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Xu M, Ren P, Tian J, Xiao L, Hu P, Chen P, Li W, Xue L. dGLYAT modulates Gadd45-mediated JNK activation and cell invasion. Cell Div 2022; 17:4. [PMID: 35933447 PMCID: PMC9357319 DOI: 10.1186/s13008-022-00080-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cell invasion is a crucial step of tumor metastasis, finding new regulators of which offers potential drug targets for cancer therapy. Aberrant GLYAT expression is associated with human cancers, yet its role in cancer remains unknown. This study aims to understand the function and mechanism of Drosophila GLYAT in cell invasion. Results We found that dGLYAT regulates Gadd45-mediated JNK pathway activation and cell invasion. Firstly, loss of dGLYAT suppressed scrib depletion- or Egr overexpression-induced JNK pathway activation and invasive cell migration. Secondary, mRNA-seq analysis identified Gadd45 as a potential transcriptional target of dGLYAT, as depletion of dGLYAT decreased Gadd45 mRNA level. Finally, Gadd45 knockdown suppressed scrib depletion-induced JNK pathway activation and cell invasion. Conclusions These evidences reveal the role of dGLYAT and Gadd45 in JNK-dependent cell invasion, and provide insight for the roles of their human homologs in cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s13008-022-00080-5.
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2
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Jiang Y, Berg MD, Genereaux J, Ahmed K, Duennwald ML, Brandl CJ, Lajoie P. Sfp1 links TORC1 and cell growth regulation to the yeast SAGA‐complex component Tra1 in response to polyQ proteotoxicity. Traffic 2019; 20:267-283. [DOI: 10.1111/tra.12637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Yuwei Jiang
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| | - Matthew D. Berg
- Department of BiochemistryThe University of Western Ontario London Ontario Canada
| | - Julie Genereaux
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
- Department of BiochemistryThe University of Western Ontario London Ontario Canada
| | - Khadija Ahmed
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| | - Martin L. Duennwald
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
- Department of Pathology and Laboratory MedicineThe University of Western Ontario London Ontario Canada
| | | | - Patrick Lajoie
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
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3
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Cai Q, Wang JJ, Fu B, Ying SH, Feng MG. Gcn5-dependent histone H3 acetylation and gene activity is required for the asexual development and virulence of Beauveria bassiana. Environ Microbiol 2018; 20:1484-1497. [PMID: 29417710 DOI: 10.1111/1462-2920.14066] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 12/11/2022]
Abstract
Gcn5 is a core histone acetyltransferase that catalyzes histone H3 acetylation on N-terminal lysine residues in yeasts and was reported to catalyze H3K9/K14 acetylation required for activating asexual development in Aspergillus. Here, we report a localization of Gcn5 ortholog in the nucleus and cytoplasm of Beauveria bassiana, a fungal insect pathogen. Deletion of gcn5 led to hypoacetylated H3 at K9/14/18/27 and 97% reduction in conidiation capacity as well as severe defects in colony growth and conidial thermotolerance. Two master conidiation genes, namely brlA and abaA, were transcriptionally repressed to undetectable level in Δgcn5, but sharply upregulated in wild-type, at the beginning time of conidiation. Based on chromatin immunoprecipitation, both DNA and acetylation levels of the distal and proximal fragments of the brlA promoter bound by acetylated H3K14 alone were upregulated in wild-type, but not in Δgcn5, at the mentioned time. In Δgcn5, normal cuticle infection was abolished while virulence through cuticle-bypassing infection was greatly attenuated, accompanied by drastically reduced activities of putative cuticle-degrading enzymes, retarded dimorphic transition and transcriptional repression of associated genes. These findings unveil a novel mechanism by which Gcn5 activates asexual development pathway by acetylating H3K14 and regulates the virulence-related cellular events in B. bassiana.
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Affiliation(s)
- Qing Cai
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Juan-Juan Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China.,School of Biological Science and Biotechnology, University of Jinan, Jinan, Shandong, 250022, People's Republic of China
| | - Bo Fu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
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4
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Korber P, Barbaric S. The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin. Nucleic Acids Res 2014; 42:10888-902. [PMID: 25190457 PMCID: PMC4176169 DOI: 10.1093/nar/gku784] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chromatin dynamics crucially contributes to gene regulation. Studies of the yeast PHO5 promoter were key to establish this nowadays accepted view and continuously provide mechanistic insight in chromatin remodeling and promoter regulation, both on single locus as well as on systems level. The PHO5 promoter is a context independent chromatin switch module where in the repressed state positioned nucleosomes occlude transcription factor sites such that nucleosome remodeling is a prerequisite for and not consequence of induced gene transcription. This massive chromatin transition from positioned nucleosomes to an extensive hypersensitive site, together with respective transitions at the co-regulated PHO8 and PHO84 promoters, became a prime model for dissecting how remodelers, histone modifiers and chaperones co-operate in nucleosome remodeling upon gene induction. This revealed a surprisingly complex cofactor network at the PHO5 promoter, including five remodeler ATPases (SWI/SNF, RSC, INO80, Isw1, Chd1), and demonstrated for the first time histone eviction in trans as remodeling mode in vivo. Recently, the PHO5 promoter and the whole PHO regulon were harnessed for quantitative analyses and computational modeling of remodeling, transcription factor binding and promoter input-output relations such that this rewarding single-locus model becomes a paradigm also for theoretical and systems approaches to gene regulatory networks.
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Affiliation(s)
- Philipp Korber
- Adolf-Butenandt-Institute, Molecular Biology, University of Munich, Munich 80336, Germany
| | - Slobodan Barbaric
- Faculty of Food Technology and Biotechnology, Laboratory of Biochemistry, University of Zagreb, Zagreb 10000, Croatia
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5
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Ansari SA, Paul E, Sommer S, Lieleg C, He Q, Daly AZ, Rode KA, Barber WT, Ellis LC, LaPorta E, Orzechowski AM, Taylor E, Reeb T, Wong J, Korber P, Morse RH. Mediator, TATA-binding protein, and RNA polymerase II contribute to low histone occupancy at active gene promoters in yeast. J Biol Chem 2014; 289:14981-95. [PMID: 24727477 DOI: 10.1074/jbc.m113.529354] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transcription by RNA polymerase II (Pol II) in eukaryotes requires the Mediator complex, and often involves chromatin remodeling and histone eviction at active promoters. Here we address the role of Mediator in recruitment of the Swi/Snf chromatin remodeling complex and its role, along with components of the preinitiation complex (PIC), in histone eviction at inducible and constitutively active promoters in the budding yeast Saccharomyces cerevisiae. We show that recruitment of the Swi/Snf chromatin remodeling complex to the induced CHA1 promoter, as well as its association with several constitutively active promoters, depends on the Mediator complex but is independent of Mediator at the induced MET2 and MET6 genes. Although transcriptional activation and histone eviction at CHA1 depends on Swi/Snf, Swi/Snf recruitment is not sufficient for histone eviction at the induced CHA1 promoter. Loss of Swi/Snf activity does not affect histone occupancy of several constitutively active promoters; in contrast, higher histone occupancy is seen at these promoters in Mediator and PIC component mutants. We propose that an initial activator-dependent, nucleosome remodeling step allows PIC components to outcompete histones for occupancy of promoter sequences. We also observe reduced promoter association of Mediator and TATA-binding protein in a Pol II (rpb1-1) mutant, indicating mutually cooperative binding of these components of the transcription machinery and indicating that it is the PIC as a whole whose binding results in stable histone eviction.
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Affiliation(s)
- Suraiya A Ansari
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Emily Paul
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Sebastian Sommer
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Corinna Lieleg
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Qiye He
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
| | - Alexandre Z Daly
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Kara A Rode
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Wesley T Barber
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Laura C Ellis
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Erika LaPorta
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
| | - Amanda M Orzechowski
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Emily Taylor
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Tanner Reeb
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Jason Wong
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Philipp Korber
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Randall H Morse
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
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6
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Xin Q, Gong Y, Lv X, Chen G, Liu W. Trichoderma reesei histone acetyltransferase Gcn5 regulates fungal growth, conidiation, and cellulase gene expression. Curr Microbiol 2013; 67:580-9. [PMID: 23748966 DOI: 10.1007/s00284-013-0396-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 04/22/2013] [Indexed: 10/26/2022]
Abstract
Gcn5 is a well-established histone acetyltransferase involved in chromatin modification by catalyzing the acetylation of specific lysine residues within the N-terminal tails of the core histones. To assess the role of chromatin remodeling in the transcriptional response of cellulolytic Trichoderma reesei to the changes of environmental conditions, we identified the T. reesei ortholog of Saccharomyces cerevisiae Gcn5 by sequence alignment and functional analysis. Heterologous expression of TrGcn5 in S. cerevisiae gcn5Δ strain restored the growth defect under nutrient limitation as well as stresses. In contrast, mutant TrGcn5 with site-directed changes of residues critical for Gcn5 histone acetyltransferase activity could not complement the growth defect. The T. reesei gcn5Δ mutant strain displayed a strongly decreased growth rate and dramatic morphological changes including misshapen hyphal cells and abolished conidiation. Moreover, the induced expression of cellulase genes was severely impaired in the gcn5Δ T. reesei with acetylation of K9 and K14 of histone H3 in the cellulase gene promoter dramatically affected in the absence of TrGcn5. The results indicate that TrGcn5 plays a critical role in filamentous growth, morphogenesis, and transcriptional activation of specific genes including cellulase encoding genes.
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Affiliation(s)
- Qi Xin
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
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7
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Flashner BM, Russo ME, Boileau JE, Leong DW, Gallicano GI. Epigenetic factors and autism spectrum disorders. Neuromolecular Med 2013; 15:339-50. [PMID: 23468062 DOI: 10.1007/s12017-013-8222-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/13/2013] [Indexed: 12/28/2022]
Abstract
Autism is a complex neurodevelopmental disorder that has significant phenotypic overlap with several diseases, many of which fall within the broader category of autism spectrum disorders (ASDs). The etiology of the disorder is unclear and seems to involve a complex interplay of polygenic as well as environmental factors. We discuss evidence that suggests that epigenetic dysregulation is highly implicated as a contributing cause of ASDs and autism. Specifically, we examine neurodevelopmental disorders that share significant phenotypic overlap with ASDs and feature the dysregulation of epigenetically modified genes including UBE3A, GABA receptor genes, and RELN. We then look at the dysregulated expression of implicated epigenetic modifiers, namely MeCP2, that yield complex and varied downstream pleiotropic effects. Finally, we examine epigenetically mediated parent-of-origin effects through which paternal gene expression dominates that of maternal contributing to contrasting phenotypes implicated in ASDs. Such preliminary evidence suggests that elucidating the complex role of epigenetic regulations involved in ASDs could prove vital in furthering our understanding of the complex etiology of autism and ASDs.
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Affiliation(s)
- Bess M Flashner
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057, USA
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8
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Pedersen JM, Fredsoe J, Roedgaard M, Andreasen L, Mundbjerg K, Kruhøffer M, Brinch M, Schierup MH, Bjergbaek L, Andersen AH. DNA Topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae. PLoS Genet 2012; 8:e1003128. [PMID: 23284296 PMCID: PMC3527272 DOI: 10.1371/journal.pgen.1003128] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/15/2012] [Indexed: 11/19/2022] Open
Abstract
To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. These genes are characterized by high transcriptional plasticity, chromatin regulation, TATA box presence, and enrichment of a nucleosome at a critical position in the promoter region, in line with a repressible/inducible mode of regulation. Single-gene studies with a range of genes belonging to this group demonstrate that topoisomerases play an important role during activation of these genes. Subsequent in-depth analysis of the inducible PHO5 gene reveals that topoisomerases are essential for binding of the Pho4p transcription factor to the PHO5 promoter, which is required for promoter nucleosome removal during activation. In contrast, topoisomerases are dispensable for constitutive transcription initiation and elongation of PHO5, as well as the nuclear entrance of Pho4p. Finally, we provide evidence that topoisomerases are required to maintain the PHO5 promoter in a superhelical state, which is competent for proper activation. In conclusion, our results reveal a hitherto unknown function of topoisomerases during transcriptional activation of genes with a repressible/inducible mode of regulation. Gene expression is controlled at many different levels to assure appropriate responses to internal and environmental changes. The effect of topological changes in the DNA double helix on gene transcription in vivo is a poorly understood factor in the regulation of eukaryotic gene expression. Topological changes are constantly generated by DNA tracking processes and may influence gene expression if not constantly removed by DNA topoisomerases. For decades it has been generally accepted that these enzymes regulate transcription by removing excess topological strain generated during tracking of the RNA polymerase, but we still lack a more holistic view of how these enzymes influence gene transcription in their native environment. Here, we examine both global and gene-specific changes in transcription following lack of DNA topoisomerases in budding yeast. Taken together, our findings show that topoisomerases play a profound role during transcriptional activation of genes with a repressible/inducible mode of regulation. For the PHO5 gene, which is investigated in more detail, we demonstrate that topoisomerases are required for binding of a transcription factor, which is crucial for promoter opening during PHO5 activation. Our data thus suggest that inducible gene promoters are highly sensitive to changes in DNA superhelicity.
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Affiliation(s)
- Jakob Madsen Pedersen
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jacob Fredsoe
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Morten Roedgaard
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Lotte Andreasen
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | - Marie Brinch
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mikkel Heide Schierup
- Bioinformatics Research Center, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Lotte Bjergbaek
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Anni Hangaard Andersen
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- * E-mail:
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9
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Abstract
Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field.
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10
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Lanza AM, Blazeck JJ, Crook NC, Alper HS. Linking yeast Gcn5p catalytic function and gene regulation using a quantitative, graded dominant mutant approach. PLoS One 2012; 7:e36193. [PMID: 22558379 PMCID: PMC3338614 DOI: 10.1371/journal.pone.0036193] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/03/2012] [Indexed: 11/18/2022] Open
Abstract
Establishing causative links between protein functional domains and global gene regulation is critical for advancements in genetics, biotechnology, disease treatment, and systems biology. This task is challenging for multifunctional proteins when relying on traditional approaches such as gene deletions since they remove all domains simultaneously. Here, we describe a novel approach to extract quantitative, causative links by modulating the expression of a dominant mutant allele to create a function-specific competitive inhibition. Using the yeast histone acetyltransferase Gcn5p as a case study, we demonstrate the utility of this approach and (1) find evidence that Gcn5p is more involved in cell-wide gene repression, instead of the accepted gene activation associated with HATs, (2) identify previously unknown gene targets and interactions for Gcn5p-based acetylation, (3) quantify the strength of some Gcn5p-DNA associations, (4) demonstrate that this approach can be used to correctly identify canonical chromatin modifications, (5) establish the role of acetyltransferase activity on synthetic lethal interactions, and (6) identify new functional classes of genes regulated by Gcn5p acetyltransferase activity—all six of these major conclusions were unattainable by using standard gene knockout studies alone. We recommend that a graded dominant mutant approach be utilized in conjunction with a traditional knockout to study multifunctional proteins and generate higher-resolution data that more accurately probes protein domain function and influence.
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Affiliation(s)
- Amanda M. Lanza
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - John J. Blazeck
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - Nathan C. Crook
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - Hal S. Alper
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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11
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Genetic evidence links the ASTRA protein chaperone component Tti2 to the SAGA transcription factor Tra1. Genetics 2012; 191:765-80. [PMID: 22505622 PMCID: PMC3389973 DOI: 10.1534/genetics.112.140459] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tra1 is a 3744-residue component of the Saccharomyces cerevisiae SAGA, NuA4, and ASTRA complexes. Tra1 contains essential C-terminal PI3K and FATC domains, but unlike other PIKK (phosphoinositide three-kinase–related kinase) family members, lacks kinase activity. To analyze functions of the FATC domain, we selected for suppressors of tra1-F3744A, an allele that results in slow growth under numerous conditions of stress. Two alleles of TTI2, tti2-F328S and tti2-I336F, acted in a partially dominant fashion to suppress the growth-related phenotypes associated with tra1-F3744A as well as its resulting defects in transcription. tti2-F328S suppressed an additional FATC domain mutation (tra1-L3733A), but not a mutation in the PI3K domain or deletions of SAGA or NuA4 components. We find eGFP-tagged Tti2 distributed throughout the cell. Tti2 is a component of the ASTRA complex, and in mammalian cells associates with molecular chaperones in complex with Tti1 and Tel2. Consistent with this finding, Tra1 levels are reduced in a strain with a temperature-sensitive allele of tel2. Further agreeing with a possible role for Tti2 in the folding or stabilization of Tra1, tra1-F3744A was mislocalized to the cytoplasm, particularly under conditions of stress. Since an intragenic mutation of tra1-R3590I also suppressed F3744A, we propose that Tti2 is required for the folding/stability of the C-terminal FATC and PI3K domains of Tra1 into their functionally active form.
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12
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Sambuk EV, Fizikova AY, Savinov VA, Padkina MV. Acid phosphatases of budding yeast as a model of choice for transcription regulation research. Enzyme Res 2011; 2011:356093. [PMID: 21785706 PMCID: PMC3137970 DOI: 10.4061/2011/356093] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/26/2011] [Indexed: 11/20/2022] Open
Abstract
Acid phosphatases of budding yeast have been studied for more than forty years. This paper covers biochemical characteristics of acid phosphatases and different aspects in expression regulation of eukaryotic genes, which were researched using acid phosphatases model. A special focus is devoted to cyclin-dependent kinase Pho85p, a negative transcriptional regulator, and its role in maintaining mitochondrial genome stability and to pleiotropic effects of pho85 mutations.
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Affiliation(s)
- Elena V Sambuk
- Genetics and Breeding Department, Biology and Soil Sciences Faculty, Saint Petersburg State University, Universitetskaya emb. 7-9, Saint Petersburg 199034, Russia
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13
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Histone H3 lysine 4 hypermethylation prevents aberrant nucleosome remodeling at the PHO5 promoter. Mol Cell Biol 2011; 31:3171-81. [PMID: 21646424 DOI: 10.1128/mcb.05017-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Recent studies have highlighted the histone H3K4 methylation (H3K4me)-dependent transcriptional repression in Saccharomyces cerevisiae; however, the underlying mechanism remains inexplicit. Here, we report that H3K4me inhibits the basal PHO5 transcription under high-phosphate conditions by suppressing nucleosome disassembly at the promoter. We found that derepression of the PHO5 promoter by SET1 deletion resulted in a labile chromatin structure, allowing more binding of RNA polymerase II (Pol II) but not the transactivators Pho2 and Pho4. We further showed that Pho23 and Cti6, two plant homeodomain (PHD)-containing proteins, cooperatively anchored the large Rpd3 (Rpd3L) complex to the H3K4-methylated PHO5 promoter. The deacetylation activity of Rpd3 on histone H3 was required for the function of Set1 at the PHO5 promoter. Taken together, our data suggest that Set1-mediated H3K4me suppresses nucleosome remodeling at the PHO5 promoter so as to reduce basal transcription of PHO5 under repressive conditions. We propose that the restriction of aberrant nucleosome remodeling contributes to strict control of gene transcription by the transactivators.
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Kimura T, Okumura F, Onodera A, Nakanishi T, Itoh N, Isobe M. Chromium (VI) inhibits mouse metallothionein-I gene transcription by modifying the transcription potential of the co-activator p300. J Toxicol Sci 2011; 36:173-80. [PMID: 21467744 DOI: 10.2131/jts.36.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The production of the heavy metal-binding proteins, the metallothioneins (MTs), is induced by heavy metals such as Zn, Cd, and Hg. MTs maintain Zn homeostasis and attenuate heavy metal-induced cytotoxicity by sequestering these metals and lowering their intracellular concentrations. Previously, we had reported that Zn induced the formation of a co-activator complex containing metal response element-binding transcription factor-1 (MTF-1) and the histone acetyltransferase (HAT), p300, which plays an essential role in the activation of MT-1 transcription. In addition, we had shown that Cr(VI) inhibits Zn-induced MT-1 transcription by preventing the Zn-dependent formation of the MTF-1-p300 complex. In the current study, we have shown that the inhibition by Cr(VI) was partially overcome by the overexpression of p300 or MTF-1 in an MT-I promoter-driven luciferase reporter assay system and have used real-time RT-PCR to determine MT-I mRNA levels. It has been reported that Cr(VI) inhibits CYP1A1 transcription by crosslinking histone deacetylase (HDAC) to the promoter. The crosslink inhibits the recruitment of p300 to the MT-1 promoter and blocks HAT-dependent transactivation by p300. However, our results demonstrate that trichostatin A, an HDAC inhibitor, could not block the inhibitory effects of Cr(VI) on MT-1 transcription and that there were no significant differences in the in vitro inhibitory effects of Cr(VI), Cr(III), and Zn on p300 HAT activity. This suggests that the inhibitory effects of Cr(VI) on MT-I transcription may be due to its effects on the HAT-independent transactivation ability rather than the HAT-dependent, HDAC release-related transactivation ability of p300.
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Affiliation(s)
- Tomoki Kimura
- Department of Toxicology, Faculty of Pharmaceutical Sciences, Setsunan University, Japan.
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Mao C, Brown CR, Falkovskaia E, Dong S, Hrabeta-Robinson E, Wenger L, Boeger H. Quantitative analysis of the transcription control mechanism. Mol Syst Biol 2011; 6:431. [PMID: 21081924 PMCID: PMC3010110 DOI: 10.1038/msb.2010.83] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 09/27/2010] [Indexed: 01/01/2023] Open
Abstract
Activated PHO5 promoter chromatin at steady state represents a statistical ensemble of distinct structures. The extent of promoter nucleosome loss depends on the strength of the transcriptional activator of PHO5, indicative of continuous disassembly and reassembly of nucleosomes at the induced promoter. PHO5 promoter nucleosome loss and expression are exponentially related, pointing at two or more steps of the expression process that are activator controlled. The intrinsic noise profile of PHO5 expression permits quantitative distinction between alternative regulatory architectures. The assumption of two activator-controlled steps, promoter nucleosome removal and assembly of the transcription machinery, is necessary and sufficient to account for the quantitative relationship between PHO5 expression, intrinsic noise, and promoter nucleosome loss.
The search for factors that interact with transcriptional activators has provided clues to the possible mechanisms of transcriptional regulation. However, the promiscuity of activator interactions has supported alternative regulatory hypotheses whose relative likelihood could not be assessed. A possible solution to the problem is suggested by recent theoretical work showing that the regulatory architecture of the gene expression process is reflected in the magnitude and frequency spectrum of steady-state fluctuations in gene expression (intrinsic noise). In this study, we analyzed promoter chromatin structure and the magnitude of intrinsic noise over a wide range of expression values for the PHO5 gene of yeast. We show that the relationship between gene expression and promoter nucleosome loss is exponential rather than linear, suggesting activator control of at least two steps of the expression process. Interpretation of our data with regard to a stochastic model of chromatin remodeling and gene expression allowed us to quantitatively distinguish between competing regulatory hypotheses, demonstrating the value of noise measurements for analysis of the gene regulatory mechanism. We show that the assumption of two activator-controlled steps, nucleosome removal and assembly of the transcription machinery, is necessary and sufficient to account for the quantitative relationship between our experimental observables. Gene transcription requires a sequence of promoter state transitions, including chromatin remodeling, assembly of the transcription machinery, and clearance of the promoter by RNA polymerase. The rate-limiting steps in this sequence are regulated by transcriptional activators that bind at specific promoter elements. As the transition kinetics of individual promoters cannot be observed, the identity of the activator-controlled steps has remained a matter of speculation. In this study, we investigated promoter chromatin structure, and the intrinsic noise of expression over a wide range of expression values for the PHO5 gene of yeast. Interpretation of our results with regard to a stochastic model of promoter chromatin remodeling and gene expression suggests that the regulatory architecture of the gene expression process is measurably reflected in its intrinsic noise profile. Our chromatin structure and noise analyses indicate that the activator of PHO5 transcription stimulates the rates of promoter nucleosome disassembly, and assembly of the transcription machinery after nucleosome removal, but no other rates of the expression process.
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Affiliation(s)
- Changhui Mao
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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16
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Naguleswaran A, Elias EV, McClintick J, Edenberg HJ, Sullivan WJ. Toxoplasma gondii lysine acetyltransferase GCN5-A functions in the cellular response to alkaline stress and expression of cyst genes. PLoS Pathog 2010; 6:e1001232. [PMID: 21179246 PMCID: PMC3003489 DOI: 10.1371/journal.ppat.1001232] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 11/16/2010] [Indexed: 12/17/2022] Open
Abstract
Parasitic protozoa such as the apicomplexan Toxoplasma gondii progress through their life cycle in response to stimuli in the environment or host organism. Very little is known about how proliferating tachyzoites reprogram their expressed genome in response to stresses that prompt development into latent bradyzoite cysts. We have previously linked histone acetylation with the expression of stage-specific genes, but the factors involved remain to be determined. We sought to determine if GCN5, which operates as a transcriptional co-activator by virtue of its histone acetyltransferase (HAT) activity, contributed to stress-induced changes in gene expression in Toxoplasma. In contrast to other lower eukaryotes, Toxoplasma has duplicated its GCN5 lysine acetyltransferase (KAT). Disruption of the gene encoding for TgGCN5-A in type I RH strain did not produce a severe phenotype under normal culture conditions, but here we show that the TgGCN5-A null mutant is deficient in responding to alkaline pH, a common stress used to induce bradyzoite differentiation in vitro. We performed a genome-wide analysis of the Toxoplasma transcriptional response to alkaline pH stress, finding that parasites deleted for TgGCN5-A fail to up-regulate 74% of the stress response genes that are induced 2-fold or more in wild-type. Using chromatin immunoprecipitation, we verify an enrichment of TgGCN5-A at the upstream regions of genes activated by alkaline pH exposure. The TgGCN5-A knockout is also incapable of up-regulating key marker genes expressed during development of the latent cyst form, and is impaired in its ability to recover from alkaline stress. Complementation of the TgGCN5-A knockout restores the expression of these stress-induced genes and reverses the stress recovery defect. These results establish TgGCN5-A as a major contributor to the alkaline stress response in RH strain Toxoplasma. Protozoan parasites cause significant disease in humans and livestock, and many of our current therapies have serious side effects or are being rendered useless due to the development of drug resistance. These parasites typically have complex life cycles involving multiple hosts and some, like Toxoplasma gondii, have the ability to remain in the host for life as a latent tissue cyst. Toxoplasma is one of the most successful parasites on Earth because the ability to develop into a tissue cyst greatly facilitates transmission through carnivores. Cyst formation also is responsible for recrudescent infection in immunocompromised patients. The conversion of Toxoplasma from its replicating cell to the cyst is triggered by stress, but we have little understanding of how the parasite stress response functions. In this study, we identify the genes involved in Toxoplasma's response to alkaline stress, which is a known trigger of cyst development. We also establish that a lysine acetyltransferase enzyme called TgGCN5-A is required for type I RH strain Toxoplasma to respond normally to alkaline stress. Parasites lacking TgGCN5-A are no longer capable of activating genes induced during cyst formation triggered by alkaline pH.
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Affiliation(s)
- Arunasalam Naguleswaran
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Eliana V. Elias
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Jeanette McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Howard J. Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - William J. Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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17
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Li L, Zhu J, Tian J, Liu X, Feng C. A role for Gcn5 in cardiomyocyte differentiation of rat mesenchymal stem cells. Mol Cell Biochem 2010; 345:309-16. [PMID: 20835911 DOI: 10.1007/s11010-010-0586-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 08/28/2010] [Indexed: 01/28/2023]
Abstract
MSCs possess the capacity of self-renewal and potential of differentiation into various kinds of specialized tissue cells including myocardiocytes. From self-renewing to oriented differentiation, chromatin is remodeled into heritable states that allow activation or maintain the repression of regulatory genes, which means specific genes in self-renewing switched off and specific genes in oriented differentiation activated (Bernstein et al. Cell 125:315-326, 2006). These epigenetic states are established and controlled largely by specific patterns of histone posttranslational modifications, in particular, histone acetylation (Li Nat Rev Genet 3:662-673, 2002). In cardiomyocyte differentiation of rat MSCs, we focused on Gcn5, which linked a known transcriptional coactivator with catalytic histone acetyltransferase activity (Brownell et al. Cell 84:843-851, 1996). To clarify participatory in vivo role of Gcn5, using an RNA interference (RNAi) strategy employing shRNA to specifically knockdown Gcn5 expression in MSCs, we found that HAT activity altered dynamically depended on the inhibition of Gcn5 during MSCs differentiation. Chromatin immunoprecipitation (ChIP) assay showed the increased binding of acetyl histone H3 to the early cardiomyocyte-specific genes GATA4 and NKx2.5 promoters in cardiomyocyte differentiation of MSCs by 5-azacytidine inducing, whereas the decreased binding with lower Gcn5 expression. Cell ultrastructure analysis revealed that MSCs induced by 5-azacytidine possess morphological characteristics of cardiomyocyte cells. The shape of MSCs transfected by Gcn5 RNAi was similar to normal MSCs, but the chromatin showed heavy electron-density and a hard-packed structure. This intermediate state of chromatin may be an inactive part of MSCs differentiation. These results demonstrate that Gcn5, possessing acetyltransferase activity, is involved in regulating chromatin configuration around GATA4 and NKx2.5 in cardiomyocyte differentiation of rat MSCs by changing the level of histone acetylation. HAT activity depending on Gcn5 is important in differentiation of MSCs into cardiomyocytes as a consequence of the remodeling of the chromatin configuration caused by modification of histone H3.
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Affiliation(s)
- Li Li
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi-An Men St., West District, 100034, Beijing, People's Republic of China.
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18
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Ertel F, Dirac-Svejstrup AB, Hertel CB, Blaschke D, Svejstrup JQ, Korber P. In vitro reconstitution of PHO5 promoter chromatin remodeling points to a role for activator-nucleosome competition in vivo. Mol Cell Biol 2010; 30:4060-76. [PMID: 20566699 PMCID: PMC2916437 DOI: 10.1128/mcb.01399-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/01/2009] [Accepted: 06/09/2010] [Indexed: 11/20/2022] Open
Abstract
The yeast PHO5 promoter is a classical model for studying the role of chromatin in gene regulation. To enable biochemical dissection of the mechanism leading to PHO5 activation, we reconstituted the process in vitro. Positioned nucleosomes corresponding to the repressed PHO5 promoter state were assembled using a yeast extract-based in vitro system. Addition of the transactivator Pho4 yielded an extensive DNase I-hypersensitive site resembling induced PHO5 promoter chromatin. Importantly, this remodeling was energy dependent. In contrast, little or no chromatin remodeling was detected at the PHO8 or PHO84 promoter in this in vitro system. Only the PHO5 promoter harbors a high-affinity intranucleosomal Pho4 binding site (UASp) where Pho4 binding can compete with nucleosome formation, prompting us to test the importance of such competition for chromatin remodeling by analysis of UASp mutants in vivo. Indeed, the intranucleosomal location of the UASp element was critical, but not essential, for complete remodeling at the PHO5 promoter in vivo. Further, binding of just the Gal4 DNA binding domain to an intranucleosomal site could increase PHO5 promoter opening. These data establish an auxiliary role for DNA binding competition between Pho4 and histones in PHO5 promoter chromatin remodeling in vivo.
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Affiliation(s)
- Franziska Ertel
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - A. Barbara Dirac-Svejstrup
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Christina Bech Hertel
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Dorothea Blaschke
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Jesper Q. Svejstrup
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Philipp Korber
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
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19
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Abstract
The budding yeast Gcn5p is a prototypic histone acetyltransferase controlling transcription of diverse genes. Here we show that Gcn5p is itself regulated by Snf1p and Spt3p. Snf1p likely controls Gcn5p via direct interaction. Mutating four residues in the Gcn5p catalytic domain, T203, S204, T211, and Y212 (TSTY), phenocopies snf1 null cells, including Gcn5p hypophosphorylation, hypoacetylation at the HIS3 promoter, and transcriptional defects of the HIS3 gene. However, overexpressing Snf1p suppresses the above phenotypes associated with the phosphodeficient TSTY mutant, suggesting that it is the interaction with Snf1p important for Gcn5p to activate HIS3. A likely mechanism by which Snf1p potentiates Gcn5p function is to antagonize Spt3p, because the HIS3 expression defects caused by snf1 knockout, or by the TSTY gcn5 mutations, can be suppressed by deleting SPT3. In vitro, Spt3p binds Gcn5p, but the interaction is drastically enhanced by the TSTY mutations, indicating that a stabilized Spt3p-Gcn5p interaction may be an underlying cause for the aforementioned HIS3 transcriptional defects. These results suggest that Gcn5p is a target regulated by the competing actions of Snf1p and Spt3p.
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20
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Ugrinova I, Pashev IG, Pasheva EA. Nucleosome binding properties and Co-remodeling activities of native and in vivo acetylated HMGB-1 and HMGB-2 proteins. Biochemistry 2009; 48:6502-7. [PMID: 19522541 DOI: 10.1021/bi9004304] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The participation of HMGB-1 and -2 proteins in chromatin remodeling is investigated. Here, the ability of these proteins and their posttranslationally acetylated forms to affect SWI/SNF and RSC-dependent nucleosome mobilization was studied. Both proteins assisted nucleosome sliding induced by the two remodelers. Following acetylation, these proteins acquire the ability to bind to core particles, a property that has not yet been documented with parental proteins. We further report that compared to the nonmodified proteins, acetylated HMGB-1 and -2 exhibited both stronger binding to linker DNA-containing nucleosomes and a higher co-remodeling activity. Acetylation of HMGB-1 and -2 proteins enhanced binding of SWI/SNF to the nucleosome but did not affect its ATPase activity.
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Affiliation(s)
- Iva Ugrinova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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21
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Abstract
Activated transcription in eukaryotes requires the aid of numerous co-factors to overcome the physical barriers chromatin poses to activation, bridge the gap between activators and polymerase, and ensure appropriate regulation. S. cerevisiae has long been a model organism for studying the role of co-activators in the steps leading up to gene activation. Detailed studies on the recruitment of these co-activators have been carried out for more than a dozen promoters. Taking a step back to survey these results, however, suggests that there are few generalizations that could be used to guide future studies of uncharacterized promoters.
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Affiliation(s)
- Rhiannon Biddick
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
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22
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Boeger H, Griesenbeck J, Kornberg RD. Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 2008; 133:716-26. [PMID: 18485878 DOI: 10.1016/j.cell.2008.02.051] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 01/13/2008] [Accepted: 02/29/2008] [Indexed: 11/24/2022]
Abstract
The rate-limiting step of transcriptional activation in eukaryotes, and thus the critical point for gene regulation, is unknown. Combining biochemical analyses of the chromatin transition at the transcriptionally induced PHO5 promoter in yeast with modeling based on a small number of simple assumptions, we demonstrate that random removal and reformation of promoter nucleosomes can account for stochastic and kinetic properties of PHO5 expression. Our analysis suggests that the disassembly of promoter nucleosomes is rate limiting for PHO5 expression, and supports a model for the underlying mechanism of promoter chromatin remodeling, which appears to conserve a single nucleosome on the promoter at all times.
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Affiliation(s)
- Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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23
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Brettingham-Moore KH, Sprod OR, Chen X, Oakford P, Shannon MF, Holloway AF. Determinants of a transcriptionally competent environment at the GM-CSF promoter. Nucleic Acids Res 2008; 36:2639-53. [PMID: 18344520 PMCID: PMC2377420 DOI: 10.1093/nar/gkn117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Granulocyte macrophage-colony stimulating factor (GM-CSF) is produced by T cells, but not B cells, in response to immune signals. GM-CSF gene activation in response to T-cell stimulation requires remodelling of chromatin associated with the gene promoter, and these changes do not occur in B cells. While the CpG methylation status of the murine GM-CSF promoter shows no correlation with the ability of the gene to respond to activation, we find that the basal chromatin environment of the gene promoter influences its ability to respond to immune signals. In unstimulated T cells but not B cells, the GM-CSF promoter is selectively marked by enrichment of histone acetylation, and association of the chromatin-remodelling protein BRG1. BRG1 is removed from the promoter upon activation concomitant with histone depletion and BRG1 is required for efficient chromatin remodelling and transcription. Increasing histone acetylation at the promoter in T cells is paralleled by increased BRG1 recruitment, resulting in more rapid chromatin remodelling, and an associated increase in GM-CSF mRNA levels. Furthermore, increasing histone acetylation in B cells removes the block in chromatin remodelling and transcriptional activation of the GM-CSF gene. These data are consistent with a model in which histone hyperacetylation and BRG1 enrichment at the GM-CSF promoter, generate a chromatin environment competent to respond to immune signals resulting in gene activation.
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Affiliation(s)
- K H Brettingham-Moore
- Menzies Research Institute, University of Tasmania, Private Bag 58, Hobart 7001, Tasmania, Australia
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24
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Zou Y, Wu J, Giannone RJ, Boucher L, Du H, Huang Y, Johnson DK, Liu Y, Wang Y. Nucleophosmin/B23 negatively regulates GCN5-dependent histone acetylation and transactivation. J Biol Chem 2007; 283:5728-37. [PMID: 18165222 DOI: 10.1074/jbc.m709932200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleophosmin/B23 is a multifunctional phosphoprotein that is overexpressed in cancer cells and has been shown to be involved in both positive and negative regulation of transcription. In this study, we first identified GCN5 acetyltransferase as a B23-interacting protein by mass spectrometry, which was then confirmed by in vivo co-immunoprecipitation. An in vitro assay demonstrated that B23 bound the PCAF-N domain of GCN5 and inhibited GCN5-mediated acetylation of both free and mononucleosomal histones, probably through interfering with GCN5 and masking histones from being acetylated. Mitotic B23 exhibited higher inhibitory activity on GCN5-mediated histone acetylation than interphase B23. Immunodepletion experiments of mitotic extracts revealed that phosphorylation of B23 at Thr 199 enhanced the inhibition of GCN5-mediated histone acetylation. Moreover, luciferase reporter and microarray analyses suggested that B23 attenuated GCN5-mediated transactivation in vivo. Taken together, our studies suggest a molecular mechanism of B23 in the mitotic inhibition of GCN5-mediated histone acetylation and transactivation.
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Affiliation(s)
- Yonglong Zou
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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25
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Jiang L, Smith JN, Anderson SL, Ma P, Mizzen CA, Kelleher NL. Global assessment of combinatorial post-translational modification of core histones in yeast using contemporary mass spectrometry. LYS4 trimethylation correlates with degree of acetylation on the same H3 tail. J Biol Chem 2007; 282:27923-34. [PMID: 17652096 DOI: 10.1074/jbc.m704194200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A global view of all core histones in yeast is provided by tandem mass spectrometry of intact histones H2A, H2B, H4, and H3. This allowed detailed characterization of >50 distinct histone forms and their semiquantitative assessment in the deletion mutants gcn5Delta, spt7Delta, ahc1Delta, and rtg2Delta, affecting the chromatin remodeling complexes SAGA, SLIK, and ADA. The "top down" mass spectrometry approach detected dramatic decreases in acetylation on H3 and H2B in gcn5Delta cells versus wild type. For H3 in wild type cells, tandem mass spectrometry revealed a direct correlation between increases of Lys(4) trimethylation and the 0, 1, 2, and 3 acetylation states of histone H3. The results show a wide swing from 10 to 80% Lys(4) trimethylation levels on those H3 tails harboring 0 or 3 acetylations, respectively. Reciprocity between these chromatin marks was apparent, since gcn5Delta cells showed a 30% decrease in trimethylation levels on Lys(4) in addition to a decrease of acetylation levels on H3 in bulk chromatin. Deletion of Set1, the Lys(4) methyltransferase, was associated with the linked disappearance of both Lys(4) methylation and Lys(14) and Lys(18) or Lys(23) acetylation on H3. In sum, we have defined the "basis set" of histone forms present in yeast chromatin using a current mass spectrometric approach that both quickly profiles global changes and directly probes the connectivity of modifications on the same histone.
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Affiliation(s)
- Lihua Jiang
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
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26
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Barbaric S, Luckenbach T, Schmid A, Blaschke D, Hörz W, Korber P. Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo. J Biol Chem 2007; 282:27610-21. [PMID: 17631505 DOI: 10.1074/jbc.m700623200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Induction of the yeast PHO5 and PHO8 genes leads to a prominent chromatin transition at their promoter regions as a prerequisite for transcription activation. Although induction of PHO8 is strictly dependent on Snf2 and Gcn5, there is no chromatin remodeler identified so far that would be essential for the opening of PHO5 promoter chromatin. Nonetheless, the nonessential but significant involvement of cofactors can be identified if the chromatin opening kinetics are delayed in the respective mutants. Using this approach, we have tested individually all 15 viable Snf2 type ATPase deletion mutants for their effect on PHO5 promoter induction and opening. Only the absence of Snf2 and Ino80 showed a strong delay in chromatin remodeling kinetics. The snf2 ino80 double mutation had a synthetic kinetic effect but eventually still allowed strong PHO5 induction. The same was true for the snf2 gcn5 and ino80 gcn5 double mutants. This strongly suggests a complex network of redundant and mutually independent parallel pathways that lead to the remodeling of the PHO5 promoter. Further, chromatin remodeling kinetics at a transcriptionally inactive TATA box-mutated PHO5 promoter were affected neither under wild type conditions nor in the absence of Snf2 or Gcn5. This demonstrates the complete independence of promoter chromatin opening from downstream PHO5 transcription processes. Finally, the histone variant Htz1 has no prominent role for the kinetics of PHO5 promoter chromatin remodeling.
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27
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Mutiu AI, Hoke SMT, Genereaux J, Liang G, Brandl CJ. The role of histone ubiquitylation and deubiquitylation in gene expression as determined by the analysis of an HTB1(K123R) Saccharomyces cerevisiae strain. Mol Genet Genomics 2007; 277:491-506. [PMID: 17447102 DOI: 10.1007/s00438-007-0212-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 01/13/2007] [Indexed: 10/23/2022]
Abstract
In Saccharomyces cerevisiae histone H2B is ubiquitylated at lysine 123 in a process requiring the E2-ubiquitin conjugase, Rad6. We have analyzed gene expression in a strain containing a variant of histone H2B with lysine 123 converted to arginine to address the mechanisms by which ubiquitylation and deubiquitylation of histone H2B affect gene expression. The SAGA complex component, Ubp8, is one of two proteases that remove the ubiquitin moiety at lysine 123. We show that changes in gene expression observed upon deletion of ubp8 are suppressed by htb1 ( K123R ), which provides genetic evidence that Ubp8 alters gene expression through deubiquitylation of histone H2B. Microarray analyses of the htb1 ( K123R ) strain show that loss of histone ubiquitylation results in a twofold or greater change in expression of approximately 1.5% of the protein coding genes with approximately 75% of these increasing. For genes in which ubiquitylation represses expression, ubiquitylation principally acts through its effects on histone methylation. In contrast, decreased expression of the CWP1 gene was not paralleled by deletions of methyltransferase components and is thus likely independent of methylation. Finally, by comparing gene expression changes in the htb1 ( K123R ) strain with those in a strain deleted for rad6, we conclude that lysine 123 affects transcription primarily because of it being a site of ubiquitylation.
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Affiliation(s)
- A Irina Mutiu
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
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28
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Morris SA, Rao B, Garcia BA, Hake SB, Diaz RL, Shabanowitz J, Hunt DF, Allis CD, Lieb JD, Strahl BD. Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification. J Biol Chem 2006; 282:7632-40. [PMID: 17189264 PMCID: PMC2811852 DOI: 10.1074/jbc.m607909200] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Histone lysine acetylation is a major mechanism by which cells regulate the structure and function of chromatin, and new sites of acetylation continue to be discovered. Here we identify and characterize histone H3K36 acetylation (H3K36ac). By mass spectrometric analyses of H3 purified from Tetrahymena thermophila and Saccharomyces cerevisiae (yeast), we find that H3K36 can be acetylated or methylated. Using an antibody specific to H3K36ac, we show that this modification is conserved in mammals. In yeast, genome-wide ChIP-chip experiments show that H3K36ac is localized predominantly to the promoters of RNA polymerase II-transcribed genes, a pattern inversely related to that of H3K36 methylation. The pattern of H3K36ac localization is similar to that of other sites of H3 acetylation, including H3K9ac and H3K14ac. Using histone acetyltransferase complexes purified from yeast, we show that the Gcn5-containing SAGA complex that regulates transcription specifically acetylates H3K36 in vitro. Deletion of GCN5 completely abolishes H3K36ac in vivo. These data expand our knowledge of the genomic targets of Gcn5, show H3K36ac is highly conserved, and raise the intriguing possibility that the transition between H3K36ac and H3K36me acts as an "acetyl/methyl switch" governing chromatin function along transcription units.
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Affiliation(s)
- Stephanie A Morris
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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29
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Imoberdorf RM, Topalidou I, Strubin M. A role for gcn5-mediated global histone acetylation in transcriptional regulation. Mol Cell Biol 2006; 26:1610-6. [PMID: 16478983 PMCID: PMC1430249 DOI: 10.1128/mcb.26.5.1610-1616.2006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional activators often require histone acetyltransferases (HATs) for full activity. The common explanation is that activators directly recruit HATs to gene promoters to locally hyperacetylate histones and thereby facilitate transcription complex formation. However, in addition to being targeted to specific loci, HATs such as Gcn5 also modify histones genome-wide. Here we provide evidence for a role of this global HAT activity in regulated transcription. We show that activation by direct recruitment of the transcriptional machinery neither recruits Gcn5 nor induces changes in histone acetylation yet can strongly depend on Gcn5 at promoters showing a high basal state of Gcn5-mediated histone acetylation. We also show that Gcn5 dependency varies among core promoters and is influenced by the strength of interaction used to recruit the machinery and by the affinity of the latter for the core promoter. These data support a role for global Gcn5 HAT activity in modulating transcription independently of its known coactivator function.
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Affiliation(s)
- Rachel Maria Imoberdorf
- Department of Microbiology and Molecular Medicine, University Medical Centre (C.M.U.), Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
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30
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Affiliation(s)
- Peter B Becker
- Adolf-Butenandt-Institut, Molekularbiologie, D-80336 München, Germany
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31
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Jessen WJ, Hoose SA, Kilgore JA, Kladde MP. Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nat Struct Mol Biol 2006; 13:256-63. [PMID: 16491089 DOI: 10.1038/nsmb1062] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Accepted: 12/29/2005] [Indexed: 01/08/2023]
Abstract
Transcriptional activation is often associated with chromatin remodeling. However, little is known about the dynamics of remodeling of nucleosome arrays in vivo. Upon induction of Saccharomyces cerevisiae PHO5, a novel kinetic assay of DNA methyltransferase accessibility showed that nucleosomes adjacent to the histone-free upstream activating sequence (UASp1) are disrupted earlier and at higher frequency in the cell population than are those more distal. Individually cloned molecules, each representing the chromatin state of a full promoter from a single cell, revealed multiple promoter classes with either no remodeling or variable numbers of disrupted nucleosomes. Individual promoters in the remodeled fraction were highly enriched for contiguous blocks of disrupted nucleosomes, the majority of which overlapped the UAS region. These results support a probabilistic model in which chromatin remodeling at PHO5 spreads from sites of transactivator association with DNA and attenuates with distance.
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Affiliation(s)
- Walter J Jessen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
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32
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Wolfram Hörz (1944–2005). Mol Cell 2006. [DOI: 10.1016/j.molcel.2006.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Korber P, Barbaric S, Luckenbach T, Schmid A, Schermer UJ, Blaschke D, Hörz W. The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters. J Biol Chem 2006; 281:5539-45. [PMID: 16407267 DOI: 10.1074/jbc.m513340200] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic gene expression starts off from a largely obstructive chromatin substrate that has to be rendered accessible by regulated mechanisms of chromatin remodeling. The yeast PHO5 promoter is a well known example for the contribution of positioned nucleosomes to gene repression and for extensive chromatin remodeling in the course of gene induction. Recently, the mechanism of this remodeling process was shown to lead to the disassembly of promoter nucleosomes and the eviction of the constituent histones in trans. This finding called for a histone acceptor in trans and thus made histone chaperones likely to be involved in this process. In this study we have shown that the histone chaperone Asf1 increases the rate of histone eviction at the PHO5 promoter. In the absence of Asf1 histone eviction is delayed, but the final outcome of the chromatin transition is not affected. The same is true for the coregulated PHO8 promoter where induction also leads to histone eviction and where the rate of histone loss is reduced in asf1 strains as well, although less severely. Importantly, the final extent of chromatin remodeling is not affected. We have also presented evidence that Asf1 and the SWI/SNF chromatin remodeling complex work in distinct parallel but functionally overlapping pathways, i.e. they both contribute toward the same outcome without being mutually strictly dependent.
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Affiliation(s)
- Philipp Korber
- Adolf-Butenandt-Institut, Universität München, Schillerstrasse 44, 80336 Münich, Germany.
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Ferreira ME, Hermann S, Prochasson P, Workman JL, Berndt KD, Wright APH. Mechanism of Transcription Factor Recruitment by Acidic Activators. J Biol Chem 2005; 280:21779-84. [PMID: 15826952 DOI: 10.1074/jbc.m502627200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many transcriptional activators are intrinsically unstructured yet display unique, defined conformations when bound to target proteins. Target-induced folding provides a mechanism by which activators could form specific interactions with an array of structurally unrelated target proteins. Evidence for such a binding mechanism has been reported previously in the context of the interaction between the cancer-related c-Myc protein and the TATA-binding protein, which can be modeled as a two-step process in which a rapidly forming, low affinity complex slowly converts to a more stable form, consistent with a coupled binding and folding reaction. To test the generality of the target-induced folding model, we investigated the binding of two widely studied acidic activators, Gal4 and VP16, to a set of target proteins, including TATA-binding protein and the Swi1 and Snf5 subunits of the Swi/Snf chromatin remodeling complex. Using surface plasmon resonance, we show that these activator-target combinations also display bi-phasic kinetics suggesting two distinct steps. A fast initial binding phase that is inhibited by high ionic strength is followed by a slow phase that is favored by increased temperature. In all cases, overall affinity increases with temperature and, in most cases, with increased ionic strength. These results are consistent with a general mechanism for recruitment of transcriptional components to promoters by naturally occurring acidic activators, by which the initial contact is mediated predominantly through electrostatic interactions, whereas subsequent target-induced folding of the activator results in a stable complex.
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Affiliation(s)
- Monica E Ferreira
- Department of Life Sciences, Södertörns Högskola, S-141 89 Huddinge, Sweden.
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35
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Dhasarathy A, Kladde MP. Promoter occupancy is a major determinant of chromatin remodeling enzyme requirements. Mol Cell Biol 2005; 25:2698-707. [PMID: 15767675 PMCID: PMC1061642 DOI: 10.1128/mcb.25.7.2698-2707.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromatin creates transcriptional barriers that are overcome by coactivator activities such as histone acetylation by Gcn5 and ATP-dependent chromatin remodeling by SWI/SNF. Factors defining the differential coactivator requirements in the transactivation of various promoters remain elusive. Induction of the Saccharomyces cerevisiae PHO5 promoter does not require Gcn5 or SWI/SNF under fully inducing conditions of no phosphate. We show that PHO5 activation is highly dependent on both coactivators at intermediate phosphate concentrations, conditions that reduce the nuclear concentration of the Pho4 transactivator and severely diminish its association with PHO5 in the absence of Gcn5 or SWI/SNF. Conversely, physiological increases in Pho4 nuclear concentration and binding at PHO5 suppress the need for both Gcn5 and SWI/SNF, suggesting that coactivator redundancy is established at high Pho4 binding site occupancy. Consistent with this, we demonstrate, using chromatin immunoprecipitation, that Gcn5 and SWI/SNF are directly recruited to PHO5 and other strongly transcribed promoters, including GAL1-10, RPL19B, RPS22B, PYK1, and EFT2, which do not require either coactivator for expression. These results show that activator concentration and binding site occupancy play crucial roles in defining the extent to which transcription requires individual chromatin remodeling enzymes. In addition, Gcn5 and SWI/SNF associate with many more genomic targets than previously appreciated.
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Affiliation(s)
- Archana Dhasarathy
- Department of Biochemistry and Biophysics, 2128 TAMU, Texas A&M University, College Station, TX 77843-2128, USA
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36
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Wang X, Michels CA. Mutations in SIN4 and RGR1 cause constitutive expression of MAL structural genes in Saccharomyces cerevisiae. Genetics 2005; 168:747-57. [PMID: 15514050 PMCID: PMC1448850 DOI: 10.1534/genetics.104.029611] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription of the Saccharomyces MAL structural genes is induced 40-fold by maltose and requires the MAL-activator and maltose permease. To identify additional players involved in regulating MAL gene expression, we carried out a genetic selection for MAL constitutive mutants. Strain CMY4000 containing MAL1 and integrated copies of MAL61promoter-HIS3 and MAL61promoter-lacZ reporter genes was used to select constitutive mutants. The 29 recessive mutants fall into at least three complementation groups. Group 1 and group 2 mutants exhibit pleiotropic phenotypes and represent alleles of Mediator component genes RGR1 and SIN4, respectively. The rgr1 and sin4 constitutive phenotype does not require either the MAL-activator or maltose permease, indicating that Mediator represses MAL basal expression. Further genetic analysis demonstrates that RGR1 and SIN4 work in a common pathway and each component of the Mediator Sin4 module plays a distinct role in regulating MAL gene expression. Additionally, the Swi/Snf chromatin-remodeling complex is required for full induction, suggesting a role for chromatin remodeling in the regulation of MAL gene expression. A sin4Delta mutation is unable to suppress the defects in MAL gene expression resulting from loss of the Swi/Snf complex component Snf2p. The role of the Mediator in MAL gene regulation is discussed.
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Affiliation(s)
- Xin Wang
- Department of Biology, Queens College and the Graduate School of City University of New York, Flushing, New York 11367, USA
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37
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Huang S, O'Shea EK. A systematic high-throughput screen of a yeast deletion collection for mutants defective in PHO5 regulation. Genetics 2005; 169:1859-71. [PMID: 15695358 PMCID: PMC1360160 DOI: 10.1534/genetics.104.038695] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In response to phosphate limitation, Saccharomyces cerevisiae induces transcription of a set of genes important for survival. One of these genes is PHO5, which encodes a secreted acid phosphatase. A phosphate-responsive signal transduction pathway (the PHO pathway) mediates this response through three central components: a cyclin-dependent kinase (CDK), Pho85; a cyclin, Pho80; and a CDK inhibitor (CKI), Pho81. While signaling downstream of the Pho81/Pho80/Pho85 complex to PHO5 expression has been well characterized, little is known about factors acting upstream of these components. To identify missing factors involved in the PHO pathway, we carried out a high-throughput, quantitative enzymatic screen of a yeast deletion collection, searching for novel mutants defective in expression of PHO5. As a result of this study, we have identified at least nine genes that were previously not known to regulate PHO5 expression. The functional diversity of these genes suggests that the PHO pathway is networked with other important cellular signaling pathways. Among these genes, ADK1 and ADO1, encoding an adenylate kinase and an adenosine kinase, respectively, negatively regulate PHO5 expression and appear to function upstream of PHO81.
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Affiliation(s)
- Sidong Huang
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, 94143-2240, USA
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38
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Korber P, Luckenbach T, Blaschke D, Hörz W. Evidence for histone eviction in trans upon induction of the yeast PHO5 promoter. Mol Cell Biol 2004; 24:10965-74. [PMID: 15572697 PMCID: PMC533982 DOI: 10.1128/mcb.24.24.10965-10974.2004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The yeast PHO5 promoter is a model system for the role of chromatin in eukaryotic gene regulation. Four positioned nucleosomes in the repressed state give way to an extended DNase I hypersensitive site upon induction. Recently this hypersensitive site was shown to be devoid of histone DNA contacts. This raises the mechanistic question of how histones are removed from the promoter. A displacement in trans or movement in cis, the latter according to the well established nucleosome sliding mechanism, are the major alternatives. In this study, we embedded the PHO5 promoter into the context of a small plasmid which severely restricts the space for nucleosome sliding along the DNA in cis. Such a construct would either preclude the chromatin transition upon induction altogether, were it to occur in cis, or gross changes in chromatin around the plasmid would be the consequence. We observed neither. Instead, promoter opening on the plasmid was indistinguishable from opening at the native chromosomal locus. This makes a sliding mechanism for the chromatin transition at the PHO5 promoter highly unlikely and points to histone eviction in trans.
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Affiliation(s)
- Philipp Korber
- Adolf-Butenandt-Institut, Universität München, Schillerstrasse 44, 80336 Munich, Germany.
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39
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Adkins MW, Howar SR, Tyler JK. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol Cell 2004; 14:657-66. [PMID: 15175160 DOI: 10.1016/j.molcel.2004.05.016] [Citation(s) in RCA: 234] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Revised: 05/17/2004] [Accepted: 05/19/2004] [Indexed: 10/26/2022]
Abstract
Nucleosome loss from a promoter region has recently been described as a potential mechanism for transcriptional regulation. We investigated whether H3/H4 histone chaperones mediate the loss of nucleosomes from the promoter of the yeast PHO5 gene during transcriptional activation. We found that antisilencing function 1 (Asf1p) mediates nucleosome disassembly from the PHO5 promoter in vivo. We show that nucleosome disassembly also occurs at a second promoter, that of the PHO8 gene, during activation, and we demonstrate that this is also mediated by Asf1p. Furthermore, we show that nucleosome disassembly is essential for PHO5 and PHO8 activation. Contrary to the current dogma, we demonstrate that nucleosome disassembly is not required to enable binding of the Pho4p activator to its PHO5 UASp2 site in vivo. Finally, we show that nucleosomes are reassembled over the PHO5 promoter during repression. As such, nucleosome disassembly and reassembly are important mechanisms for transcriptional activation and repression, respectively.
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Affiliation(s)
- Melissa W Adkins
- Department of Biochemistry and Molecular Genetics, B121, School of Medicine, University of Colorado, 4200 East Ninth Avenue, Denver, CO 80262, USA
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40
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Boeger H, Griesenbeck J, Strattan JS, Kornberg RD. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol Cell 2004; 14:667-73. [PMID: 15175161 DOI: 10.1016/j.molcel.2004.05.013] [Citation(s) in RCA: 210] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Revised: 04/07/2004] [Accepted: 04/12/2004] [Indexed: 01/08/2023]
Abstract
Previous work demonstrated the removal of nucleosomes from the PHO5 promoter upon transcriptional activation in yeast. Removal could occur by nucleosome disassembly or by sliding of nucleosomes away from the promoter. We have now activated the PHO5 promoter on chromatin circles following excision from the chromosomal locus. Whereas sliding would conserve the number of nucleosomes on the circle, we found that the number was diminished, demonstrating chromatin remodeling by nucleosome disassembly.
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Affiliation(s)
- Hinrich Boeger
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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41
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Martinez-Campa C, Politis P, Moreau JL, Kent N, Goodall J, Mellor J, Goding CR. Precise Nucleosome Positioning and the TATA Box Dictate Requirements for the Histone H4 Tail and the Bromodomain Factor Bdf1. Mol Cell 2004; 15:69-81. [PMID: 15225549 DOI: 10.1016/j.molcel.2004.05.022] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Revised: 04/02/2004] [Accepted: 04/28/2004] [Indexed: 11/24/2022]
Abstract
Acetylation of histone tails plays a key role in chromatin dynamics and is associated with the potential for gene expression. We show here that a 2-3 bp mispositioning of the nucleosome covering the TATA box at PHO5 induces a dependency on the acetylatable lysine residues of the histone H4 N-terminal region and on the TFIID-associated bromodomain factor Bdf1. This dependency arises either through fusion of the PHO5 promoter to a lacZ reporter or by mutation of the TATA box in the natural gene. The results suggest that promoters in which the TATA box is either absent or poorly accessible on the surface of a nucleosome may compensate by using Bdf1 bromodomains and acetylated H4 tails to anchor TFIID to the promoter during the initial stages of transcription activation. We propose that nucleosome positioning at the nucleotide level provides a subtle, but highly effective, mechanism for gene regulation.
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Affiliation(s)
- Carlos Martinez-Campa
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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42
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Nourani A, Utley RT, Allard S, Côté J. Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J 2004; 23:2597-607. [PMID: 15175650 PMCID: PMC449761 DOI: 10.1038/sj.emboj.7600230] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2003] [Accepted: 04/15/2004] [Indexed: 01/08/2023] Open
Abstract
The remodeling of the promoter chromatin structure is a key event for the induction of the PHO5 gene. Two DNA-binding proteins Pho2 and Pho4 are critical for this step. We found that the NuA4 histone acetyltransferase complex is essential for PHO5 transcriptional induction without affecting Pho4 translocation upon phosphate starvation. Our data also indicate that NuA4 is critical for the chromatin remodeling event that occurs over the PHO5 promoter prior to activation. Using Chromatin IP analysis, we found that Esa1-dependent histone H4 acetylation at the PHO5 promoter correlates with specific recruitment of the NuA4 complex to this locus under repressing conditions. We demonstrate that the homeodomain transcriptional activator Pho2 is responsible for this recruitment in vivo and interacts directly with the NuA4 complex. Finally, we show that Pho4 is unable to bind the PHO5 promoter without prior action of NuA4. These results indicate that, before induction, NuA4 complex recruitment by Pho2 is an essential event that presets the PHO5 promoter for subsequent binding by Pho4, chromatin remodeling and transcription.
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Affiliation(s)
- Amine Nourani
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Canada
| | - Rhea T Utley
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Canada
| | - Stéphane Allard
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Canada
| | - Jacques Côté
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Canada
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), 9 McMahon Street, Quebec City, QC G1R 2J6 Canada. Tel: +1 418 525 4444; ext. 15545; Fax: +1 418 691 5439; E-mail:
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43
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Reinke H, Hörz W. Anatomy of a hypersensitive site. ACTA ACUST UNITED AC 2004; 1677:24-9. [PMID: 15020042 DOI: 10.1016/j.bbaexp.2003.09.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2003] [Accepted: 09/10/2003] [Indexed: 01/09/2023]
Abstract
The 600-bp accessible region at the activated PHO5 promoter in S. cerevisiae has become a paradigm for hypersensitive sites. In this review, we summarize the various experimental strategies used to characterize chromatin at the active promoter and point out their virtues and their limitations. We describe the properties of chromatin at the active PHO5 promoter and what we currently know about the transition from the inactive to the active state. The implications for generating a hypersensitive region in chromatin are discussed.
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Affiliation(s)
- Hans Reinke
- Adolf-Butenandt-Institut, Molekularbiologie, Universität München, Schillerstr 44, D-80336 Munich, Germany
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44
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Geng F, Laurent BC. Roles of SWI/SNF and HATs throughout the dynamic transcription of a yeast glucose-repressible gene. EMBO J 2003; 23:127-37. [PMID: 14685262 PMCID: PMC1271673 DOI: 10.1038/sj.emboj.7600035] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2003] [Accepted: 11/12/2003] [Indexed: 11/09/2022] Open
Abstract
Eucaryotic gene expression requires chromatin-remodeling activities. We show by time-course studies that transcriptional induction of the yeast glucose-regulated SUC2 gene is rapid and shows a striking biphasic pattern, the first phase of which is partly mediated by the general stress transcription factors Msn2p/Msn4p. The SWI/SNF ATP-dependent chromatin-remodeling complex associates with the promoter in a similar biphasic manner and is essential for both phases of transcription. Two different histone acetyltransferases, Gcn5p and Esa1p, enhance the binding of SWI/SNF to the promoter during early transcription and are required for optimal SUC2 induction. Gcn5p is recruited to SUC2 simultaneously with SWI/SNF, whereas Esa1p associates constitutively with the promoter. This study reveals an unusual transcription pattern of a metabolic gene and suggests a novel strategy by which distinct chromatin remodelers cooperate for the dynamic activation of transcription.
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Affiliation(s)
- Fuqiang Geng
- Program in Molecular and Cellular Biology, Department of Microbiology and Immunology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Brehon C Laurent
- Program in Molecular and Cellular Biology, Department of Microbiology and Immunology, SUNY Downstate Medical Center, Brooklyn, NY, USA
- Program in Molecular and Cellular Biology, Department of Microbiology and Immunology, Morse Institute for Molecular Genetics, SUNY Downstate Medical Center, 450 Clarkson Avenue, Box 44, Brooklyn, NY 11203, USA. Tel.: +1 718 270 3755; Fax: +1 718 270 2656; E-mail:
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45
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Topalidou I, Papamichos-Chronakis M, Thireos G. Post-TATA binding protein recruitment clearance of Gcn5-dependent histone acetylation within promoter nucleosomes. Mol Cell Biol 2003; 23:7809-17. [PMID: 14560024 PMCID: PMC207637 DOI: 10.1128/mcb.23.21.7809-7817.2003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional activation of eukaryotic genes often requires the function of histone acetyltransferases (HATs), which is expected to result in the hyperacetylation of histones within promoter nucleosomes. In this study we show that, in Saccharomyces cerevisiae, the steady-state levels of Gcn5-dependent histone acetylation within a number of transcriptionally active promoters are inversely related to the rate of transcription. High acetylation levels were measured only when transcription was attenuated either by TATA element mutations or in a strain carrying a temperature-sensitive protein component of RNA polymerase II. In addition, we show that in one case the low levels of histone acetylation depend on the function of the Rpd3 histone deacetylase. These results point to the existence of an unexpected interplay of two opposing histone-modifying activities which operate on promoter nucleosomes following the initiation of RNA synthesis. Such interplay could ensure rapid turnover of chromatin acetylation states in continuously reprogrammed transcriptional systems.
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Affiliation(s)
- Irini Topalidou
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion 711 10, Crete, Greece
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46
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Brown K, Chen Y, Underhill TM, Mymryk JS, Torchia J. The coactivator p/CIP/SRC-3 facilitates retinoic acid receptor signaling via recruitment of GCN5. J Biol Chem 2003; 278:39402-12. [PMID: 12885766 DOI: 10.1074/jbc.m307832200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
p/CIP/SRC-3 is a member of a family of steroid receptor coactivators/nuclear receptor coactivators (SRC/NCoA) proteins that mediate the transcriptional effects of nuclear hormone receptors (NRs). Using deletion analysis we have mapped the location of two distinct activation domains in p/CIP (AD1 and AD2) capable of activating transcription in mammalian cells when fused to the Gal4-DNA binding domain. In addition to AD1 being coincident with the interaction domain for CBP, we demonstrate a novel in vivo interaction between the AD1 and GCN5. Overexpression of a Gal4-AD1 fusion protein in yeast leads to growth arrest that is relieved by mutation of genes encoding components of the SAGA complex including GCN5, ADA3, and SPT7. In addition, the AD1 of p/CIP and the ADA3 gene are shown to be essential for retinoic acid receptor alpha-dependent transcription in yeast. Transient transfection assays in mammalian cells indicate that GCN5 cooperates with p/CIP as a coactivator of RAR alpha-dependent transcription. Down-regulation of GCN5 using small interfering RNA in mammalian cells indicates that the AD1 domain and the RAR beta promoter activity are dependent, in part, on GCN5. Mutational analysis of AD1 has identified two helical motifs that are required for interactions with GCN5 and CBP. Taken together, these results support a model by which p/CIP functions as a ligand-dependent adapter, through specific protein-protein interactions with AD1, to recruit members from at least two distinct families of acetyltransferase proteins to NRs.
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Affiliation(s)
- Kirk Brown
- Department of Oncology, University of Western Ontario and the London Regional Cancer Centre, London, Ontario N6A 4L6, Canada
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47
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Carvin CD, Dhasarathy A, Friesenhahn LB, Jessen WJ, Kladde MP. Targeted cytosine methylation for in vivo detection of protein-DNA interactions. Proc Natl Acad Sci U S A 2003; 100:7743-8. [PMID: 12808133 PMCID: PMC164658 DOI: 10.1073/pnas.1332672100] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We report a technique, named targeted gene methylation (TAGM), for identifying in vivo protein-binding sites in chromatin. M.CviPI, a cytosine-5 DNA methyltransferase recognizing GC sites, is fused to a DNA-binding factor enabling simultaneous detection of targeted methylation, factor footprints, and chromatin structural changes by bisulfite genomic sequencing. Using TAGM with the yeast transactivator Pho4, methylation enrichments of up to 34- fold occur proximal to native Pho4-binding sites. Additionally, significant selective targeting of methylation is observed several hundred nucleotides away, suggesting the detection of long-range interactions due to higher-order chromatin structure. In contrast, at an extragenic locus lacking Pho4-binding sites, methylation levels are at the detection limit at early times after Pho4 transactivation. Notably, substantial amounts of methylation are targeted by Pho4-M.CviPI under repressive conditions when most of the transactivator is excluded from the nucleus. Thus, TAGM enables rapid detection of DNA-protein interactions even at low occupancies and has potential for identifying factor targets at the genome-wide level. Extension of TAGM from yeast to vertebrates, which use methylation to initiate and propagate repressed chromatin, could also provide a valuable strategy for heritable inactivation of gene expression.
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Affiliation(s)
- Christopher D Carvin
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
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Reinke H, Hörz W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol Cell 2003; 11:1599-607. [PMID: 12820972 DOI: 10.1016/s1097-2765(03)00186-2] [Citation(s) in RCA: 338] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have analyzed the histone modification status of the PHO5 promoter from yeast by the ChIP technology and have focused on changes occurring upon activation. Using various acetylation-specific antibodies, we found a dramatic loss of the acetylation signal upon induction of the promoter. This turned out to be due, however, to the progressive loss of histones altogether. The fully remodeled promoter appears to be devoid of histones as judged by ChIP analyses. Local histone hyperacetylation does indeed occur, however, prior to remodeling. This can explain the delay in chromatin remodeling in the absence of histone acetyltransferase activity of the SAGA complex that was previously documented for the PHO5 promoter. Our findings shed new light on the nucleosomal structure of fully remodeled chromatin. At the same time, they point out the need for novel controls when the ChIP technique is used to study histone modifications in the context of chromatin remodeling in vivo.
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Affiliation(s)
- Hans Reinke
- Molekularbiologie, Adolf-Butenandt-Institut, Universität München, Schillerstrasse 44, D-80336 Münich, Germany
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49
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Neef DW, Kladde MP. Polyphosphate loss promotes SNF/SWI- and Gcn5-dependent mitotic induction of PHO5. Mol Cell Biol 2003; 23:3788-97. [PMID: 12748282 PMCID: PMC155216 DOI: 10.1128/mcb.23.11.3788-3797.2003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Approximately 800 transcripts in Saccharomyces cerevisiae are cell cycle regulated. The oscillation of approximately 40% of these genes, including a prominent subclass involved in nutrient acquisition, is not understood. To address this problem, we focus on the mitosis-specific activation of the phosphate-responsive promoter, PHO5. We show that the unexpected mitotic induction of the PHO5 acid phosphatase in rich medium requires the transcriptional activators Pho4 and Pho2, the cyclin-dependent kinase inhibitor Pho81, and the chromatin-associated enzymes Gcn5 and Snf2/Swi2. PHO5 mitotic activation is repressed by addition of orthophosphate, which significantly increases cellular polyphosphate. Polyphosphate levels also fluctuate inversely with PHO5 mRNA during the cell cycle, further substantiating an antagonistic link between this phosphate polymer and PHO5 mitotic regulation. Moreover, deletion of PHM3, required for polyphosphate accumulation, leads to premature onset of PHO5 expression, as well as an increased rate, magnitude, and duration of PHO5 activation. Orthophosphate addition, however, represses mitotic PHO5 expression in a phm3delta strain. Thus, polyphosphate per se is not necessary to repress PHO transcription but, when present, replenishes cellular phosphate during nutrient depletion. These results demonstrate a dynamic mechanism of mitotic transcriptional regulation that operates mostly independently of factors that drive progression through the cell cycle.
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Affiliation(s)
- Daniel W Neef
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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Boeger H, Griesenbeck J, Strattan JS, Kornberg RD. Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell 2003; 11:1587-98. [PMID: 12820971 DOI: 10.1016/s1097-2765(03)00231-4] [Citation(s) in RCA: 338] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
It has long been known that promoter DNA is converted to a nuclease-sensitive state upon transcriptional activation. Recent findings have raised the possibility that this conversion reflects only a partial unfolding or other perturbation of nucleosomal structure, rather than the loss of nucleosomes. We report topological, sedimentation, nuclease digestion, and ChIP analyses, which demonstrate the complete unfolding of nucleosomes at the transcriptionally active PHO5 promoter of the yeast Saccharomyces cerevisiae. Although nucleosome loss occurs at all promoter sites, it is not complete at any of them, suggesting the existence of an equilibrium between the removal of nucleosomes and their reformation.
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Affiliation(s)
- Hinrich Boeger
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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