51
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Croce S, Chibon F. MED12 and uterine smooth muscle oncogenesis: State of the art and perspectives. Eur J Cancer 2015; 51:1603-10. [DOI: 10.1016/j.ejca.2015.04.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 10/23/2022]
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52
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Nagasawa S, Maeda I, Fukuda T, Wu W, Hayami R, Kojima Y, Tsugawa KI, Ohta T. MED12 exon 2 mutations in phyllodes tumors of the breast. Cancer Med 2015; 4:1117-21. [PMID: 25865354 PMCID: PMC4529349 DOI: 10.1002/cam4.462] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/08/2015] [Accepted: 03/11/2015] [Indexed: 12/24/2022] Open
Abstract
Exon 2 of MED12, a subunit of the transcriptional mediator complex, has been frequently mutated in uterine leiomyomas and breast fibroadenomas; however, it has been rarely mutated in other tumors. Although the mutations were also found in uterine leiomyosarcomas, the frequency was significantly lower than in uterine leiomyomas. Here, we examined the MED12 mutation in phyllodes tumors, another biphasic tumor with epithelial and stromal components related to breast fibroadenomas. Mutations in MED12 exon 2 were analyzed in nine fibroadenomas and eleven phyllodes tumors via Sanger sequencing. A panel of cancer- and sarcoma-related genes was also analyzed using Ion Torrent next-generation sequencing. Six mutations in fibroadenomas, including those previously reported (6/9, 67%), and five mutations in phyllodes tumors (5/11, 45%) were observed. Three mutations in the phyllodes tumors were missense mutations at Gly44, which is common in uterine leiomyomas and breast fibroadenomas. In addition, two deletion mutations (in-frame c.133_144del12 and loss of splice acceptor c.100-68_137del106) were observed in the phyllodes tumors. No other recurrent mutation was observed with next-generation sequencing. Frequent mutations in MED12 exon 2 in the phyllodes tumors suggest that it may share genetic etiology with uterine leiomyoma, a subgroup of uterine leiomyosarcomas and breast fibroadenoma.
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Affiliation(s)
- Satoi Nagasawa
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan.,Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan
| | - Ichiro Maeda
- Department of Pathology, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan
| | - Takayo Fukuda
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan
| | - Wenwen Wu
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan
| | - Ryosuke Hayami
- Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan
| | - Yasuyuki Kojima
- Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan
| | - Ko-Ichiro Tsugawa
- Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan
| | - Tomohiko Ohta
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, 216-8511, Japan
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53
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An in vivo requirement for the mediator subunit med14 in the maintenance of stem cell populations. Stem Cell Reports 2015; 4:670-84. [PMID: 25772472 PMCID: PMC4400641 DOI: 10.1016/j.stemcr.2015.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 12/24/2022] Open
Abstract
The Mediator complex has recently been shown to be a key player in the maintenance of embryonic and induced pluripotent stem cells. However, the in vivo consequences of loss of many Mediator subunits are unknown. We identified med14 as the gene affected in the zebrafish logelei (log) mutant, which displayed a morphological arrest by 2 days of development. Surprisingly, microarray analysis showed that transcription was not broadly affected in log mutants. Indeed, log cells transplanted into a wild-type environment were able to survive into adulthood. In planarians, RNAi knockdown demonstrated a requirement for med14 and many other Mediator components in adult stem cell maintenance and regeneration. Multiple stem/progenitor cell populations were observed to be reduced or absent in zebrafish med14 mutant embryos. Taken together, our results show a critical, evolutionarily conserved, in vivo function for Med14 (and Mediator) in stem cell maintenance, distinct from a general role in transcription. med14 mutant zebrafish embryos do not have global defects in transcription Mediator components are required in planaria for adult stem cell maintenance Zebrafish med14 mutant embryos have an apparent defect in stem cell maintenance Mediator has a specialized in vivo function in stem cell lineages
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54
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Allen BL, Taatjes DJ. The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol 2015; 16:155-66. [PMID: 25693131 DOI: 10.1038/nrm3951] [Citation(s) in RCA: 598] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The RNA polymerase II (Pol II) enzyme transcribes all protein-coding and most non-coding RNA genes and is globally regulated by Mediator - a large, conformationally flexible protein complex with a variable subunit composition (for example, a four-subunit cyclin-dependent kinase 8 module can reversibly associate with it). These biochemical characteristics are fundamentally important for Mediator's ability to control various processes that are important for transcription, including the organization of chromatin architecture and the regulation of Pol II pre-initiation, initiation, re-initiation, pausing and elongation. Although Mediator exists in all eukaryotes, a variety of Mediator functions seem to be specific to metazoans, which is indicative of more diverse regulatory requirements.
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Affiliation(s)
- Benjamin L Allen
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
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55
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Plaschka C, Larivière L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P. Architecture of the RNA polymerase II-Mediator core initiation complex. Nature 2015; 518:376-80. [PMID: 25652824 DOI: 10.1038/nature14229] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/14/2015] [Indexed: 12/12/2022]
Abstract
The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.
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Affiliation(s)
- C Plaschka
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - L Larivière
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - L Wenzeck
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - M Seizl
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - M Hemann
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - D Tegunov
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - E V Petrotchenko
- Department of Biochemistry and Microbiology, Genome British Columbia Protein Centre, University of Victoria, 3101-4464 Markham Street, Victoria, British Columbia V8Z7X8, Canada
| | - C H Borchers
- Department of Biochemistry and Microbiology, Genome British Columbia Protein Centre, University of Victoria, 3101-4464 Markham Street, Victoria, British Columbia V8Z7X8, Canada
| | - W Baumeister
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - F Herzog
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - E Villa
- 1] Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany [2] Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - P Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
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56
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Samanta S, Thakur JK. Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:757. [PMID: 26442070 PMCID: PMC4584954 DOI: 10.3389/fpls.2015.00757] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/04/2015] [Indexed: 05/19/2023]
Abstract
Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either increase or decrease the rate of transcription. Mediator complex is one such cofactor, and recently has drawn a lot of interest because of its integrative power to converge different signaling pathways before channeling the transcription instructions to the RNA polymerase II machinery. Like yeast and metazoans, plants do possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Genetic, and molecular analyses have unraveled important regulatory roles of Mediator subunits at every stage of plant life cycle starting from flowering to embryo and organ development, to even size determination. It also contributes immensely to the survival of plants against different environmental vagaries by the timely activation of its resistance mechanisms. Here, we have provided an overview of plant Mediator complex starting from its discovery to regulation of stoichiometry of its subunits. We have also reviewed involvement of different Mediator subunits in different processes and pathways including defense response pathways evoked by diverse biotic cues. Wherever possible, attempts have been made to provide mechanistic insight of Mediator's involvement in these processes.
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Affiliation(s)
| | - Jitendra K. Thakur
- *Correspondence: Jitendra K. Thakur, Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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57
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Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat Struct Mol Biol 2014; 21:1028-34. [PMID: 25383669 PMCID: PMC4259101 DOI: 10.1038/nsmb.2914] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/09/2014] [Indexed: 01/01/2023]
Abstract
The evolutionarily conserved Mediator complex is a critical coactivator for RNA polymerase II (Pol II)-mediated transcription. Here, we report the reconstitution of a functional 15-subunit human core Mediator complex and its characterization by functional assays and chemical cross-linking coupled to mass spectrometry (CX-MS). Whereas the reconstituted head and middle modules can stably associate, only with incorporation of MED14 into the bi-modular complex does it acquire basal and coactivator functions. This results from a dramatically enhanced ability of MED14-containing complexes to associate with Pol II. Altogether, our analyses identify MED14 as both an architectural and a functional backbone of the Mediator complex. We further establish a conditional requirement for metazoan-specific MED26 that becomes evident in the presence of heterologous nuclear factors. This general approach paves the way for systematically dissecting the multiple layers of functionalities associated with the Mediator complex.
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58
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Wang X, Sun Q, Ding Z, Ji J, Wang J, Kong X, Yang J, Cai G. Redefining the modular organization of the core Mediator complex. Cell Res 2014; 24:796-808. [PMID: 24810298 PMCID: PMC4085763 DOI: 10.1038/cr.2014.64] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 02/13/2014] [Accepted: 03/13/2014] [Indexed: 01/24/2023] Open
Abstract
The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation.
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Affiliation(s)
- Xuejuan Wang
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Qianqian Sun
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Zhenrui Ding
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Jinhua Ji
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Jianye Wang
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Xiao Kong
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Jianghong Yang
- School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
| | - Gang Cai
- 1] School of Life Sciences, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China [2] Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, 443 Huang-Shan Road, Hefei, Anhui 230027, China [3] Center for Biomedical Engineering, University of Science and Technology of China, 443 Huang-Shan Road, Hefei, Anhui 230027, China
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59
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Yin JW, Wang G. The Mediator complex: a master coordinator of transcription and cell lineage development. Development 2014; 141:977-87. [PMID: 24550107 DOI: 10.1242/dev.098392] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mediator is a multiprotein complex that is required for gene transcription by RNA polymerase II. Multiple subunits of the complex show specificity in relaying information from signals and transcription factors to the RNA polymerase II machinery, thus enabling control of the expression of specific genes. Recent studies have also provided novel mechanistic insights into the roles of Mediator in epigenetic regulation, transcriptional elongation, termination, mRNA processing, noncoding RNA activation and super enhancer formation. Based on these specific roles in gene regulation, Mediator has emerged as a master coordinator of development and cell lineage determination. Here, we describe the most recent advances in understanding the mechanisms of Mediator function, with an emphasis on its role during development and disease.
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Affiliation(s)
- Jing-wen Yin
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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60
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Jeronimo C, Robert F. Kin28 regulates the transient association of Mediator with core promoters. Nat Struct Mol Biol 2014; 21:449-55. [PMID: 24704787 PMCID: PMC3997488 DOI: 10.1038/nsmb.2810] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/11/2014] [Indexed: 12/23/2022]
Abstract
Mediator is an essential, broadly used eukaryotic transcriptional coactivator. How and what Mediator communicates from activators to RNA polymerase II (RNAPII) remains an open question. Here we performed genome-wide location profiling of Saccharomyces cerevisiae Mediator subunits. Mediator is not found at core promoters but rather occupies the upstream activating sequence, upstream of the pre-initiation complex. In the absence of Kin28 (CDK7) kinase activity or in cells in which the RNAPII C-terminal domain is mutated to replace Ser5 with alanine, however, Mediator accumulates at core promoters together with RNAPII. We propose that Mediator is released quickly from promoters after phosphorylation of Ser5 by Kin28 (CDK7), which also allows for RNAPII to escape from the promoter.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- 1] Institut de recherches cliniques de Montréal, Montréal, Québec, Canada. [2] Département de Médecine, Université de Montréal, Montréal, Québec, Canada
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61
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Nyambega B, Helbig C, Masiga DK, Clayton C, Levin MJ. Proteins associated with SF3a60 in T. brucei. PLoS One 2014; 9:e91956. [PMID: 24651488 PMCID: PMC3961280 DOI: 10.1371/journal.pone.0091956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/18/2014] [Indexed: 12/29/2022] Open
Abstract
Trypanosoma brucei relies on Spliced leader trans splicing to generate functional messenger RNAs. Trans splicing joins the specialized SL exon from the SL RNA to pre-mRNAs and is mediated by the trans-spliceosome, which is made up of small nuclear ribonucleoprotein particles and non-snRNP factors. Although the trans spliceosome is essential for trypanosomatid gene expression, not all spliceosomal protein factors are known and of these, only a few are completely characterized. In this study, we have characterized the trypanosome Splicing Factor, SF3a60, the only currently annotated SF3a component. As expected, epitope-tagged SF3a60 localizes in the trypanosome nucleus. SF3a60 is essential for cell viability but its depletion seem to have no detectable effect on trans-splicing. In addition, we used SF3a60 as bait in a Yeast-2-hybrid system screen and identified its interacting protein factors. The interactions with SF3a120, SF3a66 and SAP130 were confirmed by tandem affinity purification and mass spectrometry.
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Affiliation(s)
- Benson Nyambega
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigacíones en Ingeniería Genética y Biología Molecular (INGEBI), Buenos Aires, Argentina
- Molecular Biology and Biotechnology Department, International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Claudia Helbig
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Daniel K. Masiga
- Molecular Biology and Biotechnology Department, International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Mariano J. Levin
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigacíones en Ingeniería Genética y Biología Molecular (INGEBI), Buenos Aires, Argentina
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62
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Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
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63
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Abstract
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
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Affiliation(s)
- Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA
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64
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Carlsten JOP, Zhu X, Gustafsson CM. The multitalented Mediator complex. Trends Biochem Sci 2013; 38:531-7. [PMID: 24074826 DOI: 10.1016/j.tibs.2013.08.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/15/2013] [Accepted: 08/20/2013] [Indexed: 10/26/2022]
Abstract
The Mediator complex is needed for regulated transcription of RNA polymerase II (Pol II)-dependent genes. Initially, Mediator was only seen as a protein bridge that conveyed regulatory information from enhancers to the promoter. Later studies have added many other functions to the Mediator repertoire. Indeed, recent findings show that Mediator influences nearly all stages of transcription and coordinates these events with concomitant changes in chromatin organization. We review the multitude of activities associated with Mediator and discuss how this complex coordinates transcription with other cellular events. We also discuss the inherent difficulties associated with in vivo characterization of a coactivator complex that can indirectly affect diverse cellular processes via changes in gene transcription.
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Affiliation(s)
- Jonas O P Carlsten
- University of Gothenburg, Institute of Biomedicine, PO Box 440, 40530 Gothenburg, Sweden
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65
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Emerging roles of Cdk8 in cell cycle control. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:916-20. [DOI: 10.1016/j.bbagrm.2013.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 12/12/2022]
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66
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Aristizabal MJ, Negri GL, Benschop JJ, Holstege FCP, Krogan NJ, Kobor MS. High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8. PLoS Genet 2013; 9:e1003758. [PMID: 24009531 PMCID: PMC3757075 DOI: 10.1371/journal.pgen.1003758] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/15/2013] [Indexed: 12/21/2022] Open
Abstract
The C-terminal domain (CTD) of RNA polymerase II (RNAPII) is composed of heptapeptide repeats, which play a key regulatory role in gene expression. Using genetic interaction, chromatin immunoprecipitation followed by microarrays (ChIP-on-chip) and mRNA expression analysis, we found that truncating the CTD resulted in distinct changes to cellular function. Truncating the CTD altered RNAPII occupancy, leading to not only decreases, but also increases in mRNA levels. The latter were largely mediated by promoter elements and in part were linked to the transcription factor Rpn4. The mediator subunit Cdk8 was enriched at promoters of these genes, and its removal not only restored normal mRNA and RNAPII occupancy levels, but also reduced the abnormally high cellular amounts of Rpn4. This suggested a positive role of Cdk8 in relationship to RNAPII, which contrasted with the observed negative role at the activated INO1 gene. Here, loss of CDK8 suppressed the reduced mRNA expression and RNAPII occupancy levels of CTD truncation mutants.
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Affiliation(s)
- Maria J. Aristizabal
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Joris J. Benschop
- Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Frank C. P. Holstege
- Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, United States of America
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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67
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Lacombe T, Poh SL, Barbey R, Kuras L. Mediator is an intrinsic component of the basal RNA polymerase II machinery in vivo. Nucleic Acids Res 2013; 41:9651-62. [PMID: 23963697 PMCID: PMC3834807 DOI: 10.1093/nar/gkt701] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mediator is a prominent multisubunit coactivator that functions as a bridge between gene-specific activators and the basal RNA polymerase (Pol) II initiation machinery. Here, we study the poorly documented role of Mediator in basal, or activator-independent, transcription in vivo. We show that Mediator is still present at the promoter when the Pol II machinery is recruited in the absence of an activator, in this case through a direct fusion between a basal transcription factor and a heterologous DNA binding protein bound to the promoter. Moreover, transcription resulting from activator-independent recruitment of the Pol II machinery is impaired by inactivation of the essential Mediator subunit Med17 due to the loss of Pol II from the promoter. Our results strongly support that Mediator is an integral component of the minimal machinery essential in vivo for stable Pol II association with the promoter.
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Affiliation(s)
- Thierry Lacombe
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, affiliated with Université Paris-Sud, Gif-sur-Yvette 91198, France
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HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia. Cell 2013; 153:1327-39. [PMID: 23746844 DOI: 10.1016/j.cell.2013.04.048] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 02/26/2013] [Accepted: 04/25/2013] [Indexed: 01/17/2023]
Abstract
The transcription factor HIF1A is a key mediator of the cellular response to hypoxia. Despite the importance of HIF1A in homeostasis and various pathologies, little is known about how it regulates RNA polymerase II (RNAPII). We report here that HIF1A employs a specific variant of the Mediator complex to stimulate RNAPII elongation. The Mediator-associated kinase CDK8, but not the paralog CDK19, is required for induction of many HIF1A target genes. HIF1A induces binding of CDK8-Mediator and the super elongation complex (SEC), containing AFF4 and CDK9, to alleviate RNAPII pausing. CDK8 is dispensable for HIF1A chromatin binding and histone acetylation, but it is essential for binding of SEC and RNAPII elongation. Global analysis of active RNAPII reveals that hypoxia-inducible genes are paused and active prior to their induction. Our results provide a mechanistic link between HIF1A and CDK8, two potent oncogenes, in the cellular response to hypoxia.
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69
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Affiliation(s)
- Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich,
Germany
| | - Matthias Geyer
- Center of Advanced European Studies and Research, Group Physical Biochemistry,
Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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70
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Ansari SA, Morse RH. Mechanisms of Mediator complex action in transcriptional activation. Cell Mol Life Sci 2013; 70:2743-56. [PMID: 23361037 PMCID: PMC11113466 DOI: 10.1007/s00018-013-1265-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 12/14/2022]
Abstract
Mediator is a large multisubunit complex that plays a central role in the regulation of RNA Pol II transcribed genes. Conserved in overall structure and function among eukaryotes, Mediator comprises 25-30 protein subunits that reside in four distinct modules, termed head, middle, tail, and CDK8/kinase. Different subunits of Mediator contact other transcriptional regulators including activators, co-activators, general transcription factors, subunits of RNA Pol II, and specifically modified histones, leading to the regulated expression of target genes. This review is focused on the interactions of specific Mediator subunits with diverse transcription regulators and how those interactions contribute to Mediator function in transcriptional activation.
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Affiliation(s)
- Suraiya A. Ansari
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
| | - Randall H. Morse
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
- Department of Biomedical Science, University at Albany School of Public Health, Albany, NY USA
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71
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Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
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72
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Islam MS, Protic O, Stortoni P, Grechi G, Lamanna P, Petraglia F, Castellucci M, Ciarmela P. Complex networks of multiple factors in the pathogenesis of uterine leiomyoma. Fertil Steril 2013; 100:178-93. [DOI: 10.1016/j.fertnstert.2013.03.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 01/07/2023]
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73
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Barford D, Takagi Y, Schultz P, Berger I. Baculovirus expression: tackling the complexity challenge. Curr Opin Struct Biol 2013; 23:357-64. [PMID: 23628287 PMCID: PMC7125881 DOI: 10.1016/j.sbi.2013.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/18/2013] [Accepted: 03/29/2013] [Indexed: 10/26/2022]
Abstract
Most essential functions in eukaryotic cells are catalyzed by complex molecular machines built of many subunits. To fully understand their biological function in health and disease, it is imperative to study these machines in their entirety. The provision of many essential multiprotein complexes of higher eukaryotes including humans, can be a considerable challenge, as low abundance and heterogeneity often rule out their extraction from native source material. The baculovirus expression vector system (BEVS), specifically tailored for multiprotein complex production, has proven itself to be uniquely suited for overcoming this impeding bottleneck. Here we highlight recent major achievements in multiprotein complex structure research that were catalyzed by this versatile recombinant complex expression tool.
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Affiliation(s)
- David Barford
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
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74
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Grueter CE. Mediator complex dependent regulation of cardiac development and disease. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:151-7. [PMID: 23727265 PMCID: PMC4357813 DOI: 10.1016/j.gpb.2013.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/09/2013] [Accepted: 05/18/2013] [Indexed: 11/22/2022]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality. The risk factors for CVD include environmental and genetic components. Human mutations in genes involved in most aspects of cardiovascular function have been identified, many of which are involved in transcriptional regulation. The Mediator complex serves as a pivotal transcriptional regulator that functions to integrate diverse cellular signals by multiple mechanisms including recruiting RNA polymerase II, chromatin modifying proteins and non-coding RNAs to promoters in a context dependent manner. This review discusses components of the Mediator complex and the contribution of the Mediator complex to normal and pathological cardiac development and function. Enhanced understanding of the role of this core transcriptional regulatory complex in the heart will help us gain further insights into CVD.
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Affiliation(s)
- Chad E Grueter
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
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75
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You JS, De Carvalho DD, Dai C, Liu M, Pandiyan K, Zhou XJ, Liang G, Jones PA. SNF5 is an essential executor of epigenetic regulation during differentiation. PLoS Genet 2013; 9:e1003459. [PMID: 23637628 PMCID: PMC3636213 DOI: 10.1371/journal.pgen.1003459] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 03/04/2013] [Indexed: 12/20/2022] Open
Abstract
Nucleosome occupancy controls the accessibility of the transcription machinery to DNA regulatory regions and serves an instructive role for gene expression. Chromatin remodelers, such as the BAF complexes, are responsible for establishing nucleosome occupancy patterns, which are key to epigenetic regulation along with DNA methylation and histone modifications. Some reports have assessed the roles of the BAF complex subunits and stemness in murine embryonic stem cells. However, the details of the relationships between remodelers and transcription factors in altering chromatin configuration, which ultimately affects gene expression during cell differentiation, remain unclear. Here for the first time we demonstrate that SNF5, a core subunit of the BAF complex, negatively regulates OCT4 levels in pluripotent cells and is essential for cell survival during differentiation. SNF5 is responsible for generating nucleosome-depleted regions (NDRs) at the regulatory sites of OCT4 repressed target genes such as PAX6 and NEUROG1, which are crucial for cell fate determination. Concurrently, SNF5 closes the NDRs at the regulatory regions of OCT4-activated target genes such as OCT4 itself and NANOG. Furthermore, using loss- and gain-of-function experiments followed by extensive genome-wide analyses including gene expression microarrays and ChIP-sequencing, we highlight that SNF5 plays dual roles during differentiation by antagonizing the expression of genes that were either activated or repressed by OCT4, respectively. Together, we demonstrate that SNF5 executes the switch between pluripotency and differentiation. DNA is packaged with proteins into higher-order chromatin structures, which makes genes inherently resistant to transcription initiation. The importance of chromatin remodelers in inducing structural changes to chromatin and, therefore, in controlling the expression of genes has recently resurfaced with the realization that several of them are mutated in human cancers. SNF5, which serves as the core subunit of the BAF remodeling complex, is one such remodeler. In this study, we identify the role of SNF5 induced chromatin remodeling in cell differentiation, the commitment of embryonic cells to a mature lineage-committed state. Importantly, we find that SNF5 establishes appropriate chromatin remodeling patterns during differentiation by controlling the levels of the OCT4 protein, the master determinant of the undifferentiated state. On receipt of differentiation cues, SNF5 opens the chromatin of repressed genes that are occupied by OCT4. SNF5 also induces the closing of genes that are being actively transcribed and OCT4 bound. Further, we show that SNF5 is necessary for cell survival during differentiation, highlighting its crucial role in the process. Together, our data shed novel insights on the importance of SNF5 in maintaining the balance between the embryonic and differentiated states.
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Affiliation(s)
- Jueng Soo You
- Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angles, California, United States of America
- Department of Biochemistry, Graduate School of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Daniel D. De Carvalho
- Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angles, California, United States of America
| | - Chao Dai
- Program in Molecular and Computational Biology, University of Southern California, Los Angles, California, United States of America
| | - Minmin Liu
- Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angles, California, United States of America
| | - Kurinji Pandiyan
- Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Xianghong J. Zhou
- Program in Molecular and Computational Biology, University of Southern California, Los Angles, California, United States of America
| | - Gangning Liang
- Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angles, California, United States of America
| | - Peter A. Jones
- Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angles, California, United States of America
- * E-mail:
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76
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Mukundan B, Ansari A. Srb5/Med18-mediated termination of transcription is dependent on gene looping. J Biol Chem 2013; 288:11384-94. [PMID: 23476016 PMCID: PMC3630880 DOI: 10.1074/jbc.m112.446773] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/21/2013] [Indexed: 11/06/2022] Open
Abstract
We have earlier demonstrated the involvement of Mediator subunit Srb5/Med18 in the termination of transcription for a subset of genes in yeast. Srb5/Med18 could affect termination either indirectly by modulating CTD-Ser(2) phosphorylation near the 3' end of a gene or directly by physically interacting with the cleavage and polyadenylation factor or cleavage factor 1 (CF1) complex and facilitating their recruitment to the terminator region. Here, we show that the CTD-Ser(2) phosphorylation pattern on Srb5/Med18-dependent genes remains unchanged in the absence of Srb5 in cells. Coimmunoprecipitation analysis revealed the physical interaction of Srb5/Med18 with the CF1 complex. No such interaction of Srb5/Med18 with the cleavage and polyadenylation factor complex, however, could be detected. The Srb5/Med18-CF1 interaction was not observed in the looping defective sua7-1 strain. Srb5/Med18 cross-linking to the 3' end of genes was also abolished in the sua7-1 strain. Chromosome conformation capture analysis revealed that the looped architecture of Srb5/Med18-dependent genes was abrogated in srb5(-) cells. Furthermore, Srb5-dependent termination of transcription was compromised in the looping defective sua7-1 cells. The overall conclusion of these results is that gene looping plays a crucial role in Srb5/Med18 facilitated termination of transcription, and the looped gene architecture may have a general role in termination of transcription in budding yeast.
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Affiliation(s)
- Banupriya Mukundan
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Athar Ansari
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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77
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Zhang L, Liu N, Ma X, Jiang L. The transcriptional control machinery as well as the cell wall integrity and its regulation are involved in the detoxification of the organic solvent dimethyl sulfoxide in Saccharomyces cerevisiae. FEMS Yeast Res 2012; 13:200-18. [PMID: 23157175 DOI: 10.1111/1567-1364.12022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/08/2012] [Accepted: 11/08/2012] [Indexed: 11/30/2022] Open
Abstract
In the present study, we have identified 339 dimethyl sulfoxide (DMSO)-sensitive and nine DMSO-tolerant gene mutations in Saccharomyces cerevisiae through a functional genomics approach. Twelve of these identified DMSO-sensitive mutations are of genes involved in the general control of gene expression mediated by the SWR1 complex and the RNA polymerase II mediator complex, whereas 71 of them are of genes involved in the protein trafficking and vacuolar sorting processes. In addition, twelve of these DMSO-sensitive mutations are of genes involved in the cell wall integrity (CWI) and its regulation. DMSO-tolerant mutations are of genes mainly involved in the metabolism and the gene expression control. Therefore, the transcriptional control machinery, the CWI and its regulation as well as the protein trafficking and sorting process play critical roles in the DMSO detoxification in yeast cells.
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Affiliation(s)
- Lilin Zhang
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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78
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Sentenac A, Riva M. Odd RNA polymerases or the A(B)C of eukaryotic transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:251-7. [PMID: 23142548 DOI: 10.1016/j.bbagrm.2012.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/29/2012] [Accepted: 10/30/2012] [Indexed: 02/08/2023]
Abstract
Pioneering studies on eukaryotic transcription were undertaken with the bacterial system in mind. Will the bacterial paradigm apply to eukaryotes? Are there promoter sites scattered in the eukaryotic genome, and sigma-like proteins? Why three forms of RNA polymerase in eukaryotic cells? Why are they structurally so complex, in particular RNA polymerases I and III, compared to the bacterial enzyme? These questions and others that were raised along the way are evoked in this short historical survey of odd RNA polymerases studies, with some emphasis on the contribution of these studies to our global understanding of eukaryotic transcription systems. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- André Sentenac
- CEA-Saclay, iBiTecS, F-91191 Gif-sur-Yvette cedex, France.
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79
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Abstract
Gene transcription by RNA polymerase (Pol) II requires the coactivator complex Mediator. Mediator connects transcriptional regulators and Pol II, and is linked to human disease. Mediator from the yeast Saccharomyces cerevisiae has a molecular mass of 1.4 megadaltons and comprises 25 subunits that form the head, middle, tail and kinase modules. The head module constitutes one-half of the essential Mediator core, and comprises the conserved subunits Med6, Med8, Med11, Med17, Med18, Med20 and Med22. Recent X-ray analysis of the S. cerevisiae head module at 4.3 Å resolution led to a partial architectural model with three submodules called neck, fixed jaw and moveable jaw. Here we determine de novo the crystal structure of the head module from the fission yeast Schizosaccharomyces pombe at 3.4 Å resolution. Structure solution was enabled by new structures of Med6 and the fixed jaw, and previous structures of the moveable jaw and part of the neck, and required deletion of Med20. The S. pombe head module resembles the head of a crocodile with eight distinct elements, of which at least four are mobile. The fixed jaw comprises tooth and nose domains, whereas the neck submodule contains a helical spine and one limb, with shoulder, arm and finger elements. The arm and the essential shoulder contact other parts of Mediator. The jaws and a central joint are implicated in interactions with Pol II and its carboxy-terminal domain, and the joint is required for transcription in vitro. The S. pombe head module structure leads to a revised model of the S. cerevisiae module, reveals a high conservation and flexibility, explains known mutations, and provides the basis for unravelling a central mechanism of gene regulation.
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80
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Zhao Y, Du J, Zhao G, Jiang L. Activation of calcineurin is mainly responsible for the calcium sensitivity of gene deletion mutations in the genome of budding yeast. Genomics 2012; 101:49-56. [PMID: 23026396 DOI: 10.1016/j.ygeno.2012.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 09/18/2012] [Accepted: 09/18/2012] [Indexed: 01/20/2023]
Abstract
Here we have identified 120 gene deletion mutants that are sensitive to 0.4M calcium in Saccharomyces cerevisiae. Twenty-seven of these mutants are of genes involved in the vacuolar protein sorting pathway, including those encoding the seven components of the ESCRT complexes, and ten of them encode the components and assembly factors of the vacuolar H(+)-ATPase. Both Mediator and Paf1 complexes modulating the activity of the general transcription machinery are involved in the calcium sensitivity of yeast cells. Most of these mutants show elevated intracellular calcium contents in response to calcium stress. The calcium sensitivity of 106 mutants can be completely suppressed by 10mM Mg(2+), 56 of which can also be suppressed by the inhibitor of calcineurin, cyclosporine A. Therefore, the calcium sensitivity of nearly a half of these 120 mutations is at least partially due to the activation of calcineurin and can be modulated by magnesium ion.
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Affiliation(s)
- Yunying Zhao
- The State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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81
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Liu Z, Myers LC. Med5(Nut1) and Med17(Srb4) are direct targets of mediator histone H4 tail interactions. PLoS One 2012; 7:e38416. [PMID: 22693636 PMCID: PMC3367926 DOI: 10.1371/journal.pone.0038416] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/09/2012] [Indexed: 11/18/2022] Open
Abstract
The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. In addition to its canonical role in transcriptional activation, recent studies have demonstrated that S. cerevisiae Mediator can interact directly with nucleosomes, and their histone tails. Mutations in Mediator subunits have shown that Mediator and certain chromatin structures mutually impact each other structurally and functionally in vivo. We have taken a UV photo cross-linking approach to further delineate the molecular basis of Mediator chromatin interactions and help determine whether the impact of certain Mediator mutants on chromatin is direct. Specifically, by using histone tail peptides substituted with an amino acid analog that is a UV activatible crosslinker, we have identified specific subunits within Mediator that participate in histone tail interactions. Using Mediator purified from mutant yeast strains we have evaluated the impact of these subunits on histone tail binding. This analysis has identified the Med5 subunit of Mediator as a target for histone tail interactions and suggests that the previously observed effect of med5 mutations on telomeric heterochromatin and silencing is direct.
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Affiliation(s)
- Zhongle Liu
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Lawrence C. Myers
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America
- * E-mail:
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82
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Ranuncolo SM, Ghosh S, Hanover JA, Hart GW, Lewis BA. Evidence of the involvement of O-GlcNAc-modified human RNA polymerase II CTD in transcription in vitro and in vivo. J Biol Chem 2012; 287:23549-61. [PMID: 22605332 DOI: 10.1074/jbc.m111.330910] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA polymerase II C-terminal domain (CTD), which serves as a scaffold to recruit machinery involved in transcription, is modified post-translationally. Although the O-GlcNAc modification of RNA polymerase II CTD was documented in 1993, its functional significance remained obscure. We show that O-GlcNAc transferase (OGT) modified CTD serine residues 5 and 7. Drug inhibition of OGT and OGA (N-acetylglucosaminidase) blocked transcription during preinitiation complex assembly. Polymerase II and OGT co-immunoprecipitated, and OGT is a component of the preinitiation complex. OGT shRNA experiments showed that reduction of OGT causes a reduction in transcription and RNA polymerase II occupancy at several B-cell promoters. These data suggest that the cycling of O-GlcNAc on and off of polymerase II occurs during assembly of the preinitiation complex. Our results define unexpected roles for both the CTD and O-GlcNAc in the regulation of transcription initiation in higher eukaryotes.
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Affiliation(s)
- Stella M Ranuncolo
- Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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83
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Je EM, Kim MR, Min KO, Yoo NJ, Lee SH. Mutational analysis of MED12 exon 2 in uterine leiomyoma and other common tumors. Int J Cancer 2012; 131:E1044-7. [DOI: 10.1002/ijc.27610] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 04/10/2012] [Indexed: 11/08/2022]
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84
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Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics 2012; 189:705-36. [PMID: 22084422 DOI: 10.1534/genetics.111.127019] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Here we review recent advances in understanding the regulation of mRNA synthesis in Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been conserved in all eukaryotes, and budding yeast has been at the forefront in the discovery and dissection of these conserved mechanisms. Topics covered include upstream activation sequence and promoter structure, transcription factor classification, and examples of regulated transcription factor activity. We also examine advances in understanding the RNA polymerase II transcription machinery, conserved coactivator complexes, transcription activation domains, and the cooperation of these factors in gene regulatory mechanisms.
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85
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Zhang DW, Mosley AL, Ramisetty SR, Rodríguez-Molina JB, Washburn MP, Ansari AZ. Ssu72 phosphatase-dependent erasure of phospho-Ser7 marks on the RNA polymerase II C-terminal domain is essential for viability and transcription termination. J Biol Chem 2012; 287:8541-51. [PMID: 22235117 DOI: 10.1074/jbc.m111.335687] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) serves an important role in coordinating stage-specific recruitment and release of cellular machines during transcription. Dynamic placement and removal of phosphorylation marks on different residues of a repeating heptapeptide (YSPTSPS) of the CTD underlies the engagement of relevant cellular machinery. Whereas sequential placement of phosphorylation marks is well explored, genome-wide engagement of phosphatases that remove these CTD marks is poorly understood. In particular, identifying the enzyme that erases phospho-Ser7 (Ser7-P) marks is especially important, because we find that substituting this residue with a glutamate, a phospho-mimic, is lethal. Our observations implicate Ssu72 as a Ser7-P phosphatase. We report that removal of all phospho-CTD marks during transcription termination is mechanistically coupled. An inability to remove these marks prevents Pol II from terminating efficiently and will likely impede subsequent assembly into the pre-initiation complex.
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Affiliation(s)
- David W Zhang
- Department of Biochemistry and The Genome Center, University of Wisconsin, Madison, Wisconsin 53706, USA
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86
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Cdk8 regulates stability of the transcription factor Phd1 to control pseudohyphal differentiation of Saccharomyces cerevisiae. Mol Cell Biol 2011; 32:664-74. [PMID: 22124158 DOI: 10.1128/mcb.05420-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The yeast Saccharomyces differentiates into filamentous pseudohyphae when exposed to a poor source of nitrogen in a process involving a collection of transcription factors regulated by nutrient signaling pathways. Phd1 is important for this process in that it regulates expression of most other transcription factors involved in differentiation and can induce filamentation on its own when overproduced. In this article, we show that Phd1 is an unstable protein whose degradation is initiated through phosphorylation by Cdk8 of the RNA polymerase II mediator subcomplex. Phd1 is stabilized by cdk8 disruption, and the naturally filamenting Σ1278b strain was found to have a sequence polymorphism that eliminates a Cdk8 phosphorylation site, which both stabilizes the protein and contributes to enhanced differentiation. In nitrogen-starved cells, PHD1 expression is upregulated and the Phd1 protein becomes stabilized, which causes its accumulation during differentiation. PHD1 expression is partially dependent upon Ste12, which was also previously shown to be destabilized by Cdk8-dependent phosphorylations, but to a significantly smaller extent than Phd1. These observations demonstrate the central role that Cdk8 plays in initiation of differentiation. Cdk8 activity is inhibited in cells shifted to limiting nutrient conditions, and we argue that this effect drives the initiation of differentiation through stabilization of multiple transcription factors, including Phd1, that cause activation of genes necessary for filamentous response.
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87
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Galdieri L, Desai P, Vancura A. Facilitated assembly of the preinitiation complex by separated tail and head/middle modules of the mediator. J Mol Biol 2011; 415:464-74. [PMID: 22137896 DOI: 10.1016/j.jmb.2011.11.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 02/06/2023]
Abstract
Mediator is a general coactivator of RNA polymerase II (RNA pol II) bridging enhancer-bound transcriptional factors with RNA pol II. Mediator is organized in three distinct subcomplexes: head, middle, and tail modules. The head and middle modules interact with RNA pol II, and the tail module interacts with transcriptional activators. Deletion of one of the tail subunits SIN4 results in derepression of a subset of genes, including FLR1, by a largely unknown mechanism. Here we show that derepression of FLR1 transcription in sin4Δ cells occurs by enhanced recruitment of the mediator as well as Swi/Snf and SAGA complexes. The tail and head/middle modules of the mediator behave as separate complexes at the induced FLR1 promoter. While the tail module remains anchored to the promoter, the head/middle modules are also found in the coding region. The separation of the tail and head/middle modules in sin4Δ cells is also supported by the altered stoichiometry of the tail and head/middle modules at several tested promoters. Deletion of another subunit of the tail module MED2 in sin4Δ cells results in significantly decreased transcription of FLR1, pointing to the importance of the integrity of the separated tail module in derepression. All tested genes exhibited increased recruitment of the tail domain; however, only genes with increased occupancy of the head/middle modules also displayed increased transcription. The separated tail module thus represents a promiscuous transcriptional factor that binds to many different promoters and is necessary for derepression of FLR1 in sin4Δ cells.
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Affiliation(s)
- Luciano Galdieri
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
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88
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Schleit J, Wall VZ, Simko M, Kaeberlein M. The MDT-15 subunit of mediator interacts with dietary restriction to modulate longevity and fluoranthene toxicity in Caenorhabditis elegans. PLoS One 2011; 6:e28036. [PMID: 22132200 PMCID: PMC3221695 DOI: 10.1371/journal.pone.0028036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/31/2011] [Indexed: 11/22/2022] Open
Abstract
Dietary restriction (DR), the limitation of calorie intake while maintaining proper nutrition, has been found to extend life span and delay the onset of age-associated disease in a wide range of species. Previous studies have suggested that DR can reduce the lethality of environmental toxins. To further examine the role of DR in toxin response, we measured life spans of the nematode Caenorhabditis elegans treated with the mutagenic polyaromatic hydrocarbon, fluoranthene (FLA). FLA is a direct byproduct of combustion, and is one of U.S. Environmental Protection Agency's sixteen priority environmental toxins. Treatment with 5 µg/ml FLA shortened the life spans of ad libitum fed nematodes, and DR resulted in increased sensitivity to FLA. To determine the role of detoxifying enzymes in the toxicity of FLA, we tested nematodes with mutations in the gene encoding the MDT-15 subunit of mediator, a transcriptional coactivator that regulates genes involved in fatty acid metabolism and detoxification. Mutation of mdt-15 increased the life span of FLA treated animals compared to wild-type animals with no difference observed between DR and ad libitum fed mdt-15 animals. We also examined mutants with altered insulin-IGF-1-like signaling (IIS), which is known to modulate life span and stress resistance in C. elegans independently of DR. Mutation of the genes coding for the insulin-like receptor DAF-2 or the FOXO-family transcription factor DAF16 did not alter the animals' susceptibility to FLA compared to wild type. Taken together, our results suggest that certain compounds have increased toxicity when combined with a DR regimen through increased metabolic activation. This increased metabolic activation appears to be mediated through the MDT-15 transcription factor and is independent of the IIS pathway.
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Affiliation(s)
- Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Valerie Z. Wall
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Marissa Simko
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
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89
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Mukundan B, Ansari A. Novel role for mediator complex subunit Srb5/Med18 in termination of transcription. J Biol Chem 2011; 286:37053-7. [PMID: 21921038 PMCID: PMC3199451 DOI: 10.1074/jbc.c111.295915] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 09/13/2011] [Indexed: 11/06/2022] Open
Abstract
Mediator complex functions at the recruitment as well as the post-recruitment steps of transcription. Here we provide evidence for a novel role of Mediator in termination of transcription. Mediator subunit Srb5/Med18 cross-links to the 5' and 3' ends of INO1 and CHA1. In srb5(-) cells, recruitment of TATA-binding protein (TBP) and transcription factor IIB (TFIIB) onto the promoter of these genes remained unaffected, but cross-linking of the cleavage-polyadenylation factors Rna15 and Pta1 toward the 3' end of genes was compromised. In these cells, RNA polymerase II accumulated near the 3' end of genes and beyond. Transcription run-on analysis confirmed a transcription readthrough phenotype in the absence of Srb5/Med18. These results strongly suggest that Mediator subunit Srb5/Med18 is required for proper termination of transcription of a subset of genes in budding yeast.
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Affiliation(s)
- Banupriya Mukundan
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Athar Ansari
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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90
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Majumder P, Boss JM. Cohesin regulates MHC class II genes through interactions with MHC class II insulators. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 187:4236-44. [PMID: 21911605 PMCID: PMC3186872 DOI: 10.4049/jimmunol.1100688] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cohesin is a multiprotein, ringed complex that is most well-known for its role in stabilizing the association of sister chromatids between S phase and M. More recently, cohesin was found to be associated with transcriptional insulators, elements that are associated with the organization of chromatin into regulatory domains. The human MHC class II (MHC-II) locus contains 10 intergenic elements, termed MHC-II insulators, which bind the transcriptional insulator protein CCCTC-binding factor. MHC-II insulators interact with each other, forming a base architecture of discrete loops and potential regulatory domains. When MHC-II genes are expressed, their proximal promoter regulatory regions reorganize to the foci established by the interacting MHC-II insulators. MHC-II insulators also bind cohesin, but the functional role of cohesin in regulating this system is not known. In this article, we show that the binding of cohesin to MHC-II insulators occurred irrespective of MHC-II expression but was required for optimal expression of the HLA-DR and HLA-DQ genes. In a DNA-dependent manner, cohesin subunits interacted with CCCTC-binding factor and the MHC-II-specific transcription factors regulatory factor X and CIITA. Intriguingly, cohesin subunits were important for DNA looping interactions between the HLA-DRA promoter region and a 5' MHC-II insulator but were not required for interactions between the MHC-II insulators themselves. This latter observation introduces cohesin as a regulator of MHC-II expression by initiating or stabilizing MHC-II promoter regulatory element interactions with the MHC-II insulator elements, events that are required for maximal MHC-II transcription.
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Affiliation(s)
- Parimal Majumder
- Department of Microbiology & Immunology, 1510 Clifton Rd, Emory University School of Medicine, Atlanta, GA 30322
| | - Jeremy M. Boss
- Department of Microbiology & Immunology, 1510 Clifton Rd, Emory University School of Medicine, Atlanta, GA 30322
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91
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Chen W, Roeder RG. Mediator-dependent nuclear receptor function. Semin Cell Dev Biol 2011; 22:749-58. [PMID: 21854863 DOI: 10.1016/j.semcdb.2011.07.026] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 12/24/2022]
Abstract
As gene-specific transcription factors, nuclear receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss our current understanding of (i) pathways involved in Mediator recruitment and function through nuclear receptor target gene enhancers and promoters, (ii) conditional requirements for the strong nuclear receptor-Mediator interactions mediated by NR AF2 domains and the MED1 LXXLL motifs, (iii) Mediator functions, through different nuclear receptor-interacting subunits, in different metabolic pathways, (iv) emerging functions of Mediator as a corepressor in addition to its major role as a coactivator and (v) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. As a nuclear receptor coregulator with increasingly diverse functions, Mediator may thus modulate nuclear receptor signaling through several different mechanisms.
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Affiliation(s)
- Wei Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
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92
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Conaway RC, Conaway JW. Origins and activity of the Mediator complex. Semin Cell Dev Biol 2011; 22:729-34. [PMID: 21821140 DOI: 10.1016/j.semcdb.2011.07.021] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 11/16/2022]
Abstract
The Mediator is a large, multisubunit RNA polymerase II transcriptional regulator that was first identified in Saccharomyces cerevisiae as a factor required for responsiveness of Pol II and the general initiation factors to DNA binding transactivators. Since its discovery in yeast, Mediator has been shown to be an integral and highly evolutionarily conserved component of the Pol II transcriptional machinery with critical roles in multiple stages of transcription, from regulation of assembly of the Pol II initiation complex to regulation of Pol II elongation. Here we provide a brief overview of the evolutionary origins of Mediator, its subunit composition, and its remarkably diverse collection of activities in Pol II transcription.
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Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA.
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93
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Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y. Architecture of the Mediator head module. Nature 2011; 475:240-3. [PMID: 21725323 PMCID: PMC4109712 DOI: 10.1038/nature10162] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/28/2011] [Indexed: 01/14/2023]
Abstract
Mediator is a key regulator of eukaryotic transcription, connecting activators and repressors bound to regulatory DNA elements with RNA polymerase II (Pol II). In the yeast Saccharomyces cerevisiae, Mediator comprises 25 subunits with a total mass of more than one megadalton (refs 5, 6) and is organized into three modules, called head, middle/arm and tail. Our understanding of Mediator assembly and its role in regulating transcription has been impeded so far by limited structural information. Here we report the crystal structure of the essential Mediator head module (seven subunits, with a mass of 223 kilodaltons) at a resolution of 4.3 ångströms. Our structure reveals three distinct domains, with the integrity of the complex centred on a bundle of ten helices from five different head subunits. An intricate pattern of interactions within this helical bundle ensures the stable assembly of the head subunits and provides the binding sites for general transcription factors and Pol II. Our structural and functional data suggest that the head module juxtaposes transcription factor IIH and the carboxy-terminal domain of the largest subunit of Pol II, thereby facilitating phosphorylation of the carboxy-terminal domain of Pol II. Our results reveal architectural principles underlying the role of Mediator in the regulation of gene expression.
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Affiliation(s)
- Tsuyoshi Imasaki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202
| | - Guillermo Calero
- Department of Structural Biology, Stanford University School of Medicine, Stanford CA 94350
| | - Gang Cai
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037
| | - Kuang-Lei Tsai
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037
| | - Kentaro Yamada
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202
| | - Francesco Cardelli
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202
| | | | - Paul Tempst
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Imre Berger
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Guy Lorch Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford CA 94350
| | - Francisco J. Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037
| | - Roger D. Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford CA 94350
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202
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94
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Seizl M, Larivière L, Pfaffeneder T, Wenzeck L, Cramer P. Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization. Nucleic Acids Res 2011; 39:6291-304. [PMID: 21498544 PMCID: PMC3152362 DOI: 10.1093/nar/gkr229] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mediator is a multiprotein co-activator of RNA polymerase (Pol) II transcription. Mediator contains a conserved core that comprises the ‘head’ and ‘middle’ modules. We present here a structure–function analysis of the essential Med11/22 heterodimer, a part of the head module. Med11/22 forms a conserved four-helix bundle domain with C-terminal extensions, which bind the central head subunit Med17. A highly conserved patch on the bundle surface is required for stable transcription pre-initiation complex formation on a Pol II promoter in vitro and in vivo and may recruit the general transcription factor TFIIH. The bundle domain fold is also present in the Mediator middle module subcomplex Med7/21 and is predicted in the Mediator heterodimers Med2/3, Med4/9, Med10/14 and Med28/30. The bundle domain thus represents a common building block that has been multiplied and functionally diversified during Mediator evolution in eukaryotes.
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Affiliation(s)
- Martin Seizl
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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95
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Soutourina J, Wydau S, Ambroise Y, Boschiero C, Werner M. Direct interaction of RNA polymerase II and mediator required for transcription in vivo. Science 2011; 331:1451-4. [PMID: 21415355 DOI: 10.1126/science.1200188] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Gene transcription is highly regulated. Altered transcription can lead to cancer or developmental diseases. Mediator, a multisubunit complex conserved among eukaryotes, is generally required for RNA polymerase II (Pol II) transcription. An interaction between the two complexes is known, but its molecular nature and physiological role are unclear. We identify a direct physical interaction between the Rpb3 Pol II subunit of Saccharomyces cerevisiae and the essential Mediator subunit, Med17. Furthermore, we demonstrate a functional element in the Mediator-Pol II interface that is important for genome-wide Pol II recruitment in vivo. Our findings suggest that a direct interaction between Mediator and Pol II is generally required for transcription of class II genes in eukaryotes.
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Affiliation(s)
- Julie Soutourina
- Commissariat à l'Energie Atomique et aux Energies Alternatives, iBiTec-S, Service de Biologie Intégrative et Génétique Moléculaire, Gif-sur-Yvette cedex, France.
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96
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Herpes simplex virus 1 ICP4 forms complexes with TFIID and mediator in virus-infected cells. J Virol 2011; 85:5733-44. [PMID: 21450820 DOI: 10.1128/jvi.00385-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The infected cell polypeptide 4 (ICP4) of herpes simplex virus 1 (HSV-1) is a regulator of viral transcription that is required for productive infection. Since viral genes are transcribed by cellular RNA polymerase II (RNA pol II), ICP4 must interact with components of the pol II machinery to regulate viral gene expression. It has been shown previously that ICP4 interacts with TATA box-binding protein (TBP), TFIIB, and the TBP-associated factor 1 (TAF1) in vitro. In this study, ICP4-containing complexes were isolated from infected cells by tandem affinity purification (TAP). Forty-six proteins that copurified with ICP4 were identified by mass spectrometry. Additional copurifying proteins were identified by Western blot analysis. These included 11 components of TFIID and 4 components of the Mediator complex. The significance of the ICP4-Mediator interaction was further investigated using immunofluorescence and chromatin immunoprecipitation. Mediator was found to colocalize with ICP4 starting at early and continuing into late times of infection. In addition, Mediator was recruited to viral promoters in an ICP4-dependent manner. Taken together, the data suggest that ICP4 interacts with components of TFIID and Mediator in the context of viral infection, and this may explain the broad transactivation properties of ICP4.
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97
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Proshkina GM, Shpakovskiĭ GV. [The functional interaction of an RNA polymerase II Rpb11 subunit with the Med18 subunit (Srb5) of the Saccharomyces cerevisiae mediator complex]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 35:572-6. [PMID: 19928061 DOI: 10.1134/s1068162009040153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The SRB5 gene encoding the Med18 (Srb5) subunit of the mediator complex of the Saccharomyces cerevisiae transcription apparatus was identified in the C-terminal region of the yeast RNA polymerase II Rpb11 subunit as a multicopy suppressor of the Leu111Ala (L111A) point mutation. Thus, the functional interaction between one of the mediator components and the core of the major transcription enzyme was first shown. It is also essential that the suppressed point mutation was located in the short C-terminal region of the Rpb11subunit, which plays an important role for the evolution of the eukaryotic transcription apparatus, as was demonstrated in our previous studies.
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98
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Taatjes DJ. The human Mediator complex: a versatile, genome-wide regulator of transcription. Trends Biochem Sci 2010; 35:315-22. [PMID: 20299225 DOI: 10.1016/j.tibs.2010.02.004] [Citation(s) in RCA: 253] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 02/16/2010] [Accepted: 02/16/2010] [Indexed: 10/19/2022]
Abstract
The Mediator complex interacts extensively with the RNA polymerase II enzyme and regulates its ability to express protein-coding genes. The mechanisms by which Mediator regulates gene expression remain poorly understood, in part because the structure of Mediator and even its composition can change, depending upon the promoter context. Combined with the sheer size of the human Mediator complex (26 subunits, 1.2 MDa), this structural adaptability bestows seemingly unlimited regulatory potential within the complex. Recent efforts to understand Mediator structure and function have identified expanded roles that include control of both pre- and post-initiation events; it is also evident that Mediator performs both general and gene-specific roles to regulate gene expression.
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Affiliation(s)
- Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
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99
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Separable functions of the fission yeast Spt5 carboxyl-terminal domain (CTD) in capping enzyme binding and transcription elongation overlap with those of the RNA polymerase II CTD. Mol Cell Biol 2010; 30:2353-64. [PMID: 20231361 DOI: 10.1128/mcb.00116-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
An interaction network connecting mRNA capping enzymes, the RNA polymerase II (Pol II) carboxyl-terminal domain (CTD), elongation factor Spt5, and the Cdk7 and Cdk9 protein kinases is thought to comprise a transcription elongation checkpoint. A crux of this network is Spt5, which regulates early transcription elongation and has an imputed role in pre-mRNA processing via its physical association with capping enzymes. Schizosaccharomyces pombe Spt5 has a distinctive CTD composed of tandem nonapeptide repeats of the consensus sequence (1)TPAWNSGSK(9). The Spt5 CTD binds the capping enzymes and is a substrate for threonine phosphorylation by the Cdk9 kinase. Here we report that deletion of the S. pombe Spt5 CTD results in slow growth and aberrant cell morphology. The severity of the spt5-DeltaCTD phenotype is exacerbated by truncation of the Pol II CTD and ameliorated by overexpression of the capping enzymes RNA triphosphatase and RNA guanylyltransferase. These results suggest that the Spt5 and Pol II CTDs play functionally overlapping roles in capping enzyme recruitment. We probed structure-activity relations of the Spt5 CTD by alanine scanning of the consensus nonapeptide. The T1A change abolished CTD phosphorylation by Cdk9 but did not affect CTD binding to the capping enzymes. The T1A and P2A mutations elicited cold-sensitive (cs) and temperature-sensitive (ts) growth defects and conferred sensitivity to growth inhibition by 6-azauracil that was exacerbated by partial truncations of the Pol II CTD. The T1A phenotypes were rescued by a phosphomimetic T1E change but not by capping enzyme overexpression. These results imply a positive role for Spt5 CTD phosphorylation in Pol Il transcription elongation in fission yeast, distinct from its capping enzyme interactions. Viability of yeast cells bearing both Spt5 CTD T1A and Pol II CTD S2A mutations heralds that the Cdk9 kinase has an essential target other than Spt5 and Pol II CTD-Ser2.
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100
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Cyclin-dependent kinase 8 positively cooperates with Mediator to promote thyroid hormone receptor-dependent transcriptional activation. Mol Cell Biol 2010; 30:2437-48. [PMID: 20231357 DOI: 10.1128/mcb.01541-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mediator is a multisubunit assemblage of proteins originally identified in humans as a coactivator bound to thyroid hormone receptors (TRs) and essential for thyroid hormone (T3)-dependent transcription. Cyclin-dependent kinase 8 (CDK8), cyclin C, MED12, and MED13 form a variably associated Mediator subcomplex (termed the CDK8 module) whose functional role in TR-dependent transcription remains unclear. Using in vitro and cellular approaches, we show here that Mediator complexes containing the CDK8 module are specifically recruited into preinitiation complexes at the TR target gene type I deiodinase (DioI) together with RNA polymerase II (Pol II) in a TR- and T3-dependent manner. We found that CDK8 is essential for robust T3-dependent Dio1 transcription and that CDK8 knockdown via RNA interference decreased Pol II occupancy, and also the recruitment of the Pol II kinase CDK9, at the DioI promoter. Chromatin immunoprecipitation revealed CDK8 occupancy at the DioI promoter concurrent with active transcription, thus suggesting CDK8 involvement in transcriptional reinitiation. Mutagenesis assays showed that CDK8 kinase activity is necessary for full T3-dependent DioI activation, whereas in vitro kinase studies indicated that CDK8 may contribute to Pol II phosphorylation. Collectively, our data suggest CDK8 plays an important coactivator role in TR-dependent transcription by promoting Pol II recruitment and activation at TR target gene promoters.
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