201
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Treich I, Cairns BR, de los Santos T, Brewster E, Carlson M. SNF11, a new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2. Mol Cell Biol 1995; 15:4240-8. [PMID: 7623818 PMCID: PMC230663 DOI: 10.1128/mcb.15.8.4240] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The yeast SNF-SWI complex is required for transcriptional activation of diverse genes and has been shown to alter chromatin structure. The complex has at least 10 components, including SNF2/SWI2, SNF5, SNF6, SWI1/ADR6, and SWI3, and has been widely conserved in eukaryotes. Here we report the characterization of a new component. We identified proteins that interact in the two-hybrid system with the N-terminal region of SNF2, preceding the ATPase domain. In addition to SWI3, we recovered a new 19-kDa protein, designated SNF11. Like other SNF/SWI proteins, SNF11 functions as a transcriptional activator in genetic assays. SNF11 interacts with SNF2 in vitro and copurifies with the SNF-SWI complex from yeast cells. Using a specific antibody, we showed that SNF11 coimmunoprecipitates with members of the SNF-SWI complex and that SNF11 is tightly and stoichiometrically associated with the complex. Furthermore, SNF11 was detected in purified SNF-SWI complex by staining with Coomassie blue dye; its presence previously went unrecognized because it does not stain with silver. SNF11 interacts with a 40-residue sequence of SNF2 that is highly conserved, suggesting that SNF11 homologs exist in other organisms.
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Affiliation(s)
- I Treich
- Institute of Cancer Research, Columbia University, New York, New York 10032, USA
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202
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Varga-Weisz PD, Becker PB. Transcription factor-mediated chromatin remodelling: mechanisms and models. FEBS Lett 1995; 369:118-21. [PMID: 7641873 DOI: 10.1016/0014-5793(95)00549-o] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The association of DNA with nucleosomes in chromatin severely restricts the access of the regulatory factors that bring about transcription. In vivo active promoters are characterised by altered, almost transparent chromatin structures that allow the interaction of the transcriptional machinery. Recently, enzymatic activities have been discovered that facilitate the binding of transcription factors to chromatin by modifying nucleosomal structures in a process that requires energy. The mechanisms by which chromatin is remodelled may involve nucleosome movements, their transient unfolding, their partial or even complete disassembly. The dynamic properties of chromatin that underlie these structural changes are fundamental to the process of regulated gene expression.
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203
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Abstract
Polycomb-group proteins form chromatin complexes at target genes such as Ubx, providing a cellular memory of gene activity in early development and determining the later activity of the gene. The complexes, whose constituents vary depending on site and genomic context, initiate at specific sites, but can extend to involve larger chromatin domains. How they persist through cell proliferation and how they silence gene activity are still open issues.
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Affiliation(s)
- V Pirrotta
- Department of Zoology, University of Geneva, Switzerland
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204
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Gross CH, Shuman S. Mutational analysis of vaccinia virus nucleoside triphosphate phosphohydrolase II, a DExH box RNA helicase. J Virol 1995; 69:4727-36. [PMID: 7609038 PMCID: PMC189280 DOI: 10.1128/jvi.69.8.4727-4736.1995] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Vaccinia virus nucleoside triphosphate phosphohydrolase II (NPH-II), a 3'-to-5' RNA helicase, displays sequence similarity to members of the DExH family of nucleic acid-dependent nucleoside triphosphatases (NTPases). The contributions of the conserved GxGKT and DExH motifs to enzyme activity were assessed by alanine scanning mutagenesis. Histidine-tagged versions of NPH-II were expressed in vaccinia virus-infected BSC40 cells and purified by nickel affinity and conventional fractionation steps. Wild-type His-NPH-II was indistinguishable from native NPH-II with respect to RNA helicase, RNA binding, and nucleic acid-stimulated NTPase activities. The K-191-->A (K191A), D296A, and E297A mutant proteins bound RNA as well as wild-type His-NPH-II did, but they were severely defective in NTPase and helicase functions. The H299A mutant was active in RNA binding and NTP hydrolysis but was defective in duplex unwinding. Whereas the NTPase of wild-type NPH-II was stimulated > 10-fold by polynucleotide cofactors, the NTPase of the H299A mutant was nucleic acid independent. Because the specific NTPase activity of the H299A mutant in the absence of nucleic acid was near that of wild-type enzyme in the presence of DNA or RNA and because the Km for ATP was unaltered by the H299A substitution, we regard this mutation as a "gain-of-function" mutation and suggest that the histidine residue in the DExH box is required to couple the NTPase and helicase activities.
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Affiliation(s)
- C H Gross
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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205
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Eisen JA, Sweder KS, Hanawalt PC. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res 1995; 23:2715-23. [PMID: 7651832 PMCID: PMC307096 DOI: 10.1093/nar/23.14.2715] [Citation(s) in RCA: 566] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The SNF2 family of proteins includes representatives from a variety of species with roles in cellular processes such as transcriptional regulation (e.g. MOT1, SNF2 and BRM), maintenance of chromosome stability during mitosis (e.g. lodestar) and various aspects of processing of DNA damage, including nucleotide excision repair (e.g. RAD16 and ERCC6), recombinational pathways (e.g. RAD54) and post-replication daughter strand gap repair (e.g. RAD5). This family also includes many proteins with no known function. To better characterize this family of proteins we have used molecular phylogenetic techniques to infer evolutionary relationships among the family members. We have divided the SNF2 family into multiple subfamilies, each of which represents what we propose to be a functionally and evolutionarily distinct group. We have then used the subfamily structure to predict the functions of some of the uncharacterized proteins in the SNF2 family. We discuss possible implications of this evolutionary analysis on the general properties and evolution of the SNF2 family.
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Affiliation(s)
- J A Eisen
- Department of Biological Sciences, Stanford University, CA 94305-5020, USA
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206
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Abstract
The BDF1 gene of Saccharomyces cerevisiae is required for sporulation. Under starvation conditions, most cells from the bdf1 null mutant fail to undergo one or both meiotic divisions, and there is an absolute defect in spore formation. The Bdf1 protein localizes to the nucleus throughout all stages of the mitotic and meiotic cell cycles. Analysis of spread meiotic nuclei reveals that the Bdf1 protein is localized fairly uniformly along chromosomes, except that it is excluded specifically from the nucleolus. A bdf1 null mutant displays a reduced rate of vegetative growth and sensitivity to a DNA-damaging agent. The BDF1 gene encodes a 77-kDa protein that contains two bromodomains, sequence motifs of unknown function. Separation-of-function alleles suggest that only one of the two bromodomains is required for sporulation, whereas both are required for Bdf1 function in vegetative cells. We propose that the Bdf1 protein is a component of chromatin and that the mitotic and meiotic defects of the bdf1 null mutant result from alterations in chromatin structure.
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Affiliation(s)
- P Chua
- Department of Biology, Yale University, New Haven, Connecticut 06520-8103, USA
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207
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Li J, Broyles SS. The DNA binding domain of the vaccinia virus early transcription factor small subunit is an extended helicase-like motif. Nucleic Acids Res 1995; 23:1590-6. [PMID: 7784215 PMCID: PMC306902 DOI: 10.1093/nar/23.9.1590] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The vaccinia virus early transcription factor (VETF) is an ATP-dependent activator of the early class of viral genes. VETF is a heterodimeric protein that binds an initiator-like element surrounding the start site of transcription. Previous studies indicated that the small subunit of VETF contacts the promoter DNA. We have taken a mutational approach to determine sequences in the VETF small subunit that are important for DNA binding. Two types of sequences were targeted for mutation: ones resembling motifs that are conserved in the nucleic acid helicase family and positively charged residues in predicted alpha-helices. Mutations affecting transcription activation were clustered in two regions. One mutation that impaired DNA binding is located near the N-terminus within the putative ATP-binding pocket that comprises helicase domain I. DNA binding was also severely reduced by mutations in a sequence resembling helicase domain VI and two putative alpha-helices that flank this domain in the C-terminal third of the polypeptide. These results indicate that the DNA binding domain in the small subunit of VETF is not isolated within a separable domain as is the case with most transcription factors, but rather, spans most of the length of the 637 residue polypeptide. A model for VETF structure is suggested in which the active site for ATP hydrolysis is integrated within an extended DNA-binding domain such that the structure and function of each domain influences that of the other.
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Affiliation(s)
- J Li
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-1153, USA
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208
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Le Douarin B, Zechel C, Garnier JM, Lutz Y, Tora L, Pierrat P, Heery D, Gronemeyer H, Chambon P, Losson R. The N-terminal part of TIF1, a putative mediator of the ligand-dependent activation function (AF-2) of nuclear receptors, is fused to B-raf in the oncogenic protein T18. EMBO J 1995; 14:2020-33. [PMID: 7744009 PMCID: PMC398302 DOI: 10.1002/j.1460-2075.1995.tb07194.x] [Citation(s) in RCA: 434] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear receptors (NRs) bound to response elements mediate the effects of cognate ligands on gene expression. Their ligand-dependent activation function, AF-2, presumably acts on the basal transcription machinery through intermediary proteins/mediators. We have isolated a mouse nuclear protein, TIF1, which enhances RXR and RAR AF-2 in yeast and interacts in a ligand-dependent manner with several NRs in yeast and mammalian cells, as well as in vitro. Remarkably, these interactions require the amino acids constituting the AF-2 activating domain conserved in all active NRs. Moreover, the oestrogen receptor (ER) AF-2 antagonist hydroxytamoxifen cannot promote ER-TIF1 interaction. We propose that TIF1, which contains several conserved domains found in transcriptional regulatory proteins, is a mediator of ligand-dependent AF-2. Interestingly, the TIF1 N-terminal moiety is fused to B-raf in the mouse oncoprotein T18.
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Affiliation(s)
- B Le Douarin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Collège de France, Illkirch, Strasbourg
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209
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Yona E, Bangio H, Erlich P, Tepper SH, Katcoff DJ. The C-terminal domain of SIN1 in yeast interacts with a protein that binds the URS1 region of the yeast HO gene. MOLECULAR & GENERAL GENETICS : MGG 1995; 246:774-7. [PMID: 7898448 DOI: 10.1007/bf00290726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A protein or protein complex has previously been identified in Saccharomyces cerevisiae which both binds a short DNA sequence in URS1 of HO and interacts with SIN1. SIN1, which has some sequence similarity to mammalian HMG1, is an abundant chromatin protein in yeast and is thought to participate in the transcriptional repression of a specific family of genes. SIN1 binds DNA weakly, though it has no DNA binding specificity. Here we address the nature of the interaction between SIN1 and the specific DNA binding protein(s) to HO DNA. We show that the isolated C-terminal region of SIN1 can interact in vitro with the DNA binding protein, causing a supershift in a gel mobility shift assay. Interestingly, inclusion of the region in SIN1 which contains two acidic sequences, precludes the binding of recombinant protein to the DNA/protein complex.
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Affiliation(s)
- E Yona
- Department of Life Sciences, Bar Ilan University, Ramat Gan, Israel
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210
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Sheridan PL, Schorpp M, Voz ML, Jones KA. Cloning of an SNF2/SWI2-related protein that binds specifically to the SPH motifs of the SV40 enhancer and to the HIV-1 promoter. J Biol Chem 1995; 270:4575-87. [PMID: 7876228 DOI: 10.1074/jbc.270.9.4575] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We have isolated a human cDNA clone encoding HIP116, a protein that binds to the SPH repeats of the SV40 enhancer and to the TATA/inhibitor region of the human immunodeficiency virus (HIV)-1 promoter. The predicted HIP116 protein is related to the yeast SNF2/SWI2 transcription factor and to other members of this extended family and contains seven domains similar to those found in the vaccinia NTP1 ATPase. Interestingly, HIP116 also contains a C3HC4 zinc-binding motif (RING finger) interspersed between the ATPase motifs in an arrangement similar to that found in the yeast RAD5 and RAD16 proteins. The HIP116 amino terminus is unique among the members of this family, and houses a specific DNA-binding domain. Antiserum raised against HIP116 recognizes a 116-kDa nuclear protein in Western blots and specifically supershifts SV40 and HIV-1 protein-DNA complexes in gel shift experiments. The binding site for HIP116 on the SV40 enhancer directly overlaps the site for TEF-1, and like TEF-1, binding of HIP116 to the SV40 enhancer is destroyed by mutations that inhibit SPH enhancer activity in vivo. Purified fractions of HIP116 display strong ATPase activity that is preferentially stimulated by SPH DNA and can be inhibited specifically by antibodies to HIP116. These findings suggest that HIP116 might affect transcription, directly or indirectly, by acting as a DNA binding site-specific ATPase.
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Affiliation(s)
- P L Sheridan
- Salk Institute for Biological Studies, La Jolla, California 92037
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211
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Haviv I, Vaizel D, Shaul Y. The X protein of hepatitis B virus coactivates potent activation domains. Mol Cell Biol 1995; 15:1079-85. [PMID: 7823923 PMCID: PMC232011 DOI: 10.1128/mcb.15.2.1079] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Transactivation by hepatitis B virus X protein (pX) is promiscuous, but it requires cellular activators. To study the mode of action of pX, we coexpressed pX with Gal4-derived activators in a cotransfection system. Twelve different activators bearing different types of activation domains were compared for their response to pX. Because pX indirectly increases the amount of the activators, tools were developed to compare samples with equivalent amount of activators. We demonstrate that pX preferentially coactivates potent activators, especially those with acidic activation domains. Weak activators with nonacidic activation domains are not potentiated by pX. Interestingly, Gal4E1a, which is not rich in acidic residues but interacts with similar molecular targets, also responds to pX. The response to pX correlated with the strength of the activation domain. Collectively, these data imply that pX is a coactivator, which offers a molecular basis for the pleiotropic effects of pX on transcription.
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Affiliation(s)
- I Haviv
- Department of Molecular Genetics and Virology, Weizmann Institute of Science, Rehovot, Israel
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212
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Dunaief JL, Strober BE, Guha S, Khavari PA, Alin K, Luban J, Begemann M, Crabtree GR, Goff SP. The retinoblastoma protein and BRG1 form a complex and cooperate to induce cell cycle arrest. Cell 1994; 79:119-30. [PMID: 7923370 DOI: 10.1016/0092-8674(94)90405-7] [Citation(s) in RCA: 527] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The retinoblastoma tumor suppressor protein (RB) binds several cellular proteins involved in cell cycle progression. Using the yeast two-hybrid system, we found that RB bound specifically to the protein BRG1. BRG1 shares extensive sequence similarity to Drosophila brahma, an activator of homeotic gene expression, and the yeast transcriptional activator SNF2/SW12. BRG1 contains an RB-binding motif found in viral oncoproteins and bound to the A/B pocket and the hypophosphorylated form of RB. BRG1 did not bind RB in viral oncoprotein-transformed cells. Coimmunoprecipitation experiments suggested BRG1 associates with the RB family in vivo. In the human carcinoma cell line SW13, BRG1 exhibited tumor suppressor activity by inducing formation of flat, growth-arrested cells. This activity depended on the ability of BRG1 to cooperate and complex with RB, as both an RB-nonbinding mutant of BRG1 and the sequestration of RB by adenovirus E1A protein abolished flat cell formation.
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Affiliation(s)
- J L Dunaief
- Howard Hughes Medical Institute, Department of Microbiology, New York, New York
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213
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Auble DT, Hansen KE, Mueller CG, Lane WS, Thorner J, Hahn S. Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. Genes Dev 1994; 8:1920-34. [PMID: 7958867 DOI: 10.1101/gad.8.16.1920] [Citation(s) in RCA: 272] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Basal transcription of many genes in yeast is repressed by Mot1, an essential protein which is a member of the Snf2/Swi2 family of conserved nuclear factors. ADI is an ATP-dependent inhibitor of TATA-binding protein (TBP) binding to DNA that inhibits transcription in vitro. Here we demonstrate that ADI is encoded by the MOT1 gene. Mutation of MOT1 abolishes ADI activity and derepresses basal transcription in vitro and in vivo. Recombinant Mot1 removes TBP from DNA and Mot1 contains an ATPase activity which is essential for its function. Genetic interactions between Mot1 and TBP indicate that their functions are interlinked in vivo. These results provide a general model for understanding the mechanism of action of a large family of nuclear factors involved in processes such as transcription and DNA repair.
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Affiliation(s)
- D T Auble
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
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214
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Kwon H, Imbalzano AN, Khavari PA, Kingston RE, Green MR. Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex. Nature 1994; 370:477-81. [PMID: 8047169 DOI: 10.1038/370477a0] [Citation(s) in RCA: 621] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
CHROMATIN structure can affect the transcriptional activity of eukaryotic structural genes by blocking access of sequence-specific activator proteins (activators) to their promoter-binding sites. For example, the DNA-binding domain of the yeast GAL4 protein interacts very poorly with nucleosome cores compared with naked DNA2 (and see below), and binding of other activators is even more strongly inhibited. The way in which activators bind to nucleosomal DNA is therefore a critical aspect of transcriptional activation. Genetic studies have suggested that the multi-component SWI/SNF complex of Saccharomyces cerevisiae facilitates transcription by altering the structure of the chromatin. Here we identify and partially purify a human homologue of the yeast SWI/SNF complex (hSWI/SNF complex). We show that a partially purified hSWI/SNF complex mediates the ATP-dependent disruption of a nucleosome, thereby enabling the activators, GAL4-VP16 and GAL4-AH, to bind within a nucleosome core. We conclude that the hSWI/SNF complex acts directly to reorganize chromatin structure so as to facilitate binding of transcription factors.
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Affiliation(s)
- H Kwon
- Howard Hughes Medical Institute, Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester 01605
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215
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Renner K, Leger H, Wegner M. The POU domain protein Tst-1 and papovaviral large tumor antigen function synergistically to stimulate glia-specific gene expression of JC virus. Proc Natl Acad Sci U S A 1994; 91:6433-7. [PMID: 8022800 PMCID: PMC44216 DOI: 10.1073/pnas.91.14.6433] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Synergism between transcriptional activators is a powerful way of potentiating their function. Here we show that the glial POU domain protein Tst-1 (also known as Oct-6 and SCIP) and large tumor antigen (T antigen) synergistically increased transcription from both the early and the late promoters of papovavirus JC in glial cells. Synergism between both proteins did not require T-antigen-mediated DNA replication or direct binding of T antigen to the promoter. The ability of T antigen to functionally cooperate with Tst-1 was contained within its N-terminal region, shown by the fact that small tumor antigen (t antigen) could substitute for T antigen in transfection experiments. In addition to this functional synergism, a direct interaction between Tst-1 and T antigen was observed in vitro. Using deletion mutants of Tst-1 and T antigen, the POU domain of Tst-1 and the N-terminal region of T antigen were found to participate in this interaction. Because of the low levels of Tst-1 present in oligodendrocytes, synergism between Tst-1 and T antigen could be an important factor in establishing the lytic infection of oligodendrocytes by JC virus during the course of the fatal demyelinating disease progressive multifocal leukoencephalopathy.
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MESH Headings
- Antigens, Polyomavirus Transforming/biosynthesis
- Antigens, Polyomavirus Transforming/isolation & purification
- Antigens, Polyomavirus Transforming/metabolism
- Base Sequence
- Cell Line
- DNA Replication
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/isolation & purification
- DNA-Binding Proteins/metabolism
- Electrophoresis, Polyacrylamide Gel
- Gene Expression Regulation, Neoplastic
- Gene Expression Regulation, Viral
- Glioblastoma
- Glutathione Transferase/biosynthesis
- Humans
- Immunoblotting
- JC Virus/genetics
- JC Virus/metabolism
- Luciferases/biosynthesis
- Molecular Sequence Data
- Molecular Weight
- Mutagenesis
- Octamer Transcription Factor-6
- Plasmids
- Promoter Regions, Genetic
- Regulatory Sequences, Nucleic Acid
- Sequence Deletion
- Transcription Factors/biosynthesis
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Transcription, Genetic
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- K Renner
- Zentrum für Molekulare Neurobiologie, Universitäts-Krankenhaus Eppendorf, Hamburg, Germany
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216
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Côté J, Quinn J, Workman JL, Peterson CL. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 1994; 265:53-60. [PMID: 8016655 DOI: 10.1126/science.8016655] [Citation(s) in RCA: 659] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The SWI/SNF protein complex is required for the enhancement of transcription by many transcriptional activators in yeast. Here it is shown that the purified SWI/SNF complex is composed of 10 subunits and includes the SWI1, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products. The complex exhibited DNA-stimulated adenosine triphosphatase (ATPase) activity, but lacked helicase activity. The SWI/SNF complex caused a 10- to 30-fold stimulation in the binding of GAL4 derivatives to nucleosomal DNA in a reaction that required adenosine triphosphate (ATP) hydrolysis but was activation domain-independent. Stimulation of GAL4 binding by the complex was abolished by a mutant SWI2 subunit, and was increased by the presence of a histone-binding protein, nucleoplasmin. A direct ATP-dependent interaction between the SWI/SNF complex and nucleosomal DNA was detected. These observations suggest that a primary role of the SWI/SNF complex is to promote activator binding to nucleosomal DNA.
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Affiliation(s)
- J Côté
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802
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217
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Abstract
The yeast SNF/SWI proteins have a global role in transcriptional activation. This set of five proteins assists many gene-specific activators, most likely by altering chromatin structure to relieve repression. Recent work shows that the SNF/SWI proteins function together in a multiprotein complex and that SNF2 has DNA-dependent ATPase activity. SNF/SWI homologs have now been identified in Drosophila, mice and humans, suggesting a conserved role in transcriptional activation.
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Affiliation(s)
- M Carlson
- Department of Genetics and Development, Columbia University, New York, NY 10032
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218
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Abstract
A large 'SWI/SNF' general activator complex serves as a molecular machine to help a wide range of transcription factors overcome the specific repressive effects of chromatin.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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219
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Chiba H, Muramatsu M, Nomoto A, Kato H. Two human homologues of Saccharomyces cerevisiae SWI2/SNF2 and Drosophila brahma are transcriptional coactivators cooperating with the estrogen receptor and the retinoic acid receptor. Nucleic Acids Res 1994; 22:1815-20. [PMID: 8208605 PMCID: PMC308079 DOI: 10.1093/nar/22.10.1815] [Citation(s) in RCA: 268] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A set of genes (SWI1, SWI2/SNF2, SWI3, SNF5 and SNF6) in Saccharomyces cerevisiae are required for transcription of a variety of yeast genes. It was recently reported that the mammalian glucocorticoid receptor failed to activate transcription when transiently expressed in swi1-, swi2- or swi3- yeast strains. We report here that two highly related human cDNAs, hSNF2 alpha and -beta, encode amino acid sequences homologous to both the yeast SWI2/SNF2 and the Drosophila brahma. Similar to their yeast and Drosophila counterparts, both human cDNAs contain helicase motifs, a bromodomain, a highly charged C-terminal sequence and an N-terminal sequence rich in proline, glutamine and glycine. Tissue distribution of the mRNAs varied slightly. Transcriptional activation by the estrogen receptor and the retinoic acid receptor was enhanced by co-expression of either hSNF2 cDNA. No enhancement was observed for promoters which do not respond to nuclear receptors. We suggest that global transcriptional coactivators equivalent to the yeast SWI/SNF complex exist in mammalian cells.
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Affiliation(s)
- H Chiba
- Department of Microbiology, Institute of Medical Science, University of Tokyo, Japan
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220
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Identification and characterization of Drosophila relatives of the yeast transcriptional activator SNF2/SWI2. Mol Cell Biol 1994. [PMID: 7908117 DOI: 10.1128/mcb.14.4.2225] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Drosophila brahma (brm) gene encodes an activator of homeotic genes that is highly related to the yeast transcriptional activator SWI2 (SNF2), a potential helicase. To determine whether brm is a functional homolog of SWI2 or merely a member of a family of SWI2-related genes, we searched for additional Drosophila genes related to SWI2 and examined their function in yeast cells. In addition to brm, we identified one other Drosophila relative of SWI2: the closely related ISWI gene. The 1,027-residue ISWI protein contains the DNA-dependent ATPase domain characteristic of the SWI2 protein family but lacks the three other domains common to brm and SWI2. In contrast, the ISWI protein is highly related (70% identical) to the human hSNF2L protein over its entire length, suggesting that they may be functional homologs. The DNA-dependent ATPase domains of brm and SWI2, but not ISWI, are functionally interchangeable; a chimeric SWI2-brm protein partially rescued the slow growth of swi2- cells and supported transcriptional activation mediated by the glucocorticoid receptor in vivo in yeast cells. These findings indicate that brm is the closest Drosophila relative of SWI2 and suggest that brm and SWI2 play similar roles in transcriptional activation.
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221
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Peterson CL, Dingwall A, Scott MP. Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. Proc Natl Acad Sci U S A 1994; 91:2905-8. [PMID: 8159677 PMCID: PMC43482 DOI: 10.1073/pnas.91.8.2905] [Citation(s) in RCA: 315] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Saccharomyces cerevisiae SWI1, SWI2 (SNF2), SWI3, SNF5, and SNF6 gene products play a crucial role in the regulation of transcription. We provide here direct biochemical evidence that all five SWI/SNF polypeptides are components of a large multisubunit complex. These five polypeptides coelute from a gel-filtration column with an apparent molecular mass of approximately 2 MDa. The five SWI/SNF polypeptides do not copurify when extracts are prepared from swi- or snf- mutants. We show that SWI/SNF polypeptides also remain associated during an affinity-chromatography step followed by gel filtration. Assembly of the SWI/SNF complex is not disrupted by a mutation in the putative APT-binding site of SWI2, although this mutation eliminates SWI2 function.
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Affiliation(s)
- C L Peterson
- Program in Molecular Medicine, University of Massachussetts Medical Center, Worcester 01605
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222
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Affiliation(s)
- K LaMarco
- Tularik, Inc., South San Francisco, CA 94080
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223
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Abstract
Genetic and biochemical approaches have recently been used to demonstrate the pivotal role of chromatin structure in gene regulation at two levels of organization. The three-dimensional folding of DNA mediated by chromatin structural proteins over several hundred base pairs has been shown to be critical for the local control of both transcriptional activation and repression. Nuclear domains also exist in which the further long-range organization of chromatin over 5-50 kb exerts a global control on the transcription process.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, NICHD, NIH, Bethesda, Maryland 20892
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224
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Elfring LK, Deuring R, McCallum CM, Peterson CL, Tamkun JW. Identification and characterization of Drosophila relatives of the yeast transcriptional activator SNF2/SWI2. Mol Cell Biol 1994; 14:2225-34. [PMID: 7908117 PMCID: PMC358589 DOI: 10.1128/mcb.14.4.2225-2234.1994] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Drosophila brahma (brm) gene encodes an activator of homeotic genes that is highly related to the yeast transcriptional activator SWI2 (SNF2), a potential helicase. To determine whether brm is a functional homolog of SWI2 or merely a member of a family of SWI2-related genes, we searched for additional Drosophila genes related to SWI2 and examined their function in yeast cells. In addition to brm, we identified one other Drosophila relative of SWI2: the closely related ISWI gene. The 1,027-residue ISWI protein contains the DNA-dependent ATPase domain characteristic of the SWI2 protein family but lacks the three other domains common to brm and SWI2. In contrast, the ISWI protein is highly related (70% identical) to the human hSNF2L protein over its entire length, suggesting that they may be functional homologs. The DNA-dependent ATPase domains of brm and SWI2, but not ISWI, are functionally interchangeable; a chimeric SWI2-brm protein partially rescued the slow growth of swi2- cells and supported transcriptional activation mediated by the glucocorticoid receptor in vivo in yeast cells. These findings indicate that brm is the closest Drosophila relative of SWI2 and suggest that brm and SWI2 play similar roles in transcriptional activation.
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Affiliation(s)
- L K Elfring
- Department of Biology, University of California, Santa Cruz 95064
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225
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Cairns BR, Kim YJ, Sayre MH, Laurent BC, Kornberg RD. A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. Proc Natl Acad Sci U S A 1994; 91:1950-4. [PMID: 8127913 PMCID: PMC43282 DOI: 10.1073/pnas.91.5.1950] [Citation(s) in RCA: 313] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A complex containing the products of the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 genes and four additional polypeptides has been purified from extracts of the yeast Saccharomyces cerevisiae. Physical association of these proteins was demonstrated by copurification and coimmunoprecipitation. A potent DNA-dependent ATPase copurified with the complex, and this activity was evidently associated with SWI2/SNF2.
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Affiliation(s)
- B R Cairns
- Department of Cell Biology, Stanford University School of Medicine, CA 94305
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226
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Hörz W. [Chromatin structure and gene regulation]. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1994; 81:74-8. [PMID: 8145858 DOI: 10.1007/s001140050032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
It is becoming increasingly clear that the nucleosome, the basic repeat unit of eukaryotic chromatin, is involved also in gene regulation. In particular, the study of inducible genes has shown that nucleosomes contribute to the repressed basal state, and that they can be rearranged in response to induction. The role of the nucleosomes in gene regulation and possible mechanisms for their structural modulation are discussed.
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Affiliation(s)
- W Hörz
- Institut für Physiologische Chemie der Universität, München
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227
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228
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Matson SW, Bean DW, George JW. DNA helicases: enzymes with essential roles in all aspects of DNA metabolism. Bioessays 1994; 16:13-22. [PMID: 8141804 DOI: 10.1002/bies.950160103] [Citation(s) in RCA: 236] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
DNA helicases catalyze the disruption of the hydrogen bonds that hold the two strands of double-stranded DNA together. This energy-requiring unwinding reaction results in the formation of the single-stranded DNA required as a template or reaction intermediate in DNA replication, repair and recombination. A combination of biochemical and genetic studies have been used to probe and define the roles of the multiple DNA helicases found in E. coli. This work and similar efforts in eukaryotic cells, although far from complete, have established that DNA helicases are essential components of the machinery that interacts with the DNA molecule.
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Affiliation(s)
- S W Matson
- Department of Biology, University of North Carolina at Chapel Hill 27599
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229
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Doe CL, Murray JM, Shayeghi M, Hoskins M, Lehmann AR, Carr AM, Watts FZ. Cloning and characterisation of the Schizosaccharomyces pombe rad8 gene, a member of the SNF2 helicase family. Nucleic Acids Res 1993; 21:5964-71. [PMID: 8290359 PMCID: PMC310482 DOI: 10.1093/nar/21.25.5964] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Schizosaccharomyces pombe rad8 mutant is sensitive to both UV and gamma irradiation. We have cloned the rad8 gene by complementation of the UV sensitivity of a rad8.190 mutant strain. The gene comprises an open reading frame of 3.4 kb which does not contain any introns and is capable of encoding a 1133 amino acid protein of 129 kDa. Deletion of the gene indicates that it is not essential for cell viability. Recognisable motifs are present for a nuclear localisation signal, a RING finger and helicase domains. The predicted protein is a member of the SNF2 subfamily of proteins and shows particular homology to the Saccharomyces cerevisiae RAD5 protein. Double mutant analysis demonstrated that the rad8 mutant is not epistatic to mutants in the excision repair pathway (rad13) or checkpoint pathway (rad9). Analysis of radiation sensitivity though the cell cycle indicates that, unlike most other rad mutants, rad8 is most sensitive to irradiation during the G1/S period.
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Affiliation(s)
- C L Doe
- School of Biological Sciences, University of Sussex, Falmer, Brighton, UK
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230
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Khavari PA, Peterson CL, Tamkun JW, Mendel DB, Crabtree GR. BRG1 contains a conserved domain of the SWI2/SNF2 family necessary for normal mitotic growth and transcription. Nature 1993; 366:170-4. [PMID: 8232556 DOI: 10.1038/366170a0] [Citation(s) in RCA: 534] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Sequence-specific DNA binding activators of gene transcription may be assisted by SWI2 (SNF2), which contains a DNA-dependent ATPase domain. We have isolated a human complementary DNA encoding a 205K nuclear protein, BRG1, that contains extensive homology to SWI2 and Drosophila brahma. We report here that a SWI2/BRG1 chimera with the DNA-dependent ATPase domain replaced by corresponding human sequence restored normal mitotic growth and capacity for transcriptional activation to swi2- yeast cells. Point mutation of the conserved ATP binding site lysine abolished this complementation. This mutation in SWI2 exerted a dominant negative effect on transcription in yeast. A lysine to arginine substitution at the corresponding residue of BRG1 also generated a transcriptional dominant negative in human cells. BRG1 is exclusively nuclear and present in a high M(r) complex of about 2 x 10(6). These results show that the SWI2 family DNA-dependent ATPase domain has functional conservation between yeast and humans and suggest that a SWI/SNF protein complex is required for the activation of selective mammalian genes.
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Affiliation(s)
- P A Khavari
- Howard Hughes Medical Institute, Stanford University, California 94305
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231
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Li J, Broyles S. The DNA-dependent ATPase activity of vaccinia virus early gene transcription factor is essential for its transcription activation function. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80688-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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