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Kleiber T, Davidson G, Mengus G, Martianov I, Davidson I. Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4. Cell Death Dis 2021; 12:790. [PMID: 34385420 PMCID: PMC8361202 DOI: 10.1038/s41419-021-04067-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022]
Abstract
Regulation of gene expression involves a complex and dynamic dialogue between transcription factors, chromatin remodelling and modification complexes and the basal transcription machinery. To address the function of the Taf4 subunit of general transcription factor TFIID in the regulation of insulin signalling, it was inactivated in adult murine pancreatic beta cells. Taf4 inactivation impacted the expression of critical genes involved in beta-cell function leading to increased glycaemia, lowered plasma insulin levels and defective glucose-stimulated insulin secretion. One week after Taf4-loss, single-cell RNA-seq revealed cells with mixed beta cell, alpha and/or delta cell identities as well as a beta cell population trans-differentiating into alpha-like cells. Computational analysis of single-cell RNA-seq defines how known critical beta cell and alpha cell determinants may act in combination with additional transcription factors and the NuRF chromatin remodelling complex to promote beta cell trans-differentiation.
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Affiliation(s)
- Thomas Kleiber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Orphazyme, Ole Malloes Vej 3, 2200, Copenhagen, Danmark
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Igor Martianov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Equipe Labélisée Ligue National contre le Cancer, Alsace, France.
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2
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Sinha I, Kumar S, Poonia P, Sawhney S, Natarajan K. Functional specialization of two paralogous TAF12 variants by their selective association with SAGA and TFIID transcriptional regulatory complexes. J Biol Chem 2017; 292:6047-6055. [PMID: 28275052 PMCID: PMC5391738 DOI: 10.1074/jbc.c116.768549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/16/2017] [Indexed: 01/08/2023] Open
Abstract
TATA box-binding protein (TBP)-associated factors (TAFs), evolutionarily conserved from yeast to humans, play a central role during transcription initiation. A subset of TAF proteins is shared in transcription factor II D (TFIID) and SAGA transcription regulatory complexes. Although higher eukaryotes contain multiple TAF variants that specify tissue- and developmental stage-specific organization of TFIID or SAGA complexes, in unicellular genomes, however, each TAF is encoded by a single gene. Surprisingly, we found that the genome of Candida albicans, the predominant human fungal pathogen, contains two paralogous TAF12 genes, CaTAF12L and CaTAF12, encoding H2B-like histone-fold domain-containing variants. Of the available fungal genome sequences, only seven other closely related diploid pathogenic Candida genomes encode the two TAF12 paralogs. Using affinity purifications from C. albicans cell extracts, we demonstrate that CaTAF12L uniquely associates with the SAGA complex and CaTAF12 associates with the TFIID complex. We further show that CaTAF12, but not CaTAF12L, is essential for C. albicans growth. Conditional depletion of the two TAF12 variant proteins caused distinct cellular and colony phenotypes. Together our results define a specialized organization of the TAF12 variants and non-redundant roles for the two TAF12 variants in the unicellular C. albicans genome.
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Affiliation(s)
- Ishani Sinha
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shambhu Kumar
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Poonia
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sonal Sawhney
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Krishnamurthy Natarajan
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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3
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Gupta K, Sari-Ak D, Haffke M, Trowitzsch S, Berger I. Zooming in on Transcription Preinitiation. J Mol Biol 2016; 428:2581-2591. [PMID: 27067110 PMCID: PMC4906157 DOI: 10.1016/j.jmb.2016.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/01/2016] [Accepted: 04/01/2016] [Indexed: 02/08/2023]
Abstract
Class II gene transcription commences with the assembly of the Preinitiation Complex (PIC) from a plethora of proteins and protein assemblies in the nucleus, including the General Transcription Factors (GTFs), RNA polymerase II (RNA pol II), co-activators, co-repressors, and more. TFIID, a megadalton-sized multiprotein complex comprising 20 subunits, is among the first GTFs to bind the core promoter. TFIID assists in nucleating PIC formation, completed by binding of further factors in a highly regulated stepwise fashion. Recent results indicate that TFIID itself is built from distinct preformed submodules, which reside in the nucleus but also in the cytosol of cells. Here, we highlight recent insights in transcription factor assembly and the regulation of transcription preinitiation. Architectural models of human and yeast PIC were proposed. Mediator core–ITC complex structure reveals novel interactions. TFIID submodule residing in the cytoplasm has been discovered. Complex assembly emerges as key concept in transcription regulation.
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Affiliation(s)
- Kapil Gupta
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France; Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Duygu Sari-Ak
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France; Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Matthias Haffke
- Center for Proteomic Chemistry, Structural Biophysics, Novartis Institute for Biomedical Research NIBR, Fabrikstrasse 2, 4056 Basel, Switzerland
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main Germany
| | - Imre Berger
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France; Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France; The School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
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4
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Gazdag E, Jacobi UG, van Kruijsbergen I, Weeks DL, Veenstra GJC. Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors. Development 2016; 143:1340-50. [PMID: 26952988 PMCID: PMC4852510 DOI: 10.1242/dev.127936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/24/2016] [Indexed: 12/15/2022]
Abstract
Embryonic development relies on activating and repressing regulatory influences that are faithfully integrated at the core promoter of individual genes. In vertebrates, the basal machinery recognizing the core promoter includes TATA-binding protein (TBP) and two TBP-related factors. In Xenopus embryos, the three TBP family factors are all essential for development and are required for expression of distinct subsets of genes. Here, we report on a non-canonical TBP family-insensitive (TFI) mechanism of transcription initiation that involves mesoderm and organizer gene expression. Using TBP family single- and triple-knockdown experiments, α-amanitin treatment, transcriptome profiling and chromatin immunoprecipitation, we found that TFI gene expression cannot be explained by functional redundancy, is supported by active transcription and shows normal recruitment of the initiating form of RNA polymerase II to the promoter. Strikingly, recruitment of Gcn5 (also known as Kat2a), a co-activator that has been implicated in transcription initiation, to TFI gene promoters is increased upon depletion of TBP family factors. TFI genes are part of a densely connected TBP family-insensitive T-box-Otx2-Gsc interaction network. The results indicate that this network of genes bound by Vegt, Eomes, Otx2 and Gsc utilizes a novel, flexible and non-canonical mechanism of transcription that does not require TBP or TBP-related factors. Highlighted article: A network of embryonic genes, many of which are expressed in the mesoderm and the organiser, can initiate transcription through a non-canonical mechanism.
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Affiliation(s)
- Emese Gazdag
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Ulrike G Jacobi
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Ila van Kruijsbergen
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
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Danino YM, Even D, Ideses D, Juven-Gershon T. The core promoter: At the heart of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1116-31. [PMID: 25934543 DOI: 10.1016/j.bbagrm.2015.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.
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Affiliation(s)
- Yehuda M Danino
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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6
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Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules. Nat Commun 2015; 6:6011. [PMID: 25586196 PMCID: PMC4309443 DOI: 10.1038/ncomms7011] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/02/2014] [Indexed: 01/27/2023] Open
Abstract
General transcription factor TFIID is a cornerstone of RNA polymerase II transcription initiation in eukaryotic cells. How human TFIID-a megadalton-sized multiprotein complex composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs)-assembles into a functional transcription factor is poorly understood. Here we describe a heterotrimeric TFIID subcomplex consisting of the TAF2, TAF8 and TAF10 proteins, which assembles in the cytoplasm. Using native mass spectrometry, we define the interactions between the TAFs and uncover a central role for TAF8 in nucleating the complex. X-ray crystallography reveals a non-canonical arrangement of the TAF8-TAF10 histone fold domains. TAF2 binds to multiple motifs within the TAF8 C-terminal region, and these interactions dictate TAF2 incorporation into a core-TFIID complex that exists in the nucleus. Our results provide evidence for a stepwise assembly pathway of nuclear holo-TFIID, regulated by nuclear import of preformed cytoplasmic submodules.
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7
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Ferg M, Armant O, Yang L, Dickmeis T, Rastegar S, Strähle U. Gene transcription in the zebrafish embryo: regulators and networks. Brief Funct Genomics 2013; 13:131-43. [PMID: 24152666 DOI: 10.1093/bfgp/elt044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The precise spatial and temporal control of gene expression is a key process in the development, maintenance and regeneration of the vertebrate body. A substantial proportion of vertebrate genomes encode genes that control the transcription of the genetic information into mRNA. The zebrafish is particularly well suited to investigate gene regulatory networks underlying the control of gene expression during development due to the external development of its transparent embryos and the increasingly sophisticated tools for genetic manipulation available for this model system. We review here recent data on the analysis of cis-regulatory modules, transcriptional regulators and their integration into gene regulatory networks in the zebrafish, using the developing spinal cord as example.
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Affiliation(s)
- Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany.
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8
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Yang YC, Chang LK. Role of TAF4 in transcriptional activation by Rta of Epstein-Barr Virus. PLoS One 2013; 8:e54075. [PMID: 23326574 PMCID: PMC3542328 DOI: 10.1371/journal.pone.0054075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 12/06/2012] [Indexed: 11/23/2022] Open
Abstract
Epstein-Barr virus (EBV) expresses an immediate-early protein, Rta, to activate the transcription of EBV lytic genes. This protein usually binds to Rta-response elements or interacts with Sp1 or Zta via a mediator protein, MCAF1, to activate transcription. Rta is also known to interact with TBP and TFIIB to activate transcription. This study finds that Rta interacts with TAF4, a component of TFIID complex, in vitro and in vivo, and on the TATA sequence in the BcLF1 promoter. Rta also interacts with TAF4 and Sp1 on Sp1-binding sequences on TATA-less promoters, including those of BNLF1, BALF5, and the human androgen receptor. These interactions are important to the transcriptional activation of these genes by Rta since introducing TAF4 shRNA substantially reduces the ability of Rta to activate these promoters. This investigation reveals how Rta interacts with TFIID to stimulate transcription.
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Affiliation(s)
- Ya-Chun Yang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Li-Kwan Chang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
- * E-mail:
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9
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Katzenberger RJ, Rach EA, Anderson AK, Ohler U, Wassarman DA. The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes. PLoS One 2012; 7:e45009. [PMID: 22984601 PMCID: PMC3439415 DOI: 10.1371/journal.pone.0045009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/11/2012] [Indexed: 11/19/2022] Open
Abstract
To investigate the importance of core promoter elements for tissue-specific transcription of RNA polymerase II genes, we examined testis-specific transcription in Drosophila melanogaster. Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE). The TCE functions in the 5′ untranslated region of Mst(3)CGP mRNAs to repress translation, and it also functions in a heterologous gene to regulate transcription. We found that among genes with focused initiation patterns, the TCE is significantly enriched in core promoters of genes that are specifically expressed in testes but not in core promoters of genes that are specifically expressed in other tissues. The TCE is variably located in core promoters and is conserved in melanogaster subgroup species, but conservation dramatically drops in more distant species. In transgenic flies, short (300–400 bp) genomic regions containing a TCE directed testis-specific transcription of a reporter gene. Mutation of the TCE significantly reduced but did not abolish reporter gene transcription indicating that the TCE is important but not essential for transcription activation. Finally, mutation of testis-specific TFIID (tTFIID) subunits significantly reduced the transcription of a subset of endogenous TCE-containing but not TCE-lacking genes, suggesting that tTFIID activity is limited to TCE-containing genes but that tTFIID is not an obligatory regulator of TCE-containing genes. Thus, the TCE is a core promoter element in a subset of genes that are specifically expressed in testes. Furthermore, the TCE regulates transcription in the context of short genomic regions, from variable locations in the core promoter, and both dependently and independently of tTFIID. These findings set the stage for determining the mechanism by which the TCE regulates testis-specific transcription and understanding the dual role of the TCE in translational and transcriptional regulation.
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Affiliation(s)
- Rebeccah J. Katzenberger
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Madison, Wisconsin, United States of America
| | - Elizabeth A. Rach
- Institute for Genome Sciences and Policy, Departments of Biostatistics and Bioinformatics and Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Ashley K. Anderson
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Madison, Wisconsin, United States of America
| | - Uwe Ohler
- Institute for Genome Sciences and Policy, Departments of Biostatistics and Bioinformatics and Computer Science, Duke University, Durham, North Carolina, United States of America
- * E-mail: (DAW); (UO)
| | - David A. Wassarman
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Madison, Wisconsin, United States of America
- * E-mail: (DAW); (UO)
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Wilhelm E, Doyle MC, Nzaramba I, Magdzinski A, Dumais N, Bell B. CTGC motifs within the HIV core promoter specify Tat-responsive pre-initiation complexes. Retrovirology 2012; 9:62. [PMID: 22834489 PMCID: PMC3419132 DOI: 10.1186/1742-4690-9-62] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 07/26/2012] [Indexed: 12/12/2022] Open
Abstract
Background HIV latency is an obstacle for the eradication of HIV from infected individuals. Stable post-integration latency is controlled principally at the level of transcription. The HIV trans-activating protein, Tat, plays a key function in enhancing HIV transcriptional elongation. The HIV core promoter is specifically required for Tat-mediated trans-activation of HIV transcription. In addition, the HIV core promoter has been shown to be a potential anti-HIV drug target. Despite the pivotal role of the HIV core promoter in the control of HIV gene expression, the molecular mechanisms that couple Tat function specifically to the HIV core promoter remain unknown. Results Using electrophoretic mobility shift assays (EMSAs), the TATA box and adjacent sequences of HIV essential for Tat trans-activation were shown to form specific complexes with nuclear extracts from peripheral blood mononuclear cells, as well as from HeLa cells. These complexes, termed pre-initiation complexes of HIV (PICH), were distinct in composition and DNA binding specificity from those of prototypical eukaryotic TATA box regions such as Adenovirus major late promoter (AdMLP) or the hsp70 promoter. PICH contained basal transcription factors including TATA-binding protein and TFIIA. A mutational analysis revealed that CTGC motifs flanking the HIV TATA box are required for Tat trans-activation in living cells and correct PICH formation in vitro. The binding of known core promoter binding proteins AP-4 and USF-1 was found to be dispensable for Tat function. TAR RNA prevented stable binding of PICH-2, a complex that contains the general transcription factor TFIIA, to the HIV core promoter. The impact of TAR on PICH-2 specifically required its bulge sequence that is also known to interact with Tat. Conclusion Our data reveal that CTGC DNA motifs flanking the HIV TATA box are required for correct formation of specific pre-initiation complexes in vitro and that these motifs are also required for Tat trans-activation in living cells. The impact of TAR RNA on PICH-2 stability provides a mechanistic link by which pre-initiation complex dynamics could be coupled to the formation of the nascent transcript by the elongating transcription complex. Together, these findings shed new light on the mechanisms by which the HIV core promoter specifically responds to Tat to activate HIV gene expression.
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Affiliation(s)
- Emmanuelle Wilhelm
- RNA Group, Département de Microbiologie et d'Infectiologie, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Pavillon de Recherche Appliquée sur le Cancer, 3201 rue Jean-Migneault, Sherbrooke, Québec J1E 4K8, Canada
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Vorobyeva NE, Nikolenko JV, Krasnov AN, Kuzmina JL, Panov VV, Nabirochkina EN, Georgieva SG, Shidlovskii YV. SAYP interacts with DHR3 nuclear receptor and participates in ecdysone-dependent transcription regulation. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795411120155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Assembly of the transcription machinery: ordered and stable, random and dynamic, or both? Chromosoma 2011; 120:533-45. [PMID: 22048163 DOI: 10.1007/s00412-011-0340-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 08/22/2011] [Accepted: 08/23/2011] [Indexed: 01/12/2023]
Abstract
The assembly of the transcription machinery is a key step in gene activation, but even basic details of this process remain unclear. Here we discuss the apparent discrepancy between the classic sequential assembly model based mostly on biochemistry and an emerging dynamic assembly model based mostly on fluorescence microscopy. The former model favors a stable transcription complex with subunits that cooperatively assemble in order, whereas the latter model favors an unstable complex with subunits that may assemble more randomly. To confront this apparent discrepancy, we review the merits and drawbacks of the different experimental approaches and list potential biasing factors that could be responsible for the different interpretations of assembly. We then discuss how these biases might be overcome in the future with improved experiments or new techniques. Finally, we discuss how kinetic models for assembly may help resolve the ordered and stable vs. random and dynamic assembly debate.
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Akhtar W, Veenstra GJC. TBP-related factors: a paradigm of diversity in transcription initiation. Cell Biosci 2011; 1:23. [PMID: 21711503 PMCID: PMC3142196 DOI: 10.1186/2045-3701-1-23] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/27/2011] [Indexed: 01/24/2023] Open
Abstract
TATA binding protein (TBP) is a key component of the eukaryotic transcription initiation machinery. It functions in several complexes involved in core promoter recognition and assembly of the pre-initiation complex. Through gene duplication eukaryotes have expanded their repertoire of TATA binding proteins, leading to a variable composition of the transcription machinery. In vertebrates this repertoire consists of TBP, TBP-like factor (TLF, also known as TBPL1, TRF2) and TBP2 (also known as TBPL2, TRF3). All three factors are essential, with TLF and TBP2 playing important roles in development and differentiation, in particular gametogenesis and early embryonic development, whereas TBP dominates somatic cell transcription. TBP-related factors may compete for promoters when co-expressed, but also show preferential interactions with subsets of promoters. Initiation factor switching occurs on account of differential expression of these proteins in gametes, embryos and somatic cells. Paralogs of TFIIA and TAF subunits account for additional variation in the transcription initiation complex. This variation in core promoter recognition accommodates the expanded regulatory capacity and specificity required for germ cells and embryonic development in higher eukaryotes.
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Affiliation(s)
- Waseem Akhtar
- Radboud University Nijmegen, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.
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A plant-specific transcription factor IIB-related protein, pBRP2, is involved in endosperm growth control. PLoS One 2011; 6:e17216. [PMID: 21390310 PMCID: PMC3044737 DOI: 10.1371/journal.pone.0017216] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 01/26/2011] [Indexed: 11/19/2022] Open
Abstract
General transcription factor IIB (TFIIB) and TFIIB-related factor (BRF), are conserved RNA polymerase II/III (RNAPII/III) selectivity factors that are involved in polymerase recruitment and transcription initiation in eukaryotes. Recent findings have shown that plants have evolved a third type of B-factor, plant-specific TFIIB-related protein 1 (pBRP1), which seems to be involved in RNAPI transcription. Here, we extend the repertoire of B-factors in plants by reporting the characterization of a novel TFIIB-related protein, plant-specific TFIIB-related protein 2 (pBRP2), which is found to date only in the Brassicacea family. Unlike other B-factors that are ubiquitously expressed, PBRP2 expression is restricted to reproductive organs and seeds as shown by RT-PCR, immunofluorescence labelling and GUS staining experiments. Interestingly, pbrp2 loss-of-function specifically affects the development of the syncytial endosperm, with both parental contributions required for wild-type development. pBRP2, is the first B-factor to exhibit cell-specific expression and regulation in eukaryotes, and might play a role in enforcing bi-parental reproduction in angiosperms.
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Kuzmina JL, Panov VV, Vorobyeva NE, Soshnikova NV, Kopantseva MR, Nikolenko JV, Nabirochkina EN, Georgieva SG, Shidlovskii YV. SAYP is a novel regulator of metazoan development. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410080028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Mityaev MV, Kopantzev EP, Buzdin AA, Vinogradova TV, Sverdlov ED. Enhancer element potentially involved in human survivin gene promoter regulation in lung cancer cell lines. BIOCHEMISTRY (MOSCOW) 2010; 75:182-91. [DOI: 10.1134/s0006297910020082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Castañon-Sanchez CA, Luna-Arias JP, de Dios-Bravo MG, Herrera-Aguirre ME, Olivares-Trejo JJ, Orozco E, Hernandez JM. Entamoeba histolytica: A unicellular organism containing two active genes encoding for members of the TBP family. Protein Expr Purif 2010; 70:48-59. [DOI: 10.1016/j.pep.2009.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 12/06/2009] [Accepted: 12/09/2009] [Indexed: 10/20/2022]
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Pijnappel WP, Kolkman A, Baltissen MP, Heck AJ, Timmers HM. Quantitative mass spectrometry of TATA binding protein-containing complexes and subunit phosphorylations during the cell cycle. Proteome Sci 2009; 7:46. [PMID: 20034391 PMCID: PMC2804597 DOI: 10.1186/1477-5956-7-46] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Accepted: 12/24/2009] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Progression through the cell cycle is accompanied by tightly controlled regulation of transcription. On one hand, a subset of genes is expressed in a cell cycle-dependent manner. On the other hand, a general inhibition of transcription occurs during mitosis. Genetic and genome-wide studies suggest cell cycle regulation at the level of transcription initiation by protein complexes containing the common DNA-binding subunit TATA binding protein (TBP). TBP is a key player in regulating transcription by all three nuclear RNA polymerases. It forms at least four distinct protein complexes with TBP-associated factors (TAFs): SL1, B-TFIID, TFIID, and TFIIIB. Some TAFs are known to remain associated with TBP during the cell cycle. Here we analyze all TAFs and their phosphorylation status during the cell cycle using a quantitative mass spectrometry approach. RESULTS TBP protein complexes present in human cells at the G2/M and G1/S transitions were analyzed by combining affinity purification with quantitative mass spectrometry using stable isotope labeling with amino acids in cell culture (SILAC). Phosphorylations were mapped and quantified after enrichment of tryptic peptides by titanium dioxide. This revealed that subunit stoichiometries of TBP complexes remained intact, but their relative abundances in nuclear extracts changed during the cell cycle. Several novel phosphorylations were detected on subunits of the TBP complexes TFIID and SL1. G2/M-specific phosphorylations were detected on TAF1, TAF4, TAF7, and TAFI41/TAF1D, and G1/S-specific dephosphorylations were detected on TAF3. Many phosphorylated residues were evolutionary conserved from human to zebrafish and/or drosophila, and were present in conserved regions suggesting important regulatory functions. CONCLUSIONS This study provides the first quantitative proteomic analysis of human TBP containing protein complexes at the G2/M and G1/S transitions, and identifies new cell cycle-dependent phosphorylations on TAFs present in their protein complex. We speculate that phosphorylation of complex-specific subunits may be involved in regulating the activities of TBP protein complexes during the cell cycle.
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Affiliation(s)
- Wwm Pim Pijnappel
- Netherlands Proteomics Centre, Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Annemieke Kolkman
- Netherlands Proteomics Centre, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Faculty of Science, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marijke Pa Baltissen
- Netherlands Proteomics Centre, Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Albert Jr Heck
- Netherlands Proteomics Centre, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Faculty of Science, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ht Marc Timmers
- Netherlands Proteomics Centre, Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
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Ranjan A, Ansari SA, Srivastava R, Mantri S, Asif MH, Sawant SV, Tuli R. A T9G mutation in the prototype TATA-box TCACTATATATAG determines nucleosome formation and synergy with upstream activator sequences in plant promoters. PLANT PHYSIOLOGY 2009; 151:2174-86. [PMID: 19812181 PMCID: PMC2785982 DOI: 10.1104/pp.109.148064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 09/30/2009] [Indexed: 05/19/2023]
Abstract
We had earlier reported that mutations to G and C at the seventh and eighth positions in the prototype TATA-box TCACTATATATAG inhibited light-dependent activation of transcription from the promoter. In this study, we characterized mutations at the ninth position of the prototype TATA-box. Substitution of T at the ninth position with G or C enhanced transcription from the promoter in transgenic tobacco (Nicotiana tabacum) plants. The effect of T9G/C mutations was not light dependent, although the 9G/C TATA-box showed synergy with the light-responsive element (lre). However, the 9G/C mutants in the presence of lre failed to respond to phytochromes, sugar, and calcium signaling, in contrast to the prototype TATA-box with lre. The 9G/C mutation shifted the point of initiation of transcription, and transcription activation was dependent upon the type of activating element present upstream. The synergy in activation was noticed with lre and legumin activators but not with rbcS, Pcec, and PR-1a activators. The 9G mutation resulted in a micrococcal nuclease-sensitive region over the TATA-box, suggesting a nucleosome-free region, in contrast to the prototype promoter, which had a distinct nucleosome on the TATA-box. Thus, the transcriptional augmentation with mutation at the ninth position might be because of the loss of a repressive nucleosomal structure on the TATA-box. In agreement with our findings, the promoters containing TATAGATA as identified by genome-wide analysis of Arabidopsis (Arabidopsis thaliana) are not tightly repressed.
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Affiliation(s)
| | | | | | | | | | - Samir V. Sawant
- National Botanical Research Institute, Council of Scientific and Industrial Research, Lucknow 226001, India
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20
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Gazdag E, Santenard A, Ziegler-Birling C, Altobelli G, Poch O, Tora L, Torres-Padilla ME. TBP2 is essential for germ cell development by regulating transcription and chromatin condensation in the oocyte. Genes Dev 2009; 23:2210-23. [PMID: 19759265 PMCID: PMC2751983 DOI: 10.1101/gad.535209] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 07/27/2009] [Indexed: 02/05/2023]
Abstract
Development of the germline requires consecutive differentiation events. Regulation of these has been associated with germ cell-specific and pluripotency-associated transcription factors, but the role of general transcription factors (GTFs) remains elusive. TATA-binding protein (TBP) is a GTF involved in transcription by all RNA polymerases. During ovarian folliculogenesis in mice the vertebrate-specific member of the TBP family, TBP2/TRF3, is expressed exclusively in oocytes. To determine TBP2 function in vivo, we generated TBP2-deficient mice. We found that Tbp2(-/-) mice are viable with no apparent phenotype. However, females lacking TBP2 are sterile due to defective folliculogenesis, altered chromatin organization, and transcriptional misregulation of key oocyte-specific genes. TBP2 binds to promoters of misregulated genes, suggesting that TBP2 directly regulates their expression. In contrast, TBP ablation in the female germline results in normal ovulation and fertilization, indicating that in these cells TBP is dispensable. We demonstrate that TBP2 is essential for the differentiation of female germ cells, and show the mutually exclusive functions of these key core promoter-binding factors, TBP and TBP2, in the mouse.
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Affiliation(s)
- Emese Gazdag
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
| | - Angèle Santenard
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
- Department of Developmental and Cell Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
| | - Céline Ziegler-Birling
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
- Department of Developmental and Cell Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
| | - Gioia Altobelli
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
- Bioinformatics and Integrative Biology Laboratory, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
| | - Olivier Poch
- Bioinformatics and Integrative Biology Laboratory, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
| | - Làszlò Tora
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
| | - Maria-Elena Torres-Padilla
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
- Department of Developmental and Cell Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 Illkirch Cedex, CU de Strasbourg, France
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Transcription coactivator SAYP combines chromatin remodeler Brahma and transcription initiation factor TFIID into a single supercomplex. Proc Natl Acad Sci U S A 2009; 106:11049-54. [PMID: 19541607 DOI: 10.1073/pnas.0901801106] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription activation by RNA polymerase II is a complicated process driven by combined, precisely coordinated action of a wide array of coactivator complexes, which carry out chromatin-directed activities and nucleate the assembly of the preinitiation complex on the promoter. Using various techniques, we have shown the existence of a stable coactivator supercomplex consisting of the chromatin-remodeling factor Brahma (SWI/SNF) and the transcription initiation factor TFIID, named BTFly (Brahma and TFIID in one assembly). The coupling of Brahma and TFIID is mediated by the SAYP factor, whose evolutionarily conserved activation domain SAY can directly bind to both BAP170 subunit of Brahma and TAF5 subunit of TFIID. The integrity of BTFly is crucial for its ability to activate transcription. BTFly is distributed genome-wide and appears to be a means of effective transcription activation.
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Sprouse RO, Wells MN, Auble DT. TATA-binding protein variants that bypass the requirement for Mot1 in vivo. J Biol Chem 2009; 284:4525-35. [PMID: 19098311 PMCID: PMC2640957 DOI: 10.1074/jbc.m808951200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 12/18/2008] [Indexed: 12/27/2022] Open
Abstract
Mot1 is an essential TATA-binding protein (TBP)-associated factor and Snf2/Swi2 ATPase that both represses and activates transcription. Biochemical and structural results support a model in which ATP binding and hydrolysis induce a conformational change in Mot1 that drives local translocation along DNA, thus removing TBP. Although this activity explains transcriptional repression, it does not as easily explain Mot1-mediated transcriptional activation, and several different models have been proposed to explain how Mot1 activates transcription. To better understand the function of Mot1 in yeast cells in vivo, particularly with regard to gene activation, TBP mutants were identified that bypass the requirement for Mot1 in vivo. Although TBP has been extensively mutated and analyzed previously, this screen uncovered two novel TBP variants that are unique in their ability to bypass the requirement for Mot1. Surprisingly, in vitro analyses reveal that rather than having acquired an improved biochemical activity, one of the TBPs was defective for interaction with polymerase II preinitiation complex (PIC) components and other regulators of TBP function. The other mutant was defective for DNA binding in vitro yet was still recruited to chromatin in vivo. These results suggest that Mot1-mediated dissociation of TBP (or TBP-containing complexes) from chromatin can explain the Mot1 activation mechanism at some promoters. The results also suggest that PICs can be dynamically unstable and that appropriate PIC instability is critical for the regulation of transcription in vivo.
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Affiliation(s)
- Rebekka O Sprouse
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908, USA
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23
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Transcriptional regulation of an iron-inducible gene by differential and alternate promoter entries of multiple Myb proteins in the protozoan parasite Trichomonas vaginalis. EUKARYOTIC CELL 2009; 8:362-72. [PMID: 19151329 DOI: 10.1128/ec.00317-08] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Iron-inducible transcription of a malic enzyme gene (also reputed to be ap65-1) in Trichomonas vaginalis was previously shown to involve a Myb1 repressor and a Myb2 activator, each of which may preferentially select two closely spaced promoter sites, MRE-1/MRE-2r, which comprises overlapping promoter elements, and MRE-2f. In the present study, an iron-inducible approximately 32-kDa Myb3 nuclear protein was demonstrated to bind only the MRE-1 element. Changes in the iron supply, which produced antagonistic effects on the levels of Myb2 and Myb3 expression, also resulted in temporal and alternate entries of Myb2 and Myb3 into the ap65-1 promoter. Repression or activation of basal and iron-inducible ap65-1 transcription was detected in transfected cells when Myb3 was, respectively, substantially knocked down or overexpressed. In the latter case, increased Myb3 promoter entry was detected with concomitant decrease in Myb2 promoter entry under specific conditions, while Myb3 promoter entry was inhibited under all test conditions in cells overexpressing Myb2. In contrast, concomitant promoter entries by Myb2 and Myb3 diminished in cells overexpressing Myb1, except that Myb3 promoter entry was slightly affected under prolonged iron depletion. Together, these results suggest that Myb2 and Myb3 may coactivate basal and iron-inducible ap65-1 transcription against Myb1 through conditional and competitive promoter entries.
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Krebs A, Frontini M, Tora L. GPAT: retrieval of genomic annotation from large genomic position datasets. BMC Bioinformatics 2008; 9:533. [PMID: 19077303 PMCID: PMC2654044 DOI: 10.1186/1471-2105-9-533] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 12/15/2008] [Indexed: 11/10/2022] Open
Abstract
Background Recent genome wide transcription factor binding site or chromatin modification mapping analysis techniques, such as chromatin immunoprecipitation (ChIP) linked to DNA microarray analysis (ChIP on chip) or ChIP coupled to high throughput sequencing (ChIP-seq), generate tremendous amounts of genomic location data in the form of one-dimensional series of signals. After pre-analysis of these data (signal pre-clearing, relevant binding site detection), biologists need to search for the biological relevance of the detected genomic positions representing transcription regulation or chromatin modification events. Results To address this problem, we have developed a Genomic Position Annotation Tool (GPAT) with a simple web interface that allows the rapid and systematic labelling of thousands of genomic positions with several types of annotations. GPAT automatically extracts gene annotation information around the submitted positions from different public databases (Refseq or ENSEMBL). In addition, GPAT provides access to the expression status of the corresponding genes from either existing transcriptomic databases or from user generated expression data sets. Furthermore, GPAT allows the localisation of the genomic coordinates relative to the chromosome bands and the well characterised ENCODE regions. We successfully used GPAT to analyse ChIP on chip data and to identify genes functionally regulated by the TATA binding protein (TBP). Conclusion GPAT provides a quick, convenient and flexible way to annotate large sets of genomic positions obtained after pre-analysis of ChIP-chip, ChIP-seq or other high throughput sequencing-based techniques. Through the different annotation data displayed, GPAT facilitates the interpretation of genome wide datasets for molecular biologists.
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Affiliation(s)
- Arnaud Krebs
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 596, Université Louis Pasteur de Strasbourg, BP 10142-67404 ILLKIRCH Cedex, CU de Strasbourg, France.
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25
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Komaki-Yasuda K, Okuwaki M, Kano S, Nagata K, Kawazu SI. 5' sequence- and chromatin modification-dependent gene expression in Plasmodium falciparum erythrocytic stage. Mol Biochem Parasitol 2008; 162:40-51. [PMID: 18692528 DOI: 10.1016/j.molbiopara.2008.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 07/09/2008] [Accepted: 07/10/2008] [Indexed: 11/18/2022]
Abstract
Plasmodium falciparum, the human malaria parasite, is evolutionarily distant from other eukaryotes. Genome-wide analyses of transcription-associated proteins have revealed a relative paucity of putative regulatory transcription factors and an abundance of putative chromatin remodeling machinery, suggesting that this parasite has a transcription regulatory system that is distinct from those of other eukaryotes. Here, we have analyzed transcriptional regulation of the peroxiredoxin genes, pf1-cys-prx and pftpx-1, which show different expression patterns in P. falciparum. The reporter assays revealed the presence of putative enhancers in the 5' regions of these genes. Although pf1-cys-prx shows trophozoite/schizont stage-specific transcription, a putative cis-acting enhancer sequence in pf1-cys-prx was constitutively active when inserted into the 5' region of pftpx-1. Electrophoretic mobility shift and DNase I footprinting assays showed that this enhancer region is the target of trophozoite/schizont stage-specific DNA binding proteins. In addition, chromatin immunoprecipitation assays showed that the increased levels of histone acetylation in the 5' region of pf1-cys-prx and pftpx-1 correlate with the transcriptional activity of these genes. Recruitment of PfGCN5 histone acetyltransferase to the pf1-cys-prx enhancer in trophozoite/schizont stage was observed. These results suggest that P. falciparum possesses a sophisticated system of transcriptional regulation during intraerythrocytic stages that is managed by coordinated interactions of unique cis-elements and trans-acting factors and chromatin modifications.
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Wilhelm E, Pellay FX, Benecke A, Bell B. TAF6delta controls apoptosis and gene expression in the absence of p53. PLoS One 2008; 3:e2721. [PMID: 18628956 PMCID: PMC2444026 DOI: 10.1371/journal.pone.0002721] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 06/18/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Life and death decisions of metazoan cells hinge on the balance between the expression of pro- versus anti-apoptotic gene products. The general RNA polymerase II transcription factor, TFIID, plays a central role in the regulation of gene expression through its core promoter recognition and co-activator functions. The core TFIID subunit TAF6 acts in vitro as an essential co-activator of transcription for the p53 tumor suppressor protein. We previously identified a splice variant of TAF6, termed TAF6delta that can be induced during apoptosis. METHODOLOGY/PRINCIPAL FINDINGS To elucidate the impact of TAF6delta on cell death and gene expression, we have employed modified antisense oligonucleotides to enforce expression of endogenous TAF6delta. The induction of endogenous TAF6delta triggered apoptosis in tumor cell lines, including cells devoid of p53. Microarray experiments revealed that TAF6delta activates gene expression independently of cellular p53 status. CONCLUSIONS Our data define TAF6delta as a pivotal node in a signaling pathway that controls gene expression programs and apoptosis in the absence of p53.
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Affiliation(s)
- Emmanuelle Wilhelm
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - François-Xavier Pellay
- Institut des Hautes Études Scientifiques and Institut de Recherche Interdisciplinaire – CNRS USR3078 - Université de Lille, Bures sur Yvette, France
| | - Arndt Benecke
- Institut des Hautes Études Scientifiques and Institut de Recherche Interdisciplinaire – CNRS USR3078 - Université de Lille, Bures sur Yvette, France
| | - Brendan Bell
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 2008; 7:29-59. [PMID: 16719718 DOI: 10.1146/annurev.genom.7.080505.115623] [Citation(s) in RCA: 539] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The faithful execution of biological processes requires a precise and carefully orchestrated set of steps that depend on the proper spatial and temporal expression of genes. Here we review the various classes of transcriptional regulatory elements (core promoters, proximal promoters, distal enhancers, silencers, insulators/boundary elements, and locus control regions) and the molecular machinery (general transcription factors, activators, and coactivators) that interacts with the regulatory elements to mediate precisely controlled patterns of gene expression. The biological importance of transcriptional regulation is highlighted by examples of how alterations in these transcriptional components can lead to disease. Finally, we discuss the methods currently used to identify transcriptional regulatory elements, and the ability of these methods to be scaled up for the purpose of annotating the entire human genome.
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Affiliation(s)
- Glenn A Maston
- Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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28
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Kopytova DV, Nikolenko YV, Lebedeva LA, Nabirochkina EN, Shidlovskii YV, Georgieva SG, Krasnov AN. Study of the Drosophila melanogaster trf2 gene and its protein product. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408020026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Friedman MJ, Wang CE, Li XJ, Li S. Polyglutamine expansion reduces the association of TATA-binding protein with DNA and induces DNA binding-independent neurotoxicity. J Biol Chem 2008; 283:8283-90. [PMID: 18218637 DOI: 10.1074/jbc.m709674200] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TATA-binding protein (TBP) is essential for eukaryotic gene transcription. Human TBP contains a polymorphic polyglutamine (polyQ) domain in its N terminus and a DNA-binding domain in its highly conserved C terminus. Expansion of the polyQ domain to >42 glutamines typically results in spinocerebellar ataxia type 17 (SCA17), a neurodegenerative disorder that resembles Huntington disease. Our recent studies have demonstrated that polyQ expansion causes abnormal interaction of TBP with the general transcription factor TFIIB and induces neurodegeneration in transgenic SCA17 mice (Friedman, M. J., Shah, A. G., Fang, Z. H., Ward, E. G., Warren, S. T., Li, S., and Li, X. J. (2007) Nat. Neurosci. 10, 1519-1528). However, it remains unknown how polyQ expansion influences DNA binding by TBP. Here we report that polyQ expansion reduces in vitro binding of TBP to DNA and that mutant TBP fragments lacking an intact C-terminal DNA-binding domain are present in transgenic SCA17 mouse brains. polyQ-expanded TBP with a deletion spanning part of the DNA-binding domain does not bind DNA in vitro but forms nuclear aggregates and inhibits TATA-dependent transcription activity in cultured cells. When this TBP double mutant is expressed in transgenic mice, it forms nuclear inclusions in neurons and causes early death. These findings suggest that the polyQ tract affects the binding of TBP to promoter DNA and that polyQ-expanded TBP can induce neuronal toxicity independent of its interaction with DNA.
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Affiliation(s)
- Meyer J Friedman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Cojocaru M, Jeronimo C, Forget D, Bouchard A, Bergeron D, Côte P, Poirier GG, Greenblatt J, Coulombe B. Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription. Biochem J 2008; 409:139-47. [PMID: 17848138 PMCID: PMC4498901 DOI: 10.1042/bj20070751] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The functions ascribed to the mammalian GTFs (general transcription factors) during the various stages of the RNAPII (RNA polymerase II) transcription reaction are based largely on in vitro studies. To gain insight as to the functions of the GTFs in living cells, we have analysed the genomic location of several human GTF and RNAPII subunits carrying a TAP (tandem-affinity purification) tag. ChIP (chromatin immunoprecipitation) experiments using anti-tag beads (TAP-ChIP) allowed the systematic localization of the tagged factors. Enrichment of regions located close to the TIS (transcriptional initiation site) versus further downstream TRs (transcribed regions) of nine human genes, selected for the minimal divergence of their alternative TIS, were analysed by QPCR (quantitative PCR). We show that, in contrast with reports using the yeast system, human TFIIF (transcription factor IIF) associates both with regions proximal to the TIS and with further downstream TRs, indicating an in vivo function in elongation for this GTF. Unexpectedly, we found that the Rpb7 subunit of RNAPII, known to be required only for the initiation phase of transcription, remains associated with the polymerase during early elongation. Moreover, ChIP experiments conducted under stress conditions suggest that Rpb7 is involved in the stabilization of transcribing polymerase molecules, from initiation to late elongation stages. Together, our results provide for the first time a general picture of GTF function during the RNAPII transcription reaction in live mammalian cells and show that TFIIF and Rpb7 are involved in both early and late transcriptional stages.
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Affiliation(s)
- Marilena Cojocaru
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Célia Jeronimo
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Diane Forget
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Annie Bouchard
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Dominique Bergeron
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Pierre Côte
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Guy G. Poirier
- Centre Hospitalier Universitaire de QC, Université Laval, Québec, QC, Canada
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
- To whom correspondence should be addressed, at Laboratory of Gene Transcription and Proteomics, Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7 ()
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31
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Gazdag E, Rajkovic A, Torres-Padilla ME, Tora L. Analysis of TATA-binding protein 2 (TBP2) and TBP expression suggests different roles for the two proteins in regulation of gene expression during oogenesis and early mouse development. Reproduction 2007; 134:51-62. [PMID: 17641088 DOI: 10.1530/rep-06-0337] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Gametogenesis, the process during which germ cells are generated is essential for reproduction. In mammals, maternal mRNA and proteins present in the oocyte are required to ensure the progression of development until the embryo activates its genome after fertilisation. It is well established that the oocyte synthesises these maternal factors during oocyte growth and then undergoes a quiescent transcriptional period that will be resumed only after fertilisation. However, the mechanisms that govern transcriptional regulation and subsequent silencing during oogenesis are not well understood. Here, we have examined the expression and localisation of the TATA-binding protein (TBP) and the related protein TBP2 (also called TRF3, TBP-related factor 3) during oogenesis and in early mouse embryos. We show that TBP is expressed in the oocytes at the beginning of folliculogenesis, but it is undetectable during further stages of oocyte development, and becomes abundant again only after fertilisation. In contrast to TBP, we found that TBP2 is highly expressed in growing oocytes during folliculogenesis, declines upon ovulation, and is almost undetectable after fertilisation by the two-cell stage. The mirroring localisation profile of TBP and TBP2 suggests different roles for the two proteins in establishing specialised programs of gene expression during oocyte development and in early mouse embryos. Analysis of mutant mouse ovaries in which oocyte-specific factors have been knocked-out suggests that TBP2 is a potential candidate for regulating transcriptional control of oogenesis. Moreover, our results obtained with oocytes lacking the oocyte-specific nuclear chaperone nucleoplasmin 2 suggest that TBP2 function may be related to non-condensed chromatin conformation.
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Affiliation(s)
- Emese Gazdag
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, CNRS, INSERM, ULP, BP 10142, CU de Strasbourg, 67404 Illkirch Cedex, France
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Di Pietro C, Ragusa M, Duro L, Guglielmino MR, Barbagallo D, Carnemolla A, Laganà A, Buffa P, Angelica R, Rinaldi A, Calafato MS, Milicia I, Caserta C, Giugno R, Pulvirenti A, Giunta V, Rapisarda A, Di Pietro V, Grillo A, Messina A, Ferro A, Grzeschik KH, Purrello M. Genomics, evolution, and expression of TBPL2, a member of the TBP family. DNA Cell Biol 2007; 26:369-85. [PMID: 17570761 DOI: 10.1089/dna.2006.0527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TBPL2 is the most recently discovered and less characterized member of the TATA box binding protein (TBP) family that also comprises TBP, TATA box binding protein-like 1 (TBPL1), and Drosophila melanogaster TBP related factor (TRF). In this paper we report our in silico and in vitro data on (i) the genomics of the TBPL2 gene in Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, Gallus gallus, Xenopus tropicalis, and Takifugu rubripes; (ii) its evolution and phylogenetic relationship with TBP, TBPL1, and TRF; (iii) the structure of the TBPL2 proteins that belong to the recently identified group of the intrinsically unstructured proteins (IUPs); and (iv) TBPL2 expression in different organs and cell types of Homo sapiens and Rattus norvegicus. Similar to TBP, both the TBPL2 gene and protein are bimodular. The 3' region of the gene encoding the DNA binding domain (DBD) was well conserved during evolution. Its high homology to vertebrate TBP suggests that TBPL2 also should bind to the TATA box and interact with the proteins binding to TBP carboxy-terminal domain, such as the TBP associated factors (TAFs). As already demonstrated for TBP, TBPL2 amino-terminal segment is intrinsically unstructured and, even though variable among vertebrates, comprises a highly conserved motif not found in any other known protein. Absence of TBPL2 from the genome of invertebrates and plants demonstrates its specific origin within the subphylum of vertebrates. Our RT-PCR analysis of human and rat RNA shows that, similar to TBP, TBPL2 is ubiquitously synthesized even though at variable levels that are at least two orders of magnitude lower. Higher expression of TBPL2 in the gonads than in other organs suggests that it could perform important functions in gametogenesis. Our genomic and expression data should contribute to clarify why TBP has a general master role within the transcription apparatus (TA), whereas both TBPL1 and TBPL2 perform tissue-specific functions.
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Affiliation(s)
- Cinzia Di Pietro
- Dipartimento di Scienze Biomediche-Unità di Biologia Genetica e BioInformatica, Università di Catania, Catania, Italy, EU
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33
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Szutorisz H, Dillon N, Tora L. [Suppression of non-specific transcription by the proteasome in embryonic stem cells]. Med Sci (Paris) 2007; 23:351-3. [PMID: 17433221 DOI: 10.1051/medsci/2007234351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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34
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Müller F, Demény MA, Tora L. New problems in RNA polymerase II transcription initiation: matching the diversity of core promoters with a variety of promoter recognition factors. J Biol Chem 2007; 282:14685-9. [PMID: 17395580 DOI: 10.1074/jbc.r700012200] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Ferenc Müller
- Institute of Toxicology and Genetics, Forschungszentrum, Karlsruhe, D-76021 Germany.
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35
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Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39:457-66. [PMID: 17334365 DOI: 10.1038/ng1990] [Citation(s) in RCA: 1547] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 01/29/2007] [Indexed: 01/11/2023]
Abstract
To gain insight into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase occupancy and histone modifications at 16,000 promoters in primary human somatic and germline cells. We find CpG-poor promoters hypermethylated in somatic cells, which does not preclude their activity. This methylation is present in male gametes and results in evolutionary loss of CpG dinucleotides, as measured by divergence between humans and primates. In contrast, strong CpG island promoters are mostly unmethylated, even when inactive. Weak CpG island promoters are distinct, as they are preferential targets for de novo methylation in somatic cells. Notably, most germline-specific genes are methylated in somatic cells, suggesting additional functional selection. These results show that promoter sequence and gene function are major predictors of promoter methylation states. Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation.
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Affiliation(s)
- Michael Weber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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36
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Gendra E, Colgan DF, Meany B, Konarska MM. A sequence motif in the simian virus 40 (SV40) early core promoter affects alternative splicing of transcribed mRNA. J Biol Chem 2007; 282:11648-57. [PMID: 17331949 DOI: 10.1074/jbc.m611126200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To identify new sequence elements in the promoter that affect splicing patterns of pre-mRNAs, we analyzed effects of different promoters on alternative splicing of model reporter genes. We compared the E1a alternative splicing pattern in transcripts expressed from the full-length cytomegalovirus, SV40 early, or a hybrid cytomegalovirus/SV40 early promoter and found that the hybrid promoter improved selection of the suboptimal E1a 5'SS-1. Expressing RNA from the hybrid promoter also enhanced selection of suboptimal splice sites in other alternatively spliced reporter genes, demonstrating the generality of this effect. Unlike previously defined promoter elements shown to affect alternative splicing, which were located in the enhancer/upstream activating sequences, the motif identified in this work is positioned within the core promoter; it is comprised of eight T-residues directly upstream of the SV40 early TATA box. This motif was previously implicated in DNA bending and negative regulation of transcription. Together, these results suggest that the identity of transcription complex assembled in the core promoter-dependent fashion can affect splice site selection during pre-mRNA splicing, perhaps by influencing the processivity of transcription elongation.
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37
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Abstract
The general transcription factor TFIIB (transcription factor IIB) plays a critical role in the assembly of the RNA polymerase II pre-initiation complex. TFIIB can make sequence-specific DNA contacts both upstream and downstream of the TATA box. This has led to the definition of two core promoter BREs (TFIIB-recognition elements), one upstream [BRE(u) (upstream BRE)] and one downstream of TATA box [BRE(d) (downstream BRE)]. TFIIB-BRE(u) and TFIIB-BRE(d) contacts are mediated by two independent DNA-recognition motifs within the core domain of TFIIB. Both the BRE(u) and the BRE(d) modulate the transcriptional potency of a promoter. However, the net effect of the BREs on promoter activity is dependent on the specific blend of elements present within a core promoter.
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Affiliation(s)
- W Deng
- Faculty of Life Sciences, The Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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38
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Szutorisz H, Georgiou A, Tora L, Dillon N. The proteasome restricts permissive transcription at tissue-specific gene loci in embryonic stem cells. Cell 2007; 127:1375-88. [PMID: 17190601 DOI: 10.1016/j.cell.2006.10.045] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 08/28/2006] [Accepted: 10/13/2006] [Indexed: 12/28/2022]
Abstract
The ability of stem cells to activate different gene expression programs requires the choreographed assembly of trans-acting factors at enhancers and promoters during cell differentiation. In this study, we show that the proteasome acts on specific regulatory regions in embryonic stem (ES) cells to prevent incorrect transcriptional initiation. Chemical or siRNA-mediated inhibition of proteasome activity results in increased transcription factor and RNA polymerase II binding and leads to activation of cryptic promoters. Analysis of the binding profiles of different proteasome subunits in normal ES cells and following RNAi knockdown of individual subunits provides evidence for a targeted assembly of the 26S proteasome at specific regulatory elements. Our results suggest that the proteasome promotes a dynamic turnover of transcription factor and Pol II binding at tissue-specific gene domains in ES cells, thereby restricting permissive transcriptional activity and keeping the genes in a potentiated state, ready for activation at later stages.
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Affiliation(s)
- Henrietta Szutorisz
- Gene Regulation and Chromatin Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Campus, Du Cane Road, London W12 ONN, UK.
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Acquaah-Mensah GK, Misra V, Biswal S. Ethanol sensitivity: a central role for CREB transcription regulation in the cerebellum. BMC Genomics 2006; 7:308. [PMID: 17147806 PMCID: PMC1698922 DOI: 10.1186/1471-2164-7-308] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Accepted: 12/05/2006] [Indexed: 01/18/2023] Open
Abstract
Background Lowered sensitivity to the effects of ethanol increases the risk of developing alcoholism. Inbred mouse strains have been useful for the study of the genetic basis of various drug addiction-related phenotypes. Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice differentially express a number of genes thought to be implicated in sensitivity to the effects of ethanol. Concomitantly, there is evidence for a mediating role of cAMP/PKA/CREB signalling in aspects of alcoholism modelled in animals. In this report, the extent to which CREB signalling impacts the differential expression of genes in ILS and ISS mouse cerebella is examined. Results A training dataset for Machine Learning (ML) and Exploratory Data Analyses (EDA) was generated from promoter region sequences of a set of genes known to be targets of CREB transcription regulation and a set of genes whose transcription regulations are potentially CREB-independent. For each promoter sequence, a vector of size 132, with elements characterizing nucleotide composition features was generated. Genes whose expressions have been previously determined to be increased in ILS or ISS cerebella were identified, and their CREB regulation status predicted using the ML scheme C4.5. The C4.5 learning scheme was used because, of four ML schemes evaluated, it had the lowest predicted error rate. On an independent evaluation set of 21 genes of known CREB regulation status, C4.5 correctly classified 81% of instances with F-measures of 0.87 and 0.67 respectively for the CREB-regulated and CREB-independent classes. Additionally, six out of eight genes previously determined by two independent microarray platforms to be up-regulated in the ILS or ISS cerebellum were predicted by C4.5 to be transcriptionally regulated by CREB. Furthermore, 64% and 52% of a cross-section of other up-regulated cerebellar genes in ILS and ISS mice, respectively, were deemed to be CREB-regulated. Conclusion These observations collectively suggest that ethanol sensitivity, as it relates to the cerebellum, may be associated with CREB transcription activity.
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Affiliation(s)
- George K Acquaah-Mensah
- Department of Pharmaceutical Sciences, School of Pharmacy-Worcester, Massachusetts College of Pharmacy and Health Sciences, 19 Foster Street, Worcester MA 01608-1715, USA
| | - Vikas Misra
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe St., Baltimore MD 21205, USA
| | - Shyam Biswal
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe St., Baltimore MD 21205, USA
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40
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Kopytova DV, Krasnov AN, Kopantceva MR, Nabirochkina EN, Nikolenko JV, Maksimenko O, Kurshakova MM, Lebedeva LA, Yerokhin MM, Simonova OB, Korochkin LI, Tora L, Georgiev PG, Georgieva SG. Two isoforms of Drosophila TRF2 are involved in embryonic development, premeiotic chromatin condensation, and proper differentiation of germ cells of both sexes. Mol Cell Biol 2006; 26:7492-505. [PMID: 17015475 PMCID: PMC1636870 DOI: 10.1128/mcb.00349-06] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Drosophila TATA box-binding protein (TBP)-related factor 2 (TRF2 or TLF) was shown to control a subset of genes different from that controlled by TBP. Here, we have investigated the structure and functions of the trf2 gene. We demonstrate that it encodes two protein isoforms: the previously described 75-kDa TRF2 and a newly identified 175-kDa version in which the same sequence is preceded by a long N-terminal domain with coiled-coil motifs. Chromatography of Drosophila embryo extracts revealed that the long TRF2 is part of a multiprotein complex also containing ISWI. Both TRF2 forms are detected at the same sites on polytene chromosomes and have the same expression patterns, suggesting that they fulfill similar functions. A study of the manifestations of the trf2 mutation suggests an essential role of TRF2 during embryonic Drosophila development. The trf2 gene is strongly expressed in germ line cells of adult flies. High levels of TRF2 are found in nuclei of primary spermatocytes and trophocytes with intense transcription. In ovaries, TRF2 is present both in actively transcribing nurse cells and in the transcriptionally inactive oocyte nuclei. Moreover, TRF2 is essential for premeiotic chromatin condensation and proper differentiation of germ cells of both sexes.
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Affiliation(s)
- Daria V Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov St. 34/5, Moscow 119334, Russian Federation
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41
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Katzenberger RJ, Marengo MS, Wassarman DA. ATM and ATR pathways signal alternative splicing of Drosophila TAF1 pre-mRNA in response to DNA damage. Mol Cell Biol 2006; 26:9256-67. [PMID: 17030624 PMCID: PMC1698527 DOI: 10.1128/mcb.01125-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alternative pre-mRNA splicing is a major mechanism utilized by eukaryotic organisms to expand their protein-coding capacity. To examine the role of cell signaling in regulating alternative splicing, we analyzed the splicing of the Drosophila melanogaster TAF1 pre-mRNA. TAF1 encodes a subunit of TFIID, which is broadly required for RNA polymerase II transcription. We demonstrate that TAF1 alternative splicing generates four mRNAs, TAF1-1, TAF1-2, TAF1-3, and TAF1-4, of which TAF1-2 and TAF1-4 encode proteins that directly bind DNA through AT hooks. TAF1 alternative splicing was regulated in a tissue-specific manner and in response to DNA damage induced by ionizing radiation or camptothecin. Pharmacological inhibitors and RNA interference were used to demonstrate that ionizing-radiation-induced upregulation of TAF1-3 and TAF1-4 splicing in S2 cells was mediated by the ATM (ataxia-telangiectasia mutated) DNA damage response kinase and checkpoint kinase 2 (CHK2), a known ATM substrate. Similarly, camptothecin-induced upregulation of TAF1-3 and TAF1-4 splicing was mediated by ATR (ATM-RAD3 related) and CHK1. These findings suggest that inducible TAF1 alternative splicing is a mechanism to regulate transcription in response to developmental or DNA damage signals and provide the first evidence that the ATM/CHK2 and ATR/CHK1 signaling pathways control gene expression by regulating alternative splicing.
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Affiliation(s)
- Rebeccah J Katzenberger
- University of Wisconsin School of Medicine and Public Health, Department of Pharmacology, Madison, WI 53706, USA
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42
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Abstract
TATA-binding protein-associated factor 1 (TAF1) is an essential component of the general transcription factor IID (TFIID), which nucleates assembly of the preinitiation complex for transcription by RNA polymerase II. TATA-binding protein and TAF1.TAF2 heterodimers are the only components of TFIID shown to bind specific DNA sequences (the TATA box and initiator, respectively), raising the question of how TFIID localizes to gene promoters that lack binding sites for these proteins. Here we demonstrate that Drosophila TAF1 protein isoforms TAF1-2 and TAF1-4 directly bind DNA independently of TAF2. DNA binding by TAF1 isoforms is mediated by cooperative interactions of two identical AT-hook motifs, one of which is encoded by an alternatively spliced exon. Electrophoretic mobility shift assays revealed that TAF1-2 bound the minor groove of adenine-thymine-rich DNA with a preference for the sequence AAT. Alanine-scanning mutagenesis of the alternatively spliced AT-hook indicated that Lys and Arg residues made essential DNA contacts, whereas Gly and Pro residues within the Arg-Gly-Arg-Pro core sequence were less important for DNA binding, suggesting that AT-hooks are more divergent than previously predicted. TAF1-2 bound with variable affinity to the transcription start site of several Drosophila genes, and binding to the hsp70 promoter was reduced by mutation of a single base pair at the transcription start site. Collectively, these data indicate that AT-hooks serve to anchor TAF1 isoforms to the minor groove of adenine-thymine-rich Drosophila gene promoters and suggest a model in which regulated expression of TAF1 isoforms by alternative splicing contributes to gene-specific transcription.
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Affiliation(s)
- Chad E Metcalf
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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Wierstra I, Alves J. FOXM1c transactivates the human c-myc promoter directly via the two TATA boxes P1 and P2. FEBS J 2006; 273:4645-67. [PMID: 16965535 DOI: 10.1111/j.1742-4658.2006.05468.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
FOXM1c transactivates the c-myc promoter via the P1 and P2 TATA boxes using a new mechanism. Whereas the P1 TATA box TATAATGC requires its sequence context to be FOXM1c responsive, the P2 TATA box TATAAAAG alone is sufficient to confer FOXM1c responsiveness to any minimal promoter. FOXM1c transactivates by binding to the TATA box as well as directly to TATA-binding protein, transcription factor IIB and transcription factor IIA. This new transactivation mechanism is clearly distinguished from the function of FOXM1c as a conventional transcription factor. The central domain of FOXM1c functions as an essential domain for activation via the TATA box, but as an inhibitory domain (retinoblastoma protein-independent transrepression domain and retinoblastoma protein-recruiting negative regulatory domain) for transactivation via conventional FOXM1c-binding sites. Each promoter with the P2 TATA box TATAAAAG is postulated to be transactivated by FOXM1c. This was demonstrated for the promoters of c-fos, hsp70 and histone H2B/a. A database search revealed almost 300 probable FOXM1c target genes, many of which function in proliferation and tumorigenesis. Accordingly, dominant-negative FOXM1c proteins reduced cell growth approximately threefold, demonstrating a proliferation-stimulating function for wild-type FOXM1c.
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Affiliation(s)
- Inken Wierstra
- Institute of Molecular Biology, Medical School Hannover, Germany.
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44
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Boldt ABW, Culpi L, Tsuneto LT, de Souza IR, Kun JFJ, Petzl-Erler ML. Diversity of the MBL2 gene in various Brazilian populations and the case of selection at the mannose-binding lectin locus. Hum Immunol 2006; 67:722-34. [PMID: 17002903 DOI: 10.1016/j.humimm.2006.05.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 05/10/2006] [Indexed: 11/15/2022]
Abstract
The mannose binding lectin (MBL2) polymorphism is responsible for a common immunodeficiency in the human species. There were suggestions that the MBL2 polymorphism has been under balancing selection, based on the high global frequency of alleles generating MBL deficiency and on the worldwide distribution of diseases negatively associated with them. To describe the distribution of MBL2 allelic haplotypes in Brazilian populations and to discuss the evolution of this polymorphism, we analyzed six South Brazilian populations (152 Guarani Amerindian, 239 Kaingang Amerindian, 107 admixed, Brazilian 32 Afro-Brazilian, 202 Euro-Brazilian and 16 Oriental-Brazilian). Eight haplotypes were observed: MBL2*HYPA, LYQA, LYPA, LXPA, LYPB, LYQC, HYPD, and LYPD. In addition, through sequencing of the promoter and exon 1 from Amerindian and Oriental individuals, three new single-nucleotide polymorphisms (SNPs) were found in the MBL2 promoter region in the Kaingang. Analysis of the sequencing data by neutrality tests (Tajima's D and Fu and Li's D* and F*) revealed no deviation from selective neutrality equilibrium in the Guarani and Kaingang. Significant Fay and Wu's H results are explained by the recent gene flow in these populations. Contrarily to previous thoughts, stochastic evolutionary factors seem therefore to have had a predominant role in shaping the MBL2 polymorphism, at least in the Amerindians.
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Affiliation(s)
- A B W Boldt
- Kun Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
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45
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Donati G, Imbriano C, Mantovani R. Dynamic recruitment of transcription factors and epigenetic changes on the ER stress response gene promoters. Nucleic Acids Res 2006; 34:3116-27. [PMID: 16757577 PMCID: PMC1475745 DOI: 10.1093/nar/gkl304] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Response to stresses that alter the function of the endoplasmic reticulum is an important cellular function, which relies on the activation of specific genes. Several transcription factors (TFs) are known to affect this pathway. Using RT-PCR and ChIP assays, we studied the recruitment of promoter-specific TFs, general TFs and epigenetic marks in activated promoters. H3-K4 di- and tri-methylation and H3-K79 di-methylation are present before induction. H3 acetylation is generally high before induction, and H4 acetylation shows a promoter-specific increase. Interestingly, there is a depletion of histone H3 under maximal induction, explaining an apparent decrease of H3-K4 tri-methylation and H3-K79 di-methylation. Pol II is found enriched on some promoters under basal conditions, unlike TBP and p300, which are recruited selectively. Most genes are bound by XBP-1 after induction, some before induction, presumably by the inactive isoform. ATF6 and CHOP associate to largely different set of genes. C/EBPbeta is selective and binding to the CHOP promoter precedes that of XBP-1, ATF6 and CHOP. Finally, one of the ER-stress inducible genes analyzed, HRD1, is not bound by any of these factors. Among the constitutive TFs, NF-Y, but not Sp1, is found on all genes before induction. Intriguingly, siRNA interference of the NF-YB subunit indicates transcriptional impairment of some, but not all genes. These data highlight a previously unappreciated complexity of TFs binding and epigenetic changes, pointing to different TFs-specific pathways within this broad response.
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Affiliation(s)
| | - Carol Imbriano
- Dipartimento di Biologia Animale, Università di Modena e ReggioVia Campi 287/d, 41100 Modena, Italy
| | - Roberto Mantovani
- To whom correspondence should be addressed. Tel: +39 02 50315005; Fax: +39 02 50315044;
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46
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Ong SJ, Hsu HM, Liu HW, Chu CH, Tai JH. Multifarious transcriptional regulation of adhesion protein gene ap65-1 by a novel Myb1 protein in the protozoan parasite Trichomonas vaginalis. EUKARYOTIC CELL 2006; 5:391-9. [PMID: 16467479 PMCID: PMC1405892 DOI: 10.1128/ec.5.2.391-399.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The transcription efficiency of an adhesion protein gene, ap65-1, in Trichomonas vaginalis varies with changes in the iron supply and with the growth stage. In the present study, two Myb recognition elements, MRE-1/MRE-2r and MRE-2f, were found to play antagonistic roles in regulating the iron-inducible activity of an ap65-1 reporter gene. Intriguingly, either of these elements was shown to be sufficient to repress basal activity, but together they were also shown to activate growth-related activity of the reporter gene in iron-depleted cells. A myb1 gene which encodes a 24-kDa protein containing a Myb-like R2R3 DNA binding domain was identified from Southwestern screening of MRE-2f-binding proteins. The Myb1 protein was detected as a major 35-kDa protein which exhibited variations in nuclear concentration with changes in the iron supply. A recombinant Myb1 protein was shown to differentially interact with MRE-1/MRE-2r and MRE-2f in vitro. Overexpression of hemagglutinin-tagged Myb1 in T. vaginalis resulted in repression or activation of ap65-1 transcription in iron-depleted cells at an early and a late stage of cell growth, respectively, while iron-inducible ap65-1 transcription was constitutively repressed. The hemagglutinin-tagged Myb1 protein was found to constantly occupy the chromosomal ap65-1 promoter at a proximal site, but it also selected two more distal sites only at the late growth stage. Together, these observations suggest that Myb1 critically regulates multifarious ap65-1 transcription, possibly via differential selection of multiple promoter sites upon environmental changes.
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Affiliation(s)
- Shiou-Jeng Ong
- Division of Infectious Diseases, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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Kapadia F, Johnson LF. Introduction of an initiator element in the mouse thymidylate synthase promoter alters S phase regulation but has no effect on promoter bidirectionality. J Cell Biochem 2006; 97:599-608. [PMID: 16215980 DOI: 10.1002/jcb.20666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The promoter of the mouse thymidylate synthase (TS) gene lacks a TATAA box and an initiator element, is bidirectional and initiates transcription at multiple start sites across broad initiation windows upstream and downstream of the 30 nt essential promoter region. The TS promoter also plays an essential role in the post-transcription regulation of TS gene expression during the G(1)-S phase transition. The goal of this study was to determine if the addition of a TATAA box or an initiator element would have a significant effect on start-site pattern, promoter bidirectionality and S phase regulation of the TS gene. A TATAA box and/or an initiator element were inserted downstream of the TS essential promoter region, and the modified promoters were used to drive expression of indicator genes. The engineered genes were transfected into cultured mammalian cells, and the effects of the mutations were determined. Addition of the TATAA box and especially the initiator element had a significant effect on the transcription start site pattern, indicating that the elements were functional. Unexpectedly, addition of one or both of these elements had no effect on promoter bidirectionality. However, inclusion of the initiator element led to a significant reduction in S phase regulation of TS mRNA levels, indicating that changes in promoter architecture can perturb normal S phase regulation of TS gene expression.
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Affiliation(s)
- Fehmida Kapadia
- Department of Molecular Genetics and The Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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Copik AJ, Webb MS, Miller AL, Wang Y, Kumar R, Thompson EB. Activation function 1 of glucocorticoid receptor binds TATA-binding protein in vitro and in vivo. Mol Endocrinol 2006; 20:1218-30. [PMID: 16469772 DOI: 10.1210/me.2005-0257] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The mechanism through which the glucocorticoid receptor (GR) stimulates transcription is still unclear, although it is clear that the GR affects assembly of the transcriptional machinery. The binding of the TATA-binding protein (TBP) to the TATA-box is accepted as essential in this process. It is known that the GR can interact in vitro with TBP, but the direct interaction of TBP with GR has not been previously characterized quantitatively and has not been appreciated as an important step in assembling the transcriptional complex. Herein, we demonstrate that the TBP-GR interaction is functionally significant by characterizing the association of TBP and GR in vitro by a combination of techniques and confirming the role of this interaction in vivo. Combined analysis, using native gel electrophoresis, sedimentation equilibrium, and isothermal microcalorimetry titrations, characterize the stoichiometry, affinity, and thermodynamics of the TBP-GR interaction. TBP binds recombinant GR activation function 1 (AF1) with a 1:2 stoichiometry and a dissociation constant in the nanomolar range. In vivo fluorescence resonance energy transfer experiments, using fluorescently labeled TBP and various GR constructs, transiently transfected into CV-1 cells, show GR-TBP interactions, dependent on AF1. AF1-deletion variants showed fluorescence resonance energy transfer efficiencies on the level of coexpressed cyan fluorescent protein and yellow fluorescent protein, indicating that the interaction is dependent on AF1 domain. To demonstrate the functional role of the in vivo GR-TBP interaction, increased amounts of TBP expressed in vivo stimulated expression of GR-driven reporters and endogenous genes, and the effect was also specifically dependent on AF1.
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Affiliation(s)
- Alicja J Copik
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1068, USA
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DeJong J. Basic mechanisms for the control of germ cell gene expression. Gene 2006; 366:39-50. [PMID: 16326034 DOI: 10.1016/j.gene.2005.10.012] [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] [Received: 06/09/2005] [Revised: 09/23/2005] [Accepted: 10/10/2005] [Indexed: 11/17/2022]
Abstract
The patterns of gene expression in spermatocytes and oocytes are quite different from those in somatic cells. The messenger RNAs produced by these cells are not only required to support germ cell development but, in the case of oocytes, they are also used for maturation, fertilization, and early embryogenesis. Recent studies have begun to provide an explanation for how germ-cell-specific programs of gene expression are generated. Part of the answer comes from the observation that germ cells express core promoter-associated regulatory factors that are different from those expressed in somatic cells. These factors supplement or replace their somatic counterparts to direct expression during meiosis and gametogenesis. In addition, germ cell transcription involves the recognition and use of specialized core promoter sequences. Finally, transcription must occur on chromosomal DNA templates that are reorganized into new chromatin-packaging configurations using alternate histone subunits. This article will review recent advances in our understanding of the factors and mechanisms that control transcription in ovary and testis and will discuss models for germ cell gene expression.
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Affiliation(s)
- Jeff DeJong
- Department of Molecular and Cell Biology, University of Texas at Dallas, 2601 N. Floyd Road, Richardson, TX 75080, United States.
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Abstract
In response to various stresses, p53 is rapidly activated and transcriptionally regulates a number of target genes by which p53 modulates a variety of cellular activities. The transcriptional activity of p53 is delicately regulated by a plethora of cellular factors, independently or synergistically, in multiple ways in order to achieve a specific response. This article reviewed the role of the basal transcriptional machinery, co-activators, and co-repressors involved in p53-dependent transcription, and the underlying mechanism by which the p53 transcriptional activity is regulated. We also discussed some potentially interesting questions and future directions in the field.
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Affiliation(s)
- Gang Liu
- Department of Cell Biology, The University of Alabama at Birmingham, 1918 University Boulevard, Birmingham, AL 35294, USA
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