muscle relies on the differentiation and fusion of mono-nucleated muscle progenitor cells into the multi-nucleated muscle fiber syncytium. The temporally-controlled cellular and morphogenetic changes underlying this process are initiated by a series of highly coordinated transcription programs. At the core, the myogenic differentiation cascade is driven by muscle-specific transcription factors, i.e., the Myogenic Regulatory Factors (MRFs). Despite extensive knowledge on the function of individual MRFs, very little is known about how they are coordinated. Ultimately, highly specific coordination of these transcription programs is critical for their masterfully timed transitions, which in turn facilitates the intricate generation of skeletal muscle fibers from a naïve pool of progenitor cells. The Mediator complex links basal transcriptional machinery and transcription factors to regulate transcription and could be the integral component that coordinates transcription factor function during muscle differentiation, growth, and maturation. In this study, we systematically deciphered the changes in Mediator complex subunit expression in skeletal muscle development, regeneration, aging, and disease. We incorporated our in vitro and in vivo experimental results with analysis of publicly available RNA-seq and single nuclei RNA-seq datasets and uncovered the regulation of Mediator subunits in different physiological and temporal contexts. Our experimental results revealed that Mediator subunit expression during myogenesis is highly dynamic. We also discovered unique temporal patterns of Mediator expression in muscle stem cells after injury and during the early regeneration period, suggesting that Mediator subunits may have unique contributions to directing muscle stem cell fate. Although we observed few changes in Mediator subunit expression in aging muscles compared to younger muscles, we uncovered extensive heterogeneity of Mediator subunit expression in dystrophic muscle nuclei, characteristic of chronic muscle degeneration and regeneration cycles. Taken together, our study provides a glimpse of the complex regulation of Mediator subunit expression in the skeletal muscle cell lineage and serves as a springboard for mechanistic studies into the function of individual Mediator subunits in skeletal muscle.
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Affiliation(s)
- Dominic W. Kolonay
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Kristina M. Sattler
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Corinne Strawser
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Jill Rafael-Fortney
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Maria M. Mihaylova
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Katherine E. Miller
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Christoph Lepper
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Kedryn K. Baskin
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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4
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Ling YH, Ye Z, Liang C, Yu C, Park G, Corden JL, Wu C. Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets. Nat Cell Biol 2024; 26:581-592. [PMID: 38548891 PMCID: PMC11210292 DOI: 10.1038/s41556-024-01382-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/21/2024] [Indexed: 04/09/2024]
Abstract
Efficient gene expression requires RNA polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in three-dimensional nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. In the present study, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation and reduces transcription bursting. The present study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.
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Affiliation(s)
- Yick Hin Ling
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Ziyang Ye
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Chloe Liang
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Chuofan Yu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Giho Park
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffry L Corden
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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5
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Blomberg J, Tasselius V, Vergara A, Karamat F, Imran QM, Strand Å, Rosvall M, Björklund S. Pseudomonas syringae infectivity correlates to altered transcript and metabolite levels of Arabidopsis mediator mutants. Sci Rep 2024; 14:6771. [PMID: 38514763 PMCID: PMC10958028 DOI: 10.1038/s41598-024-57192-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16, med18, med25 and cdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in med16 and cdk8, but increased in med25, which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that MED16, MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infections.
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Affiliation(s)
- Jeanette Blomberg
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Viktor Tasselius
- Department of Physics, Umeå University, 901 87, Umeå, Sweden
- Biostatistics, School of Public Health and Community Medicine, Gothenburg University, P.O. Box 463, 405 30, Gothenburg, Sweden
| | | | - Fazeelat Karamat
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Qari Muhammad Imran
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Åsa Strand
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87, Umeå, Sweden
| | - Martin Rosvall
- Department of Physics, Umeå University, 901 87, Umeå, Sweden
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.
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6
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Ling YH, Ye Z, Liang C, Yu C, Park G, Corden JL, Wu C. Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551302. [PMID: 37577667 PMCID: PMC10418089 DOI: 10.1101/2023.07.31.551302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Efficient gene expression requires RNA Polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in 3D nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. Here, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation, and reduces transcription bursting. This study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.
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Affiliation(s)
- Yick Hin Ling
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Ziyang Ye
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Chloe Liang
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Chuofan Yu
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Giho Park
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Jeffry L Corden
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
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7
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Flores-Solis D, Lushpinskaia IP, Polyansky AA, Changiarath A, Boehning M, Mirkovic M, Walshe J, Pietrek LM, Cramer P, Stelzl LS, Zagrovic B, Zweckstetter M. Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nat Commun 2023; 14:5979. [PMID: 37749095 PMCID: PMC10519987 DOI: 10.1038/s41467-023-41633-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/10/2023] [Indexed: 09/27/2023] Open
Abstract
Eukaryotic gene regulation and pre-mRNA transcription depend on the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. Due to its highly repetitive, intrinsically disordered sequence, the CTD enables clustering and phase separation of Pol II. The molecular interactions that drive CTD phase separation and Pol II clustering are unclear. Here, we show that multivalent interactions involving tyrosine impart temperature- and concentration-dependent self-coacervation of the CTD. NMR spectroscopy, molecular ensemble calculations and all-atom molecular dynamics simulations demonstrate the presence of diverse tyrosine-engaging interactions, including tyrosine-proline contacts, in condensed states of human CTD and other low-complexity proteins. We further show that the network of multivalent interactions involving tyrosine is responsible for the co-recruitment of the human Mediator complex and CTD during phase separation. Our work advances the understanding of the driving forces of CTD phase separation and thus provides the basis to better understand CTD-mediated Pol II clustering in eukaryotic gene transcription.
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Affiliation(s)
- David Flores-Solis
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany
| | - Irina P Lushpinskaia
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany
| | - Anton A Polyansky
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Arya Changiarath
- Faculty of Biology, Johannes Gutenberg University Mainz (JGU), Gresemundweg 2, 55128, Mainz, Germany
- KOMET1, Institute of Physics, Johannes Gutenberg University Mainz (JGU), Staudingerweg 9, 55099, Mainz, Germany
| | - Marc Boehning
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Milana Mirkovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - James Walshe
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Lisa M Pietrek
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Strasße 3, 60438, Frankfurt am Main, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Lukas S Stelzl
- Faculty of Biology, Johannes Gutenberg University Mainz (JGU), Gresemundweg 2, 55128, Mainz, Germany
- KOMET1, Institute of Physics, Johannes Gutenberg University Mainz (JGU), Staudingerweg 9, 55099, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Bojan Zagrovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany.
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany.
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8
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Pal S, Biswas D. Promoter-proximal regulation of gene transcription: Key factors involved and emerging role of general transcription factors in assisting productive elongation. Gene 2023:147571. [PMID: 37331491 DOI: 10.1016/j.gene.2023.147571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The pausing of RNA polymerase II (Pol II) at the promoter-proximal sites is a key rate-limiting step in gene expression. Cells have dedicated a specific set of proteins that sequentially establish pause and then release the Pol II from promoter-proximal sites. A well-controlled pausing and subsequent release of Pol II is crucial for thefine tuning of expression of genes including signal-responsive and developmentally-regulated ones. The release of paused Pol II broadly involves its transition from initiation to elongation. In this review article, we will discuss the phenomenon of Pol II pausing, the underlying mechanism, and also the role of different known factors, with an emphasis on general transcription factors, involved in this overall regulation. We will further discuss some recent findings suggesting a possible role (underexplored) of initiation factors in assisting the transition of transcriptionally-engaged paused Pol II into productive elongation.
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Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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9
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Lambert É, Puwakdandawa K, Tao YF, Robert F. From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J 2023; 290:286-309. [PMID: 34698446 DOI: 10.1111/febs.16250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 02/05/2023]
Abstract
Mediator is a large modular protein assembly whose function as a coactivator of transcription is conserved in all eukaryotes. The Mediator complex can integrate and relay signals from gene-specific activators bound at enhancers to activate the general transcription machinery located at promoters. It has thus been described as a bridge between these elements during initiation of transcription. Here, we review recent studies on Mediator relating to its structure, gene specificity and general requirement, roles in chromatin architecture as well as novel concepts involving phase separation and transcriptional bursting. We revisit the mechanism of action of Mediator and ultimately put forward models for its mode of action in gene activation.
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Affiliation(s)
- Élie Lambert
- Institut de recherches cliniques de Montréal, Canada
| | | | - Yi Fei Tao
- Institut de recherches cliniques de Montréal, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Canada
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10
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Morse RH. Function and dynamics of the Mediator complex: novel insights and new frontiers. Transcription 2022; 13:39-52. [PMID: 35708525 PMCID: PMC9467533 DOI: 10.1080/21541264.2022.2085502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The Mediator complex was discovered in the early 1990s as a biochemically fractionated factor from yeast extracts that was necessary for activator-stimulated transcriptional activation to be observed in in vitro transcription assays. The structure of this large, multi-protein complex is now understood in great detail, and novel genetic approaches have provided rich insights into its dynamics during transcriptional activation and the mechanism by which it facilitates activated transcription. Here I review recent findings and unanswered questions regarding Mediator dynamics, the roles of individual subunits, and differences between its function in yeast and metazoan cells.
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Affiliation(s)
- Randall H Morse
- Wadsworth Center, New York State Department of Health, Albany, NY, United States.,Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, United States
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11
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Role of the Mediator Complex and MicroRNAs in Breast Cancer Etiology. Genes (Basel) 2022; 13:genes13020234. [PMID: 35205279 PMCID: PMC8871970 DOI: 10.3390/genes13020234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
Transcriptional coactivators play a key role in RNA polymerase II transcription and gene regulation. One of the most important transcriptional coactivators is the Mediator (MED) complex, which is an evolutionary conserved large multiprotein complex. MED transduces the signal between DNA-bound transcriptional activators (gene-specific transcription factors) to the RNA polymerase II transcription machinery to activate transcription. It is known that MED plays an essential role in ER-mediated gene expression mainly through the MED1 subunit, since estrogen receptor (ER) can interact with MED1 by specific protein–protein interactions; therefore, MED1 plays a fundamental role in ER-positive breast cancer (BC) etiology. Additionally, other MED subunits also play a role in BC etiology. On the other hand, microRNAs (miRNAs) are a family of small non-coding RNAs, which can regulate gene expression at the post-transcriptional level by binding in a sequence-specific fashion at the 3′ UTR of the messenger RNA. The miRNAs are also important factors that influence oncogenic signaling in BC by acting as both tumor suppressors and oncogenes. Moreover, miRNAs are involved in endocrine therapy resistance of BC, specifically to tamoxifen, a drug that is used to target ER signaling. In metazoans, very little is known about the transcriptional regulation of miRNA by the MED complex and less about the transcriptional regulation of miRNAs involved in BC initiation and progression. Recently, it has been shown that MED1 is able to regulate the transcription of the ER-dependent miR-191/425 cluster promoting BC cell proliferation and migration. In this review, we will discuss the role of MED1 transcriptional coactivator in the etiology of BC and in endocrine therapy-resistance of BC and also the contribution of other MED subunits to BC development, progression and metastasis. Lastly, we identified miRNAs that potentially can regulate the expression of MED subunits.
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12
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Petrenko N, Struhl K. Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species. eLife 2021; 10:67964. [PMID: 34515029 PMCID: PMC8463073 DOI: 10.7554/elife.67964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The preinitiation complex (PIC) for transcriptional initiation by RNA polymerase (Pol) II is composed of general transcription factors that are highly conserved. However, analysis of ChIP-seq datasets reveals kinetic and compositional differences in the transcriptional initiation process among eukaryotic species. In yeast, Mediator associates strongly with activator proteins bound to enhancers, but it transiently associates with promoters in a form that lacks the kinase module. In contrast, in human, mouse, and fly cells, Mediator with its kinase module stably associates with promoters, but not with activator-binding sites. This suggests that yeast and metazoans differ in the nature of the dynamic bridge of Mediator between activators and Pol II and the composition of a stable inactive PIC-like entity. As in yeast, occupancies of TATA-binding protein (TBP) and TBP-associated factors (Tafs) at mammalian promoters are not strictly correlated. This suggests that within PICs, TFIID is not a monolithic entity, and multiple forms of TBP affect initiation at different classes of genes. TFIID in flies, but not yeast and mammals, interacts strongly at regions downstream of the initiation site, consistent with the importance of downstream promoter elements in that species. Lastly, Taf7 and the mammalian-specific Med26 subunit of Mediator also interact near the Pol II pause region downstream of the PIC, but only in subsets of genes and often not together. Species-specific differences in PIC structure and function are likely to affect how activators and repressors affect transcriptional activity.
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Affiliation(s)
- Natalia Petrenko
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
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13
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A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions. Methods Mol Biol 2021. [PMID: 34382181 DOI: 10.1007/978-1-0716-1597-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Knowledge in gene transcription and chromatin regulation has been intensely studied for decades, but thanks to next-generation sequencing (NGS) techniques there has been a major leap forward in the last few years. Historically, identification of specific enhancer elements has led to the identification of master transcription factors (TFs) in the 1990s. Genetic and biochemical experiments have identified the key regulators controlling RNA polymerase II (RNAPII) transcription and structurally analyses have elucidated detailed mechanisms. NGS and the development of chromatin immunoprecipitation (ChIP) have accelerated the gain of knowledge in the recent years. By now, we have a dazzling wealth of techniques that are currently used to put gene expression into a genome-wide context. This book is an attempt to assemble useful protocols for many researchers within and nearby research areas. In general, these innovative techniques focus on enhancer and promoter studies. The techniques should also be of interest for related fields such as DNA repair and replication.
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Shirra MK, Kocik RA, Ellison MA, Arndt KM. Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2021; 11:6360461. [PMID: 34499735 PMCID: PMC8527469 DOI: 10.1093/g3journal/jkab298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022]
Abstract
Maintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B. In Saccharomyces cerevisiae, amino acid substitutions in the Rtf1 subunit of Paf1C greatly diminish H2B ubiquitylation and cause transcription to initiate at a cryptic promoter within the coding region of the FLO8 gene, an indicator of chromatin disruption. In a genetic screen to identify factors that functionally interact with Paf1C, we identified mutations in HDA3, a gene encoding a subunit of the Hda1C histone deacetylase (HDAC), as suppressors of an rtf1 mutation. Absence of Hda1C also suppresses the cryptic initiation phenotype of other mutants defective in H2B ubiquitylation. The genetic interactions between Hda1C and the H2B ubiquitylation pathway appear specific: loss of Hda1C does not suppress the cryptic initiation phenotypes of other chromatin mutants and absence of other HDACs does not suppress the absence of H2B ubiquitylation. Providing further support for an appropriate balance of histone acetylation in regulating cryptic initiation, absence of the Sas3 histone acetyltransferase elevates cryptic initiation in rtf1 mutants. Our data suggest that the H2B ubiquitylation pathway and Hda1C coordinately regulate chromatin structure during transcription elongation and point to a potential role for a HDAC in supporting chromatin accessibility.
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Affiliation(s)
- Margaret K Shirra
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Rachel A Kocik
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mitchell A Ellison
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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15
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Tang M, Pei G, Su D, Wang C, Feng X, Srivastava M, Chen Z, Zhao Z, Chen J. Genome-wide CRISPR screens reveal cyclin C as synthetic survival target of BRCA2. Nucleic Acids Res 2021; 49:7476-7491. [PMID: 34197614 PMCID: PMC8287926 DOI: 10.1093/nar/gkab540] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/04/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023] Open
Abstract
Poly (ADP-ribose) polymerase inhibitor (PARPi)-based therapies initially reduce tumor burden but eventually lead to acquired resistance in cancer patients with BRCA1 or BRCA2 mutation. To understand the potential PARPi resistance mechanisms, we performed whole-genome CRISPR screens to discover genetic alterations that change the gene essentiality in cells with inducible depletion of BRCA2. We identified that several RNA Polymerase II transcription Mediator complex components, especially Cyclin C (CCNC) as synthetic survival targets upon BRCA2 loss. Total mRNA sequencing demonstrated that loss of CCNC could activate the transforming growth factor (TGF)-beta signaling pathway and extracellular matrix (ECM)-receptor interaction pathway, however the inhibition of these pathways could not reverse cell survival in BRCA2 depleted CCNC-knockout cells, indicating that the activation of these pathways is not required for the resistance. Moreover, we showed that the improved survival is not due to restoration of homologous recombination repair although decreased DNA damage signaling was observed. Interestingly, loss of CCNC could restore replication fork stability in BRCA2 deficient cells, which may contribute to PARPi resistance. Taken together, our data reveal CCNC as a critical genetic determinant upon BRCA2 loss of function, which may help the development of novel therapeutic strategies that overcome PARPi resistance.
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Affiliation(s)
- Mengfan Tang
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Youn DY, Xiaoli AM, Zong H, Okada J, Liu L, Pessin J, Pessin JE, Yang F. The Mediator complex kinase module is necessary for fructose regulation of liver glycogen levels through induction of glucose-6-phosphatase catalytic subunit (G6pc). Mol Metab 2021; 48:101227. [PMID: 33812059 PMCID: PMC8099662 DOI: 10.1016/j.molmet.2021.101227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE Liver glycogen levels are dynamic and highly regulated by nutrient availability as the levels decrease during fasting and are restored during the feeding cycle. However, feeding in the presence of fructose in water suppresses glycogen accumulation in the liver by upregulating the expression of the glucose-6-phosphatase catalytic subunit (G6pc) gene, although the exact mechanism is unknown. We generated liver-specific knockout MED13 mice that lacked the transcriptional Mediator complex kinase module to examine its effect on the transcriptional activation of inducible target gene expression, such as the ChREBP- and FOXO1-dependent control of the G6pc gene promoter. METHODS The relative changes in liver expression of lipogenic and gluconeogenic genes as well as glycogen levels were examined in response to feeding standard low-fat laboratory chow supplemented with water or water containing sucrose or fructose in control (Med13fl/fl) and liver-specific MED13 knockout (MED13-LKO) mice. RESULTS Although MED13 deficiency had no significant effect on constitutive gene expression, all the dietary inducible gene transcripts were significantly reduced despite the unchanged insulin sensitivity in the MED13-LKO mice compared to that in the control mice. G6pc gene transcription displayed the most significant difference between the Med13 fl/fl and MED13-LKO mice, particularly when fed fructose. Following fasting that depleted liver glycogen, feeding induced the restoration of glycogen levels except in the presence of fructose. MED13 deficiency rescued the glycogen accumulation defect in the presence of fructose. This resulted from the suppression of G6pc expression and thus G6PC enzymatic activity. Among two transcriptional factors that regulate G6pc gene expression, FOXO1 binding to the G6pc promoter was not affected, whereas ChREBP binding was dramatically reduced in MED13-LKO hepatocytes. In addition, there was a marked suppression of FOXO1 and ChREBP-β transcriptional activities in MED13-LKO hepatocytes. CONCLUSIONS Taken together, our data suggest that the kinase module of the Mediator complex is necessary for the transcriptional activation of metabolic genes such as G6pc and has an important role in regulating glycogen levels in the liver through altering transcription factor binding and activity at the G6pc promoter.
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Affiliation(s)
- Dou Yeon Youn
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Alus M Xiaoli
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Haihong Zong
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Junichi Okada
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Li Liu
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jacob Pessin
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jeffrey E Pessin
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Fajun Yang
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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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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18
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Tourigny JP, Schumacher K, Saleh MM, Devys D, Zentner GE. Architectural Mediator subunits are differentially essential for global transcription in Saccharomyces cerevisiae. Genetics 2021; 217:iyaa042. [PMID: 33789343 PMCID: PMC8045717 DOI: 10.1093/genetics/iyaa042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/16/2020] [Indexed: 12/18/2022] Open
Abstract
Mediator is a modular coactivator complex involved in the transcription of the majority of RNA polymerase II-regulated genes. However, the degrees to which individual core subunits of Mediator contribute to its activity have been unclear. Here, we investigate the contribution of two essential architectural subunits of Mediator to transcription in Saccharomyces cerevisiae. We show that acute depletion of the main complex scaffold Med14 or the head module nucleator Med17 is lethal and results in global transcriptional downregulation, though Med17 removal has a markedly greater negative effect. Consistent with this, Med17 depletion impairs preinitiation complex (PIC) assembly to a greater extent than Med14 removal. Co-depletion of Med14 and Med17 reduced transcription and TFIIB promoter occupancy similarly to Med17 ablation alone, indicating that the contributions of Med14 and Med17 to Mediator function are not additive. We propose that, while the structural integrity of complete Mediator and the head module are both important for PIC assembly and transcription, the head module plays a greater role in this process and is thus the key functional module of Mediator in this regard.
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Affiliation(s)
- Jason P Tourigny
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kenny Schumacher
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France
- U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Moustafa M Saleh
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France
- U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
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19
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Garg A, Shuman S, Schwer B. A genetic screen for suppressors of hyper-repression of the fission yeast PHO regulon by Pol2 CTD mutation T4A implicates inositol 1-pyrophosphates as agonists of precocious lncRNA transcription termination. Nucleic Acids Res 2020; 48:10739-10752. [PMID: 33010152 PMCID: PMC7641756 DOI: 10.1093/nar/gkaa776] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/03/2020] [Accepted: 09/29/2020] [Indexed: 12/23/2022] Open
Abstract
Fission yeast phosphate homeostasis genes are repressed in phosphate-rich medium by transcription of upstream lncRNAs that interferes with activation of the flanking mRNA promoters. lncRNA control of PHO gene expression is influenced by the Thr4 phospho-site in the RNA polymerase II CTD and the 3′ processing/termination factors CPF and Rhn1, mutations of which result in hyper-repression of the PHO regulon. Here, we performed a forward genetic screen for mutations that de-repress Pho1 acid phosphatase expression in CTD-T4A cells. Sequencing of 18 independent STF (Suppressor of Threonine Four) isolates revealed, in every case, a mutation in the C-terminal pyrophosphatase domain of Asp1, a bifunctional inositol pyrophosphate (IPP) kinase/pyrophosphatase that interconverts 5-IP7 and 1,5-IP8. Focused characterization of two STF strains identified 51 coding genes coordinately upregulated vis-à-vis the parental T4A strain, including all three PHO regulon genes (pho1, pho84, tgp1). Whereas these STF alleles—asp1-386(Stop) and asp1-493(Stop)—were lethal in a wild-type CTD background, they were viable in combination with mutations in CPF and Rhn1, in which context Pho1 was also de-repressed. Our findings implicate Asp1 pyrophosphatase in constraining 1,5-IP8 or 1-IP7 synthesis by Asp1 kinase, without which 1-IPPs can accumulate to toxic levels that elicit precocious termination by CPF/Rhn1.
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Affiliation(s)
- Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
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20
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André KM, Sipos EH, Soutourina J. Mediator Roles Going Beyond Transcription. Trends Genet 2020; 37:224-234. [PMID: 32921511 DOI: 10.1016/j.tig.2020.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022]
Abstract
Dysfunctions of nuclear processes including transcription and DNA repair lead to severe human diseases. Gaining an understanding of how these processes operate in the crowded context of chromatin can be particularly challenging. Mediator is a large multiprotein complex conserved in eukaryotes with a key coactivator role in the regulation of RNA polymerase (Pol) II transcription. Despite intensive studies, the molecular mechanisms underlying Mediator function remain to be fully understood. Novel findings have provided insights into the relationship between Mediator and chromatin architecture, revealed its role in connecting transcription with DNA repair and proposed an emerging mechanism of phase separation involving Mediator condensates. Recent developments in the field suggest multiple functions of Mediator going beyond transcriptional processes per se that would explain its involvement in various human pathologies.
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Affiliation(s)
- Kévin M André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Eliet H Sipos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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21
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Transcriptional regulatory proteins in central carbon metabolism of Pichia pastoris and Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:7273-7311. [PMID: 32651601 DOI: 10.1007/s00253-020-10680-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 01/21/2023]
Abstract
System-wide interactions in living cells and discovery of the diverse roles of transcriptional regulatory proteins that are mediator proteins with catalytic domains and regulatory subunits and transcription factors in the cellular pathways have become crucial for understanding the cellular response to environmental conditions. This review provides information for future metabolic engineering strategies through analyses on the highly interconnected regulatory networks in Saccharomyces cerevisiae and Pichia pastoris and identifying their components. We discuss the current knowledge on the carbon catabolite repression (CCR) mechanism, interconnecting regulatory system of the central metabolic pathways that regulate cell metabolism based on nutrient availability in the industrial yeasts. The regulatory proteins and their functions in the CCR signalling pathways in both yeasts are presented and discussed. We highlight the importance of metabolic signalling networks by signifying ways on how effective engineering strategies can be designed for generating novel regulatory circuits, furthermore to activate pathways that reconfigure the network architecture. We summarize the evidence that engineering of multilayer regulation is needed for directed evolution of the cellular network by putting the transcriptional control into a new perspective for the regulation of central carbon metabolism of the industrial yeasts; furthermore, we suggest research directions that may help to enhance production of recombinant products in the widely used, creatively engineered, but relatively less studied P. pastoris through de novo metabolic engineering strategies based on the discovery of components of signalling pathways in CCR metabolism. KEY POINTS: • Transcriptional regulation and control is the key phenomenon in the cellular processes. • Designing de novo metabolic engineering strategies depends on the discovery of signalling pathways in CCR metabolism. • Crosstalk between pathways occurs through essential parts of transcriptional machinery connected to specific catalytic domains. • In S. cerevisiae, a major part of CCR metabolism is controlled through Snf1 kinase, Glc7 phosphatase, and Srb10 kinase. • In P. pastoris, signalling pathways in CCR metabolism have not yet been clearly known yet. • Cellular regulations on the transcription of promoters are controlled with carbon sources.
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22
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Quintero-Cadena P, Lenstra TL, Sternberg PW. RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting. Mol Cell 2020; 79:207-220.e8. [DOI: 10.1016/j.molcel.2020.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/09/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
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Yarrington RM, Yu Y, Yan C, Bai L, Stillman DJ. A Role for Mediator Core in Limiting Coactivator Recruitment in Saccharomyces cerevisiae. Genetics 2020; 215:407-420. [PMID: 32327563 PMCID: PMC7268993 DOI: 10.1534/genetics.120.303254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/21/2020] [Indexed: 01/12/2023] Open
Abstract
Mediator is an essential, multisubunit complex that functions as a transcriptional coactivator in yeast and other eukaryotic organisms. Mediator has four conserved modules, Head, Middle, Tail, and Kinase, and has been implicated in nearly all aspects of gene regulation. The Tail module has been shown to recruit the Mediator complex to the enhancer or upstream activating sequence (UAS) regions of genes via interactions with transcription factors, and the Kinase module facilitates the transition of Mediator from the UAS/enhancer to the preinitiation complex via protein phosphorylation. Here, we analyze expression of the Saccharomyces cerevisiaeHO gene using a sin4 Mediator Tail mutation that separates the Tail module from the rest of the complex; the sin4 mutation permits independent recruitment of the Tail module to promoters without the rest of Mediator. Significant increases in recruitment of the SWI/SNF and SAGA coactivators to the HO promoter UAS were observed in a sin4 mutant, along with increased gene activation. These results are consistent with recent studies that have suggested that the Kinase module functions negatively to inhibit activation by the Tail. However, we found that Kinase module mutations did not mimic the effect of a sin4 mutation on HO expression. This suggests that at HO the core Mediator complex (Middle and Head modules) must play a role in limiting Tail binding to the promoter UAS and gene activation. We propose that the core Mediator complex helps modulate Mediator binding to the UAS regions of genes to limit coactivator recruitment and ensure proper regulation of gene transcription.
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Affiliation(s)
- Robert M Yarrington
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Yaxin Yu
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Chao Yan
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Lu Bai
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
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Selective Mediator dependence of cell-type-specifying transcription. Nat Genet 2020; 52:719-727. [PMID: 32483291 PMCID: PMC7610447 DOI: 10.1038/s41588-020-0635-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite this pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Notably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.
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25
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Cramer P. Eukaryotic Transcription Turns 50. Cell 2020; 179:808-812. [PMID: 31675494 DOI: 10.1016/j.cell.2019.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/15/2022]
Abstract
This year we celebrate the 50th anniversary of the discovery of the three eukaryotic RNA polymerases. Ever since this seminal event in 1969, researchers have investigated the intricate mechanisms of gene transcription with great dedication. The transcription field continues to influence developmental, stem cell, and cancer biology.
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Affiliation(s)
- Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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Abstract
RNA polymerase II (Pol II) transcribes all protein-coding genes and many noncoding RNAs in eukaryotic genomes. Although Pol II is a complex, 12-subunit enzyme, it lacks the ability to initiate transcription and cannot consistently transcribe through long DNA sequences. To execute these essential functions, an array of proteins and protein complexes interact with Pol II to regulate its activity. In this review, we detail the structure and mechanism of over a dozen factors that govern Pol II initiation (e.g., TFIID, TFIIH, and Mediator), pausing, and elongation (e.g., DSIF, NELF, PAF, and P-TEFb). The structural basis for Pol II transcription regulation has advanced rapidly in the past decade, largely due to technological innovations in cryoelectron microscopy. Here, we summarize a wealth of structural and functional data that have enabled a deeper understanding of Pol II transcription mechanisms; we also highlight mechanistic questions that remain unanswered or controversial.
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Affiliation(s)
- Allison C Schier
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
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27
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Georges A, Gopaul D, Denby Wilkes C, Giordanengo Aiach N, Novikova E, Barrault MB, Alibert O, Soutourina J. Functional interplay between Mediator and RNA polymerase II in Rad2/XPG loading to the chromatin. Nucleic Acids Res 2019; 47:8988-9004. [PMID: 31299084 PMCID: PMC6753472 DOI: 10.1093/nar/gkz598] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/30/2022] Open
Abstract
Transcription and maintenance of genome integrity are fundamental cellular functions. Deregulation of transcription and defects in DNA repair lead to serious pathologies. The Mediator complex links RNA polymerase (Pol) II transcription and nucleotide excision repair via Rad2/XPG endonuclease. However, the functional interplay between Rad2/XPG, Mediator and Pol II remains to be determined. In this study, we investigated their functional dynamics using genomic and genetic approaches. In a mutant affected in Pol II phosphorylation leading to Mediator stabilization on core promoters, Rad2 genome-wide occupancy shifts towards core promoters following that of Mediator, but decreases on transcribed regions together with Pol II. Specific Mediator mutations increase UV sensitivity, reduce Rad2 recruitment to transcribed regions, lead to uncoupling of Rad2, Mediator and Pol II and to colethality with deletion of Rpb9 Pol II subunit involved in transcription-coupled repair. We provide new insights into the functional interplay between Rad2, Mediator and Pol II and propose that dynamic interactions with Mediator and Pol II are involved in Rad2 loading to the chromatin. Our work contributes to the understanding of the complex link between transcription and DNA repair machineries, dysfunction of which leads to severe diseases.
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Affiliation(s)
- Adrien Georges
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Diyavarshini Gopaul
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Giordanengo Aiach
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Elizaveta Novikova
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie-Bénédicte Barrault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | | | - Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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28
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Roeder RG. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 2019; 26:783-791. [PMID: 31439941 DOI: 10.1038/s41594-019-0287-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
The landmark 1969 discovery of nuclear RNA polymerases I, II and III in diverse eukaryotes represented a major turning point in the field that, with subsequent elucidation of the distinct structures and functions of these enzymes, catalyzed an avalanche of further studies. In this Review, written from a personal and historical perspective, I highlight foundational biochemical studies that led to the discovery of an expanding universe of the components of the transcriptional and regulatory machineries, and a parallel complexity in gene-specific mechanisms that continue to be explored to the present day.
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Affiliation(s)
- Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, USA.
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29
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Youn DY, Xiaoli AM, Kwon H, Yang F, Pessin JE. The subunit assembly state of the Mediator complex is nutrient-regulated and is dysregulated in a genetic model of insulin resistance and obesity. J Biol Chem 2019; 294:9076-9083. [PMID: 31028171 PMCID: PMC6556571 DOI: 10.1074/jbc.ra119.007850] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/18/2019] [Indexed: 01/22/2023] Open
Abstract
The Mediator complex plays a critical role in the regulation of transcription by linking transcription factors to RNA polymerase II. By examining mouse livers, we have found that in the fasted state, the Mediator complex exists primarily as an approximately 1.2-MDa complex, consistent with the size of the large Mediator complex, whereas following feeding, it converts to an approximately 600-kDa complex, consistent with the size of the core Mediator complex. This dynamic change is due to the dissociation and degradation of the kinase module that includes the MED13, MED12, cyclin-dependent kinase 8 (CDK8), and cyclin C (CCNC) subunits. The dissociation and degradation of the kinase module are dependent upon nutrient activation of mTORC1 that is necessary for the induction of lipogenic gene expression because pharmacological or genetic inhibition of mTORC1 in the fed state restores the kinase module. The degradation but not dissociation of the kinase module depends upon the E3 ligase, SCFFBW7 In addition, genetically insulin-resistant and obese db/db mice in the fasted state displayed elevated lipogenic gene expression and loss of the kinase module that was reversed following mTORC1 inhibition. These data demonstrate that the assembly state of the Mediator complex undergoes physiologic regulation during normal cycles of fasting and feeding in the mouse liver. Furthermore, the assembly state of the Mediator complex is dysregulated in states of obesity and insulin resistance.
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Affiliation(s)
- Dou Yeon Youn
- From the Departments of Medicine
- Molecular Pharmacology and
| | - Alus M Xiaoli
- From the Departments of Medicine
- Developmental and Molecular Biology, and
| | - Hyokjoon Kwon
- the Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901
| | - Fajun Yang
- From the Departments of Medicine
- Developmental and Molecular Biology, and
- the Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461 and
| | - Jeffrey E Pessin
- From the Departments of Medicine,
- Molecular Pharmacology and
- the Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461 and
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30
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Trnka MJ, Pellarin R, Robinson PJ. Role of integrative structural biology in understanding transcriptional initiation. Methods 2019; 159-160:4-22. [PMID: 30890443 PMCID: PMC6617507 DOI: 10.1016/j.ymeth.2019.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022] Open
Abstract
Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest. Most commonly cross-linking data sets are employed alongside electron microscopy maps, crystallographic structures, and other data by computational methods that integrate all known information and produce structural models at a level of resolution that is appropriate to the input data. The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the same protein, and structural and compositional heterogeneity. In recent years integrative structural biology approaches have been successfully applied to a range of RNA polymerase II complexes. Here we will provide a general background to integrative structural biology, a description of how it should be practically implemented and how it has furthered our understanding of the biology of large transcriptional assemblies. Finally, in the context of recent breakthroughs in microscope and direct electron detector technology, where increasingly EM is capable of resolving structural features directly without the aid of other structural techniques, we will discuss the future role of integrative structural techniques.
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Affiliation(s)
- Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Riccardo Pellarin
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France
| | - Philip J Robinson
- Department of Biological Sciences, Birkbeck University of London, Institute of Structural and Molecular Biology, London, United Kingdom.
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31
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Ofori K, Fernandes H, Cummings M, Colby T, Saqi A. Benign metastasizing leiomyoma presenting with miliary pattern and fatal outcome: Case report with molecular analysis & review of the literature. Respir Med Case Rep 2019; 27:100831. [PMID: 30989050 PMCID: PMC6446132 DOI: 10.1016/j.rmcr.2019.100831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 11/17/2022] Open
Abstract
Benign metastasizing leiomyoma (BML) is a rare benign smooth muscle neoplasm that originates in the uterus and metastasizes to distant sites—most commonly the lungs. BMLs are often found incidentally in patients with a history of uterine leiomyoma(s) and tend to be indolent. Occasionally they may be symptomatic and rarely follow an aggressive clinical course. We report an unusual case of BML presenting in a 46-year-old woman as a miliary nodular pattern bilaterally in the lungs and progressive respiratory failure. Her past medical history was significant for uterine “leiomyomas” of at least 9 years' duration. Post mortem histologic evaluation of the uterine and lung lesions revealed benign smooth muscle neoplasms (leiomyomas and BMLs, respectively), and molecular analyses demonstrated identical clonal MED12 mutation, though with greater mutant allelic frequency in the uterus. We document a rare aggressive clinical course in a patient with BML, which presented as a miliary radiologic pattern mimicking an infectious etiology or interstitial lung disease.
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Affiliation(s)
- Kenneth Ofori
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Matthew Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia, University Medical Center, New York, USA
| | | | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
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32
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Twenty years of Mediator complex structural studies. Biochem Soc Trans 2019; 47:399-410. [PMID: 30733343 PMCID: PMC6393861 DOI: 10.1042/bst20180608] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/18/2022]
Abstract
Mediator is a large multiprotein complex conserved in all eukaryotes that plays an essential role in transcriptional regulation. Mediator comprises 25 subunits in yeast and 30 subunits in humans that form three main modules and a separable four-subunit kinase module. For nearly 20 years, because of its size and complexity, Mediator has posed a formidable challenge to structural biologists. The first two-dimensional electron microscopy (EM) projection map of Mediator leading to the canonical view of its division in three topological modules named Head, Middle and Tail, was published in 1999. Within the last few years, optimization of Mediator purification combined with technical and methodological advances in cryo-electron microscopy (cryo-EM) have revealed unprecedented details of Mediator subunit organization, interactions with RNA polymerase II and parts of its core structure at high resolution. To celebrate the twentieth anniversary of the first Mediator EM reconstruction, we look back on the structural studies of Mediator complex from a historical perspective and discuss them in the light of our current understanding of its role in transcriptional regulation.
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33
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Dannappel MV, Sooraj D, Loh JJ, Firestein R. Molecular and in vivo Functions of the CDK8 and CDK19 Kinase Modules. Front Cell Dev Biol 2019; 6:171. [PMID: 30693281 PMCID: PMC6340071 DOI: 10.3389/fcell.2018.00171] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/06/2018] [Indexed: 12/21/2022] Open
Abstract
CDK8 and its paralog, CDK19, collectively termed ‘Mediator Kinase,’ are cyclin-dependent kinases that have been implicated as key rheostats in cellular homeostasis and developmental programming. CDK8 and CDK19 are incorporated, in a mutually exclusive manner, as part of a 4-protein complex called the Mediator kinase module. This module reversibly associates with the Mediator, a 26 subunit protein complex that regulates RNA Polymerase II mediated gene expression. As part of this complex, the Mediator kinases have been implicated in diverse process such as developmental signaling, metabolic homeostasis and in innate immunity. In recent years, dysregulation of Mediator kinase module proteins, including CDK8/19, has been implicated in the development of different human diseases, and in particular cancer. This has led to intense efforts to understand how CDK8/19 regulate diverse biological outputs and develop Mediator kinase inhibitors that can be exploited therapeutically. Herein, we review both context and function of the Mediator kinases at a molecular, cellular and animal level. In so doing, we illuminate emerging concepts underpinning Mediator kinase biology and highlight certain aspects that remain unsolved.
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Affiliation(s)
- Marius Volker Dannappel
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Dhanya Sooraj
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Jia Jian Loh
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Ron Firestein
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
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34
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Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation. G3-GENES GENOMES GENETICS 2018; 8:3093-3108. [PMID: 30049745 PMCID: PMC6118316 DOI: 10.1534/g3.118.200573] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Mediator complex is a central component of transcriptional regulation in Eukaryotes. The complex is structurally divided into four modules known as the head, middle, tail and kinase modules, and in Arabidopsis thaliana, comprises 28-34 subunits. Here, we explore the functions of four Arabidopsis Mediator tail subunits, MED2, MED5a/b, MED16, and MED23, by comparing the impact of mutations in each on the Arabidopsis transcriptome. We find that these subunits affect both unique and overlapping sets of genes, providing insight into the functional and structural relationships between them. The mutants primarily exhibit changes in the expression of genes related to biotic and abiotic stress. We find evidence for a tissue specific role for MED23, as well as in the production of alternative transcripts. Together, our data help disentangle the individual contributions of these MED subunits to global gene expression and suggest new avenues for future research into their functions.
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35
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Postrecruitment Function of Yeast Med6 Protein during the Transcriptional Activation by Mediator Complex. Biochem Res Int 2018; 2018:6406372. [PMID: 29992056 PMCID: PMC5818915 DOI: 10.1155/2018/6406372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/29/2017] [Indexed: 11/17/2022] Open
Abstract
Med6 protein (Med6p) is a hallmark component of evolutionarily conserved Mediator complexes, and the genuine role of Med6p in Mediator functions remains elusive. For the functional analysis of Saccharomyces cerevisiae Med6p (scMed6p), we generated a series of scMed6p mutants harboring a small internal deletion. Genetic analysis of these mutants revealed that three regions (amino acids 33-42 (Δ2), 125-134 (Δ5), and 157-166 (Δ6)) of scMed6p are required for cell viability and are located at highly conserved regions of Med6 homologs. Notably, the Med6p-Δ2 mutant was barely detectable in whole-cell extracts and purified Mediator, suggesting a loss of Mediator association and concurrent rapid degradation. Consistent with this, the recombinant forms of Med6p having these mutations partially (Δ2) restore or fail (Δ5 and Δ6) to restore in vitro transcriptional defects caused by temperature-sensitive med6 mutation. In an artificial recruitment assay, Mediator containing a LexA-fused wild-type Med6p or Med6p-Δ5 was recruited to the lexA operator region with TBP and activated reporter gene expression. However, the recruitment of Mediator containing LexA-Med6p-Δ6 to lexA operator region resulted in neither TBP recruitment nor reporter gene expression. This result demonstrates a pivotal role of Med6p in the postrecruitment function of Mediator, which is essential for transcriptional activation by Mediator.
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36
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Nitta R, Imasaki T, Nitta E. Recent progress in structural biology: lessons from our research history. Microscopy (Oxf) 2018; 67:4996565. [PMID: 29771342 DOI: 10.1093/jmicro/dfy022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
The recent 'resolution revolution' in structural analyses of cryo-electron microscopy (cryo-EM) has drastically changed the research strategy for structural biology. In addition to X-ray crystallography and nuclear magnetic resonance spectroscopy, cryo-EM has achieved the structural analysis of biological molecules at near-atomic resolution, resulting in the Nobel Prize in Chemistry 2017. The effect of this revolution has spread within the biology and medical science fields affecting everything from basic research to pharmaceutical development by visualizing atomic structure. As we have used cryo-EM as well as X-ray crystallography since 2000 to elucidate the molecular mechanisms of the fundamental phenomena in the cell, here we review our research history and summarize our findings. In the first half of the review, we describe the structural mechanisms of microtubule-based motility of molecular motor kinesin by using a joint cryo-EM and X-ray crystallography method. In the latter half, we summarize our structural studies on transcriptional regulation by X-ray crystallography of in vitro reconstitution of a multi-protein complex.
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Affiliation(s)
- Ryo Nitta
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
- RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsuyoshi Imasaki
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
- RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Eriko Nitta
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
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37
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Abstract
Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.
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Affiliation(s)
- Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, Commissariat à l'énergie Atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), University Paris Sud, University Paris Saclay, F-91198 Gif-sur-Yvette, France
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38
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Eychenne T, Werner M, Soutourina J. Toward understanding of the mechanisms of Mediator function in vivo: Focus on the preinitiation complex assembly. Transcription 2017; 8:328-342. [PMID: 28841352 DOI: 10.1080/21541264.2017.1329000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mediator is a multisubunit complex conserved in eukaryotes that plays an essential coregulator role in RNA polymerase (Pol) II transcription. Despite intensive studies of the Mediator complex, the molecular mechanisms of its function in vivo remain to be fully defined. In this review, we will discuss the different aspects of Mediator function starting with its interactions with specific transcription factors, its recruitment to chromatin and how, as a coregulator, it contributes to the assembly of transcription machinery components within the preinitiation complex (PIC) in vivo and beyond the PIC formation.
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Affiliation(s)
- Thomas Eychenne
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France.,b Institut Pasteur, (Epi)genomics of Animal Development Unit , Development and Stem Cell Biology Department, CNRS UMR3778 , Paris , France
| | - Michel Werner
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
| | - Julie Soutourina
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
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39
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Petrenko N, Jin Y, Wong KH, Struhl K. Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo. eLife 2017; 6. [PMID: 28699889 PMCID: PMC5529107 DOI: 10.7554/elife.28447] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 07/09/2017] [Indexed: 12/27/2022] Open
Abstract
The Mediator complex has been described as a general transcription factor, but it is unclear if it is essential for Pol II transcription and/or is a required component of the preinitiation complex (PIC) in vivo. Here, we show that depletion of individual subunits, even those essential for cell growth, causes a general but only modest decrease in transcription. In contrast, simultaneous depletion of all Mediator modules causes a drastic decrease in transcription. Depletion of head or middle subunits, but not tail subunits, causes a downstream shift in the Pol II occupancy profile, suggesting that Mediator at the core promoter inhibits promoter escape. Interestingly, a functional PIC and Pol II transcription can occur when Mediator is not detected at core promoters. These results provide strong evidence that Mediator is essential for Pol II transcription and stimulates PIC formation, but it is not a required component of the PIC in vivo. DOI:http://dx.doi.org/10.7554/eLife.28447.001
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Affiliation(s)
- Natalia Petrenko
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Boston, United States
| | - Yi Jin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Boston, United States
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Boston, United States
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40
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Yuan CT, Huang WC, Lee CH, Lin MC, Lee CH, Kao YC, Huang HY, Kuo KT, Lee JC. Comprehensive screening forMED12mutations in gynaecological mesenchymal tumours identified morphologically distinctive mixed epithelial and stromal tumours. Histopathology 2017; 70:954-965. [DOI: 10.1111/his.13156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/19/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Chang-Tsu Yuan
- Department and Graduate Institute of Pathology; National Taiwan University Hospital; National Taiwan University College of Medicine; Taipei Taiwan
| | - Wen-Chih Huang
- Department of Pathology; Far-Eastern Memorial Hospital; New Taipei City Taiwan
| | - Cheng-Han Lee
- Department of Pathology; British Columbia Cancer Agency; Vancouver British Columbia
- University of Alberta; Edmonton Alberta Canada
| | - Ming-Chieh Lin
- Department and Graduate Institute of Pathology; National Taiwan University Hospital; National Taiwan University College of Medicine; Taipei Taiwan
| | - Chen-Hui Lee
- Department of Pathology and Laboratory Medicine; Taichung Veterans General Hospital; Taichung Taiwan
| | - Yu-Chien Kao
- Department of Pathology; Shuang Ho Hospital; Taipei Medical University; Taipei Taiwan
| | - Hsuan-Ying Huang
- Department of Pathology; Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine; Kaohsiung Taiwan
| | - Kuan-Ting Kuo
- Department and Graduate Institute of Pathology; National Taiwan University Hospital; National Taiwan University College of Medicine; Taipei Taiwan
| | - Jen-Chieh Lee
- Department and Graduate Institute of Pathology; National Taiwan University Hospital; National Taiwan University College of Medicine; Taipei Taiwan
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41
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Abstract
Mediator is a conserved and essential coactivator complex broadly required for RNA polymerase II (RNAPII) transcription. Recent genome-wide studies of Mediator binding in budding yeast have revealed new insights into the functions of this critical complex and raised new questions about its role in the regulation of gene expression.
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Affiliation(s)
- Sebastian Grünberg
- a Basic Sciences Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
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42
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Petrenko N, Jin Y, Wong KH, Struhl K. Mediator Undergoes a Compositional Change during Transcriptional Activation. Mol Cell 2016; 64:443-454. [PMID: 27773675 DOI: 10.1016/j.molcel.2016.09.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/01/2016] [Accepted: 09/09/2016] [Indexed: 10/20/2022]
Abstract
Mediator is a transcriptional co-activator recruited to enhancers by DNA-binding activators, and it also interacts with RNA polymerase (Pol) II as part of the preinitiation complex (PIC). We demonstrate that a single Mediator complex associates with the enhancer and core promoter in vivo, indicating that it can physically bridge these transcriptional elements. However, the Mediator kinase module associates strongly with the enhancer, but not with the core promoter, and it dissociates from the enhancer upon depletion of the TFIIH kinase. Severing the kinase module from Mediator by removing the connecting subunit Med13 does not affect Mediator association at the core promoter but increases occupancy at enhancers. Thus, Mediator undergoes a compositional change in which the kinase module, recruited via Mediator to the enhancer, dissociates from Mediator to permit association with Pol II and the PIC. As such, Mediator acts as a dynamic bridge between the enhancer and core promoter.
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Affiliation(s)
- Natalia Petrenko
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Jin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Koon Ho Wong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Faculty of Health Sciences, University of Macau, Macau SAR, China.
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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43
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Vernimmen D, Bickmore WA. The Hierarchy of Transcriptional Activation: From Enhancer to Promoter. Trends Genet 2016; 31:696-708. [PMID: 26599498 DOI: 10.1016/j.tig.2015.10.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/18/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Regulatory elements (enhancers) that are remote from promoters play a critical role in the spatial, temporal, and physiological control of gene expression. Studies on specific loci, together with genome-wide approaches, suggest that there may be many common mechanisms involved in enhancer-promoter communication. Here, we discuss the multiprotein complexes that are recruited to enhancers and the hierarchy of events taking place between regulatory elements and promoters.
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Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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44
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Morrill SA, Exner AE, Babokhov M, Reinfeld BI, Fuchs SM. DNA Instability Maintains the Repeat Length of the Yeast RNA Polymerase II C-terminal Domain. J Biol Chem 2016; 291:11540-50. [PMID: 27026700 PMCID: PMC4882425 DOI: 10.1074/jbc.m115.696252] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/06/2022] Open
Abstract
The C-terminal domain (CTD) of RNA polymerase II in eukaryotes is comprised of tandemly repeating units of a conserved seven-amino acid sequence. The number of repeats is, however, quite variable across different organisms. Furthermore, previous studies have identified evidence of rearrangements within the CTD coding region, suggesting that DNA instability may play a role in regulating or maintaining CTD repeat number. The work described here establishes a clear connection between DNA instability and CTD repeat number in Saccharomyces cerevisiae First, analysis of 36 diverse S. cerevisiae isolates revealed evidence of numerous past rearrangements within the DNA sequence that encodes the CTD. Interestingly, the total number of CTD repeats was relatively static (24-26 repeats in all strains), suggesting a balancing act between repeat expansion and contraction. In an effort to explore the genetic plasticity within this region, we measured the rates of repeat expansion and contraction using novel reporters and a doxycycline-regulated expression system for RPB1 In efforts to determine the mechanisms leading to CTD repeat variability, we identified the presence of DNA secondary structures, specifically G-quadruplex-like DNA, within the CTD coding region. Furthermore, we demonstrated that mutating PIF1, a G-quadruplex-specific helicase, results in increased CTD repeat length polymorphisms. We also determined that RAD52 is necessary for CTD repeat expansion but not contraction, identifying a role for recombination in repeat expansion. Results from these DNA rearrangements may help explain the CTD copy number variation seen across eukaryotes, as well as support a model of CTD expansion and contraction to maintain CTD integrity and overall length.
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Affiliation(s)
- Summer A Morrill
- From the Department of Biology, Tufts University, Medford, Massachusetts 02155
| | - Alexandra E Exner
- From the Department of Biology, Tufts University, Medford, Massachusetts 02155
| | - Michael Babokhov
- From the Department of Biology, Tufts University, Medford, Massachusetts 02155
| | - Bradley I Reinfeld
- From the Department of Biology, Tufts University, Medford, Massachusetts 02155
| | - Stephen M Fuchs
- From the Department of Biology, Tufts University, Medford, Massachusetts 02155
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45
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Plaschka C, Nozawa K, Cramer P. Mediator Architecture and RNA Polymerase II Interaction. J Mol Biol 2016; 428:2569-2574. [PMID: 26851380 DOI: 10.1016/j.jmb.2016.01.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 12/18/2022]
Abstract
Integrated structural biology recently elucidated the architecture of Mediator and its position on RNA polymerase II. Here we summarize these achievements and list open questions on Mediator structure and mechanism.
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Affiliation(s)
- Clemens Plaschka
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Kayo Nozawa
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany.
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46
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Laughery MF, Hunter T, Brown A, Hoopes J, Ostbye T, Shumaker T, Wyrick JJ. New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae. Yeast 2015; 32:711-20. [PMID: 26305040 PMCID: PMC4715497 DOI: 10.1002/yea.3098] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/10/2015] [Accepted: 08/18/2015] [Indexed: 01/19/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is an important tool for genome editing because the Cas9 endonuclease can induce targeted DNA double-strand breaks. Targeting of the DNA break is typically controlled by a single-guide RNA (sgRNA), a chimeric RNA containing a structural segment important for Cas9 binding and a 20mer guide sequence that hybridizes to the genomic DNA target. Previous studies have demonstrated that CRISPR-Cas9 technology can be used for efficient, marker-free genome editing in Saccharomyces cerevisiae. However, introducing the 20mer guide sequence into yeast sgRNA expression vectors often requires cloning procedures that are complex, time-consuming and/or expensive. To simplify this process, we have developed a new sgRNA expression cassette with internal restriction enzyme sites that permit rapid, directional cloning of 20mer guide sequences. Here we describe a flexible set of vectors based on this design for cloning and expressing sgRNAs (and Cas9) in yeast using different selectable markers. We anticipate that the Cas9-sgRNA expression vector with the URA3 selectable marker (pML104) will be particularly useful for genome editing in yeast, since the Cas9 machinery can be easily removed by counter-selection using 5-fluoro-orotic acid (5-FOA) following successful genome editing. The availability of new vectors that simplify and streamline the technical steps required for guide sequence cloning should help accelerate the use of CRISPR-Cas9 technology in yeast genome editing.
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Affiliation(s)
- Marian F. Laughery
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Tierra Hunter
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Alexander Brown
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - James Hoopes
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Travis Ostbye
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Taven Shumaker
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
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47
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Schneider M, Hellerschmied D, Schubert T, Amlacher S, Vinayachandran V, Reja R, Pugh BF, Clausen T, Köhler A. The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression. Cell 2015; 162:1016-28. [PMID: 26317468 PMCID: PMC4644235 DOI: 10.1016/j.cell.2015.07.059] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 05/05/2015] [Accepted: 07/06/2015] [Indexed: 11/27/2022]
Abstract
Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription, and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with the Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent at specific genes. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing. Our data provide mechanistic insight into how an NPC-associated adaptor complex accesses the core transcription machinery. The nuclear pore-associated TREX-2 complex directly interacts with Mediator TREX-2 regulates Mediator association with Cdk8 and RNA Pol II Ser5 phosphorylation TREX-2 and the Med31 submodule co-regulate specific inducible and constitutive genes A similar TREX-2 surface promotes both transcription and mRNA export
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Affiliation(s)
- Maren Schneider
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Doris Hellerschmied
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Tobias Schubert
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Stefan Amlacher
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Vinesh Vinayachandran
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - Rohit Reja
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - Tim Clausen
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alwin Köhler
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria.
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48
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Nagulapalli M, Maji S, Dwivedi N, Dahiya P, Thakur JK. Evolution of disorder in Mediator complex and its functional relevance. Nucleic Acids Res 2015; 44:1591-612. [PMID: 26590257 PMCID: PMC4770211 DOI: 10.1093/nar/gkv1135] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 10/18/2015] [Indexed: 12/27/2022] Open
Abstract
Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of ‘junction-MoRF’ has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein–protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms.
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Affiliation(s)
- Malini Nagulapalli
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pradeep Dahiya
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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49
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McCleland ML, Soukup TM, Liu SD, Esensten JH, de Sousa e Melo F, Yaylaoglu M, Warming S, Roose-Girma M, Firestein R. Cdk8 deletion in the Apc(Min) murine tumour model represses EZH2 activity and accelerates tumourigenesis. J Pathol 2015; 237:508-19. [PMID: 26235356 DOI: 10.1002/path.4596] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 07/09/2015] [Accepted: 07/28/2015] [Indexed: 01/29/2023]
Abstract
CDK8 is a dissociable kinase module of the Mediator complex and has been shown to play an important role in transcriptional regulation in organisms as diverse as yeast and humans. Recent studies suggest that CDK8 functions as an oncoprotein in melanoma and colon cancer. Importantly, these studies were conducted using in vitro cell line models and the role of CDK8 in tumourigenesis in vivo has not been explored. We have generated a mouse with a Cdk8 conditional knockout allele and examined the consequences of Cdk8 loss on normal tissue homeostasis and tumour development in vivo. Cdk8 deletion in the young adult mouse did not induce any gross or histopathological abnormalities, implying that Cdk8 is largely dispensable for somatic cellular homeostasis. In contrast, Cdk8 deletion in the Apc(Min) intestinal tumour model shortened the animals' survival and increased tumour burden. Although Cdk8 deletion did not affect tumour initiation, intestinal tumour size and growth rate were significantly increased in Cdk8-null animals. Transcriptome analysis performed on Cdk8-null intestinal cells revealed up-regulation of genes that are governed by the Polycomb group (PcG) complex. In support of these findings, Cdk8-null intestinal cells and tumours displayed a reduction in histone H3K27 trimethylation, both globally and at the promoters of a number of PcG-regulated genes involved in oncogenic signalling. Together, our findings uncover a tumour suppressor function for CDK8 in vivo and suggest that the role of CDK8 activity in driving oncogenesis is context-specific. Sequencing data were deposited at GEO (Accession No. GSE71385).
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Affiliation(s)
- Mark L McCleland
- Department of Pathology, Genentech Inc, South San Francisco, CA, USA
| | - Tim M Soukup
- Department of Molecular Biology, Genentech Inc, South San Francisco, CA, USA
| | - Scot D Liu
- Department of Pathology, Genentech Inc, South San Francisco, CA, USA
| | | | | | - Murat Yaylaoglu
- Department of Pathology, Genentech Inc, South San Francisco, CA, USA
| | - Soren Warming
- Department of Molecular Biology, Genentech Inc, South San Francisco, CA, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech Inc, South San Francisco, CA, USA
| | - Ron Firestein
- Department of Pathology, Genentech Inc, South San Francisco, CA, USA
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50
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Eyboulet F, Wydau-Dematteis S, Eychenne T, Alibert O, Neil H, Boschiero C, Nevers MC, Volland H, Cornu D, Redeker V, Werner M, Soutourina J. Mediator independently orchestrates multiple steps of preinitiation complex assembly in vivo. Nucleic Acids Res 2015; 43:9214-31. [PMID: 26240385 PMCID: PMC4627066 DOI: 10.1093/nar/gkv782] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/21/2015] [Indexed: 12/20/2022] Open
Abstract
Mediator is a large multiprotein complex conserved in all eukaryotes, which has a crucial coregulator function in transcription by RNA polymerase II (Pol II). However, the molecular mechanisms of its action in vivo remain to be understood. Med17 is an essential and central component of the Mediator head module. In this work, we utilised our large collection of conditional temperature-sensitive med17 mutants to investigate Mediator's role in coordinating preinitiation complex (PIC) formation in vivo at the genome level after a transfer to a non-permissive temperature for 45 minutes. The effect of a yeast mutation proposed to be equivalent to the human Med17-L371P responsible for infantile cerebral atrophy was also analyzed. The ChIP-seq results demonstrate that med17 mutations differentially affected the global presence of several PIC components including Mediator, TBP, TFIIH modules and Pol II. Our data show that Mediator stabilizes TFIIK kinase and TFIIH core modules independently, suggesting that the recruitment or the stability of TFIIH modules is regulated independently on yeast genome. We demonstrate that Mediator selectively contributes to TBP recruitment or stabilization to chromatin. This study provides an extensive genome-wide view of Mediator's role in PIC formation, suggesting that Mediator coordinates multiple steps of a PIC assembly pathway.
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Affiliation(s)
- Fanny Eyboulet
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Sandra Wydau-Dematteis
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Thomas Eychenne
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | | | - Helen Neil
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Claire Boschiero
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Marie-Claire Nevers
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, F-91191 Gif sur Yvette cedex, France
| | - Hervé Volland
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, F-91191 Gif sur Yvette cedex, France
| | - David Cornu
- CNRS, Centre de Recherche de Gif, SICaPS, F-91198 Gif-sur-Yvette cedex, France
| | - Virginie Redeker
- CNRS, Centre de Recherche de Gif, SICaPS, F-91198 Gif-sur-Yvette cedex, France
| | - Michel Werner
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
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