101
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Albert T, Wells J, Funk JO, Pullner A, Raschke EE, Stelzer G, Meisterernst M, Farnham PJ, Eick D. The chromatin structure of the dual c-myc promoter P1/P2 is regulated by separate elements. J Biol Chem 2001; 276:20482-90. [PMID: 11279041 DOI: 10.1074/jbc.m100265200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proto-oncogene c-myc is transcribed from a dual promoter P1/P2, with transcription initiation sites 160 base pairs apart. Here we have studied the transcriptional activation of both promoters on chromatin templates. c-myc chromatin was reconstituted on stably transfected, episomal, Epstein-Barr virus-derived vectors in a B cell line. Episomal P1 and P2 promoters showed only basal activity but were strongly inducible by histone deacetylase inhibitors. The effect of promoter mutations on c-myc activity, chromatin structure, and E2F binding was studied. The ME1a1 binding site between P1 and P2 was required for the maintenance of an open chromatin configuration of the dual c-myc promoters. Mutation of this site strongly reduced the sensitivity of the core promoter region of P1/P2 to micrococcal nuclease and prevented binding of polymerase II (pol II) at the P2 promoter. In contrast, mutation of the P2 TATA box also abolished binding of pol II at the P2 promoter but did not affect the chromatin structure of the P1/P2 core promoter region. The E2F binding site adjacent to ME1a1 is required for repression of the P2 promoter but not the P1 promoter, likely by recruitment of histone deacetylase activity. Chromatin precipitation experiments with E2F-specific antibodies revealed binding of E2F-1, E2F-2, and E2F-4 to the E2F site of the c-myc promoter in vivo if the E2F site was intact. Taken together, the analyses support a model with a functional hierarchy for regulatory elements in the c-myc promoter region; binding of proteins to the ME1a1 site provides a nucleosome-free region of chromatin near the P2 start site, binding of E2F results in transcriptional repression without affecting polymerase recruitment, and the TATA box is required for polymerase recruitment.
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Affiliation(s)
- T Albert
- Institute of Clinical Molecular Biology and Tumor Genetics, Department for Protein Chemistry, Research Centre for Environment and Health (GSF), Marchioninistrasse 25, D-81377 München, Germany
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102
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Abstract
Chromatin is thought to repress transcription by limiting access of the DNA to transcription factors. Using a yeast heat shock gene flanked by mating-type silencers as a model system, we find that repressive, SIR-generated heterochromatin is permissive to the constitutive binding of an activator, HSF, and two components of the preinitiation complex (PIC), TBP and Pol II. These factors cohabitate the promoter with Sir silencing proteins and deacetylated nucleosomal histones. The heterochromatic HMRa1 promoter is also occupied by TBP and Pol II, suggesting that SIR regulates gene expression not by restricting factor access to DNA but rather by blocking a step downstream of PIC recruitment. Interestingly, activation of silent promoter chromatin occurs in the absence of histone displacement and without change in histone acetylation state.
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Affiliation(s)
- E A Sekinger
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
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103
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Guyon JR, Narlikar GJ, Sullivan EK, Kingston RE. Stability of a human SWI-SNF remodeled nucleosomal array. Mol Cell Biol 2001; 21:1132-44. [PMID: 11158300 PMCID: PMC99567 DOI: 10.1128/mcb.21.4.1132-1144.2001] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2000] [Accepted: 11/03/2000] [Indexed: 11/20/2022] Open
Abstract
SWI-SNF alters DNA-histone interactions within a nucleosome in an ATP-dependent manner. These alterations cause changes in the topology of a closed circular nucleosomal array that persist after removal of ATP from the reaction. We demonstrate here that a remodeled closed circular array will revert toward its original topology when ATP is removed, indicating that the remodeled array has a higher energy than that of the starting state. However, reversion occurs with a half-life measured in hours, implying a high energy barrier between the remodeled and standard states. The addition of competitor DNA accelerates reversion of the remodeled array by more than 10-fold, and we interpret this result to mean that binding of human SWI-SNF (hSWI-SNF), even in the absence of ATP hydrolysis, stabilizes the remodeled state. In addition, we also show that SWI-SNF is able to remodel a closed circular array in the absence of topoisomerase I, demonstrating that hSWI-SNF can induce topological changes even when conditions are highly energetically unfavorable. We conclude that the remodeled state is less stable than the standard state but that the remodeled state is kinetically trapped by the high activation energy barrier separating it from the unremodeled conformation.
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Affiliation(s)
- J R Guyon
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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104
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105
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Santisteban MS, Kalashnikova T, Smith MM. Histone H2A.Z regulats transcription and is partially redundant with nucleosome remodeling complexes. Cell 2000; 103:411-22. [PMID: 11081628 DOI: 10.1016/s0092-8674(00)00133-1] [Citation(s) in RCA: 252] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nucleosomes impose a block to transcription that can be overcome in vivo by remodeling complexes such as SNF/SWI and histone modification complexes such as SAGA. Mutations in the major core histones relieve transcriptional repression and bypass the requirement for SNF/SWI and SAGA. We have found that the variant histone H2A.Z regulates gene transcription, and deletion of the gene encoding H2A.Z strongly increases the requirement for SNF/SWI and SAGA. This synthetic genetic interaction is seen at the level of single genes and acts downstream of promoter nucleosome reorganization. H2A.Z is preferentially crosslinked in vivo to intergenic DNA at the PH05 and GAL1 loci, and this association changes with transcriptional activation. These results describe a novel pathway for regulating transcription using variant histones to modulate chromatin structure.
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MESH Headings
- Adenosine Triphosphatases
- Alleles
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/physiology
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/physiology
- Fungal Proteins/genetics
- Fungal Proteins/physiology
- Gene Deletion
- Gene Expression Regulation, Fungal
- Genes, Essential/genetics
- Genes, Fungal/genetics
- Genes, Fungal/physiology
- Histones/chemistry
- Histones/genetics
- Histones/metabolism
- Hot Temperature
- Macromolecular Substances
- Membrane Transport Proteins/genetics
- Molecular Conformation
- Nuclear Proteins
- Nucleosomes/chemistry
- Nucleosomes/genetics
- Nucleosomes/metabolism
- Phenotype
- Phosphate Transport Proteins
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Kinases/genetics
- Protein Kinases/physiology
- Protein Subunits
- Recombinant Fusion Proteins
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Suppression, Genetic/genetics
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- M S Santisteban
- Department of Microbiology and Cancer Center, University of Virginia, Charlottesville 22908, USA
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106
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Costa PJ, Arndt KM. Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics 2000; 156:535-47. [PMID: 11014804 PMCID: PMC1461271 DOI: 10.1093/genetics/156.2.535] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Strong evidence indicates that transcription elongation by RNA polymerase II (pol II) is a highly regulated process. Here we present genetic results that indicate a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. A screen for synthetic lethal mutations was carried out with an rtf1 deletion mutation to identify factors that interact with Rtf1 or regulate the same process as Rtf1. The screen uncovered mutations in SRB5, CTK1, FCP1, and POB3. These genes encode an Srb/mediator component, a CTD kinase, a CTD phosphatase, and a protein involved in the regulation of transcription by chromatin structure, respectively. All of these gene products have been directly or indirectly implicated in transcription elongation, indicating that Rtf1 may also regulate this process. In support of this view, we show that RTF1 functionally interacts with genes that encode known elongation factors, including SPT4, SPT5, SPT16, and PPR2. We also show that a deletion of RTF1 causes sensitivity to 6-azauracil and mycophenolic acid, phenotypes correlated with a transcription elongation defect. Collectively, our results suggest that Rtf1 may function as a novel transcription elongation factor in yeast.
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Affiliation(s)
- P J Costa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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107
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Citterio E, Van Den Boom V, Schnitzler G, Kanaar R, Bonte E, Kingston RE, Hoeijmakers JH, Vermeulen W. ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor. Mol Cell Biol 2000; 20:7643-53. [PMID: 11003660 PMCID: PMC86329 DOI: 10.1128/mcb.20.20.7643-7653.2000] [Citation(s) in RCA: 296] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Cockayne syndrome B protein (CSB) is required for coupling DNA excision repair to transcription in a process known as transcription-coupled repair (TCR). Cockayne syndrome patients show UV sensitivity and severe neurodevelopmental abnormalities. CSB is a DNA-dependent ATPase of the SWI2/SNF2 family. SWI2/SNF2-like proteins are implicated in chromatin remodeling during transcription. Since chromatin structure also affects DNA repair efficiency, chromatin remodeling activities within repair are expected. Here we used purified recombinant CSB protein to investigate whether it can remodel chromatin in vitro. We show that binding of CSB to DNA results in an alteration of the DNA double-helix conformation. In addition, we find that CSB is able to remodel chromatin structure at the expense of ATP hydrolysis. Specifically, CSB can alter DNase I accessibility to reconstituted mononucleosome cores and disarrange an array of nucleosomes regularly spaced on plasmid DNA. In addition, we show that CSB interacts not only with double-stranded DNA but also directly with core histones. Finally, intact histone tails play an important role in CSB remodeling. CSB is the first repair protein found to play a direct role in modulating nucleosome structure. The relevance of this finding to the interplay between transcription and repair is discussed.
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Affiliation(s)
- E Citterio
- Medical Genetic Center, Department of Cell Biology and Genetics, Center for Biomedical Genetics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
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108
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Abstract
The machinery that transcribes protein-coding genes in eukaryotic cells must contend with repressive chromatin structures in order to find its target DNA sequences. Diverse arrays of proteins modify the structure of chromatin at gene promoters to help transcriptional regulatory proteins access their DNA recognition sites. The way in which disruption of chromatin structure at a promoter is transmitted through a whole gene has not been defined. Recent breakthroughs suggest that the passage of an RNA polymerase through a gene is coupled to mechanisms that propagate the breakdown of chromatin.
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Affiliation(s)
- G Orphanides
- Zeneca Central Toxicology Laboratory, Alderley Park, Cheshire, UK
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109
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Fivaz J, Bassi MC, Price M, Pinaud S, Mirkovitch J. Precisely positioned nucleosomes are not essential for c-fos gene regulation in vivo. Gene 2000; 255:169-84. [PMID: 11024277 DOI: 10.1016/s0378-1119(00)00339-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Chromatin architecture plays a decisive role in many aspects of transcription regulation. We have tested the role of specific chromatin structures in c-fos gene regulation, using a gene transfer system based on episomes derived from the Epstein-Barr virus (EBV). This system reproduces in several respects the chromatin structure and regulation of the chromosomal c-fos gene. Using this approach, we first demonstrate that the pausing of RNA polymerase II downstream of the transcriptional start site does not require precisely positioned nucleosomes. Indeed, changing the pattern of MNase hypersensitive sites along the transcribed sequence does not perturb RNA polymerase II pausing or the regulation of the c-fos gene. Next, we show that a putative nucleosome positioned between the SIE/SRE elements (-300) and the CRE/TATA elements (-36) is not necessary for activation by a variety of inducers. Accordingly, total or partial deletion of the putative nucleosome sequence does not disturb c-fos regulation while the two regulatory sites flanking the nucleosome sequence remain hypersensitive to MNase. As described in this paper, EBV episomes are useful vectors to critically examine the role of the chromatin structure in gene transcription for human cells.
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Affiliation(s)
- J Fivaz
- Swiss Institute for Experimental Cancer Research (ISREC), Chemin des Boveresses 155, CH-1066, Epalinges, Switzerland
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110
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Phelan ML, Schnitzler GR, Kingston RE. Octamer transfer and creation of stably remodeled nucleosomes by human SWI-SNF and its isolated ATPases. Mol Cell Biol 2000; 20:6380-9. [PMID: 10938115 PMCID: PMC86113 DOI: 10.1128/mcb.20.17.6380-6389.2000] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromatin remodeling complexes help regulate the structure of chromatin to facilitate transcription. The multisubunit human (h) SWI-SNF complex has been shown to remodel mono- and polynucleosome templates in an ATP-dependent manner. The isolated hSWI-SNF ATPase subunits BRG1 and hBRM also have these activities. The intact complex has been shown to produce a stable remodeled dimer of mononucleosomes as a product. Here we show that the hSWI-SNF ATPases alone can also produce this product. In addition, we show that hSWI-SNF and its ATPases have the ability to transfer histone octamers from donor nucleosomes to acceptor DNA. These two reactions are characterized and compared. Our results are consistent with both products of SWI-SNF action being formed as alternative outcomes of a single remodeling mechanism. The ability of the isolated ATPase subunits to catalyze these reactions suggests that these subunits play a key role in determining the mechanistic capabilities of the SWI-SNF family of remodeling complexes.
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Affiliation(s)
- M L Phelan
- Department of Molecular Biology, Massachusetts General Hospital, Boston 02114, USA
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111
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Meininghaus M, Chapman RD, Horndasch M, Eick D. Conditional expression of RNA polymerase II in mammalian cells. Deletion of the carboxyl-terminal domain of the large subunit affects early steps in transcription. J Biol Chem 2000; 275:24375-82. [PMID: 10825165 DOI: 10.1074/jbc.m001883200] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The carboxyl-terminal domain (CTD) of the large subunit of mammalian RNA polymerase II contains 52 repeats of a heptapeptide that is the target of a variety of kinases. The hyperphosphorylated CTD recruits important factors for mRNA capping, splicing, and 3'-processing. The role of the CTD for the transcription process in vivo, however, is not yet clear. We have conditionally expressed an alpha-amanitin-resistant large subunit with an almost entirely deleted CTD (LS*Delta5) in B-cells. These cells have a defect in global transcription of cellular genes in the presence of alpha-amanitin. Moreover, pol II harboring LS*Delta5 failed to transcribe up to the promoter-proximal pause sites in the hsp70A and c-fos gene promoters. The results indicate that the CTD is already required for steps that occur before promoter-proximal pausing and maturation of mRNA.
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Affiliation(s)
- M Meininghaus
- Institute for Clinical Molecular Biology and Tumor Genetics, GSF-Research Center for Environment and Health, Marchioninistrasse 25, D-81377 Munich, Germany
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112
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Sudarsanam P, Winston F. The Swi/Snf family nucleosome-remodeling complexes and transcriptional control. Trends Genet 2000; 16:345-51. [PMID: 10904263 DOI: 10.1016/s0168-9525(00)02060-6] [Citation(s) in RCA: 262] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Swi/Snf family of nucleosome-remodeling complexes has been shown to play important roles in gene expression throughout eukaryotes. Genetic and biochemical studies previously suggested that Swi/Snf activates transcription by remodeling nucleosomes, thereby permitting increased access of transcription factors for their binding sites. Recent studies have identified additional Swi/Snf biochemical activities and have suggested possible mechanisms by which Swi/Snf is targeted to specific promoters. Surprisingly, studies have also revealed that, besides being necessary for activation, Swi/Snf is required for transcriptional repression of some genes. These analyses have transformed our understanding of the function of the Swi/Snf family of complexes and suggest that they control transcription in diverse ways.
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Affiliation(s)
- P Sudarsanam
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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113
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Abstract
The elongation stage of eukaryotic mRNA synthesis can be regulated by transcription factors that interact directly with the RNA polymerase II (pol II) elongation complex and by activities that modulate the structure of its chromatin template. Recent studies have revealed new elongation factors and have implicated the general initiation factors TFIIE, TFIIF and TFIIH, as well as the C-terminal domain (CTD) of the largest subunit of pol II, in elongation. The recently reported high-resolution crystal structure of RNA polymerase II, which provides insight into the architecture of the elongation complex, marks a new era of investigation into transcription elongation.
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Affiliation(s)
- J W Conaway
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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114
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Davie JK, Kane CM. Genetic interactions between TFIIS and the Swi-Snf chromatin-remodeling complex. Mol Cell Biol 2000; 20:5960-73. [PMID: 10913179 PMCID: PMC86073 DOI: 10.1128/mcb.20.16.5960-5973.2000] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2000] [Accepted: 05/16/2000] [Indexed: 11/20/2022] Open
Abstract
The eukaryotic transcript elongation factor TFIIS enables RNA polymerase II to read through blocks to elongation in vitro and interacts genetically with a variety of components of the transcription machinery in vivo. In Saccharomyces cerevisiae, the gene encoding TFIIS (PPR2) is not essential, and disruption strains exhibit only mild phenotypes and an increased sensitivity to 6-azauracil. The nonessential nature of TFIIS encouraged the use of a synthetic lethal screen to elucidate the in vivo roles of TFIIS as well as provide more information on other factors involved in the regulation of transcript elongation. Several genes were identified that are necessary for either cell survival or robust growth when the gene encoding TFIIS has been disrupted. These include UBP3, KEX2, STT4, and SWI2/SNF2. SWI1 and SNF5 disruptions were also synthetically lethal with ppr2Delta, suggesting that the reduced ability to remodel chromatin confers the synthetic phenotype. The synthetic phenotypes show marked osmosensitivity and cytoskeletal defects, including a terminal hyperelongated bud phenotype with the Swi-Snf complex. These results suggest that genes important in osmoregulation, cell membrane synthesis and integrity, and cell division may require the Swi-Snf complex and TFIIS for efficient transcription. The detection of these genetic interactions provides another functional link between the Swi-Snf complex and the elongation machinery.
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Affiliation(s)
- J K Davie
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202, USA
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115
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Abstract
Protein-protein interactions between human heat shock transcription factor 1 (hHSF1) and general transcription factors TFIIA-gamma, TFIIB, TBP, TAF(II)32, and TAF(II)55 and positive coactivator PC4 were characterized in order to identify potential targets of contact in the transcriptional preinitiation complex. These contacts represent one of the final steps in the signal transfer of heat stress to the transcriptional apparatus. TATA-binding protein (TBP) and transcription factor IIB (TFIIB) were identified as major targets for HSF1 transcriptional activation domains AD1 and AD2 based on in vitro interaction assays. TBP showed affinity for AD2 and a fragment containing AD1, while the core domain of TFIIB interacted primarily with the AD1 fragment. Interactions were also detected between full-length HSF1 and the small subunit (gamma) of TFIIA. PC4 interacted weakly with HSF2 and showed even less affinity for HSF1. Coimmunoprecipitation of transiently expressed TBP in HeLa cells demonstrated that HSF1 AD2 and AD1+AD2 are able to bind TBP in vivo. Assays based on transcriptional interference confirmed predictions that both TBP and TFIIB can interact with HSF1 activation domains in HeLa cells. The negative regulatory region (NR) of HSF1 did not interact with any general factors tested in vitro but did bind TFIID in nuclear extracts through contacts that probably involve TATA associated proteins (TAFs). These results suggest a model for transcriptional regulation by HSF1 that involves a shift between formation of dysfunctional TFIID complexes with the NR and transcriptionally competent complexes with the C-terminal activation domains.
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Affiliation(s)
- Chao-Xing Yuan
- Department of Microbiology and Cell Science, Program in Plant Molecular and Cellular Biology, University of Florida, PO Box 110700, Gainesville, FL 32611-0700 USA
| | - William B Gurley
- Department of Microbiology and Cell Science, Program in Plant Molecular and Cellular Biology, University of Florida, PO Box 110700, Gainesville, FL 32611-0700 USA
- Correspondence to: William B. Gurley, Tel: 352 392-1568; Fax: 352 392-5922; .
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116
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John S, Howe L, Tafrov ST, Grant PA, Sternglanz R, Workman JL. The Something About Silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF II30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)–FACT complex. Genes Dev 2000. [DOI: 10.1101/gad.14.10.1196] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have purified and characterized a Gcn5-independent nucleosomal histone H3 HAT complex, NuA3 (NucleosomalAcetyltransferase of histone H3). Peptide sequencing of proteins from the purified NuA3 complex identified Sas3 as the catalytic HAT subunit of the complex. Sas3 is the yeast homolog of the human MOZ oncogene. Sas3 is required for both the HAT activity and the integrity of the NuA3 complex. In addition, NuA3 contains the TBP- associated factor, yTAFII30, which is also a component of the TFIID, TFIIF, and SWI/SNF complexes. Sas3 mediates interaction of the NuA3 complex with Spt16 both in vivo and in vitro. Spt16 functions as a component of the yeast CP (Cdc68/Pob3) and mammalian FACT (facilitateschromatin transcription) complexes, which are involved in transcription elongation and DNA replication. This interaction suggests that the NuA3 complex might function in concert with FACT–CP to stimulate transcription or replication elongation through nucleosomes by providing a coupled acetyltransferase activity.
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117
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Abstract
The assembly of eukaryotic DNA into folded nucleosomal arrays has drastic consequences for many nuclear processes that require access to the DNA sequence, including RNA transcription, DNA replication, recombination, and repair. Two types of highly conserved chromatin remodeling enzymes have been implicated as regulators of the repressive nature of chromatin structure: ATP-dependent remodeling complexes and nuclear histone acetyltransferases (HATs). Recent studies indicate that both types of enzymes can be recruited to chromosomal loci through either physical interactions with transcriptional activators or via the global accessibility of chromatin during S phase of the cell cycle. Here we review these recent observations and discuss the implications for gene-specific regulation by chromatin remodeling machines.
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Affiliation(s)
- C L Peterson
- Program in Molecular Medicine and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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118
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Tang H, Liu Y, Madabusi L, Gilmour DS. Promoter-proximal pausing on the hsp70 promoter in Drosophila melanogaster depends on the upstream regulator. Mol Cell Biol 2000; 20:2569-80. [PMID: 10713179 PMCID: PMC85473 DOI: 10.1128/mcb.20.7.2569-2580.2000] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase II pauses in the promoter-proximal region of many genes during transcription. In the case of the hsp70 promoter from Drosophila melanogaster, this pause is long-lived and occurs even when the gene is not induced. Paused polymerase escapes during heat shock when the transcriptional activator heat shock factor associates with the promoter. However, pausing is still evident, especially when induction is at an intermediate level. Yeast Gal4 protein (Gal4p) will induce transcription of the hsp70 promoter in Drosophila when binding sites for Gal4p are positioned upstream from the hsp70 TATA element. To further our understanding of promoter-proximal pausing, we have analyzed the effect of Gal4p on promoter-proximal pausing in salivary glands of Drosophila larvae. Using permanganate genomic footprinting, we observed that various levels of Gal4p induction resulted in an even distribution of RNA polymerase throughout the first 76 nucleotides of the transcribed region. In contrast, promoter-proximal pausing still occurs on endogenous and transgenic hsp70 promoters in salivary glands when these promoters are induced by heat shock. We also determined that mutations introduced into the region where the polymerase pauses do not inhibit pausing in a cell-free system. Taken together, these results indicate that promoter-proximal pausing is dictated by the regulatory proteins interacting upstream from the core promoter region.
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Affiliation(s)
- H Tang
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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119
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Lis JT, Mason P, Peng J, Price DH, Werner J. P-TEFb kinase recruitment and function at heat shock loci. Genes Dev 2000. [DOI: 10.1101/gad.14.7.792] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
P-TEFb, a heterodimer of the kinase Cdk9 and cyclin T, was isolated as a factor that stimulates formation of productive transcription elongation complexes in vitro. Here, we show that P-TEFb is located at >200 distinct sites on Drosophila polytene chromosomes. Upon heat shock, P-TEFb, like the regulatory factor HSF, is rapidly recruited to heat shock loci, and this recruitment is blocked in an HSF mutant. Yet, HSF binding to DNA is not sufficient to recruit P-TEFb in vivo, and HSF and P-TEFb immunostainings within a heat shock locus are not coincident. Insight to the function of P-TEFb is offered by experiments showing that the direct recruitment of a Gal4-binding domain P-TEFb hybrid to an hsp70 promoter in Drosophilacells is sufficient to activate transcription in the absence of heat shock. Analyses of point mutants show this P-TEFb stimulation is dependent on Cdk9 kinase activity and on Cdk9's interaction with cyclin T. These results, coupled with the frequent colocalization of P-TEFb and the hypophosphorylated form of RNA polymerase II (Pol II) found at promoter-pause sites, support a model in which P-TEFb acts to stimulate promoter-paused Pol II to enter into productive elongation.
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120
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de La Serna IL, Carlson KA, Hill DA, Guidi CJ, Stephenson RO, Sif S, Kingston RE, Imbalzano AN. Mammalian SWI-SNF complexes contribute to activation of the hsp70 gene. Mol Cell Biol 2000; 20:2839-51. [PMID: 10733587 PMCID: PMC85505 DOI: 10.1128/mcb.20.8.2839-2851.2000] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
ATP-dependent chromatin-remodeling complexes are conserved among all eukaryotes and function by altering nucleosome structure to allow cellular regulatory factors access to the DNA. Mammalian SWI-SNF complexes contain either of two highly conserved ATPase subunits: BRG1 or BRM. To identify cellular genes that require mammalian SWI-SNF complexes for the activation of gene expression, we have generated cell lines that inducibly express mutant forms of the BRG1 or BRM ATPases that are unable to bind and hydrolyze ATP. The mutant subunits physically associate with at least two endogenous members of mammalian SWI-SNF complexes, suggesting that nonfunctional, dominant negative complexes may be formed. We determined that expression of the mutant BRG1 or BRM proteins impaired the ability of cells to activate the endogenous stress response gene hsp70 in response to arsenite, a metabolic inhibitor, or cadmium, a heavy metal. Activation of hsp70 by heat stress, however, was unaffected. Activation of the heme oxygenase 1 promoter by arsenite or cadmium and activation of the cadmium-inducible metallothionein promoter also were unaffected by the expression of mutant SWI-SNF components. Analysis of a subset of constitutively expressed genes revealed no or minimal effects on transcript levels. We propose that the requirement for mammalian SWI-SNF complexes in gene activation events will be specific to individual genes and signaling pathways.
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Affiliation(s)
- I L de La Serna
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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121
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Affiliation(s)
- M Vignali
- Howard Hughes Medical Institute, Department of Biochemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-4500, USA
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122
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Neely KE, Hassan AH, Wallberg AE, Steger DJ, Cairns BR, Wright AP, Workman JL. Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol Cell 1999; 4:649-55. [PMID: 10549297 DOI: 10.1016/s1097-2765(00)80216-6] [Citation(s) in RCA: 208] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The yeast SWI/SNF complex is required for the transcription of several yeast genes and has been shown to alter nucleosome structure in an ATP-dependent reaction. In this study, we show that the complex stimulated in vitro transcription from nucleosome templates in an activation domain-dependent manner. Transcription stimulation by SWI/SNF required an activation domain with which it directly interacts. The acidic activation domains of VP16, Gcn4, Swi5, and Hap4 interacted directly with the purified SWI/SNF complex and with the SWI/SNF complex in whole-cell extracts. The similarity of activation domain interactions and transcriptional stimulation between SWI/SNF and the SAGA histone acetyltransferase complex may account for their apparent overlapping functions in vivo.
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Affiliation(s)
- K E Neely
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802, USA
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123
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Bednar J, Studitsky VM, Grigoryev SA, Felsenfeld G, Woodcock CL. The nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryomicroscopy. Mol Cell 1999; 4:377-86. [PMID: 10518218 DOI: 10.1016/s1097-2765(00)80339-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcribing SP6 RNA polymerase was arrested at unique positions in the nucleosome core, and the complexes were analyzed using biochemical methods and electron cryomicroscopy. As the polymerase enters the nucleosome, it disrupts DNA-histone interactions behind and up to approximately 20 bp ahead of the elongation complex. After the polymerase proceeds 30-40 bp into the nucleosome, two intermediates are observed. In one, only the DNA ahead of the polymerase reassociates with the octamer. In the other, DNA both ahead of and behind the enzyme reassociates. These intermediates present a barrier to elongation. When the polymerase approaches the nucleosome dyad, it displaces the octamer, which is transferred to promoter-proximal DNA.
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Affiliation(s)
- J Bednar
- Department of Biology, University of Massachusetts-Amherst 01003, USA
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124
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Luse DS, Samkurashvili I. The transition from initiation to elongation by RNA polymerase II. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:289-300. [PMID: 10384293 DOI: 10.1101/sqb.1998.63.289] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- D S Luse
- Department of Molecular Biology, Lerner Research Institute, Cleveland Clinic Foundation, Ohio 44195, USA
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125
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Schnitzler GR, Sif S, Kingston RE. A model for chromatin remodeling by the SWI/SNF family. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:535-43. [PMID: 10384318 DOI: 10.1101/sqb.1998.63.535] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- G R Schnitzler
- Department of Molecular Biology, Massachusetts General Hospital, Boston 02114, USA
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126
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Varga-Weisz PD, Bonte EJ, Becker PB. Analysis of modulators of chromatin structure in Drosophila. Methods Enzymol 1999; 304:742-57. [PMID: 10372394 DOI: 10.1016/s0076-6879(99)04045-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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127
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Pfeifer GP, Chen HH, Komura J, Riggs AD. Chromatin structure analysis by ligation-mediated and terminal transferase-mediated polymerase chain reaction. Methods Enzymol 1999; 304:548-71. [PMID: 10372381 DOI: 10.1016/s0076-6879(99)04032-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- G P Pfeifer
- Department of Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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128
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Sathyanarayana UG, Freeman LA, Lee MS, Garrard WT. RNA polymerase-specific nucleosome disruption by transcription in vivo. J Biol Chem 1999; 274:16431-6. [PMID: 10347204 DOI: 10.1074/jbc.274.23.16431] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nucleosomal chromatin structure within genes is disrupted upon transcription by RNA polymerase II. To determine whether this disruption is caused by transcription per se as opposed to the RNA polymerase source, we engineered the yeast chromosomal HSP82 gene to be exclusively transcribed by bacteriophage T7 RNA polymerase in vivo. Interestingly, we found that a fraction of the T7-generated transcripts were 3' end processed and polyadenylated at or near the 3' ends of the hsp82 and the immediately downstream CIN2 genes. Surprisingly, the nucleosomal structure of the T7-transcribed hsp82 gene remained intact, in marked contrast to the disrupted structure generated by much weaker, basal level transcription of the wild type gene by RNA polymerase II under non-heat shock conditions. Therefore, disruption of chromatin structure by transcription is dependent on the RNA polymerase source. We propose that the observed RNA polymerase dependence for transcription-induced nucleosome disruption may be related either to the differential recruitment of chromatin remodeling complexes, the rates of histone octamer translocation and nucleosome reformation during polymerase traversal, and/or the degree of transient torsional stress generated by the elongating polymerase.
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Affiliation(s)
- U G Sathyanarayana
- Department of Molecular Biology and Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75235-9140, USA
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129
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Sudarsanam P, Cao Y, Wu L, Laurent BC, Winston F. The nucleosome remodeling complex, Snf/Swi, is required for the maintenance of transcription in vivo and is partially redundant with the histone acetyltransferase, Gcn5. EMBO J 1999; 18:3101-6. [PMID: 10357821 PMCID: PMC1171391 DOI: 10.1093/emboj/18.11.3101] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Snf/Swi, a nucleosome remodeling complex, is important for overcoming nucleosome-mediated repression of transcription in Saccharomyces cerevisiae. We have addressed the mechanism by which Snf/Swi controls transcription in vivo of an Snf/Swi-dependent promoter, that of the SUC2 gene. By single-cell analysis, our results show that Snf/Swi is required for activated levels of SUC2 expression in every cell of a population. In addition, Snf/Swi is required for maintenance of SUC2 transcription, suggesting that continuous chromatin remodeling is necessary to maintain an active transcriptional state. Finally, Snf/Swi and Gcn5, a histone acetyltransferase, have partially redundant roles in the control of SUC2 transcription, suggesting a functional overlap between two different mechanisms believed to overcome repression by nucleosomes, nucleosome remodeling and histone acetylation.
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MESH Headings
- Acetyltransferases/genetics
- Acetyltransferases/metabolism
- Carrier Proteins/genetics
- Chromosomal Proteins, Non-Histone
- DNA-Binding Proteins
- Epistasis, Genetic
- Fungal Proteins/genetics
- Fungal Proteins/metabolism
- Gene Expression Regulation, Fungal
- Genes, Reporter/genetics
- Green Fluorescent Proteins
- Histone Acetyltransferases
- Luminescent Proteins/analysis
- Luminescent Proteins/genetics
- Membrane Transport Proteins
- Models, Genetic
- Molecular Conformation
- Mutation
- Nucleosomes/chemistry
- Nucleosomes/genetics
- Plant Proteins/genetics
- Protein Kinases/genetics
- Protein Kinases/metabolism
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Temperature
- Templates, Genetic
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic/genetics
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Affiliation(s)
- P Sudarsanam
- Department of Genetics, Harvard Medical School, Boston, 200 Longwood Avenue, MA 02115, USA
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130
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Reines D, Conaway RC, Conaway JW. Mechanism and regulation of transcriptional elongation by RNA polymerase II. Curr Opin Cell Biol 1999; 11:342-6. [PMID: 10395562 PMCID: PMC3371606 DOI: 10.1016/s0955-0674(99)80047-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Over the past few years, biochemical and genetic studies have shed considerable light on the structure and function of the RNA polymerase II (pol II) elongation complex and the transcription factors that control it. Novel elongation factors have been identified and their mechanisms of action characterized in increasing detail; new insights into the biological roles of elongation factors have been gained from genetic studies of the regulation of mRNA synthesis in yeast; and intriguing links between the pol II elongation machinery and the pathways of DNA repair and recombination have emerged.
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Affiliation(s)
- D Reines
- Department of Biochemistry, Emory University School of Medicine, Rollins Research Center, 1510 Clifton Road, Atlanta, GA 30322, USA
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131
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Zaret K. Developmental competence of the gut endoderm: genetic potentiation by GATA and HNF3/fork head proteins. Dev Biol 1999; 209:1-10. [PMID: 10208738 DOI: 10.1006/dbio.1999.9228] [Citation(s) in RCA: 183] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A long-standing problem in developmental biology has been to understand how the embryonic germ layers gain the competence to differentiate into distinct cell types. Genetic studies have shown that members of the GATA and HNF3/fork head transcription factor families are essential for the formation and differentiation of gut endoderm tissues in worms, flies, and mammals. Recent in vivo footprinting studies have shown that GATA and HNF3 binding sites in chromatin are occupied on a silent gene in endoderm that has the potential to be activated solely in that germ layer. These and other data indicate that these evolutionarily conserved factors help impart the competence of a gene to be activated in development, a phenomenon called genetic potentiation. The mechanistic implications of genetic potentiation and its general significance are discussed.
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Affiliation(s)
- K Zaret
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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132
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Guyon JR, Narlikar GJ, Sif S, Kingston RE. Stable remodeling of tailless nucleosomes by the human SWI-SNF complex. Mol Cell Biol 1999; 19:2088-97. [PMID: 10022896 PMCID: PMC84002 DOI: 10.1128/mcb.19.3.2088] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/1998] [Accepted: 12/13/1998] [Indexed: 12/22/2022] Open
Abstract
The histone N-terminal tails have been shown previously to be important for chromatin assembly, remodeling, and stability. We have tested the ability of human SWI-SNF (hSWI-SNF) to remodel nucleosomes whose tails have been cleaved through a limited trypsin digestion. We show that hSWI-SNF is able to remodel tailless mononucleosomes and nucleosomal arrays, although hSWI-SNF remodeling of tailless nucleosomes is less effective than remodeling of nucleosomes with tails. Analogous to previous observations with tailed nucleosomal templates, we show both (i) that hSWI-SNF-remodeled trypsinized mononucleosomes and arrays are stable for 30 min in the remodeled conformation after removal of ATP and (ii) that the remodeled tailless mononucleosome can be isolated on a nondenaturing acrylamide gel as a novel species. Thus, nucleosome remodeling by hSWI-SNF can occur via interactions with a tailless nucleosome core.
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Affiliation(s)
- J R Guyon
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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133
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Abstract
Chromatin disruption and modification are associated with transcriptional regulation by diverse coactivators and corepressors. Here we discuss the possible structural basis and functional consequences of the observed alterations in chromatin associated with transcriptional activation and repression. Recent advances in defining the roles of individual histones and their domains in the assembly and maintenance of regulatory architectures provide a framework for understanding how chromatin remodelling machines, histone acetyltransferases and deacetylases function.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, Natational Institute of Child Health and Human Development, NIH, Building 18T, Room 106, Bethesda, MD 20892-5431, USA.
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134
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Abstract
The synthesis of mature and functional messenger RNA by eukaryotic RNA polymerase II (Pol II) is a complex, multistage process requiring the cooperative action of many cellular proteins. This process, referred to collectively as the transcription cycle, proceeds via five stages: preinitiation, initiation, promoter clearance, elongation, and termination. During the past few years, fundamental studies of the elongation stage of transcription have demonstrated the existence of several families of Pol II elongation factors governing the activity of Pol II. It is now clear that the elongation stage of transcription is a critical stage for the regulation of gene expression. In fact, two of these elongation factors, ELL and elongin, have been implicated in human cancer. This article will review the proteins involved in the regulation of the elongation stage of transcription by Pol II, describing the recent experimental findings that have propelled vigorous research on the properties and function of the elongating RNA polymerase II. --Shilatifard, A. Factors regulating the transcriptional elongation activity of RNA polymerase II.
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Affiliation(s)
- A Shilatifard
- Department of Biochemistry, St. Louis University School of Medicine, St. Louis, Missouri 63104, USA.
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135
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Piruat JI, Aguilera A. A novel yeast gene, THO2, is involved in RNA pol II transcription and provides new evidence for transcriptional elongation-associated recombination. EMBO J 1998; 17:4859-72. [PMID: 9707445 PMCID: PMC1170815 DOI: 10.1093/emboj/17.16.4859] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have identified two novel yeast genes, THO1 and THO2, that partially suppress the transcription defects of hpr1Delta mutants by overexpression. We show by in vivo transcriptional and recombinational analysis of tho2Delta cells that THO2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats, as previously shown for HPR1. The tho2Delta mutation reduces the transcriptional efficiency of yeast DNA sequences down to 25% of the wild-type levels and abolishes transcription of the lacZ sequence. In addition, tho2Delta causes a strong increase in the frequency of recombination between direct repeats (>2000-fold above wild-type levels). Some DNA repeats cannot even be maintained in the cell. This hyper-recombination phenotype is dependent on transcription and is not observed in DNA repeats that are not transcribed. The higher the impairment of transcription caused by tho2Delta, the higher the frequency of recombination of a particular DNA region. The tho2Delta mutation also increases the frequency of plasmid loss. Our work not only identifies a novel yeast gene, THO2, with similar function to HPR1, but also provides new evidence for transcriptional blocks as a source of recombination. We propose that there is a set of proteins including Hpr1p and Tho2p, in the absence of which RNA pol II transcription is stalled or blocked, causing genetic instability.
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Affiliation(s)
- J I Piruat
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Sevilla, Spain
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136
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Wu SY, Kershnar E, Chiang CM. TAFII-independent activation mediated by human TBP in the presence of the positive cofactor PC4. EMBO J 1998; 17:4478-90. [PMID: 9687514 PMCID: PMC1170779 DOI: 10.1093/emboj/17.15.4478] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
TFIID is a multiprotein complex comprised of the TATA-binding protein (TBP) and an array of TBP-associated factors (TAFIIs). Whereas TBP is sufficient for basal transcription in conjunction with other general transcription factors and RNA polymerase II, TAFIIs are additionally required for activator-dependent transcription in mammalian cell-free transcription systems. However, recent in vivo studies carried out in yeast suggest that TAFIIs are not globally required for activator function. The discrepancy between in vivo yeast studies and in vitro mammalian cell-free systems remains to be resolved. In this study, we describe a mammalian cell-free transcription system reconstituted with only recombinant proteins and epitope-tagged multiprotein complexes. Transcriptional activation can be recapitulated in this highly purified in vitro transcription system in the absence of TAFIIs. This TBP-mediated activation is not induced by human mediator, another transcriptional coactivator complex potentially implicated in activator response. In contrast, general transcription factors TFIIH and TFIIA play a significant role in TBP-mediated activation, which can be detected in vitro with Gal4 fusion proteins containing various transcriptional activation domains. Our data, therefore, suggest that TFIIH and TFIIA can mediate activator function in the absence of TAFIIs.
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Affiliation(s)
- S Y Wu
- Department of Biochemistry, University of Illinois, Urbana 61801, USA
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137
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Pinaud S, Mirkovitch J. Regulation of c-fos expression by RNA polymerase elongation competence. J Mol Biol 1998; 280:785-98. [PMID: 9671550 DOI: 10.1006/jmbi.1998.1905] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The molecular mechanisms underlying transcription elongation and their role in gene regulation are poorly characterized in eukaryotes. A number of genes, however, have been proposed to be regulated at the level of transcription elongation, including c-myc, c-fos and c-myb. Here, we analyze the control of transcription elongation at the mouse c-fos gene at the nucleotide level in intact cells. We find that RNA polymerases are engaged in the promoter-proximal part of the gene in the absence of gene activation signals and mRNA synthesis. Importantly, we determine that the engaged RNA polymerases originate from a continuous initiation of transcription which, in the absence of gene activation signals, terminate close to the promoter. We also observe that the c-fos gene presents an active chromatin conformation, with the promoter and upstream regulatory sequences constitutively occupied by proteins, accounting for the continuous initiation of RNA polymerase complexes. We propose that activation of c-fos gene expression results primarily from the assembly of elongation-competent RNA polymerases that can transcribe the complete gene. Our results suggest that the engaged RNA polymerases found downstream of a number of other eukaryotic promoters may be associated with transcription termination of elongation-incompetent polymerases in the absence of activating signals.
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Affiliation(s)
- S Pinaud
- Swiss Institute for Experimental Cancer Research (ISREC), Chemin des Boveresses 155, Epalinges, CH-1066, Switzerland
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138
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Abstract
Chromatin has shifted into the focus of attention as a key to understanding the regulation of nuclear processes such as transcription. Protein machines have been described that use the energy of ATP to render chromatin dynamic and hence active, but which may also be involved in chromatin assembly. The discovery of three different Drosophila nucleosome remodeling complexes that contain imitation switch (ISWI), an ATPase with a high degree of sequence conservation from yeast to human, points to a central function of this ATPase in chromatin dynamics.
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139
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Brown SA, Weirich CS, Newton EM, Kingston RE. Transcriptional activation domains stimulate initiation and elongation at different times and via different residues. EMBO J 1998; 17:3146-54. [PMID: 9606196 PMCID: PMC1170653 DOI: 10.1093/emboj/17.11.3146] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcriptional activators can stimulate multiple steps in the transcription process. We have used GAL4 fusion proteins to characterize the ability of different transcriptional activation domains to stimulate transcriptional elongation on the hsp70 gene in vitro. Stimulation of elongation apparently occurs via a mechanistic pathway different from that of stimulation of initiation: the herpes simplex virus VP16, heat shock factor 1 (HSF1) and amphipathic helix (AH) activation domains all stimulate initiation, but only VP16 and HSF1 stimulate elongation; and mutations in hydrophobic residues of the HSF1 activation domains impair stimulation of elongation but not of initiation, while mutations in adjacent acidic residues impair stimulation of initiation more than of elongation. Experiments in which activators were exchanged between initiation and elongation demonstrate that the elongation function of HSF1 will stimulate RNA polymerase that has initiated and is transcriptionally engaged. Transcriptional activators thus appear to have at least two distinct functions that reside in the same domain, and that act at different times to stimulate initiation and elongation.
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Affiliation(s)
- S A Brown
- Department of Genetics, Harvard Medical School, and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
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140
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Abstract
Transcription initiation by RNA polymerase II (RNA pol II) requires interaction between cis-acting promoter elements and trans-acting factors. The eukaryotic promoter consists of core elements, which include the TATA box and other DNA sequences that define transcription start sites, and regulatory elements, which either enhance or repress transcription in a gene-specific manner. The core promoter is the site for assembly of the transcription preinitiation complex, which includes RNA pol II and the general transcription fctors TBP, TFIIB, TFIIE, TFIIF, and TFIIH. Regulatory elements bind gene-specific factors, which affect the rate of transcription by interacting, either directly or indirectly, with components of the general transcriptional machinery. A third class of transcription factors, termed coactivators, is not required for basal transcription in vitro but often mediates activation by a broad spectrum of activators. Accordingly, coactivators are neither gene-specific nor general transcription factors, although gene-specific coactivators have been described in metazoan systems. Transcriptional repressors include both gene-specific and general factors. Similar to coactivators, general transcriptional repressors affect the expression of a broad spectrum of genes yet do not repress all genes. General repressors either act through the core transcriptional machinery or are histone related and presumably affect chromatin function. This review focuses on the global effectors of RNA polymerase II transcription in yeast, including the general transcription factors, the coactivators, and the general repressors. Emphasis is placed on the role that yeast genetics has played in identifying these factors and their associated functions.
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Affiliation(s)
- M Hampsey
- Department of Biochemistry, Division of Nucleic Acids Enzymology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854-5635, USA.
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141
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Nightingale KP, Wellinger RE, Sogo JM, Becker PB. Histone acetylation facilitates RNA polymerase II transcription of the Drosophila hsp26 gene in chromatin. EMBO J 1998; 17:2865-76. [PMID: 9582280 PMCID: PMC1170627 DOI: 10.1093/emboj/17.10.2865] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A number of activators are known to increase transcription by RNA polymerase (pol) II through protein acetylation. While the physiological substrates for those acetylases are poorly defined, possible targets include general transcription factors, activator proteins and histones. Using a cell-free system to reconstitute chromatin with increased histone acetylation levels, we directly tested for a causal role of histone acetylation in transcription by RNA pol II. Chromatin, containing either control or acetylated histones, was reconstituted to comparable nucleosome densities and characterized by electron microscopy after psoralen cross-linking as well as by in vitro transcription. While H1-containing control chromatin severely repressed transcription of our model hsp26 gene, highly acetylated chromatin was significantly less repressive. Acetylation of histones, and particularly of histone H4, affected transcription at the level of initiation. Monitoring the ability of the transcription machinery to associate with the promoter in chromatin, we found that heat shock factor, a crucial regulator of heat shock gene transcription, profited most from histone acetylation. These experiments demonstrate that histone acetylation can modulate activator access to their target sites in chromatin, and provide a causal link between histone acetylation and enhanced transcription initiation of RNA pol II in chromatin.
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Affiliation(s)
- K P Nightingale
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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142
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El Kharroubi A, Piras G, Zensen R, Martin MA. Transcriptional activation of the integrated chromatin-associated human immunodeficiency virus type 1 promoter. Mol Cell Biol 1998; 18:2535-44. [PMID: 9566873 PMCID: PMC110633 DOI: 10.1128/mcb.18.5.2535] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The regulation of human immunodeficiency virus type 1 (HIV-1) gene expression involves a complex interplay between cellular transcription factors, chromatin-associated proviral DNA, and the virus-encoded transactivator protein, Tat. Here we show that Tat transactivates the integrated HIV-1 long terminal repeat (LTR), even in the absence of detectable basal promoter activity, and this transcriptional activation is accompanied by chromatin remodeling downstream of the transcription initiation site, as monitored by increased accessibility to restriction endonucleases. However, with an integrated promoter lacking both Sp1 and NF-kappaB sites, Tat was unable to either activate transcription or induce changes in chromatin structure even when it was tethered to the HIV-1 core promoter upstream of the TATA box. Tat responsiveness was observed only when Sp1 or NF-kappaB was bound to the promoter, implying that Tat functions subsequent to the formation of a specific transcription initiation complex. Unlike Tat, NF-kappaB failed to stimulate the integrated transcriptionally silent HIV-1 promoter. Histone acetylation renders the inactive HIV-1 LTR responsive to NF-kappaB, indicating that a suppressive chromatin structure must be remodeled prior to transcriptional activation by NF-kappaB. Taken together, these results suggest that Sp1 and NF-kappaB are required for the assembly of transcriptional complexes on the integrated viral promoter exhibiting a continuum of basal activities, all of which are fully responsive to Tat.
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Affiliation(s)
- A El Kharroubi
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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143
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Ryan MP, Jones R, Morse RH. SWI-SNF complex participation in transcriptional activation at a step subsequent to activator binding. Mol Cell Biol 1998; 18:1774-82. [PMID: 9528749 PMCID: PMC121407 DOI: 10.1128/mcb.18.4.1774] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/1997] [Accepted: 01/06/1998] [Indexed: 02/07/2023] Open
Abstract
The SWI-SNF complex in yeast and related complexes in higher eukaryotes have been implicated in assisting gene activation by overcoming the repressive effects of chromatin. We show that the ability of the transcriptional activator GAL4 to bind to a site in a positioned nucleosome is not appreciably impaired in swi mutant yeast cells. However, chromatin remodeling that depends on a transcriptional activation domain shows a considerable, although not complete, SWI-SNF dependence, suggesting that the SWI-SNF complex exerts its major effect at a step subsequent to activator binding. We tested this idea further by comparing the SWI-SNF dependence of a reporter gene based on the GAL10 promoter, which has an accessible upstream activating sequence and a nucleosomal TATA element, with that of a CYC1-lacZ reporter, which has a relatively accessible TATA element. We found that the GAL10-based reporter gene showed a much stronger SWI-SNF dependence than did the CYC1-lacZ reporter with several different activators. Remarkably, transcription of the GAL10-based reporter by a GAL4-GAL11 fusion protein showed a nearly complete requirement for the SWI-SNF complex, strongly suggesting that SWI-SNF is needed to allow access of TFIID or the RNA polymerase II holoenzyme. Taken together, our results demonstrate that chromatin remodeling in vivo can occur by both SWI-SNF-dependent and -independent avenues and suggest that the SWI-SNF complex exerts its major effect in transcriptional activation at a step subsequent to transcriptional activator-promoter recognition.
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Affiliation(s)
- M P Ryan
- Molecular Genetics Program, Wadsworth Center, New York State Department of Health, and State University of New York School of Public Health, Albany 12201-2002, USA
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144
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Law A, Hirayoshi K, O'Brien T, Lis JT. Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila. Nucleic Acids Res 1998; 26:919-24. [PMID: 9461448 PMCID: PMC147354 DOI: 10.1093/nar/26.4.919] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A new method is described for cloning DNA sequences occupied by a specific protein on chromatin in vivo . The approach uses UV cross-linking to couple proteins covalently to DNA and the resulting complexes are then purified under stringent conditions. Particular adducts are immunoprocipitated with antibody to the protein of interest. The resulting DNA (iDNA) is amplified by PCR, cloned and characterized. The model system used was RNA polymerase II (Pol II), whose density on particular DNAs under various conditions is well documented. Pol II can exist in several states on DNA. While Pol II can simply be bound to DNA, the bulk of DNA-associated Pol II is transcriptionally engaged in either the transcribing or paused states. Paused Pol IIs that have previously been characterized are found at promoters and have the distinctive property that their transcription in isolated nuclei is stimulated by sarkosyl or high salt. Here we isolate and sequence DNAs that cross-link to Pol II molecules. We identify by nuclear run-on assays those DNAs that have Pol II engaged in transcription. Twenty one percent of the iDNA clones that have detectable transcriptionally engaged Pol II appear to be paused, in that they display sarkosyl-stimulated trancription in a nuclear run-on transcription assay. At least some of these map to the 5'-ends of genes. These results suggest that transcriptional pausing of Pol II is a general phenomenon in vivo.
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Affiliation(s)
- A Law
- Section of Biochemsitry, Molecular and Cellular Biology, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
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145
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Benjamin LR, Gilmour DS. Nucleosomes are not necessary for promoter-proximal pausing in vitro on the Drosophila hsp70 promoter. Nucleic Acids Res 1998; 26:1051-5. [PMID: 9461467 PMCID: PMC147342 DOI: 10.1093/nar/26.4.1051] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RNA polymerase II has been found to pause stably on several metazoan genes in a promoter-proximal region located 20-40 nt downstream from the start site of transcription. Escape of polymerase from this paused state has been proposed to be a rate limiting step in transcription of some genes. A study of the human hsp70 promoter showed that a nucleosome positioned downstream from the transcription start was a key component in establishing a stably paused polymerase in one cell-free system. We tested whether these results could be extended to the Drosophila hsp70 promoter in a Drosophila cell-free system and found that polymerase paused stably on the promoter even when the length of DNA downstream from the transcription start was not sufficient for assembly of a nucleosome. Our results indicate that a downstream nucleosome is not a universal requirement for stably pausing RNA polymerase in the promoter-proximal region.
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Affiliation(s)
- L R Benjamin
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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146
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Hartzog GA, Wada T, Handa H, Winston F. Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev 1998; 12:357-69. [PMID: 9450930 PMCID: PMC316481 DOI: 10.1101/gad.12.3.357] [Citation(s) in RCA: 375] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/1997] [Accepted: 12/08/1997] [Indexed: 02/05/2023]
Abstract
Previous characterization of the Saccharomyces cerevisiae Spt4, Spt5, and Spt6 proteins suggested that these proteins act as transcription factors that modify chromatin structure. In this work, we report new genetic and biochemical studies of Spt4, Spt5, and Spt6 that reveal a role for these factors in transcription elongation. We have isolated conditional mutations in SPT5 that can be suppressed in an allele-specific manner by mutations in the two largest subunits of RNA polymerase II (Pol II). Strikingly, one of these RNA Pol II mutants is defective for transcription elongation and the others cause phenotypes consistent with an elongation defect. In addition, we show that spt4, spt5, and spt6 mutants themselves have phenotypes suggesting defects in transcription elongation in vivo. Consistent with these findings, we show that Spt5 is physically associated with RNA Pol II in vivo, and have identified a region of sequence similarity between Spt5 and NusG, an Escherichia coli transcription elongation factor that binds directly to RNA polymerase. Finally, we show that Spt4 and Spt5 are tightly associated in a complex that does not contain Spt6. These results, taken together with the biochemical identification of a human Spt4-Spt5 complex as a transcription elongation factor (Wada et al. 1998), provide strong evidence that these factors are important for transcription elongation in vivo.
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Affiliation(s)
- G A Hartzog
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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147
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Wada T, Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, Sugimoto S, Yano K, Hartzog GA, Winston F, Buratowski S, Handa H. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev 1998; 12:343-56. [PMID: 9450929 PMCID: PMC316480 DOI: 10.1101/gad.12.3.343] [Citation(s) in RCA: 583] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/1997] [Accepted: 12/04/1997] [Indexed: 02/05/2023]
Abstract
We report the identification of a transcription elongation factor from HeLa cell nuclear extracts that causes pausing of RNA polymerase II (Pol II) in conjunction with the transcription inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). This factor, termed DRB sensitivity-inducing factor (DSIF), is also required for transcription inhibition by H8. DSIF has been purified and is composed of 160-kD (p160) and 14-kD (p14) subunits. Isolation of a cDNA encoding DSIF p160 shows it to be a homolog of the Saccharomyces cerevisiae transcription factor Spt5. Recombinant Supt4h protein, the human homolog of yeast Spt4, is functionally equivalent to DSIF p14, indicating that DSIF is composed of the human homologs of Spt4 and Spt5. In addition to its negative role in elongation, DSIF is able to stimulate the rate of elongation by RNA Pol II in a reaction containing limiting concentrations of ribonucleoside triphosphates. A role for DSIF in transcription elongation is further supported by the fact that p160 has a region homologous to the bacterial elongation factor NusG. The combination of biochemical studies on DSIF and genetic analysis of Spt4 and Spt5 in yeast, also in this issue, indicates that DSIF associates with RNA Pol II and regulates its processivity in vitro and in vivo.
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Affiliation(s)
- T Wada
- Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226, Japan
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148
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Orphanides G, LeRoy G, Chang CH, Luse DS, Reinberg D. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 1998; 92:105-16. [PMID: 9489704 DOI: 10.1016/s0092-8674(00)80903-4] [Citation(s) in RCA: 498] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The requirements for transcriptional activation by RNA polymerase II were examined using chromatin templates assembled in vitro and a transcription system composed of the human general transcription factors and RNA polymerase II. Activator-induced, energy-dependent chromatin remodeling promoted efficient preinitiation complex formation and transcription initiation, but was not sufficient for productive transcription. Polymerases that initiated transcription on remodeled chromatin templates encountered a block to transcription proximal to the promoter. Entry into productive transcription required an accessory factor present in HeLa cell nuclear extract, FACT (facilitates chromatin transcription), which we have purified. FACT acts subsequent to transcription initiation to release RNA polymerase II from a nucleosome-induced block to productive transcription. The biochemical properties and polypeptide composition of FACT suggest that it is a novel protein factor that facilitates transcript elongation through nucleosomes.
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Affiliation(s)
- G Orphanides
- Howard Hughes Medical Institute, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway 08854, USA
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149
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Yamaguchi Y, Wada T, Handa H. Interplay between positive and negative elongation factors: drawing a new view of DRB. Genes Cells 1998; 3:9-15. [PMID: 9581978 DOI: 10.1046/j.1365-2443.1998.00162.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DRB is a classic inhibitor of transcription by RNA polymerase II (pol II). Although it has been demonstrated that DRB inhibits the elongation step of transcription, its mode of action has been elusive. DRB also markedly inhibits human immunodeficiency virus (HIV) transcription, by targeting the elongation which is enhanced by the HIV-encoded transactivator Tat. Two factors essential for DRB action have recently been identified. These factors, positive transcription elongation factor b (P-TEFb) and DRB sensitivity-inducing factor (DSIF), positively and negatively regulate pol II elongation, and are likely to be relevant to the function of Tat. In this review, we summarize the recent findings on these factors, and discuss a possible model for the molecular mechanism of DRB action.
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Affiliation(s)
- Y Yamaguchi
- Department of Biomolecular Engineering, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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150
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Abstract
Eukaryotic messenger RNA (mRNA) synthesis is a complex multi-stage process that requires the concerted action of many cellular factors to generate a mature functional message. This elaborate process by RNA polymerase II (pol II) proceeds via multiple stages-preinitiation, initiation (Figure 1), promoter clearance, elongation (Figure 1) and termination - which have come to be referred to collectively as the transcription cycle. Although the preinitiation and initiation stages of transcription have received the most attention during the past decade, the past few years have been a watershed for biochemical studies of the pol II elongation complex. Recent studies have demonstrated the existence of several families of pol II elongation factors and nuclear proteins that can govern the activity of pol II during mRNA chain elongation. New findings have revealed that the elongation stage of transcription is a critical site for the regulation of gene expression. Evidence obtained to date suggests that eukaryotes regulate elongation by both 'general' and 'activator dependent' mechanisms. These mechanisms necessitate alteration of pol II's catalytic site, modification of chromatin structure, phosphorylation of the pol II carboxyl-terminal domain (CTD) and involvement of other components of the transcription machinery to increase the rate and efficiency of transcription elongation. This minireview is an annotation on the recent progress in studies of the biochemical mechanism and molecular regulation of the elongation stages of eukaryotic mRNA synthesis. The recent developments that have guided our understanding and propelled current research on transcription elongation by mammalian pol II will be described here.
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Affiliation(s)
- A Shilatifard
- Saint Louis University School of Medicine, Edward A. Doisy Department of Biochemistry and Molecular Biology, MO 63104, USA
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