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Jishage M, Malik S, Wagner U, Uberheide B, Ishihama Y, Hu X, Chait BT, Gnatt A, Ren B, Roeder RG. Transcriptional regulation by Pol II(G) involving mediator and competitive interactions of Gdown1 and TFIIF with Pol II. Mol Cell 2012; 45:51-63. [PMID: 22244332 DOI: 10.1016/j.molcel.2011.12.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/06/2011] [Accepted: 12/12/2011] [Indexed: 11/30/2022]
Abstract
Pol II(G) is a distinct form of RNA polymerase II that contains the tightly associated Gdown1 polypeptide (encoded by POLR2M). Unlike Pol II, Pol II(G) is highly dependent upon Mediator for robust activator-dependent transcription in a biochemically defined in vitro system. Here, in vitro studies show that Gdown1 competes with TFIIF for binding to the RPB1 and RPB5 subunits of Pol II, thereby inhibiting an essential function of TFIIF in preinitiation complex assembly, but also that Mediator can actually facilitate Pol II(G) binding to the promoter prior to subsequent Mediator functions. Complementary ChIP and RNAi analyses reveal that Pol II(G) is recruited to promoter regions of subsets of actively transcribed genes, where it appears to restrict transcription. These and other results suggest that Pol II(G) may act to modulate some genes while simultaneously, as a poised (noninitiated) polymerase, setting the stage for Mediator-dependent enhancement of their activity.
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Affiliation(s)
- Miki Jishage
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
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52
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Abstract
In this issue of Molecular Cell, papers by the Price and Roeder labs reveal how the Gdown1 protein antagonizes the general transcription factor TFIIF during RNAPII initiation and elongation and how the Mediator complex intervenes in this molecular tug-of-war to activate RNAPII.
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53
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Cheng B, Li T, Rahl PB, Adamson TE, Loudas NB, Guo J, Varzavand K, Cooper JJ, Hu X, Gnatt A, Young RA, Price DH. Functional association of Gdown1 with RNA polymerase II poised on human genes. Mol Cell 2012; 45:38-50. [PMID: 22244331 DOI: 10.1016/j.molcel.2011.10.022] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 08/05/2011] [Accepted: 10/20/2011] [Indexed: 10/14/2022]
Abstract
Most human genes are loaded with promoter-proximally paused RNA polymerase II (Pol II) molecules that are poised for release into productive elongation by P-TEFb. We present evidence that Gdown1, the product of the POLR2M gene that renders Pol II responsive to Mediator, is involved in Pol II elongation control. During in vitro transcription, Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. Supporting these mechanistic insights, ChIP-Seq demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Our results establish that Gdown1 stabilizes poised polymerases while maintaining their responsiveness to P-TEFb and suggest that Mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function.
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Affiliation(s)
- Bo Cheng
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA 52242, USA
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54
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Close P, East P, Dirac-Svejstrup AB, Hartmann H, Heron M, Maslen S, Chariot A, Söding J, Skehel M, Svejstrup JQ. DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. Nature 2012; 484:386-9. [PMID: 22446626 PMCID: PMC3378035 DOI: 10.1038/nature10925] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 02/07/2012] [Indexed: 11/18/2022]
Abstract
Alternative messenger RNA splicing is the main reason that vast mammalian proteomic complexity can be achieved with a limited number of genes. Splicing is physically and functionally coupled to transcription, and is greatly affected by the rate of transcript elongation. As the nascent pre-mRNA emerges from transcribing RNA polymerase II (RNAPII), it is assembled into a messenger ribonucleoprotein (mRNP) particle; this is the functional form of the nascent pre-mRNA and determines the fate of the mature transcript. However, factors that connect the transcribing polymerase with the mRNP particle and help to integrate transcript elongation with mRNA splicing remain unclear. Here we characterize the human interactome of chromatin-associated mRNP particles. This led us to identify deleted in breast cancer 1 (DBC1) and ZNF326 (which we call ZNF-protein interacting with nuclear mRNPs and DBC1 (ZIRD)) as subunits of a novel protein complex--named DBIRD--that binds directly to RNAPII. DBIRD regulates alternative splicing of a large set of exons embedded in (A + T)-rich DNA, and is present at the affected exons. RNA-interference-mediated DBIRD depletion results in region-specific decreases in transcript elongation, particularly across areas encompassing affected exons. Together, these data indicate that the DBIRD complex acts at the interface between mRNP particles and RNAPII, integrating transcript elongation with the regulation of alternative splicing.
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Affiliation(s)
- Pierre Close
- Mechanisms of Transcription Laboratory, Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, UK
- Unit of Medical Chemistry, GIGA-Signal Transduction, GIGA-R, University of Liege, CHU, Sart-Tilman, Liege, Belgium
| | - Philip East
- Bioinformatics & Biostatistics Group, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London, WC2A 3LY
| | - A. Barbara Dirac-Svejstrup
- Mechanisms of Transcription Laboratory, Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, UK
| | - Holger Hartmann
- Gene Center and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Mark Heron
- Gene Center and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Sarah Maslen
- Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK, London Research Institute, South Mimms, EN6 3LD, UK
| | - Alain Chariot
- Unit of Medical Chemistry, GIGA-Signal Transduction, GIGA-R, University of Liege, CHU, Sart-Tilman, Liege, Belgium
| | - Johannes Söding
- Gene Center and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Mark Skehel
- Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK, London Research Institute, South Mimms, EN6 3LD, UK
| | - Jesper Q. Svejstrup
- Mechanisms of Transcription Laboratory, Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, UK
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55
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Wild T, Cramer P. Biogenesis of multisubunit RNA polymerases. Trends Biochem Sci 2012; 37:99-105. [PMID: 22260999 DOI: 10.1016/j.tibs.2011.12.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 12/08/2011] [Accepted: 12/16/2011] [Indexed: 01/11/2023]
Abstract
Gene transcription in the nucleus of eukaryotic cells is carried out by three related multisubunit RNA polymerases, Pol I, Pol II and Pol III. Although the structure and function of the polymerases have been studied extensively, little is known about their biogenesis and their transport from the cytoplasm (where the subunits are synthesized) to the nucleus. Recent studies have revealed polymerase assembly intermediates and putative assembly factors, as well as factors required for Pol II nuclear import. In this review, we integrate the available data into a model of Pol II biogenesis that provides a framework for future analysis of the biogenesis of all RNA polymerases.
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Affiliation(s)
- Thomas Wild
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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56
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Ye X, Xiao P, Hu X, Chen Y, Zhang L, Xie W, Hu X. Crystallization and preliminary X-ray analysis of the RPB5 subunit of human RNA polymerase II. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1391-3. [PMID: 22102239 PMCID: PMC3212458 DOI: 10.1107/s1744309111033288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 08/16/2011] [Indexed: 11/11/2022]
Abstract
RPB5 is an essential subunit of eukaryotic RNA polymerase II. It has been proposed to interact with DNA and several key transcription factors during transcription. These interactions are crucial for transcription and its regulation. Here, prior to obtaining complex structures of human RPB5 and its binding partners, recombinant human RPB5 was crystallized alone by vapour diffusion in hanging drops. A complete data set was collected from a single frozen crystal employing an in-house X-ray source. The crystal diffracted to 2.8 Å resolution and belonged to space group P4(3)2(1)2. The likely Matthews coefficient and solvent content of 2.67 Å(3) Da(-1) and 53.92%, respectively, suggested the presence of two protein subunits in the asymmetric unit. The structure was solved using molecular replacement.
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Affiliation(s)
- Xingyou Ye
- School of Pharmaceutical Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Ping Xiao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Xiaowei Hu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, People’s Republic of China
| | - Yunyun Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Liping Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Wei Xie
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, People’s Republic of China
| | - Xiaopeng Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, Guangdong 510006, People’s Republic of China
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57
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Hein PP, Palangat M, Landick R. RNA transcript 3'-proximal sequence affects translocation bias of RNA polymerase. Biochemistry 2011; 50:7002-14. [PMID: 21739957 DOI: 10.1021/bi200437q] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Translocation of RNA polymerase on DNA is thought to involve oscillations between pretranslocated and posttranslocated states that are rectified by nucleotide addition or pyrophosphorolysis. The pretranslocated register is also a precursor to transcriptional pause states that mediate regulation of transcript elongation. However, the determinants of bias between the pretranslocated and posttranslocated states are incompletely understood. To investigate translocation bias in multisubunit RNA polymerases, we measured rates of pyrophosphorolysis, which occurs in the pretranslocated register, in minimal elongation complexes containing T. thermophilus or E. coli RNA polymerase. Our results suggest that the identity of RNA:DNA nucleotides in the active site are strong determinants of susceptibility to pyrophosphorolysis, and thus translocation bias, with the 3' RNA nucleotide favoring the pretranslocated state in the order U > C > A > G. The preference of 3' U vs G for the pretranslocated register appeared to be universal among both bacterial and eukaryotic RNA polymerases and was confirmed by exonuclease III footprinting of defined elongation complexes. However, the relationship of pyrophosphate concentration to the rate of pyrophosphorolysis of 3' U-containing versus 3' G-containing elongation complexes did not match predictions of a simple mechanism in which 3'-RNA seqeunce affects only translocation bias and pyrophosphate (PPi) binds only to the pretranslocated state.
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Affiliation(s)
- Pyae P Hein
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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58
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Jun SH, Reichlen MJ, Tajiri M, Murakami KS. Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol 2011; 46:27-40. [PMID: 21250781 DOI: 10.3109/10409238.2010.538662] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To elucidate the mechanism of transcription by cellular RNA polymerases (RNAPs), high-resolution X-ray crystal structures together with structure-guided biochemical, biophysical, and genetics studies are essential. The recently solved X-ray crystal structures of archaeal RNAP allow a structural comparison of the transcription machinery among all three domains of life. The archaea were once thought of closely related to bacteria, but they are now considered to be more closely related to the eukaryote at the molecular level than bacteria. According to these structures, the archaeal transcription apparatus, which includes RNAP and general transcription factors (GTFs), is similar to the eukaryotic transcription machinery. Yet, the transcription regulators, activators and repressors, encoded by archaeal genomes are closely related to bacterial factors. Therefore, archaeal transcription appears to possess an intriguing hybrid of eukaryotic-type transcription apparatus and bacterial-like regulatory mechanisms. Elucidating the transcription mechanism in archaea, which possesses a combination of bacterial and eukaryotic transcription mechanisms that are commonly regarded as separate and mutually exclusive, can provide data that will bring basic transcription mechanisms across all life forms.
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Affiliation(s)
- Sung-Hoon Jun
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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59
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Nechaev S, Adelman K. Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1809:34-45. [PMID: 21081187 DOI: 10.1016/j.bbagrm.2010.11.001] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 11/06/2010] [Accepted: 11/09/2010] [Indexed: 01/12/2023]
Abstract
Proper regulation of gene expression is essential for the differentiation, development and survival of all cells and organisms. Recent work demonstrates that transcription of many genes, including key developmental and stimulus-responsive genes, is regulated after the initiation step, by pausing of RNA polymerase II during elongation through the promoter-proximal region. Thus, there is great interest in better understanding the events that follow transcription initiation and the ways in which the efficiency of early elongation can be modulated to impact expression of these highly regulated genes. Here we describe our current understanding of the steps involved in the transition from an unstable initially transcribing complex into a highly stable and processive elongation complex. We also discuss the interplay between factors that affect early transcript elongation and the potential physiological consequences for genes that are regulated through transcriptional pausing.
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Affiliation(s)
- Sergei Nechaev
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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60
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Malik S, Roeder RG. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet 2010; 11:761-72. [PMID: 20940737 DOI: 10.1038/nrg2901] [Citation(s) in RCA: 535] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Mediator is an evolutionarily conserved, multiprotein complex that is a key regulator of protein-coding genes. In metazoan cells, multiple pathways that are responsible for homeostasis, cell growth and differentiation converge on the Mediator through transcriptional activators and repressors that target one or more of the almost 30 subunits of this complex. Besides interacting directly with RNA polymerase II, Mediator has multiple functions and can interact with and coordinate the action of numerous other co-activators and co-repressors, including those acting at the level of chromatin. These interactions ultimately allow the Mediator to deliver outputs that range from maximal activation of genes to modulation of basal transcription to long-term epigenetic silencing.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.
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61
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Takahashi H, Martin-Brown S, Washburn MP, Florens L, Conaway JW, Conaway RC. Proteomics reveals a physical and functional link between hepatocyte nuclear factor 4alpha and transcription factor IID. J Biol Chem 2009; 284:32405-12. [PMID: 19805548 DOI: 10.1074/jbc.m109.017954] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Proteomic analyses have contributed substantially to our understanding of diverse cellular processes. Improvements in the sensitivity of mass spectrometry approaches are enabling more in-depth analyses of protein-protein networks and, in some cases, are providing surprising new insights into well established, longstanding problems. Here, we describe such a proteomic analysis that exploits MudPIT mass spectrometry and has led to the discovery of a physical and functional link between the orphan nuclear receptor hepatocyte nuclear factor 4alpha (HNF4alpha) and transcription factor IID (TFIID). A systematic characterization of the HNF4alpha-TFIID link revealed that the HNF4alpha DNA-binding domain binds directly to the TATA box-binding protein (TBP) and, through this interaction, can target TBP or TFIID to promoters containing HNF4alpha-binding sites in vitro. Supporting the functional significance of this interaction, an HNF4alpha mutation that blocks binding of TBP to HNF4alpha interferes with HNF4alpha transactivation activity in cells. These findings identify an unexpected role for the HNF4alpha DNA-binding domain in mediating key regulatory interactions and provide new insights into the roles of HNF4alpha and TFIID in RNA polymerase II transcription.
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Affiliation(s)
- Hidehisa Takahashi
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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62
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Mosley AL, Pattenden SG, Carey M, Venkatesh S, Gilmore JM, Florens L, Workman JL, Washburn MP. Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation. Mol Cell 2009; 34:168-78. [PMID: 19394294 DOI: 10.1016/j.molcel.2009.02.025] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 02/03/2009] [Accepted: 02/23/2009] [Indexed: 11/16/2022]
Abstract
Messenger RNA processing is coupled to RNA polymerase II (RNAPII) transcription through coordinated recruitment of accessory proteins to the Rpb1 C-terminal domain (CTD). Dynamic changes in CTD phosphorylation during transcription elongation are responsible for their recruitment, with serine 5 phosphorylation (S5-P) occurring toward the 5' end of genes and serine 2 phosphorylation (S2-P) occurring toward the 3' end. The proteins responsible for regulation of the transition state between S5-P and S2-P CTD remain elusive. We show that a conserved protein of unknown function, Rtr1, localizes within coding regions, with maximum levels of enrichment occurring between the peaks of S5-P and S2-P RNAPII. Upon deletion of Rtr1, the S5-P form of RNAPII accumulates in both whole-cell extracts and throughout coding regions; additionally, RNAPII transcription is decreased, and termination defects are observed. Functional characterization of Rtr1 reveals its role as a CTD phosphatase essential for the S5-to-S2-P transition.
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Affiliation(s)
- Amber L Mosley
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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63
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Takahashi H, Kasahara K, Kokubo T. Saccharomyces cerevisiaeMed9 comprises two functionally distinct domains that play different roles in transcriptional regulation. Genes Cells 2009; 14:53-67. [DOI: 10.1111/j.1365-2443.2008.01250.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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64
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GRINL1A colocalizes with N-methyl D-aspartate receptor NR1 subunit and reduces N-methyl D-aspartate toxicity. Neuroreport 2008; 19:1721-6. [PMID: 18849881 DOI: 10.1097/wnr.0b013e328317f05f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We hypothesized that proteins from the GRINL1A complex transcription unit called Gcom proteins modulate glutamatergic neurotransmission through interaction with the NR1 subunit of the N-methyl D-aspartate (NMDA) receptor. Cotransfection of hemagglutinin-tagged Gcom1 (GRINL1A combined transcript 1) and NR1 cDNAs into HEK293 cells revealed overlapping fluorescent signals in the plasma membrane. Coimmunoprecipitation studies demonstrated reciprocal coimmunoprecipitation from rat brain protein isolates, suggesting an interaction between GRINL1A proteins and the NMDA receptor. Anti-Gcom1 and anti-NR1 antibodies revealed colocalization of postsynaptic immunoreactivity in rat cortical and hippocampal neurons. Finally, anti-Gcom1 antibodies specifically inhibited NMDA excitotoxicity in rat cortical neurons, suggesting a functional interaction of Gcom and NR1 proteins. Our results are consistent with a facilatory role of GRINL1A proteins in glutamatergic signal transduction through interaction with the NMDA receptor.
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65
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Abstract
Adding to the concept that Mediator acts as an "integrative hub,"Ding et al. (2008) report in this issue of Molecular Cell that, by facilitating the recruitment of the G9a methyl transferase, Mediator can also promote epigenetic silencing of selected genes.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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66
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Cheng TF, Hu X, Gnatt A, Brooks PJ. Differential blocking effects of the acetaldehyde-derived DNA lesion N2-ethyl-2'-deoxyguanosine on transcription by multisubunit and single subunit RNA polymerases. J Biol Chem 2008; 283:27820-27828. [PMID: 18669632 DOI: 10.1074/jbc.m804086200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acetaldehyde, the first metabolite of ethanol, reacts with DNA to form adducts, including N(2)-ethyl-2'-deoxyguanosine (N(2)-Et-dG). Although the effects of N(2)-Et-dG on DNA polymerases have been well studied, nothing is known about possible effects of this lesion on transcription by RNA polymerases (RNAPs). Using primer extension assays in vitro, we found that a single N(2)-Et-dG lesion is a strong block to both mammalian RNAPII and two other multisubunit RNAPs, (yeast RNAPII and Escherichia coli RNAP), as well as to T7 RNAP. However, the mechanism of transcription blockage appears to differ between the multisubunit RNAPs and T7 RNAP. Specifically, all three of the multisubunit RNAPs can incorporate a single rNTP residue opposite the lesion, whereas T7 RNAP is essentially unable to do so. Using the mammalian RNAPII, we found that CMP is exclusively incorporated opposite the N(2)-Et-dG lesion. In addition, we also show that the accessory transcription factor TFIIS does not act as a lesion bypass factor, as it does for other nonbulky DNA lesions; instead, it stimulates the polymerase to remove the CMP incorporated opposite the lesion by mammalian RNAPII. We also include models of the N(2)-Et-dG within the active site of yeast RNAPII, which are compatible with our observations.
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Affiliation(s)
- Tsu-Fan Cheng
- Section on Molecular Neurobiology, Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, Maryland 20892
| | - Xiaopeng Hu
- Department of Pharmacology and Experimental Therapeutics, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Averell Gnatt
- Department of Pharmacology and Experimental Therapeutics, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Philip J Brooks
- Section on Molecular Neurobiology, Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, Maryland 20892.
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67
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Hahn S. Transcriptional regulation. Meeting on regulatory mechanisms in eukaryotic transcription. EMBO Rep 2008; 9:612-6. [PMID: 18535623 PMCID: PMC2530034 DOI: 10.1038/embor.2008.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 04/30/2008] [Indexed: 11/08/2022] Open
Affiliation(s)
- Steven Hahn
- Fred Hutchinson Cancer Research Centre, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.
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68
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Hubbard K, Catalano J, Puri RK, Gnatt A. Knockdown of TFIIS by RNA silencing inhibits cancer cell proliferation and induces apoptosis. BMC Cancer 2008; 8:133. [PMID: 18474089 PMCID: PMC2390572 DOI: 10.1186/1471-2407-8-133] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 05/12/2008] [Indexed: 01/11/2023] Open
Abstract
Background A common element among cancer cells is the presence of improperly controlled transcription. In these cells, the degree of specific activation of some genes is abnormal, and altering the aberrant transcription may therefore directly target cancer. TFIIS is a transcription elongation factor, which directly binds the transcription motor, RNA Polymerase II and allows it to read through various transcription arrest sites. We report on RNA interference of TFIIS, a transcription elongation factor, and its affect on proliferation of cancer cells in culture. Methods RNA interference was performed by transfecting siRNA to specifically knock down TFIIS expression in MCF7, MCF10A, PL45 and A549 cells. Levels of TFIIS expression were determined by the Quantigene method, and relative protein levels of TFIIS, c-myc and p53 were determined by C-ELISA. Induction of apoptosis was determined by an enzymatic Caspase 3/7 assay, as well as a non-enzymatic assay detecting cytoplasmic mono- and oligonucleosomes. A gene array analysis was conducted for effects of TFIIS siRNA on MCF7 and MCF10A cell lines. Results Knockdown of TFIIS reduced cancer cell proliferation in breast, lung and pancreatic cancer cell lines. More specifically, TFIIS knockdown in the MCF7 breast cancer cell line induced cancer cell death and increased c-myc and p53 expression whereas TFIIS knockdown in the non-cancerous breast cell line MCF10A was less affected. Differential effects of TFIIS knockdown in MCF7 and MCF10A cells included the estrogenic, c-myc and p53 pathways, as observed by C-ELISA and gene array, and were likely involved in MCF7 cell-death. Conclusion Although transcription is a fundamental process, targeting select core transcription factors may provide for a new and potent avenue for cancer therapeutics. In the present study, knockdown of TFIIS inhibited cancer cell proliferation, suggesting that TFIIS could be studied as a potential cancer target within the transcription machinery.
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Affiliation(s)
- Kyle Hubbard
- Pharmacology and Experimental Therapeutics, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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69
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Pygopus activates Wingless target gene transcription through the mediator complex subunits Med12 and Med13. Proc Natl Acad Sci U S A 2008; 105:6644-9. [PMID: 18451032 DOI: 10.1073/pnas.0709749105] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wnt target gene transcription is mediated by nuclear translocation of stabilized beta-catenin, which binds to TCF and recruits Pygopus, a cofactor with an unknown mechanism of action. The mediator complex is essential for the transcription of RNA polymerase II-dependent genes; it associates with an accessory subcomplex consisting of the Med12, Med13, Cdk8, and Cyclin C subunits. We show here that the Med12 and Med13 subunits of the Drosophila mediator complex, encoded by kohtalo and skuld, are essential for the transcription of Wingless target genes. kohtalo and skuld act downstream of beta-catenin stabilization both in vivo and in cell culture. They are required for transcriptional activation by the N-terminal domain of Pygopus, and their physical interaction with Pygopus depends on this domain. We propose that Pygopus promotes Wnt target gene transcription by recruiting the mediator complex through interactions with Med12 and Med13.
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Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga JT. The RNA polymerase II core promoter - the gateway to transcription. Curr Opin Cell Biol 2008; 20:253-9. [PMID: 18436437 DOI: 10.1016/j.ceb.2008.03.003] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Accepted: 03/11/2008] [Indexed: 10/22/2022]
Abstract
The RNA polymerase II core promoter is generally defined to be the sequence that directs the initiation of transcription. This simple definition belies a diverse and complex transcriptional module. There are two major types of core promoters - focused and dispersed. Focused promoters contain either a single transcription start site or a distinct cluster of start sites over several nucleotides, whereas dispersed promoters contain several start sites over 50-100 nucleotides and are typically found in CpG islands in vertebrates. Focused promoters are more ancient and widespread throughout nature than dispersed promoters; however, in vertebrates, dispersed promoters are more common than focused promoters. In addition, core promoters may contain many different sequence motifs, such as the TATA box, BRE, Inr, MTE, DPE, DCE, and XCPE1, that specify different mechanisms of transcription and responses to enhancers. Thus, the core promoter is a sophisticated gateway to transcription that determines which signals will lead to transcription initiation.
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Affiliation(s)
- Tamar Juven-Gershon
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347, USA
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71
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Casamassimi A, Napoli C. Mediator complexes and eukaryotic transcription regulation: an overview. Biochimie 2007; 89:1439-46. [PMID: 17870225 DOI: 10.1016/j.biochi.2007.08.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 08/02/2007] [Indexed: 10/23/2022]
Abstract
Mediator is an essential component of the RNA polymerase II-mediated transcription machinery. This component plays a key role both in the stimulation of basal transcription and in the regulation of eukaryotic mRNA synthesis. The Saccharomyces cerevisiae Mediator complex was the first to be studied and consists of at least 20 different subunits with multiple activities. Afterwards, its subunit composition was determined and related functions of C. elegans, Drosophila and mammalian complexes show a striking evolutionary conservation both of the structure and function from yeast to man. Recently, yeast studies strongly suggest additional roles for Mediator in coordinating transcription initiation with downstream transcriptional events in the coding region of genes; consequently, new models of recruitment-coupled regulation have been indicated. Further studies on transcription machinery should expand our knowledge of the pathways in which variant components of Mediator, or variant proteins interacting directly or in complexes, represent risk factors for complex inheritable disease.
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Affiliation(s)
- Amelia Casamassimi
- Department of General Pathology, Division of Clinical Pathology, 1st School of Medicine, II University of Naples, Via L. De Crecchio 7, 80138-Naples, Italy
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Jeronimo C, Forget D, Bouchard A, Li Q, Chua G, Poitras C, Thérien C, Bergeron D, Bourassa S, Greenblatt J, Chabot B, Poirier GG, Hughes TR, Blanchette M, Price DH, Coulombe B. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell 2007; 27:262-274. [PMID: 17643375 PMCID: PMC4498903 DOI: 10.1016/j.molcel.2007.06.027] [Citation(s) in RCA: 341] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 05/16/2007] [Accepted: 06/22/2007] [Indexed: 01/20/2023]
Abstract
We have performed a survey of soluble human protein complexes containing components of the transcription and RNA processing machineries using protein affinity purification coupled to mass spectrometry. Thirty-two tagged polypeptides yielded a network of 805 high-confidence interactions. Remarkably, the network is significantly enriched in proteins that regulate the formation of protein complexes, including a number of previously uncharacterized proteins for which we have inferred functions. The RNA polymerase II (RNAP II)-associated proteins (RPAPs) are physically and functionally associated with RNAP II, forming an interface between the enzyme and chaperone/scaffolding proteins. BCDIN3 is the 7SK snRNA methylphosphate capping enzyme (MePCE) present in an snRNP complex containing both RNA processing and transcription factors, including the elongation factor P-TEFb. Our results define a high-density protein interaction network for the mammalian transcription machinery and uncover multiple regulatory factors that target the transcription machinery.
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Affiliation(s)
- Célia Jeronimo
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Diane Forget
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Annie Bouchard
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Qintong Li
- Biochemistry Department, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Gordon Chua
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Christian Poitras
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Cynthia Thérien
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Dominique Bergeron
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Sylvie Bourassa
- Centre hospitalier universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Benoit Chabot
- Département de microbiologie et infectiologie, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Guy G Poirier
- Centre hospitalier universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada
| | - Timothy R Hughes
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics, McGill University, Montréal, QC H3A 2B4, Canada
| | - David H Price
- Biochemistry Department, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Benoit Coulombe
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
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73
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Malik S, Barrero MJ, Jones T. Identification of a regulator of transcription elongation as an accessory factor for the human Mediator coactivator. Proc Natl Acad Sci U S A 2007; 104:6182-7. [PMID: 17404243 PMCID: PMC1851085 DOI: 10.1073/pnas.0608717104] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The multiprotein Mediator coactivator complex is universally required for transcription of metazoan genes. It has been proposed to function by interfacing between transcriptional activators and the RNA polymerase II machinery. However, in vitro transcription systems reconstituted from homogeneous preparations of RNA polymerase II, the general transcription initiation factors, and the cofactor PC4 display relatively robust activator (HNF-4)-dependent activity, which, nonetheless, can be further stimulated by Mediator. By contrast, an unfractionated nuclear extract-based system in which Mediator has been immunodepleted displays a near-absolute dependence on ectopic Mediator. Here, we identified and purified an activity, MSA-2, that confers extract-like Mediator responsiveness to our reconstituted system. Mass spectrometric analyses identified its two constituent polypeptides as hSpt5 and hSpt4, which also comprise the elongation factor DSIF. Mechanistically, MSA-2/DSIF acts by restricting overall transcription in the pure system, thereby imposing a strong Mediator dependence. Our data thus point to potential mechanisms for Mediator function beyond its presently believed role in promoting the initial formation of the RNA polymerase II-containing preinitiation complex.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10021, USA.
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