1
|
Maji S, Waseem M, Sharma MK, Singh M, Singh A, Dwivedi N, Thakur P, Cooper DG, Bisht NC, Fassler JS, Subbarao N, Khurana JP, Bhavesh NS, Thakur JK. MediatorWeb: a protein-protein interaction network database for the RNA polymerase II Mediator complex. FEBS J 2024. [PMID: 38975839 DOI: 10.1111/febs.17225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 04/24/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
The protein-protein interaction (PPI) network of the Mediator complex is very tightly regulated and depends on different developmental and environmental cues. Here, we present an interactive platform for comparative analysis of the Mediator subunits from humans, baker's yeast Saccharomyces cerevisiae, and model plant Arabidopsis thaliana in a user-friendly web-interface database called MediatorWeb. MediatorWeb provides an interface to visualize and analyze the PPI network of Mediator subunits. The database facilitates downloading the untargeted and unweighted network of Mediator complex, its submodules, and individual Mediator subunits to better visualize the importance of individual Mediator subunits or their submodules. Further, MediatorWeb offers network visualization of the Mediator complex and interacting proteins that are functionally annotated. This feature provides clues to understand functions of Mediator subunits in different processes. In an additional tab, MediatorWeb provides quick access to secondary and tertiary structures, as well as residue-level contact information for Mediator subunits in each of the three model organisms. Another useful feature of MediatorWeb is detection of interologs based on orthologous analyses, which can provide clues to understand the functions of Mediator complex in less explored kingdoms. Thus, MediatorWeb and its features can help the user to understand the role of Mediator complex and its subunits in the transcription regulation of gene expression.
Collapse
Grants
- BT/PR40146/BTIS/137/4/2020 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR40169/BTIS/137/71/2023 Department of Biotechnology, Ministry of Science and Technology, India
- BT/HRD/MK-YRFP/50/27/2021 Department of Biotechnology, Ministry of Science and Technology, India
- BT/HRD/MK-YRFP/50/26/2021 Department of Biotechnology, Ministry of Science and Technology, India
- SERB, Government of India
- ICMR
- Council of Scientific and Industrial Research, India
Collapse
Affiliation(s)
- Sourobh Maji
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mohd Waseem
- National Institute of Plant Genome Research, New Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Maninder Singh
- National Institute of Plant Genome Research, New Delhi, India
| | - Anamika Singh
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nidhi Dwivedi
- National Institute of Plant Genome Research, New Delhi, India
| | - Pallabi Thakur
- National Institute of Plant Genome Research, New Delhi, India
| | - David G Cooper
- Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN, USA
| | - Naveen C Bisht
- National Institute of Plant Genome Research, New Delhi, India
| | | | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jitendra P Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Jitendra Kumar Thakur
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- National Institute of Plant Genome Research, New Delhi, India
| |
Collapse
|
2
|
Targeting transcription in heart failure via CDK7/12/13 inhibition. Nat Commun 2022; 13:4345. [PMID: 35896549 PMCID: PMC9329381 DOI: 10.1038/s41467-022-31541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
Heart failure with reduced ejection fraction (HFrEF) is associated with high mortality, highlighting an urgent need for new therapeutic strategies. As stress-activated cardiac signaling cascades converge on the nucleus to drive maladaptive gene programs, interdicting pathological transcription is a conceptually attractive approach for HFrEF therapy. Here, we demonstrate that CDK7/12/13 are critical regulators of transcription activation in the heart that can be pharmacologically inhibited to improve HFrEF. CDK7/12/13 inhibition using the first-in-class inhibitor THZ1 or RNAi blocks stress-induced transcription and pathologic hypertrophy in cultured rodent cardiomyocytes. THZ1 potently attenuates adverse cardiac remodeling and HFrEF pathogenesis in mice and blocks cardinal features of disease in human iPSC-derived cardiomyocytes. THZ1 suppresses Pol II enrichment at stress-transactivated cardiac genes and inhibits a specific pathologic gene program in the failing mouse heart. These data identify CDK7/12/13 as druggable regulators of cardiac gene transactivation during disease-related stress, suggesting that HFrEF features a critical dependency on transcription that can be therapeutically exploited.
Collapse
|
3
|
Liu Q, Bischof S, Harris CJ, Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE. The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis. Nat Commun 2020; 11:2798. [PMID: 32493925 PMCID: PMC7271234 DOI: 10.1038/s41467-020-16651-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022] Open
Abstract
Mediator 12 (MED12) and MED13 are components of the Mediator multi-protein complex, that facilitates the initial steps of gene transcription. Here, in an Arabidopsis mutant screen, we identify MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially required for the expression of genes depleted in active chromatin marks, a chromatin signature shared with morc1 re-activated loci. We further discover that MED12 tends to interact with genes that are responsive to environmental stimuli, including light and radiation. We demonstrate that light-induced transient gene expression depends on MED12, and is accompanied by a concomitant increase in MED12 enrichment during induction. In contrast, the steady-state expression level of these genes show little dependence on MED12, suggesting that MED12 is primarily required to aid the expression of genes in transition from less-active to more active states. Mediator is a multiprotein complex required to activate gene transcription by RNAPII. Here, the authors report that MED12 and MED13 are conditional positive regulators that facilitate the expression of genes depleted in active chromatin marks and the induction of gene expression in response to environmental stimuli in Arabidopsis.
Collapse
Affiliation(s)
- Qikun Liu
- School of Advanced Agricultural Sciences, Peking University, 100871, Beijing, China. .,Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| | - Sylvain Bischof
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.,Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.,Basic Forestry and Proteomics Center, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Lingyu Zhan
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Calvin Nguyen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Andrew Rashoff
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Magdalena Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolome
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jeffrey A Long
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA. .,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| |
Collapse
|
4
|
Cooper DG, Fassler JS. Med15: Glutamine-Rich Mediator Subunit with Potential for Plasticity. Trends Biochem Sci 2019; 44:737-751. [PMID: 31036407 DOI: 10.1016/j.tibs.2019.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/16/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023]
Abstract
The Mediator complex is required for basal activity of the RNA polymerase (Pol) II transcriptional apparatus and for responsiveness to some activator proteins. Med15, situated in the Mediator tail, plays a role in transmitting regulatory information from distant DNA-bound transcription factors to the transcriptional apparatus poised at promoters. Yeast Med15 and its orthologs share an unusual, glutamine-rich amino acid composition. Here, we discuss this sequence feature and the tendency of polyglutamine tracts to vary in length among strains of Saccharomyces cerevisiae, and we propose that different polyglutamine tract lengths may be adaptive within certain domestication habitats.
Collapse
Affiliation(s)
- David G Cooper
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Jan S Fassler
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| |
Collapse
|
5
|
Nagpal N, Sharma S, Maji S, Durante G, Ferracin M, Thakur JK, Kulshreshtha R. Essential role of MED1 in the transcriptional regulation of ER-dependent oncogenic miRNAs in breast cancer. Sci Rep 2018; 8:11805. [PMID: 30087366 PMCID: PMC6081450 DOI: 10.1038/s41598-018-29546-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 07/12/2018] [Indexed: 01/24/2023] Open
Abstract
Mediator complex has been extensively shown to regulate the levels of several protein-coding genes; however, its role in the regulation of miRNAs in humans remains unstudied so far. Here we show that MED1, a Mediator subunit in the Middle module of Mediator complex, is overexpressed in breast cancer and is a negative prognostic factor. The levels of several miRNAs (miR-100-5p, -191-5p, -193b-3p, -205-5p, -326, -422a and -425-5p) were found to be regulated by MED1. MED1 induces miR-191/425 cluster in an estrogen receptor-alpha (ER-α) dependent manner. Occupancy of MED1 on estrogen response elements (EREs) upstream of miR-191/425 cluster is estrogen and ER-α-dependent and ER-α-induced expression of these miRNAs is MED1-dependent. MED1 mediates induction of cell proliferation and migration and the genes associated with it (JUN, FOS, EGFR, VEGF, MMP1, and ERBB4) in breast cancer, which is abrogated when used together with miR-191-inhibition. Additionally, we show that MED1 also regulates the levels of direct miR-191 target genes such as SATB1, CDK6 and BDNF. Overall, the results show that MED1/ER-α/miR-191 axis promotes breast cancer cell proliferation and migration and may serve as a novel target for therapy.
Collapse
Affiliation(s)
- Neha Nagpal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.,Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shivani Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Sourobh Maji
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Giorgio Durante
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126, Bologna, Italy
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
| |
Collapse
|
6
|
Malik N, Agarwal P, Tyagi A. Emerging functions of multi-protein complex Mediator with special emphasis on plants. Crit Rev Biochem Mol Biol 2017; 52:475-502. [DOI: 10.1080/10409238.2017.1325830] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Akhilesh Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| |
Collapse
|
7
|
Abstract
Transcription and splicing are fundamental steps in gene expression. These processes have been studied intensively over the past four decades, and very recent findings are challenging some of the formerly established ideas. In particular, splicing was shown to occur much faster than previously thought, with the first spliced products observed as soon as splice junctions emerge from RNA polymerase II (Pol II). Splicing was also found coupled to a specific phosphorylation pattern of Pol II carboxyl-terminal domain (CTD), suggesting a new layer of complexity in the CTD code. Moreover, phosphorylation of the CTD may be scarcer than expected, and other post-translational modifications of the CTD are emerging with unanticipated roles in gene expression regulation.
Collapse
Affiliation(s)
- Noélia Custódio
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
| | - Maria Carmo-Fonseca
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
| |
Collapse
|
8
|
Tsutsui T, Fukasawa R, Tanaka A, Hirose Y, Ohkuma Y. Identification of target genes for the CDK subunits of the Mediator complex. Genes Cells 2015; 16:1208-18. [PMID: 22117896 DOI: 10.1111/j.1365-2443.2011.01565.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mediator is a large complex containing up to 30 subunits that consist of four modules each: head, middle, tail and CDK/Cyclin. Recent studies have shown that CDK8, a subunit of the CDK/Cyclin module, is one of the key subunits of Mediator that mediates its pivotal roles in transcriptional regulation. In addition to CDK8, CDK19 was identified in human Mediator with a great deal of similarity to CDK8 but was conserved only in vertebrates. Previously, we reported that human CDK19 could form the Mediator complexes independent of CDK8. To further investigate the in vivo transcriptional activities of the complexes, we used a luciferase assay in combined with siRNA-mediated knockdown to show that CDK8 and CDK19 possess opposing functions in viral activator VP16-dependent transcriptional regulation. CDK8 supported transcriptional activation, whereas CDK19, however, counteracted it. In this study, we further characterized CDK19. We used microarrays to identify target genes for each CDK, and we selected six genes: two target genes of CDK8, two target genes of CDK19 and two genes that were targets for both. Surprisingly, it turned out that both CDKs bound to all six target genes, regardless of their effects in transcription upon binding, suggesting Mediator as a context-specific transcriptional regulator.
Collapse
Affiliation(s)
- Taiki Tsutsui
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | | | | | | | | |
Collapse
|
9
|
Clark AD, Oldenbroek M, Boyer TG. Mediator kinase module and human tumorigenesis. Crit Rev Biochem Mol Biol 2015; 50:393-426. [PMID: 26182352 DOI: 10.3109/10409238.2015.1064854] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mediator is a conserved multi-subunit signal processor through which regulatory informatiosn conveyed by gene-specific transcription factors is transduced to RNA Polymerase II (Pol II). In humans, MED13, MED12, CDK8 and Cyclin C (CycC) comprise a four-subunit "kinase" module that exists in variable association with a 26-subunit Mediator core. Genetic and biochemical studies have established the Mediator kinase module as a major ingress of developmental and oncogenic signaling through Mediator, and much of its function in signal-dependent gene regulation derives from its resident CDK8 kinase activity. For example, CDK8-targeted substrate phosphorylation impacts transcription factor half-life, Pol II activity and chromatin chemistry and functional status. Recent structural and biochemical studies have revealed a precise network of physical and functional subunit interactions required for proper kinase module activity. Accordingly, pathologic change in this activity through altered expression or mutation of constituent kinase module subunits can have profound consequences for altered signaling and tumor formation. Herein, we review the structural organization, biological function and oncogenic potential of the Mediator kinase module. We focus principally on tumor-associated alterations in kinase module subunits for which mechanistic relationships as opposed to strictly correlative associations are established. These considerations point to an emerging picture of the Mediator kinase module as an oncogenic unit, one in which pathogenic activation/deactivation through component change drives tumor formation through perturbation of signal-dependent gene regulation. It follows that therapeutic strategies to combat CDK8-driven tumors will involve targeted modulation of CDK8 activity or pharmacologic manipulation of dysregulated CDK8-dependent signaling pathways.
Collapse
Affiliation(s)
- Alison D Clark
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| | - Marieke Oldenbroek
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| | - Thomas G Boyer
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| |
Collapse
|
10
|
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.
Collapse
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
| | | |
Collapse
|
11
|
Serrat N, Sebastian C, Pereira-Lopes S, Valverde-Estrella L, Lloberas J, Celada A. The Response of Secondary Genes to Lipopolysaccharides in Macrophages Depends on Histone Deacetylase and Phosphorylation of C/EBPβ. THE JOURNAL OF IMMUNOLOGY 2013; 192:418-26. [DOI: 10.4049/jimmunol.1203500] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
12
|
Affiliation(s)
- Jiannan Guo
- Biochemistry Department, University of Iowa , Iowa City, Iowa 52242, United States
| | | |
Collapse
|
13
|
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
| |
Collapse
|
14
|
Tsutsui T, Fukasawa R, Shinmyouzu K, Nakagawa R, Tobe K, Tanaka A, Ohkuma Y. Mediator complex recruits epigenetic regulators via its two cyclin-dependent kinase subunits to repress transcription of immune response genes. J Biol Chem 2013; 288:20955-20965. [PMID: 23749998 DOI: 10.1074/jbc.m113.486746] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Mediator complex (Mediator) plays pivotal roles in activating transcription by RNA polymerase II, but relatively little is known about its roles in repression. Here, we identified the histone arginine methyltransferase PRMT5 and WD repeat protein 77/methylosome protein 50 (WDR77/MEP50) as Mediator cyclin-dependent kinase (CDK)-interacting proteins and studied the roles of PRMT5 in the transcriptional regulation of CCAAT enhancer-binding protein (C/EBP) β target genes. First, we purified CDK8- and CDK19-containing complexes from HeLa nuclear extracts and subjected these purified complexes to mass spectrometric analyses. These experiments revealed that two Mediator CDKs, CDK8 and CDK19, individually interact with PRMT5 and WDR77, and their interactions with PRMT5 cause transcriptional repression of C/EBPβ target genes by regulating symmetric dimethylation of histone H4 arginine 3 (H4R3me2s) in the promoter regions of those genes. Furthermore, the recruitment of the DNA methyltransferase DNMT3A correlated with H4R3 dimethylation potentially leading to DNA methylation at the promoter proximal region and tight inhibition of preinitiation complex formation. In vertebrates, C/EBPβ regulates many genes involved in immune responses and cell differentiation. These findings shed light on the molecular mechanisms of the repressive roles of Mediator CDKs in transcription of C/EBPβ target genes and might provide clues that enable future studies of the functional associations between Mediators and epigenetic regulation.
Collapse
Affiliation(s)
- Taiki Tsutsui
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Rikiya Fukasawa
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Kaori Shinmyouzu
- the Mass Spectrometry Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Reiko Nakagawa
- the Mass Spectrometry Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kazuyuki Tobe
- the First Department of Internal Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
| | - Aki Tanaka
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Yoshiaki Ohkuma
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and.
| |
Collapse
|
15
|
Steimel A, Suh J, Hussainkhel A, Deheshi S, Grants JM, Zapf R, Moerman DG, Taubert S, Hutter H. The C. elegans CDK8 Mediator module regulates axon guidance decisions in the ventral nerve cord and during dorsal axon navigation. Dev Biol 2013; 377:385-98. [PMID: 23458898 DOI: 10.1016/j.ydbio.2013.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 01/21/2013] [Accepted: 02/14/2013] [Indexed: 11/30/2022]
Abstract
Receptors expressed on the growth cone of outgrowing axons detect cues required for proper navigation. The pathway choices available to an axon are in part defined by the set of guidance receptors present on the growth cone. Regulated expression of receptors and genes controlling the localization and activity of receptors ensures that axons respond only to guidance cues relevant for reaching their targets. In genetic screens for axon guidance mutants, we isolated an allele of let-19/mdt-13, a component of the Mediator, a large ~30 subunit protein complex essential for gene transcription by RNA polymerase II. LET-19/MDT-13 is part of the CDK8 module of the Mediator. By testing other Mediator components, we found that all subunits of the CDK8 module as well as some other Mediator components are required for specific axon navigation decisions in a subset of neurons. Expression profiling demonstrated that let-19/mdt-13 regulates the expression of a large number of genes in interneurons. A mutation in the sax-3 gene, encoding a receptor for the repulsive guidance cue SLT-1, suppresses the commissure navigation defects found in cdk-8 mutants. This suggests that the CDK8 module specifically represses the SAX-3/ROBO pathway to ensure proper commissure navigation.
Collapse
Affiliation(s)
- Andreas Steimel
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Hsin JP, Manley JL. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 2012; 26:2119-37. [PMID: 23028141 DOI: 10.1101/gad.200303.112] [Citation(s) in RCA: 463] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The C-terminal domain (CTD) of the RNA polymerase II largest subunit consists of multiple heptad repeats (consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), varying in number from 26 in yeast to 52 in vertebrates. The CTD functions to help couple transcription and processing of the nascent RNA and also plays roles in transcription elongation and termination. The CTD is subject to extensive post-translational modification, most notably phosphorylation, during the transcription cycle, which modulates its activities in the above processes. Therefore, understanding the nature of CTD modifications, including how they function and how they are regulated, is essential to understanding the mechanisms that control gene expression. While the significance of phosphorylation of Ser2 and Ser5 residues has been studied and appreciated for some time, several additional modifications have more recently been added to the CTD repertoire, and insight into their function has begun to emerge. Here, we review findings regarding modification and function of the CTD, highlighting the important role this unique domain plays in coordinating gene activity.
Collapse
Affiliation(s)
- Jing-Ping Hsin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | | |
Collapse
|
17
|
The Mediator complex in thyroid hormone receptor action. Biochim Biophys Acta Gen Subj 2012; 1830:3867-75. [PMID: 22402254 DOI: 10.1016/j.bbagen.2012.02.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/16/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND Mediator is an evolutionarily conserved multisubunit complex that plays an essential regulatory role in eukaryotic transcription of protein-encoding genes. The human complex was first isolated as a transcriptional coactivator bound to the thyroid hormone receptor (TR) and has since been shown to play a key coregulatory role for a broad range of nuclear hormone receptors (NRs) as well as other signal-activated transcription factors. SCOPE OF REVIEW We provide a general overview of Mediator structure and function, summarize the mechanisms by which Mediator is targeted to NRs, and outline recent evidence revealing Mediator as a regulatory axis for other distinct coregulatory factors, chromatin modifying enzymes and cellular signal transduction pathways. MAJOR CONCLUSIONS Besides serving as a functional interface with the RNA polymerase II basal transcription machinery, Mediator plays a more versatile role in regulating transcription including the ability to: a) facilitate gene-specific chromatin looping events; b) coordinate chromatin modification events with preinitiation complex assembly; and c) regulate critical steps that occur during transcriptional elongation. The variably associated MED1 subunit continues to emerge as a pivotal player in Mediator function, not only as the primary interaction site for NRs, but also as a crucial interaction hub for other coregulatory factors, and as an important regulatory target for signal-activated kinases. GENERAL SIGNIFICANCE Mediator plays an integral coregulatory role at NR target genes by functionally interacting with the basal transcription apparatus and by coordinating the action of chromatin modifying enzymes and transcription elongation factors. This article is part of a Special Issue entitled Thyroid hormone signalling.
Collapse
|
18
|
Bernecky C, Taatjes DJ. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. J Mol Biol 2012; 417:387-94. [PMID: 22343046 DOI: 10.1016/j.jmb.2012.02.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 02/07/2012] [Indexed: 01/07/2023]
Abstract
The human Mediator complex controls RNA polymerase II (pol II) function in ways that remain incompletely understood. Activator-Mediator binding alters Mediator structure, and these activator-induced structural shifts appear to play key roles in regulating transcription. A recent cryo-electron microscopy (EM) analysis revealed that pol II adopted a stable orientation within a Mediator-pol II-TFIIF assembly in which Mediator was bound to the activation domain of viral protein 16 (VP16). Whereas TFIIF was shown to be important for orienting pol II within this assembly, the potential role of the activator was not assessed. To determine how activator binding might affect pol II orientation, we isolated human Mediator-pol II-TFIIF complexes in which Mediator was not bound to an activator. Cryo-EM analysis of this assembly, coupled with pol II crystal structure docking, revealed that pol II binds Mediator at the same general location; however, in contrast to VP16-bound Mediator, pol II does not appear to stably orient in the absence of an activator. Variability in pol II orientation might be important mechanistically, perhaps to enable sense and antisense transcription at human promoters. Because Mediator interacts extensively with pol II, these results suggest that Mediator structural shifts induced by activator binding help stably orient pol II prior to transcription initiation.
Collapse
Affiliation(s)
- Carrie Bernecky
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | | |
Collapse
|
19
|
Chen W, Roeder RG. Mediator-dependent nuclear receptor function. Semin Cell Dev Biol 2011; 22:749-58. [PMID: 21854863 DOI: 10.1016/j.semcdb.2011.07.026] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 12/24/2022]
Abstract
As gene-specific transcription factors, nuclear receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss our current understanding of (i) pathways involved in Mediator recruitment and function through nuclear receptor target gene enhancers and promoters, (ii) conditional requirements for the strong nuclear receptor-Mediator interactions mediated by NR AF2 domains and the MED1 LXXLL motifs, (iii) Mediator functions, through different nuclear receptor-interacting subunits, in different metabolic pathways, (iv) emerging functions of Mediator as a corepressor in addition to its major role as a coactivator and (v) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. As a nuclear receptor coregulator with increasingly diverse functions, Mediator may thus modulate nuclear receptor signaling through several different mechanisms.
Collapse
Affiliation(s)
- Wei Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
| | | |
Collapse
|
20
|
Interactions between subunits of the Mediator complex with gene-specific transcription factors. Semin Cell Dev Biol 2011; 22:759-68. [PMID: 21839847 DOI: 10.1016/j.semcdb.2011.07.022] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 07/26/2011] [Accepted: 07/28/2011] [Indexed: 11/24/2022]
Abstract
The Mediator complex forms the bridge between gene-specific transcription factors and the RNA polymerase II (RNAP II) machinery. Mediator is a large polypetide complex consisting of about thirty polypeptides that are mostly conserved from yeast to human. Mediator coordinates RNAP II recruitment, phosphorylation of the C-terminal domain of RNAP II, enhancer-loop formation and post-initiation events. The focus of the review is to summarize the current knowledge of transcription factor/Mediator interactions in higher eukaryotes and illuminate the physiological and gene-selective roles of Mediator.
Collapse
|
21
|
Mediator and human disease. Semin Cell Dev Biol 2011; 22:776-87. [PMID: 21840410 DOI: 10.1016/j.semcdb.2011.07.024] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/25/2011] [Accepted: 07/28/2011] [Indexed: 01/21/2023]
Abstract
Since the identification of a metazoan counterpart to yeast Mediator nearly 15 years ago, a convergent body of biochemical and molecular genetic studies have confirmed their structural and functional relationship as an integrative hub through which regulatory information conveyed by signal activated transcription factors is transduced to RNA polymerase II. Nonetheless, metazoan Mediator complexes have been shaped during evolution by substantive diversification and expansion in both the number and sequence of their constituent subunits, with important implications for the development of multicellular organisms. The appearance of unique interaction surfaces within metazoan Mediator complexes for transcription factors of diverse species-specific origins extended the role of Mediator to include an essential function in coupling developmentally coded signals with precise gene expression output sufficient to specify cell fate and function. The biological significance of Mediator in human development, suggested by genetic studies in lower metazoans, is emphatically illustrated by an expanding list of human pathologies linked to genetic variation or aberrant expression of its individual subunits. Here, we review our current body of knowledge concerning associations between individual Mediator subunits and specific pathological disorders. When established, molecular etiologies underlying genotype-phenotype correlations are addressed, and we anticipate that future progress in this critical area will help identify therapeutic targets across a range of human pathologies.
Collapse
|
22
|
Abstract
Mediator, a conserved multiprotein complex in animals, plants, and fungi, is a cofactor of RNA Polymerase II (Pol II). It is known to promote basal Pol II-mediated transcription as well as bridge sequence-specific transcriptional regulators and Pol II to integrate regulatory information. Pol II transcribes not only protein-coding genes but also intergenic regions to generate noncoding RNAs such as small RNAs (microRNAs and small interfering RNAs) and long noncoding RNAs. Intriguingly, two plant-specific polymerases, Pol IV and Pol V, have evolved from Pol II and play a role in the production of small interfering RNAs and long noncoding RNAs at heterochromatic regions to maintain genome stability through transcriptional gene silencing (TGS). Recent studies have defined the composition of the plant Mediator and evaluated its role in noncoding RNA production in relationship to Pol II, Pol IV and Pol V. Here, we review the functions of Mediator and that of noncoding RNAs generated by Pol II, Pol IV and Pol V in plants, and discuss a role of Mediator in epigenetic regulation via noncoding RNA production.
Collapse
Affiliation(s)
- Yun Ju Kim
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | | |
Collapse
|
23
|
Carey MF, Peterson CL, Smale ST. Purification of mediator from HeLa cell lines expressing a flag-tagged mediator subunit. Cold Spring Harb Protoc 2010; 2010:pdb.prot5451. [PMID: 20647355 DOI: 10.1101/pdb.prot5451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The Mediator (Med) complex plays a key role in promoter-specific activation of transcription by RNA polymerase II (Pol II). Med is a major target of activators and can be used in many types of affinity binding and immobilized template studies to evaluate interactions with individual activators. Additionally, all of the Med subunits have been cloned and can be subjected to individual structure-function analyses to learn how a specific activator interacts with a particular subunit. This protocol presents a simple affinity-based method to purify Med complex from HeLa cells stably expressing the Flag-tagged Intersex protein.
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
| |
Collapse
|
25
|
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.
Collapse
|
26
|
MED14 tethers mediator to the N-terminal domain of peroxisome proliferator-activated receptor gamma and is required for full transcriptional activity and adipogenesis. Mol Cell Biol 2010; 30:2155-69. [PMID: 20194623 DOI: 10.1128/mcb.01238-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Mediator subunit MED1/TRAP220/DRIP205/PBP interacts directly with many nuclear receptors and was long thought to be responsible for tethering Mediator to peroxisome proliferator-activated receptor (PPAR)-responsive promoters. However, it was demonstrated recently that PPARgamma can recruit Mediator by MED1-independent mechanisms. Here, we show that target gene activation by ectopically expressed PPARgamma and PPARalpha is independent of MED1. Consistent with this finding, recruitment of PPARgamma, MED6, MED8, TATA box-binding protein (TBP), and RNA polymerase II (RNAPII) to the enhancer and proximal promoter of the PPARgamma target gene Fabp4 is also independent of MED1. Using a small interfering RNA (siRNA)-based approach, we identify MED14 as a novel critical Mediator component for PPARgamma-dependent transactivation, and we demonstrate that MED14 interacts directly with the N terminus of PPARgamma in a ligand-independent manner. Interestingly, MED14 knockdown does not affect the recruitment of PPARgamma, MED6, and MED8 to the Fabp4 enhancer but does reduce their occupancy of the Fabp4 proximal promoter. In agreement with the necessity of MED14 for PPARgamma transcriptional activity, we show that knockdown of MED14 impairs adipogenesis of 3T3-L1 cells. Thus, MED14 constitutes a novel anchoring point between Mediator and the N-terminal domain of PPARgamma that is necessary for functional PPARgamma-mediated recruitment of Mediator and transactivation of PPARgamma subtype-specific target genes.
Collapse
|
27
|
Knuesel MT, Meyer KD, Bernecky C, Taatjes DJ. The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function. Genes Dev 2009; 23:439-51. [PMID: 19240132 DOI: 10.1101/gad.1767009] [Citation(s) in RCA: 255] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The human CDK8 subcomplex (CDK8, cyclin C, Med12, and Med13) negatively regulates transcription in ways not completely defined; past studies suggested CDK8 kinase activity was required for its repressive function. Using a reconstituted transcription system together with recombinant or endogenous CDK8 subcomplexes, we demonstrate that, in fact, Med12 and Med13 are critical for subcomplex-dependent repression, whereas CDK8 kinase activity is not. A hallmark of activated transcription is efficient reinitiation from promoter-bound scaffold complexes that recruit a series of pol II enzymes to the gene. Notably, the CDK8 submodule strongly represses even reinitiation events, suggesting a means to fine tune transcript levels. Structural and biochemical studies confirm the CDK8 submodule binds the Mediator leg/tail domain via the Med13 subunit, and this submodule-Mediator association precludes pol II recruitment. Collectively, these results reveal the CDK8 subcomplex functions as a simple switch that controls the Mediator-pol II interaction to help regulate transcription initiation and reinitiation events. As Mediator is generally required for expression of protein-coding genes, this may reflect a common mechanism by which activated transcription is shut down in human cells.
Collapse
Affiliation(s)
- Matthew T Knuesel
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | | | | | | |
Collapse
|
28
|
Gilchrist DA, Fargo DC, Adelman K. Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods 2009; 48:398-408. [PMID: 19275938 DOI: 10.1016/j.ymeth.2009.02.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/25/2009] [Accepted: 02/27/2009] [Indexed: 10/21/2022] Open
Abstract
Transcription is a sophisticated multi-step process in which RNA polymerase II (Pol II) transcribes a DNA template into RNA in concert with a broad array of transcription initiation, elongation, capping, termination, and histone modifying factors. Recent global analyses of Pol II distribution have indicated that many genes are regulated during the elongation phase, shedding light on a previously underappreciated mechanism for controlling gene expression. Understanding how various factors regulate transcription elongation in living cells has been greatly aided by chromatin immunoprecipitation (ChIP) studies, which can provide spatial and temporal resolution of protein-DNA binding events. The coupling of ChIP with DNA microarray and high-throughput sequencing technologies (ChIP-chip and ChIP-seq) has significantly increased the scope of ChIP studies and genome-wide maps of Pol II or elongation factor binding sites can now be readily produced. However, while ChIP-chip/ChIP-seq data allow for high-resolution localization of protein-DNA binding sites, they are not sufficient to dissect protein function. Here we describe techniques for coupling ChIP-chip/ChIP-seq with genetic, chemical, and experimental manipulation to obtain mechanistic insight from genome-wide protein-DNA binding studies. We have employed these techniques to discern immature promoter-proximal Pol II from productively elongating Pol II, and infer a critical role for the transition between initiation and full elongation competence in regulating development and gene induction in response to environmental signals.
Collapse
Affiliation(s)
- Daniel A Gilchrist
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | | | | |
Collapse
|
29
|
Bromodomain protein Brd4 regulates human immunodeficiency virus transcription through phosphorylation of CDK9 at threonine 29. J Virol 2008; 83:1036-44. [PMID: 18971272 DOI: 10.1128/jvi.01316-08] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Positive transcription elongation factor b (P-TEFb), composed of cyclin-dependent kinase 9 (CDK9) and cyclin T, is a global transcription factor for eukaryotic gene expression, as well as a key factor for human immunodeficiency virus (HIV) transcription elongation. P-TEFb phosphorylates the carboxyl-terminal domain (CTD) of the large subunit of RNA polymerase II (RNAP II), facilitating the transition from nonprocessive to processive transcription elongation. Recently, the bromodomain protein Brd4 has been shown to interact with the low-molecular-weight, active P-TEFb complex and recruit P-TEFb to the HIV type 1 long terminal repeat (LTR) promoter. However, the subsequent events through which Brd4 regulates CDK9 kinase activity and RNAP II-dependent transcription are not clearly understood. Here we provide evidence that Brd4 regulates P-TEFb kinase activity by inducing a negative pathway. Moreover, by analyzing stepwise initiation and elongation complexes, we demonstrate that P-TEFb activity is regulated in the transcription complex. Brd4 induces phosphorylation of CDK9 at threonine 29 (T29) in the HIV transcription initiation complex, inhibiting CDK9 kinase activity. P-TEFb inhibition is transient, as Brd4 is released from the transcription complex between positions +14 and +36. Removal of the phosphate group at T29 by an incoming phosphatase released P-TEFb activity, resulting in increased RNAP II CTD phosphorylation and transcription. Finally, we present chromatin immunoprecipitation studies showing that CDK9 with phosphorylated T29 is associated with the HIV promoter region in the integrated and transcriptionally silent HIV genome.
Collapse
|
30
|
Ding N, Zhou H, Esteve PO, Chin HG, Kim S, Xu X, Joseph SM, Friez MJ, Schwartz CE, Pradhan S, Boyer TG. Mediator links epigenetic silencing of neuronal gene expression with x-linked mental retardation. Mol Cell 2008; 31:347-59. [PMID: 18691967 DOI: 10.1016/j.molcel.2008.05.023] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Revised: 04/20/2008] [Accepted: 05/29/2008] [Indexed: 11/18/2022]
Abstract
Mediator occupies a central role in RNA polymerase II transcription as a sensor, integrator, and processor of regulatory signals that converge on protein-coding gene promoters. Compared to its role in gene activation, little is known regarding the molecular mechanisms and biological implications of Mediator as a transducer of repressive signals. Here we describe a protein interaction network required for extraneuronal gene silencing comprising Mediator, G9a histone methyltransferase, and the RE1 silencing transcription factor (REST; also known as neuron restrictive silencer factor, NRSF). We show that the MED12 interface in Mediator links REST with G9a-dependent histone H3K9 dimethylation to suppress neuronal genes in nonneuronal cells. Notably, missense mutations in MED12 causing the X-linked mental retardation (XLMR) disorders FG syndrome and Lujan syndrome disrupt its REST corepressor function. These findings implicate Mediator in epigenetic restriction of neuronal gene expression to the nervous system and suggest a pathologic basis for MED12-associated XLMR involving impaired REST-dependent neuronal gene regulation.
Collapse
Affiliation(s)
- Ning Ding
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Tsutsui T, Umemura H, Tanaka A, Mizuki F, Hirose Y, Ohkuma Y. Human mediator kinase subunit CDK11 plays a negative role in viral activator VP16-dependent transcriptional regulation. Genes Cells 2008; 13:817-26. [PMID: 18651850 DOI: 10.1111/j.1365-2443.2008.01208.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mediator is an essential transcriptional cofactor of RNA polymerase II (Pol II) in eukaryotes. This cofactor is a large complex containing up to 30 subunits and consisting of four modules: head, middle, tail, and CDK/Cyclin. Generally, Mediator connects transcriptional regulators, cofactors, chromatin regulators, and chromatin remodellers, with the pre-initiation complex to provide a platform for the assembly of these factors. Many previous studies have revealed that CDK8, a subunit of the CDK/Cyclin module, is one of the key subunits mediating the pivotal roles of Mediator in transcriptional regulation. In addition to CDK8, CDK11 is conserved among vertebrates as a Mediator subunit and closely resembles CDK8. While the role of CDK8 has been studied extensively, little is known of the role of CDK11 in Mediator. We purified human CDK11 (hCDK11)-containing protein complexes from an epitope-tagged hCDK11-expressing HeLa cell line and found that hCDK11 could independently form Mediator complexes devoid of human CDK8 (hCDK8). To investigate the in vivo transcriptional activity of the complex, we employed a luciferase assay. Although hCDK11 has nearly 80% amino acid sequence identity to hCDK8, siRNA-knockdown study revealed that hCDK8 and hCDK11 possess opposing functions in viral activator VP16-dependent transcriptional regulation.
Collapse
Affiliation(s)
- Taiki Tsutsui
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | | | | | | | | | | |
Collapse
|
32
|
Clayton JE, van den Heuvel SJL, Saito RM. Transcriptional control of cell-cycle quiescence during C. elegans development. Dev Biol 2008; 313:603-13. [PMID: 18082681 PMCID: PMC2386670 DOI: 10.1016/j.ydbio.2007.10.051] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 10/25/2007] [Accepted: 10/30/2007] [Indexed: 11/27/2022]
Abstract
During the development of the C. elegans reproductive system, cells that give rise to the vulva, the vulval precursor cells (VPCs), remain quiescent for two larval stages before resuming cell division in the third larval stage. We have identified several transcriptional regulators that contribute to this temporary cell-cycle arrest. Mutation of lin-1 or lin-31, two downstream targets of the Receptor Tyrosine kinase (RTK)/Ras/MAP kinase cascade that controls VPC cell fate, disrupts the temporary VPC quiescence. We found that the LIN-1/Ets and LIN-31/FoxB transcription factors promote expression of CKI-1, a member of the p27 family of cyclin-dependent kinase inhibitors (CKIs). LIN-1 and LIN-31 promote cki-1/Kip-1 transcription prior to their inhibition through RTK/Ras/MAPK activation. Another mutation identified in the screen defined the mdt-13 TRAP240 Mediator subunit. Further analysis of the multi-subunit Mediator complex revealed that a specific subset of its components act in VPC quiescence. These components substantially overlap with the CDK-8 module implicated in transcriptional repression. Taken together, strict control of cell-cycle quiescence during VPC development involves transcriptional induction of CKI-1 and transcriptional regulation through the Mediator complex. These transcriptional regulators represent potential molecular connections between development and the basic cell-cycle machinery.
Collapse
Affiliation(s)
- Joseph E Clayton
- Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA
| | | | | |
Collapse
|
33
|
Westerling T, Kuuluvainen E, Mäkelä TP. Cdk8 is essential for preimplantation mouse development. Mol Cell Biol 2007; 27:6177-82. [PMID: 17620419 PMCID: PMC1952144 DOI: 10.1128/mcb.01302-06] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Cdk8 kinase and associated proteins form a nonessential transcriptional repressor module of the Mediator in the budding yeast Saccharomyces cerevisiae. Genetic analyses of this module have demonstrated functions ranging from environmental responses in budding yeast to organogenesis and development in worms, flies, and zebrafish. Here we have investigated the function of mammalian Cdk8 using mice harboring a gene trap insertion at the Cdk8 locus inactivating this kinase. No phenotypes were noted in heterozygote Cdk8+/- mice, but intercrossing these did not produce homozygous Cdk8-/- offspring. Developmental analysis demonstrated a requirement for Cdk8 prior to implantation at embryonic days 2.5 to 3.0. Cdk8-/- preimplantation embryos had fragmented blastomeres and did not proceed to compaction. As Cdk8 deficiency in cultured metazoan cells did not affect cell viability, the results suggest that transcriptional repression of genes critical for early-cell-fate determination underlies the requirement of Cdk8 in embryogenesis.
Collapse
Affiliation(s)
- Thomas Westerling
- Genome-Scale Biology Program and Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, P.O. Box 63, 00014 Helsinki, Finland
| | | | | |
Collapse
|
34
|
Gonzalez D, Bowen AJ, Carroll TS, Conlan RS. The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription. Mol Cell Biol 2007; 27:5306-15. [PMID: 17526732 PMCID: PMC1952085 DOI: 10.1128/mcb.01912-06] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription corepressors are general regulators controlling the expression of genes involved in multiple signaling pathways and developmental programs. Repression is mediated through mechanisms including the stabilization of a repressive chromatin structure over control regions and regulation of Mediator function inhibiting RNA polymerase II activity. Using whole-genome arrays we show that the Arabidopsis thaliana corepressor LEUNIG, a member of the GroTLE transcription corepressor family, regulates the expression of multiple targets in vivo. LEUNIG has a role in the regulation of genes involved in a number of different physiological processes including disease resistance, DNA damage response, and cell signaling. We demonstrate that repression of in vivo LEUNIG targets is achieved through histone deacetylase (HDAC)-dependent and -independent mechanisms. HDAC-dependent mechanisms involve direct interaction with HDA19, a class 1 HDAC, whereas an HDAC-independent repression activity involves interactions with the putative Arabidopsis Mediator components AtMED14/SWP and AtCDK8/HEN3. We suggest that changes in chromatin structure coupled with regulation of Mediator function are likely to be utilized by LEUNIG in the repression of gene transcription.
Collapse
Affiliation(s)
- Deyarina Gonzalez
- Institute of Life Science, School of Medicine, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, United Kingdom
| | | | | | | |
Collapse
|
35
|
Furumoto T, Tanaka A, Ito M, Malik S, Hirose Y, Hanaoka F, Ohkuma Y. A kinase subunit of the human mediator complex, CDK8, positively regulates transcriptional activation. Genes Cells 2007; 12:119-32. [PMID: 17212659 DOI: 10.1111/j.1365-2443.2007.01036.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human thyroid hormone receptor-associated proteins (TRAP)/Mediator and related complexes mediate transcription through regulatory factors. To further understand the structural and functional diversity of these complexes we established three HeLa cell lines each expressing one of three epitope-tagged human TRAP/Mediator subunits, MED6, MED7, and CDK8 and isolated the complexes in which these subunits were contained by affinity and HPLC-gel filtration chromatography. The largest complexes from each cell line had a molecular mass of 1.5 MDa and possessed almost identical subunit compositions; we designated these complexes TRAP/Mediator-like complex 1 (TMLC1). Two potential subcomplexes were additionally observed: a 1-MDa complex from the CDK8-cell line (TMLC2) and a 600-kDa complex from the MED6-cell line (TMLC3). All three complexes regulated transcription in vitro; TMLC1 and TMLC3 augmented transcriptional activation, whereas TMLC2 repressed it. TMLC1 and TMLC2 phosphorylated RNA polymerase II (Pol II), but TMLC3 did not. Furthermore, TMLC1 predominantly interacted with the general transcription factors TFIIE, TFIIF, and TFIIH, which function during transcription initiation and the transition to elongation. In a final experiment, knockdown of CDK8 using RNA interference prevented transcriptional activation by Gal4-VP16 in a luciferase-assay. This, together with the effect of TMLC1 on transcription in vitro, suggests that CDK8 play positive roles in transcriptional activation.
Collapse
Affiliation(s)
- Tadashi Furumoto
- Graduate School of Frontier Biosciences, Osaka Universuty, Suita, Osaka 565-0871, Japan
| | | | | | | | | | | | | |
Collapse
|
36
|
Kang BG, Shin JH, Yi JK, Kang HC, Lee JJ, Heo HS, Chae JH, Shin I, Kim CG. Corepressor MMTR/DMAP1 is involved in both histone deacetylase 1- and TFIIH-mediated transcriptional repression. Mol Cell Biol 2007; 27:3578-88. [PMID: 17371848 PMCID: PMC1899998 DOI: 10.1128/mcb.01808-06] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A transcription corepressor, MAT1-mediated transcriptional repressor (MMTR), was found in mouse embryonic stem cell lines. MMTR orthologs (DMAP1) are found in a wide variety of life forms from yeasts to humans. MMTR down-regulation in differentiating mouse embryonic stem cells in vitro resulted in activation of many unrelated genes, suggesting its role as a general transcriptional repressor. In luciferase reporter assays, the transcriptional repression activity resided at amino acids 221 to 468. Histone deacetylase 1 (HDAC1) interacts with MMTR both in vitro and in vivo and also interacts with MMTR in the nucleus. Interestingly, MMTR activity was only partially rescued by competition with dominant-negative HDAC1(H141A) or by treatment with an HDAC inhibitor, trichostatin A (TSA). To identify the protein responsible for HDAC1-independent MMTR activity, we performed a yeast two-hybrid screen with the full-length MMTR coding sequence as bait and found MAT1. MAT1 is an assembly/targeting factor for cyclin-dependent kinase-activating kinase which constitutes a subcomplex of TFIIH. The coiled-coil domain in the middle of MAT1 was confirmed to interact with the C-terminal half of MMTR, and the MMTR-mediated transcriptional repression activity was completely restored by MAT1 in the presence of TSA. Moreover, intact MMTR was required to inhibit phosphorylation of the C-terminal domain in the RNA polymerase II largest subunit by TFIIH kinase in vitro. Taken together, these data strongly suggest that MMTR is part of the basic cellular machinery for a wide range of transcriptional regulation via interaction with TFIIH and HDAC.
Collapse
Affiliation(s)
- Bong Gu Kang
- Department of Life Science, College of Natural Sciences, Hanyang University, Haengdang 17, Sungdong-gu, Seoul 133-791, South Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Lee J, Safe S. Coactivation of estrogen receptor alpha (ER alpha)/Sp1 by vitamin D receptor interacting protein 150 (DRIP150). Arch Biochem Biophys 2007; 461:200-10. [PMID: 17306756 PMCID: PMC1978170 DOI: 10.1016/j.abb.2006.12.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 12/24/2006] [Indexed: 11/30/2022]
Abstract
Vitamin D receptor interacting protein (DRIP150) coactivates estrogen receptor alpha (ERalpha)-mediated transactivation in breast cancer cell lines transfected with a construct (pERE(3)) containing three estrogen responsive elements (EREs). In this study, we show that DRIP150 also coactivates ERalpha/Sp1-mediated transactivation in ZR-75, MCF-7, and MDA-MB-231 breast cancer cells transfected with a construct (pSp1(3)) containing three consensus GC-rich motifs. Studies on coactivation of wild-type and variant ERalpha/Sp1 by DRIP150 indicates that the DNA-binding domain and helix 12 in the ligand binding domain of ERalpha are required and the coactivation response is squelched by overexpressing an NR-box peptide that contains two LXXLL motifs from GRIP2. In contrast, coactivation of ERalpha/Sp1 by wild-type and mutant DRIP150 expression plasmids show that coactivation of ERalpha/Sp1 by DRIP150 is independent of the NR-boxes. Deletion analysis of DRIP150 demonstrates that coactivation requires an alpha-helical NIFSEVRVYN (amino acids 795-804) motif within 23 amino acid sequence (789-811) in the central region of DRIP150 and similar results were obtained for coactivation of ERalpha by DRIP150. Thus, although different domains of ERalpha are required for hormone-dependent activation of ERalpha and ERalpha/Sp1, coactivation of these transcription factors by DRIP150 requires the alpha-helical amino acids 795-804. This is the first report of a coactivator that enhances ERalpha/Sp1-mediated transactivation in breast cancer cells.
Collapse
Affiliation(s)
- Jeongeun Lee
- Department of Veterinary Physiology and Pharmacology, Texas A&M University College Station, TX 77843-4466
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology, Texas A&M University College Station, TX 77843-4466
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030-3303
| |
Collapse
|
38
|
Matsushita A, Sasaki S, Kashiwabara Y, Nagayama K, Ohba K, Iwaki H, Misawa H, Ishizuka K, Nakamura H. Essential role of GATA2 in the negative regulation of thyrotropin beta gene by thyroid hormone and its receptors. Mol Endocrinol 2007; 21:865-84. [PMID: 17244762 DOI: 10.1210/me.2006-0208] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Previously we reported that the negative regulation of the TSHbeta gene by T(3) and its receptor [thyroid hormone receptor (TR)] is observed in CV1 cells when GATA2 and Pit1 are introduced. Using this system, we further studied the mechanism of TSHbeta inhibition. The negative regulatory element (NRE), which had been reported to mediate T(3)-bound TR (T(3)-TR)-dependent inhibition, is dispensable, because deletion or mutation of NRE did not impair suppression. The reporter construct, TSHbeta-D4-chloramphenicol acetyltransferase, which possesses only the binding sites for Pit1 and GATA2, was activated by GATA2 alone, and this transactivation was specifically inhibited by T(3)-TR. The Zn finger region of GATA2 interacts with the DNA-binding domain of TR in a T(3)-independent manner. The suppression by T(3)-TR was impaired by overexpression of a dominant-negative type TR-associated protein (TRAP) 220, an N- and C-terminal deletion construct, indicating the participation of TRAP220. Chromatin immunoprecipitation assays with a thyrotroph cell line, TalphaT1, revealed that T(3) treatment recruited histone deacetylase 3, reduced the acetylation of histone H4, and caused the dissociation of TRAP220 within 15-30 min. The reduction of histone H4 acetylation was transient, whereas the dissociation of TRAP220 persisted for a longer period. In the negative regulation of the TSHbeta gene by T(3)-TR we report that 1) GATA2 is the major transcriptional activator of the TSHbeta gene, 2) the putative NRE previously reported is not required, 3) TR-DNA-binding domain directly interacts with the Zn finger region of GATA2, and 4) histone deacetylation and TRAP220 dissociation are important.
Collapse
Affiliation(s)
- Akio Matsushita
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Sukiennicki TL, Fowell DJ. Distinct molecular program imposed on CD4+ T cell targets by CD4+CD25+ regulatory T cells. THE JOURNAL OF IMMUNOLOGY 2007; 177:6952-61. [PMID: 17082610 DOI: 10.4049/jimmunol.177.10.6952] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CD4+CD25+ regulatory T cells (Tregs) are key modulators of immunity, but their mechanism of action is unclear. To elucidate the molecular consequences of Treg encounter, we analyzed changes in gene expression in CD4+ T cell targets activated in the presence or absence of CD4+CD25+ Tregs. Tregs did not alter the early activation program of CD4+ T cells, but had reversed many of the activation-induced changes by 36 h. It is not known whether Tregs simply induce a set of transcriptional changes common to other nonproliferative states or whether instead Tregs mediate a distinct biological activity. Therefore, we compared the gene profile of T cells following Treg encounter with that of T cells made anergic, TGF-beta-treated, or IL-2-deprived; all possible modes of Treg action. Strikingly, all genes down-regulated in suppressed cells were indeed common to these nonproliferative states. In contrast, Treg encounter led to elevated expression of a unique set of genes in the target T cells. Although different from the nonproliferative states tested, the Treg-imposed gene program is exemplified by expression of many genes associated with growth arrest or inhibition of proliferation. We suggest that Tregs function by the induction of a distinct set of negative regulatory factors that initiate or maintain target T cells in a nonproliferative state.
Collapse
Affiliation(s)
- Teresa L Sukiennicki
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester, Rochester, NY 14642, USA
| | | |
Collapse
|
40
|
Abstract
The C-terminal repeat domain (CTD), an unusual extension appended to the C terminus of the largest subunit of RNA polymerase II, serves as a flexible binding scaffold for numerous nuclear factors; which factors bind is determined by the phosphorylation patterns on the CTD repeats. Changes in phosphorylation patterns, as polymerase transcribes a gene, are thought to orchestrate the association of different sets of factors with the transcriptase and strongly influence functional organization of the nucleus. In this review we appraise what is known, and what is not known, about patterns of phosphorylation on the CTD of RNA polymerases II at the beginning, the middle, and the end of genes; the proposal that doubly phosphorylated repeats are present on elongating polymerase is explored. We discuss briefly proteins known to associate with the phosphorylated CTD at the beginning and ends of genes; we explore in more detail proteins that are recruited to the body of genes, the diversity of their functions, and the potential consequences of tethering these functions to elongating RNA polymerase II. We also discuss accumulating structural information on phosphoCTD-binding proteins and how it illustrates the variety of binding domains and interaction modes, emphasizing the structural flexibility of the CTD. We end with a number of open questions that highlight the extent of what remains to be learned about the phosphorylation and functions of the CTD.
Collapse
Affiliation(s)
- Hemali P Phatnani
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | |
Collapse
|
41
|
Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Conaway JW, Florens L, Washburn MP. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A 2006; 103:18928-33. [PMID: 17138671 PMCID: PMC1672612 DOI: 10.1073/pnas.0606379103] [Citation(s) in RCA: 422] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Components of multiprotein complexes are routinely determined by using proteomic approaches. However, this information lacks functional content except when new complex members are identified. To analyze quantitatively the abundance of proteins in human Mediator we used normalized spectral abundance factors generated from shotgun proteomics data sets. With this approach we define a common core of mammalian Mediator subunits shared by alternative forms that variably associate with the kinase module and RNA polymerase (pol) II. Although each version of affinity-purified Mediator contained some kinase module and RNA pol II, Mediator purified through F-Med26 contained the most RNA pol II and the least kinase module as demonstrated by the normalized spectral abundance factor approach. The distinct forms of Mediator were functionally characterized by using a transcriptional activity assay, where F-Med26 Mediator/RNA pol II was the most active. This method of protein complex visualization has important implications for the analysis of multiprotein complexes and assembly of protein interaction networks.
Collapse
Affiliation(s)
| | - Tari J. Parmely
- *Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Shigeo Sato
- *Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Dongxiao Zhu
- *Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Ronald C. Conaway
- *Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160; and
| | - Joan Weliky Conaway
- *Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160; and
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190
| | | | - Michael P. Washburn
- *Stowers Institute for Medical Research, Kansas City, MO 64110
- To whom correspondence should be addressed at: Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110. E-mail:
| |
Collapse
|
42
|
Uhlmann T, Boeing S, Lehmbacher M, Meisterernst M. The VP16 activation domain establishes an active mediator lacking CDK8 in vivo. J Biol Chem 2006; 282:2163-73. [PMID: 17135252 DOI: 10.1074/jbc.m608451200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
VP16 has been widely used to unravel the mechanisms underlying gene transcription. Much of the previous work has been conducted in reconstituted in vitro systems. Here we study the formation of transcription complexes at stable reporters under the control of an inducible Tet-VP16 activator in living cells. In this simplified model for gene activation VP16 recruits the general factors and the cofactors Mediator, GCN5, CBP, and PC4, within minutes to the promoter region. Activation is accompanied by only minor changes in histone acetylation and H3K4 methylation but induces a marked promoter-specific increase in H3K79 methylation. Mediated through contacts with VP16 several subunits of the cleavage and polyadenylation factor (CPSF/CstF) are concentrated at the promoter region. We provide in vitro and in vivo evidence that VP16 activates transcription through a specific MED25-associated Mediator, which is deficient in CDK8.
Collapse
Affiliation(s)
- Thomas Uhlmann
- Gene Expression, National Research Center for Environment and Health, Marchionini-Strasse 25, D-81377 Munich, Germany
| | | | | | | |
Collapse
|
43
|
Abstract
In eukaryotes, the core promoter serves as a platform for the assembly of transcription preinitiation complex (PIC) that includes TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II (pol II), which function collectively to specify the transcription start site. PIC formation usually begins with TFIID binding to the TATA box, initiator, and/or downstream promoter element (DPE) found in most core promoters, followed by the entry of other general transcription factors (GTFs) and pol II through either a sequential assembly or a preassembled pol II holoenzyme pathway. Formation of this promoter-bound complex is sufficient for a basal level of transcription. However, for activator-dependent (or regulated) transcription, general cofactors are often required to transmit regulatory signals between gene-specific activators and the general transcription machinery. Three classes of general cofactors, including TBP-associated factors (TAFs), Mediator, and upstream stimulatory activity (USA)-derived positive cofactors (PC1/PARP-1, PC2, PC3/DNA topoisomerase I, and PC4) and negative cofactor 1 (NC1/HMGB1), normally function independently or in combination to fine-tune the promoter activity in a gene-specific or cell-type-specific manner. In addition, other cofactors, such as TAF1, BTAF1, and negative cofactor 2 (NC2), can also modulate TBP or TFIID binding to the core promoter. In general, these cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators. Here we review the roles of these cofactors and GTFs, as well as TBP-related factors (TRFs), TAF-containing complexes (TFTC, SAGA, SLIK/SALSA, STAGA, and PRC1) and TAF variants, in pol II-mediated transcription, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.
Collapse
Affiliation(s)
- Mary C Thomas
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4935, USA
| | | |
Collapse
|
44
|
Abstract
Cells often fine-tune gene expression at the level of transcription to generate the appropriate response to a given environmental or developmental stimulus. Both positive and negative influences on gene expression must be balanced to produce the correct level of mRNA synthesis. To this end, the cell uses several classes of regulatory coactivator complexes including two central players, TFIID and Mediator (MED), in potentiating activated transcription. Both of these complexes integrate activator signals and convey them to the basal apparatus. Interestingly, many promoters require both regulatory complexes, although at first glance they may seem to be redundant. Here we have used RNA interference (RNAi) in Drosophila cells to selectively deplete subunits of the MED and TFIID complexes to dissect the contribution of each of these complexes in modulating activated transcription. We exploited the robust response of the metallothionein genes to heavy metal as a model for transcriptional activation by analyzing direct factor recruitment in both heterogeneous cell populations and at the single-cell level. Intriguingly, we find that MED and TFIID interact functionally to modulate transcriptional response to metal. The metal response element-binding transcription factor-1 (MTF-1) recruits TFIID, which then binds promoter DNA, setting up a "checkpoint complex" for the initiation of transcription that is subsequently activated upon recruitment of the MED complex. The appropriate expression level of the endogenous metallothionein genes is achieved only when the activities of these two coactivators are balanced. Surprisingly, we find that the same activator (MTF-1) requires different coactivator subunits depending on the context of the core promoter. Finally, we find that the stability of multi-subunit coactivator complexes can be compromised by loss of a single subunit, underscoring the potential for combinatorial control of transcription activation.
Collapse
Affiliation(s)
- Michael T Marr
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | | | | | | |
Collapse
|
45
|
Mitra AP, Almal AA, George B, Fry DW, Lenehan PF, Pagliarulo V, Cote RJ, Datar RH, Worzel WP. The use of genetic programming in the analysis of quantitative gene expression profiles for identification of nodal status in bladder cancer. BMC Cancer 2006; 6:159. [PMID: 16780590 PMCID: PMC1550424 DOI: 10.1186/1471-2407-6-159] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 06/16/2006] [Indexed: 11/30/2022] Open
Abstract
Background Previous studies on bladder cancer have shown nodal involvement to be an independent indicator of prognosis and survival. This study aimed at developing an objective method for detection of nodal metastasis from molecular profiles of primary urothelial carcinoma tissues. Methods The study included primary bladder tumor tissues from 60 patients across different stages and 5 control tissues of normal urothelium. The entire cohort was divided into training and validation sets comprised of node positive and node negative subjects. Quantitative expression profiling was performed for a panel of 70 genes using standardized competitive RT-PCR and the expression values of the training set samples were run through an iterative machine learning process called genetic programming that employed an N-fold cross validation technique to generate classifier rules of limited complexity. These were then used in a voting algorithm to classify the validation set samples into those associated with or without nodal metastasis. Results The generated classifier rules using 70 genes demonstrated 81% accuracy on the validation set when compared to the pathological nodal status. The rules showed a strong predilection for ICAM1, MAP2K6 and KDR resulting in gene expression motifs that cumulatively suggested a pattern ICAM1>MAP2K6>KDR for node positive cases. Additionally, the motifs showed CDK8 to be lower relative to ICAM1, and ANXA5 to be relatively high by itself in node positive tumors. Rules generated using only ICAM1, MAP2K6 and KDR were comparably robust, with a single representative rule producing an accuracy of 90% when used by itself on the validation set, suggesting a crucial role for these genes in nodal metastasis. Conclusion Our study demonstrates the use of standardized quantitative gene expression values from primary bladder tumor tissues as inputs in a genetic programming system to generate classifier rules for determining the nodal status. Our method also suggests the involvement of ICAM1, MAP2K6, KDR, CDK8 and ANXA5 in unique mathematical combinations in the progression towards nodal positivity. Further studies are needed to identify more class-specific signatures and confirm the role of these genes in the evolution of nodal metastasis in bladder cancer.
Collapse
Affiliation(s)
- Anirban P Mitra
- Department of Pathology, University of Southern California Keck School of Medicine, 2011 Zonal Avenue, HMR 312, Los Angeles CA 90033, USA
| | - Arpit A Almal
- Genetics Squared Inc., 210 South 5th Avenue, Suite A, Ann Arbor MI 48104, USA
| | - Ben George
- Department of Internal Medicine, Gundersen Lutheran Medical Center, 1900 South Avenue, La Crosse WI 54601, USA
| | - David W Fry
- Genetics Squared Inc., 210 South 5th Avenue, Suite A, Ann Arbor MI 48104, USA
| | - Peter F Lenehan
- Genetics Squared Inc., 210 South 5th Avenue, Suite A, Ann Arbor MI 48104, USA
| | - Vincenzo Pagliarulo
- Dipartimento Emergenza e Trapianti d'Organo, Sezione di Urologia, Università di Bari, Piazza G. Cesare 11, Bari 70124, Italy
| | - Richard J Cote
- Department of Pathology, University of Southern California Keck School of Medicine, 2011 Zonal Avenue, HMR 312, Los Angeles CA 90033, USA
| | - Ram H Datar
- Department of Pathology, University of Southern California Keck School of Medicine, 2011 Zonal Avenue, HMR 312, Los Angeles CA 90033, USA
| | - William P Worzel
- Genetics Squared Inc., 210 South 5th Avenue, Suite A, Ann Arbor MI 48104, USA
| |
Collapse
|
46
|
Zhou M, Lu H, Park H, Wilson-Chiru J, Linton R, Brady JN. Tax interacts with P-TEFb in a novel manner to stimulate human T-lymphotropic virus type 1 transcription. J Virol 2006; 80:4781-91. [PMID: 16641271 PMCID: PMC1472077 DOI: 10.1128/jvi.80.10.4781-4791.2006] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human T-lymphotropic virus type 1 (HTLV-1) encodes a transcriptional activator, Tax, whose function is essential for viral transcription and replication. Tax transactivates the viral long-terminal repeat through a series of protein-protein interactions which facilitate CREB and CBP/p300 binding. In addition, Tax dissociates transcription repressor histone deacetylase 1 interaction with the CREB response element. The subsequent events through which Tax interacts and communicates with RNA polymerase II and cyclin-dependent kinases (CDKs) are not clearly understood. Here we present evidence that Tax recruits positive transcription elongation factor b (P-TEFb) (CDK9/cyclin T1) to the viral promoter. This recruitment likely involves protein-protein interactions since Tax associates with P-TEFb in vitro as demonstrated by glutathione S-transferase fusion protein pull-down assays and in vivo as shown by co-immunoprecipitation assays. Functionally, small interfering RNA directed toward CDK9 inhibited Tax transactivation in transient assays. Consistent with these findings, the depletion of CDK9 from nuclear extracts inhibited Tax transactivation in vitro. Reconstitution of the reaction with wild-type P-TEFb, but not a kinase-dead mutant, recovered HTLV-1 transcription. Moreover, the addition of the CDK9 inhibitor flavopiridol blocked Tax transactivation in vitro and in vivo. Interestingly, we found that Tax regulates CDK9 kinase activity through a novel autophosphorylation pathway.
Collapse
Affiliation(s)
- Meisheng Zhou
- Virus Tumor Biology Section, Laboratory of Cellular Oncology, Center for Cancer Research, NCI/NIH, , Bethesda, MD 20892, USA
| | | | | | | | | | | |
Collapse
|
47
|
Belakavadi M, Fondell JD. Role of the mediator complex in nuclear hormone receptor signaling. Rev Physiol Biochem Pharmacol 2006; 156:23-43. [PMID: 16634145 DOI: 10.1007/s10254-005-0002-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mediator is an evolutionarily conserved multisubunit protein complex that plays a key role in regulating transcription by RNA polymerase II. The complex functions by serving as a molecular bridge between DNA-bound transcriptional activators and the basal transcription apparatus. In humans, Mediator was first characterized as a thyroid hormone receptor (TR)-associated protein (TRAP) complex that facilitates ligand-dependent transcriptional activation by TR. More recently, Mediator has been established as an essential coactivator for a broad range of nuclear hormone receptors (NRs) as well as several other types of gene-specific transcriptional activators. A single subunit of the complex, MED1/TRAP220, is required for direct ligand-dependent interactions with NRs. Mediator coactivates NR-regulated gene expression by facilitating the recruitment and activation of the RNA polymerase II-associated basal transcription apparatus. Importantly, Mediator acts in concert with other NR coactivators involved in chromatin remodeling to initiate transcription of NR target genes in a multistep manner. In this review, we summarize the functional role of Mediator in NR signaling pathways with an emphasis on the underlying molecular mechanisms by which the complex interacts with NRs and subsequently facilitates their action. We also focus on recent advances in our understanding of TRAP/Mediator's pathophysiological role in mammalian disease and development.
Collapse
Affiliation(s)
- M Belakavadi
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ 08854, USA
| | | |
Collapse
|
48
|
Zhu X, Wirén M, Sinha I, Rasmussen NN, Linder T, Holmberg S, Ekwall K, Gustafsson CM. Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions. Mol Cell 2006; 22:169-78. [PMID: 16630887 DOI: 10.1016/j.molcel.2006.03.032] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 02/14/2006] [Accepted: 03/22/2006] [Indexed: 11/25/2022]
Abstract
Mediator exists in a free form containing the Med12, Med13, CDK8, and CycC subunits (the Srb8-11 module) and a smaller form, which lacks these four subunits and associates with RNA polymerase II (Pol II), forming a holoenzyme. We use chromatin immunoprecipitation (ChIP) and DNA microarrays to investigate genome-wide localization of Mediator and the Srb8-11 module in fission yeast. Mediator and the Srb8-11 module display similar binding patterns, and interactions with promoters and upstream activating sequences correlate with increased transcription activity. Unexpectedly, Mediator also interacts with the downstream coding region of many genes. These interactions display a negative bias for positions closer to the 5' ends of open reading frames (ORFs) and appear functionally important, because downregulation of transcription in a temperature-sensitive med17 mutant strain correlates with increased Mediator occupancy in the coding region. We propose that Mediator coordinates transcription initiation with transcriptional events in the coding region of eukaryotic genes.
Collapse
Affiliation(s)
- Xuefeng Zhu
- Department Laboratory Medicine, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Abstract
Signal transduction within the canonical Wnt/beta-catenin pathway drives development and carcinogenesis through programmed or unprogrammed changes in gene transcription. Although the upstream events linked to signal-induced activation of beta-catenin in the cytoplasm have been deciphered in considerable detail, much less is known regarding the mechanism by which beta-catenin stimulates target gene transcription in the nucleus. Here, we show that beta-catenin physically and functionally targets the MED12 subunit in Mediator to activate transcription. The beta-catenin transactivation domain bound directly to isolated MED12 and intact Mediator both in vitro and in vivo, and Mediator was recruited to Wnt-responsive genes in a beta-catenin-dependent manner. Disruption of the beta-catenin/MED12 interaction through dominant-negative interference- or RNA interference-mediated MED12 suppression inhibited beta-catenin transactivation in response to Wnt signaling. This study thus identifies the MED12 interface within Mediator as a new component and a potential therapeutic target in the Wnt/beta-catenin pathway.
Collapse
Affiliation(s)
- Seokjoong Kim
- Department of Molecular Medicine and the Institute of Biotechnology, University of Texas Health Science Center, San Antonio, Texas 78245-3207, USA
| | | | | | | |
Collapse
|
50
|
Abstract
Others have shown that yeast strains bearing a ts mutation in the Srb4 subunit of Mediator cease transcription of all mRNA at the restrictive temperature, in a manner virtually indistinguishable from a strain bearing a ts mutation in the largest subunit of RNA polymerase II. We find that srb4ts Mediator is defective for the stimulation of basal RNA polymerase II transcription at the restrictive temperature in vitro. Taken together, these findings lead to the suggestion that Mediator is required for basal RNA polymerase II transcription in vivo. On this basis, Mediator is identified as a general transcription factor, comparable in importance to RNA polymerase II and other general factors for the initiation of transcription. The possibility that Mediator serves as an anti-inhibitor, opposing the effects of global negative regulators, is largely excluded.
Collapse
Affiliation(s)
- Yuichiro Takagi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5400, USA
| | | |
Collapse
|