1
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Flores Cortes E, Saddoris SM, Owens AK, Gibeault R, Depledge DP, Schang LM. Histone H2A variant H2A.B is enriched in transcriptionally active and replicating HSV-1 lytic chromatin. J Virol 2024; 98:e0201523. [PMID: 38451083 PMCID: PMC11019955 DOI: 10.1128/jvi.02015-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections but the precise mechanisms are not fully defined. Nucleosomes are dynamic: they slide, breathe, assemble, and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent, whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X, and macroH2A were enhanced in infected cells, whereas those of H2A.B were uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, as well as ectopic and endogenous H2B were assembled into HSV-1 chromatin evenly throughout the genome but canonical H2A was relatively depleted whereas H2A.B was enriched, particularly in the most dynamic viral chromatin. When viral transcription and DNA replication were restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants. IMPORTANCE Herpes simplex virus 1 (HSV-1) transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed epigenetic mechanisms of regulation of HSV-1 transcription have not been fully characterized and may differ from those regulating cellular transcription. Whereas lytic HSV-1 chromatin is unusually dynamic, latent silenced HSV-1 chromatin is not. The mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment of the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding of its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
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Affiliation(s)
- Esteban Flores Cortes
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Sarah M. Saddoris
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Arryn K. Owens
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Rebecca Gibeault
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel P. Depledge
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
| | - Luis M. Schang
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Flores E, Saddoris SM, Owens AK, Gibeault R, Depledge DP, Schang LM. Histone H2A variant H2A.B is enriched in transcriptionally active HSV-1 lytic chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573075. [PMID: 38187672 PMCID: PMC10769327 DOI: 10.1101/2023.12.22.573075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections, but the precise mechanisms are not fully defined. Nucleosomes are dynamic; they slide, breathe, assemble and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X and macroH2A were enhanced in infected cells, whereas those of H2A.B uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, ectopic, and endogenous H2B, were assembled into HSV-1 chromatin evenly throughout the genome, but canonical H2A was relatively depleted from the viral chromatin whereas H2A.B was enriched in the most dynamic viral chromatin. When viral transcription was restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency, and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants. Importance HSV-1 transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed mechanisms of regulation of HSV-1 transcription by epigenetics have not been fully characterized and may differ from those regulating cellular transcription. In particular, the lytic HSV-1 chromatin is unusually dynamic, whereas the latent silenced one is not, but the mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment on the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding for its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
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3
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Dionisi S, Piera K, Baumschlager A, Khammash M. Implementation of a Novel Optogenetic Tool in Mammalian Cells Based on a Split T7 RNA Polymerase. ACS Synth Biol 2022; 11:2650-2661. [PMID: 35921263 PMCID: PMC9396705 DOI: 10.1021/acssynbio.2c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Optogenetic tools are widely used to control gene expression
dynamics
both in prokaryotic and eukaryotic cells. These tools are used in
a variety of biological applications from stem cell differentiation
to metabolic engineering. Despite some tools already available in
bacteria, no light-inducible system currently exists to control gene
expression independently from mammalian transcriptional and/or translational
machineries thus working orthogonally to endogenous regulatory mechanisms.
Such a tool would be particularly important in synthetic biology,
where orthogonality is advantageous to achieve robust activation of
synthetic networks. Here we implement, characterize, and optimize
a new optogenetic tool in mammalian cells based on a previously published
system in bacteria called Opto-T7RNAPs. The tool is orthogonal to
the cellular machinery for transcription and consists of a split T7
RNA polymerase coupled with the blue light-inducible magnets system
(mammalian OptoT7–mOptoT7). In our study we exploited the T7
polymerase’s viral origins to tune our system’s expression
level, reaching up to an almost 20-fold change activation over the
dark control. mOptoT7 is used here to generate mRNA for protein expression,
shRNA for protein inhibition, and Pepper aptamer for RNA visualization.
Moreover, we show that mOptoT7 can mitigate the gene expression burden
when compared to another optogenetic construct. These properties make
mOptoT7 a powerful new tool to use when orthogonality and viral RNA
species (that lack endogenous RNA modifications) are desired.
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Affiliation(s)
- Sara Dionisi
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Karol Piera
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Armin Baumschlager
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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4
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Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy. Ultramicroscopy 2010; 110:682-8. [DOI: 10.1016/j.ultramic.2010.02.032] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Thakar A, Gupta P, McAllister WT, Zlatanova J. Histone Variant H2A.Z Inhibits Transcription in Reconstituted Nucleosomes. Biochemistry 2010; 49:4018-26. [DOI: 10.1021/bi1001618] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Amit Thakar
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071
| | - Pooja Gupta
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071
| | - William T. McAllister
- Department of Cell Biology, University of Medicine and Dentistry of New Jersey, Stratford, New Jersey 08084
| | - Jordanka Zlatanova
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071
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6
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Phosphorylation of histone H3T6 by PKCbeta(I) controls demethylation at histone H3K4. Nature 2010; 464:792-6. [PMID: 20228790 DOI: 10.1038/nature08839] [Citation(s) in RCA: 230] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 01/19/2010] [Indexed: 12/11/2022]
Abstract
Demethylation at distinct lysine residues in histone H3 by lysine-specific demethylase 1 (LSD1) causes either gene repression or activation. As a component of co-repressor complexes, LSD1 contributes to target gene repression by removing mono- and dimethyl marks from lysine 4 of histone H3 (H3K4). In contrast, during androgen receptor (AR)-activated gene expression, LSD1 removes mono- and dimethyl marks from lysine 9 of histone H3 (H3K9). Yet, the mechanisms that control this dual specificity of demethylation are unknown. Here we show that phosphorylation of histone H3 at threonine 6 (H3T6) by protein kinase C beta I (PKCbeta(I), also known as PRKCbeta) is the key event that prevents LSD1 from demethylating H3K4 during AR-dependent gene activation. In vitro, histone H3 peptides methylated at lysine 4 and phosphorylated at threonine 6 are no longer LSD1 substrates. In vivo, PKCbeta(I) co-localizes with AR and LSD1 on target gene promoters and phosphorylates H3T6 after androgen-induced gene expression. RNA interference (RNAi)-mediated knockdown of PKCbeta(I) abrogates H3T6 phosphorylation, enhances demethylation at H3K4, and inhibits AR-dependent transcription. Activation of PKCbeta(I) requires androgen-dependent recruitment of the gatekeeper kinase protein kinase C (PKC)-related kinase 1 (PRK1). Notably, increased levels of PKCbeta(I) and phosphorylated H3T6 (H3T6ph) positively correlate with high Gleason scores of prostate carcinomas, and inhibition of PKCbeta(I) blocks AR-induced tumour cell proliferation in vitro and cancer progression of tumour xenografts in vivo. Together, our data establish that androgen-dependent kinase signalling leads to the writing of the new chromatin mark H3T6ph, which in consequence prevents removal of active methyl marks from H3K4 during AR-stimulated gene expression.
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Abstract
Chromatin is a highly regulated nucleoprotein complex through which genetic material is structured and maneuvered to elicit cellular processes, including transcription, cell division, differentiation, and DNA repair. In eukaryotes, the core of this structure is composed of nucleosomes, or repetitive histone octamer units typically enfolded by 147 base pairs of DNA. DNA is arranged and indexed through these nucleosomal structures to adjust local chromatin compaction and accessibility. Histones are subject to multiple covalent posttranslational modifications, some of which alter intrinsic chromatin properties, others of which present or hinder binding modules for non-histone, chromatin-modifying complexes. Although certain histone marks correlate with different biological outputs, we have yet to fully appreciate their effects on transcription and other cellular processes. Tremendous advancements over the past years have uncovered intriguing histone-related matters and raised important related questions. This review revisits past breakthroughs and discusses novel developments that pertain to histone posttranslational modifications and the affects they have on transcription and DNA packaging.
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Affiliation(s)
- Eric I Campos
- Department of Biochemistry, Howard Hughes Medical Institute, NYU School of Medicine, New York, New York 10016, USA
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8
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9
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Hizume K, Nakai T, Araki S, Prieto E, Yoshikawa K, Takeyasu K. Removal of histone tails from nucleosome dissects the physical mechanisms of salt-induced aggregation, linker histone H1-induced compaction, and 30-nm fiber formation of the nucleosome array. Ultramicroscopy 2009; 109:868-73. [PMID: 19328628 DOI: 10.1016/j.ultramic.2009.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In order to reveal the roles of histone tails in the formation of higher-order chromatin structures, we employed atomic force microscopy (AFM), and an in vitro reconstitution system to examine the properties of reconstituted chromatin composed of tail-less histones and a long DNA (106-kb plasmid) template. The tail-less nucleosomes did not aggregate at high salt concentrations or with an excess amount of core histones, in contrast with the behavior of nucleosomal arrays composed of nucleosomes containing normal, N-terminal tails. Analysis of our nucleosome distributions reveals that the attractive interaction between tail-less nucleosomes is weakened. Addition of linker histone H1 into the tail-less nucleosomal array failed to promote the formation of 30nm chromatin fibers that are usually formed in the normal nucleosomal array. These results demonstrate that the attractive interaction between nucleosomes via histone tails plays a critical role in the formation of the uniform 30-nm chromatin fiber.
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Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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10
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Oduro AK, Fritsch MK, Murdoch FE. Chromatin context dominates estrogen regulation of pS2 gene expression. Exp Cell Res 2008; 314:2796-810. [PMID: 18662686 DOI: 10.1016/j.yexcr.2008.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 07/07/2008] [Accepted: 07/07/2008] [Indexed: 12/29/2022]
Abstract
Chromatin structure and transcription factor activity collaborate to set the transcription level of a gene. Our understanding of the relative contributions of each of these factors at a specific gene is limited. We studied the effects of an altered chromatin environment on the activity of the estrogen-responsive pS2 promoter. We created stable cell lines with the pS2 promoter situated in an alternative chromatin site in addition to it being in its native site. Both promoters were estrogen-responsive for estrogen receptor alpha (ERalpha) recruitment, but transcription was inducible only at the native site. At the recombinant site, transcription was high and constitutive. Higher histone H3 and H4 acetylation (acH3 and acH4), as well as trimethylated lysine 4 on histone H3 levels, was observed at the recombinant site compared to the native site in vehicle treated cells. Inhibition of histone deacetylases (HDACs) resulted in increased acH4, but only modest increases in acH3, ERalpha binding and basal transcription at the native pS2 site. Inhibiting HDACs had no effect on transcription from the recombinant site. These data suggest that highly active chromatin is not only permissive for transcription, but can override the requirement for the transcription factor at an inducible promoter.
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Affiliation(s)
- Akua K Oduro
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, MSC 5250, 1300 University Avenue, Madison, WI 53706, USA
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11
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Metzger E, Yin N, Wissmann M, Kunowska N, Fischer K, Friedrichs N, Patnaik D, Higgins JMG, Potier N, Scheidtmann KH, Buettner R, Schüle R. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation. Nat Cell Biol 2007; 10:53-60. [PMID: 18066052 DOI: 10.1038/ncb1668] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Accepted: 11/23/2007] [Indexed: 12/14/2022]
Abstract
Posttranslational modifications of histones such as methylation, acetylation and phosphorylation regulate chromatin structure and gene expression. Here we show that protein-kinase-C-related kinase 1 (PRK1) phosphorylates histone H3 at threonine 11 (H3T11) upon ligand-dependent recruitment to androgen receptor target genes. PRK1 is pivotal to androgen receptor function because PRK1 knockdown or inhibition impedes androgen receptor-dependent transcription. Blocking PRK1 function abrogates androgen-induced H3T11 phosphorylation and inhibits androgen-induced demethylation of histone H3. Moreover, serine-5-phosphorylated RNA polymerase II is no longer observed at androgen receptor target promoters. Phosphorylation of H3T11 by PRK1 accelerates demethylation by the Jumonji C (JmjC)-domain-containing protein JMJD2C. Thus, phosphorylation of H3T11 by PRK1 establishes a novel chromatin mark for gene activation, identifying PRK1 as a gatekeeper of androgen receptor-dependent transcription. Importantly, levels of PRK1 and phosphorylated H3T11 correlate with Gleason scores of prostate carcinomas. Finally, inhibition of PRK1 blocks proliferation of androgen receptor-induced tumour cell proliferation, making PRK1 a promising therapeutic target.
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Affiliation(s)
- Eric Metzger
- Universitäts-Frauenklinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, 79106 Freiburg, Germany
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12
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Hizume K, Araki S, Yoshikawa K, Takeyasu K. Topoisomerase II, scaffold component, promotes chromatin compaction in vitro in a linker-histone H1-dependent manner. Nucleic Acids Res 2007; 35:2787-99. [PMID: 17430970 PMCID: PMC1885653 DOI: 10.1093/nar/gkm116] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
TopoisomeraseII (Topo II) is a major component of chromosomal scaffolds and essential for mitotic chromosome condensation, but the mechanism of this action remains unknown. Here, we used an in vitro chromatin reconstitution system in combination with atomic force and fluorescence microscopic analyses to determine how Topo II affects chromosomal structure. Topo II bound to bare DNA and clamped the two DNA strands together, even in the absence of ATP. In addition, Topo II promoted chromatin compaction in a manner dependent on histone H1 but independent of ATP. Histone H1-induced 30-nm chromatin fibers were converted into a large complex by Topo II. Fluorescence microscopic analysis of the Brownian motion of chromatin stained with 4′,6-diamidino-2-phenylindole showed that the reconstituted chromatin became larger following the addition of Topo II in the presence but not the absence of histone H1. Based on these findings, we propose that chromatin packing is triggered by histone H1-dependent, Topo II-mediated clamping of DNA strands.
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Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan and Department of Physics, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Sumiko Araki
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan and Department of Physics, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kenichi Yoshikawa
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan and Department of Physics, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kunio Takeyasu
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan and Department of Physics, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- *To whom correspondence should be addressed +81-75-753-6852+81-75-753-6852
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13
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Wissmann M, Yin N, Müller JM, Greschik H, Fodor BD, Jenuwein T, Vogler C, Schneider R, Günther T, Buettner R, Metzger E, Schüle R. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat Cell Biol 2007; 9:347-53. [PMID: 17277772 DOI: 10.1038/ncb1546] [Citation(s) in RCA: 462] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 01/02/2007] [Indexed: 01/27/2023]
Abstract
Posttranslational modifications of histones, such as methylation, regulate chromatin structure and gene expression. Recently, lysine-specific demethylase 1 (LSD1), the first histone demethylase, was identified. LSD1 interacts with the androgen receptor and promotes androgen-dependent transcription of target genes by ligand-induced demethylation of mono- and dimethylated histone H3 at Lys 9 (H3K9) only. Here, we identify the Jumonji C (JMJC) domain-containing protein JMJD2C as the first histone tridemethylase regulating androgen receptor function. JMJD2C interacts with androgen receptor in vitro and in vivo. Assembly of ligand-bound androgen receptor and JMJD2C on androgen receptor-target genes results in demethylation of trimethyl H3K9 and in stimulation of androgen receptor-dependent transcription. Conversely, knockdown of JMJD2C inhibits androgen-induced removal of trimethyl H3K9, transcriptional activation and tumour cell proliferation. Importantly, JMJD2C colocalizes with androgen receptor and LSD1 in normal prostate and in prostate carcinomas. JMJD2C and LSD1 interact and both demethylases cooperatively stimulate androgen receptor-dependent gene transcription. In addition, androgen receptor, JMJD2C and LSD1 assemble on chromatin to remove methyl groups from mono, di and trimethylated H3K9. Thus, our data suggest that specific gene regulation requires the assembly and coordinate action of demethylases with distinct substrate specificities.
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MESH Headings
- Animals
- Cell Line
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Chlorocebus aethiops
- Gene Expression Regulation/drug effects
- HeLa Cells
- Histone Demethylases
- Histones/metabolism
- Humans
- Jumonji Domain-Containing Histone Demethylases
- Male
- Metribolone/pharmacology
- MicroRNAs/genetics
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oxidoreductases, N-Demethylating/genetics
- Oxidoreductases, N-Demethylating/metabolism
- Prostate-Specific Antigen/genetics
- Prostate-Specific Antigen/metabolism
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Protein Binding/drug effects
- RNA, Small Interfering/genetics
- Receptors, Androgen/analysis
- Receptors, Androgen/metabolism
- Receptors, Glucocorticoid/genetics
- Receptors, Glucocorticoid/metabolism
- Receptors, Progesterone/genetics
- Receptors, Progesterone/metabolism
- Response Elements/genetics
- Tissue Kallikreins/genetics
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transfection
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Affiliation(s)
- Melanie Wissmann
- Universitäts-Frauenklinik und Zentrum für Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, 79106 Freiburg, Germany
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14
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Hizume K, Yoshimura SH, Kumeta M, Takeyasu K. Structural organization of dynamic chromatin. Subcell Biochem 2007; 41:3-28. [PMID: 17484121 DOI: 10.1007/1-4020-5466-1_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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15
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Lavelle C. Transcription elongation through a chromatin template. Biochimie 2006; 89:516-27. [PMID: 17070642 DOI: 10.1016/j.biochi.2006.09.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 09/26/2006] [Indexed: 10/24/2022]
Abstract
DNA transaction events occurring during cell life (replication, transcription, recombination, repair, cell division) are always linked to severe changes in the topological state of the double helix. However, since naked DNA almost does not exist in eukaryote nucleus but rather interacts with various proteins, including ubiquitous histones, these topological changes happen in a chromatin context. This review focuses on the role of chromatin fiber structure and dynamics in the regulation of transcription, with an almost exclusive emphasis on the elongation step. Beside a brief overview of our knowledge about transcribed chromatin, we will see how recent mechanistic and biochemical studies give us new insights into the way cell could modulate DNA supercoiling and chromatin conformational dynamics. The participation of topoisomerases in this complex ballet is discussed, since recent data suggest that their role could be closely related to the precise chromatin structure. Lastly, some future prospects to carry on are proposed, hoping this review will help in stimulating discussions and further investigations in the field.
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Affiliation(s)
- Christophe Lavelle
- Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif, France.
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16
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Hublitz P, Kunowska N, Mayer UP, Müller JM, Heyne K, Yin N, Fritzsche C, Poli C, Miguet L, Schupp IW, van Grunsven LA, Potiers N, van Dorsselaer A, Metzger E, Roemer K, Schüle R. NIR is a novel INHAT repressor that modulates the transcriptional activity of p53. Genes Dev 2006; 19:2912-24. [PMID: 16322561 PMCID: PMC1315397 DOI: 10.1101/gad.351205] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Most transcriptional repression pathways depend on the targeted deacetylation of histone tails. In this report, we characterize NIR, a novel transcriptional corepressor with inhibitor of histone acetyltransferase (INHAT) activity. NIR (Novel INHAT Repressor) is ubiquitously expressed throughout embryonic development and adulthood. NIR is a potent transcriptional corepressor that is not blocked by histone deacetylase inhibitors and is capable of silencing both basal and activator-driven transcription. NIR directly binds to nucleosomes and core histones and prevents acetylation by histone acetyltransferases, thus acting as a bona fide INHAT. Using a tandem affinity purification approach, we identified the tumor suppressor p53 as a NIR-interacting partner. Association of p53 and NIR was verified in vitro and in vivo. Upon recruitment by p53, NIR represses transcription of both p53-dependent reporters and endogenous target genes. Knock-down of NIR by RNA interference significantly enhances histone acetylation at p53-regulated promoters. Moreover, p53-dependent apoptosis is robustly increased upon depletion of NIR. In summary, our findings describe NIR as a novel INHAT that plays an important role in the control of p53 function.
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Affiliation(s)
- Philip Hublitz
- Frauenklinik der Albert-Ludwigs-Universität Freiburg, Zentrale Klinische Forschung, D-79106 Freiburg, Germany
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17
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Hizume K, Yoshimura SH, Takeyasu K. Linker histone H1 per se can induce three-dimensional folding of chromatin fiber. Biochemistry 2005; 44:12978-89. [PMID: 16185066 DOI: 10.1021/bi050623v] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Higher-order architectures of chromosomes play important roles in the regulation of genome functions. To understand the molecular mechanism of genome packing, an in vitro chromatin reconstitution method and a single-molecule imaging technique (atomic force microscopy) were combined. In 50 mM NaCl, well-stretched beads-on-a-string chromatin fiber was observed. However, in 100 mM NaCl, salt-induced interaction between nucleosomes caused partial aggregation. Addition of histone H1 promoted a further folding of the fiber into thicker fibers 20-30 nm in width. Micrococcal nuclease digestion of these thicker fibers produced an approximately 170 bp fragment of nucleosomal DNA, which was approximately 20 bp longer than in the absence of histone H1 ( approximately 150 bp), indicating that H1 is correctly placed at the linker region. The width of the fiber depended on the ionic strength. Widths of 20 nm in 50 mM NaCl became 30 nm as the ionic strength was changed to 100 mM. On the basis of these results, a flexible model of chromatin fiber formation was proposed, where the mode of the fiber compaction changes depending both on salt environment and linker histone H1. The biological significance of this property of the chromatin architecture will be apparent in the closed segments ( approximately 100 kb) between SAR/MAR regions.
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Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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18
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Yoshikawa Y, Hizume K, Oda Y, Takeyasu K, Araki S, Yoshikawa K. Protective effect of vitamin C against double-strand breaks in reconstituted chromatin visualized by single-molecule observation. Biophys J 2005; 90:993-9. [PMID: 16284271 PMCID: PMC1367124 DOI: 10.1529/biophysj.105.069963] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Direct attack to genomic DNA by reactive oxygen species causes various types of lesions, including base modifications and strand breaks. The most significant lesion is considered to be an unrepaired double-strand break that can lead to fatal cell damage. We directly observed double-strand breaks of DNA in reconstituted chromatin stained by a fluorescent cyanine dye, YOYO (quinolinium, 1,1'-[1,3- propanediylbis[(dimethyliminio)-3,1- propanediyl]]bis[4-[(3-methyl-2(3H)-benzoxazolylidene)methyl]]-, tetraiodide), in solution, where YOYO is known to have the ability to photo-cleave DNAs by generating reactive oxygen species. Reconstituted chromatin was assembled from large circular DNA (106 kbp) with core histone proteins. We also investigated the effect of vitamin C (ascorbic acid) on preventing photo-induced double-strand breaks in a quantitative manner. We found that DNA is protected against double-strand breaks by the addition of ascorbic acid, and this protective effect is dose dependent. The effective kinetic constant of the breakage reaction in the presence of 5 mM ascorbic acid is 20 times lower than that in the absence of ascorbic acid. This protective effect of ascorbic acid in reconstituted chromatin is discussed in relation to the highly compacted polynucleosomal structure. The results highlight the fact that single-molecule observation is a useful tool for studying double-strand breaks in giant DNA and chromatin.
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Affiliation(s)
- Yuko Yoshikawa
- Department of Food and Nutrition, Nagoya Bunri College, Nagoya 451-0077, Japan.
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19
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Metzger E, Wissmann M, Yin N, Müller JM, Schneider R, Peters AHFM, Günther T, Buettner R, Schüle R. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 2005; 437:436-9. [PMID: 16079795 DOI: 10.1038/nature04020] [Citation(s) in RCA: 1315] [Impact Index Per Article: 69.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 07/08/2005] [Indexed: 12/11/2022]
Abstract
Gene regulation in eukaryotes requires the coordinate interaction of chromatin-modulating proteins with specific transcription factors such as the androgen receptor. Gene activation and repression is specifically regulated by histone methylation status at distinct lysine residues. Here we show that lysine-specific demethylase 1 (LSD1; also known as BHC110) co-localizes with the androgen receptor in normal human prostate and prostate tumour. LSD1 interacts with androgen receptor in vitro and in vivo, and stimulates androgen-receptor-dependent transcription. Conversely, knockdown of LSD1 protein levels abrogates androgen-induced transcriptional activation and cell proliferation. Chromatin immunoprecipitation analyses demonstrate that androgen receptor and LSD1 form chromatin-associated complexes in a ligand-dependent manner. LSD1 relieves repressive histone marks by demethylation of histone H3 at lysine 9 (H3-K9), thereby leading to de-repression of androgen receptor target genes. Furthermore, we identify pargyline as an inhibitor of LSD1. Pargyline blocks demethylation of H3-K9 by LSD1 and consequently androgen-receptor-dependent transcription. Thus, modulation of LSD1 activity offers a new strategy to regulate androgen receptor functions. Here, we link demethylation of a repressive histone mark with androgen-receptor-dependent gene activation, thus providing a mechanism by which demethylases control specific gene expression.
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Affiliation(s)
- Eric Metzger
- Universitäts-Frauenklinik und Zentrum für Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, 79106 Freiburg, Germany
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20
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Levchenko V, Jackson B, Jackson V. Histone release during transcription: displacement of the two H2A-H2B dimers in the nucleosome is dependent on different levels of transcription-induced positive stress. Biochemistry 2005; 44:5357-72. [PMID: 15807529 DOI: 10.1021/bi047786o] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Both indirect (transcription-induced stress) and direct effects of polymerase elongation on histone-DNA interactions were studied on closed circular DNA that was either moderately or positively coiled. The templates were reconstituted with (3)H-labeled H2A, H2B, H3, and H4 to form nucleosomes, and transcription was done with T7 RNA polymerase in the presence of a negatively coiled competitor DNA (reconstituted with unlabeled H3 and H4). The first of the two labeled H2A-H2B dimers readily displaced from the highly positively coiled template to the competitor even in the absence of transcription, while the indirect effect of transcription-induced stress was required for the moderately coiled template. The second labeled H2A-H2B dimer required transcription-induced stress for both moderately and highly positively coiled DNA. The displacement of the labeled H3-H4 tetramer also occurred, provided it was associated with an H2A-H2B dimer and a moderately positively coiled DNA. This displacement occurred independent of transcription-induced stress and is likely due to the direct effect of polymerase disruption of histone-DNA interactions. The inclusion of the histone chaperone, NAP1, greatly enhanced the release of both of the two H2A-H2B dimers. These observations are consistent with in vivo observations which indicate that during transcription H2A and H2B are significantly more mobile than H3 and H4 and indicate that transcription-induced positive stress is a likely cause for this selective movement.
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Affiliation(s)
- Vladislav Levchenko
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
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21
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Levchenko V, Jackson V. Histone Release during Transcription: NAP1 Forms a Complex with H2A and H2B and Facilitates a Topologically Dependent Release of H3 and H4 from the Nucleosome†. Biochemistry 2004; 43:2359-72. [PMID: 14992573 DOI: 10.1021/bi035737q] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcription through a multinucleosomal template was studied to determine why histones are released to the nascent RNA. It was first determined in competition experiments between DNA and RNA that histones H2A and H2B have a 20-fold preference for binding RNA over DNA; a preference was not seen for histones H3 and H4. Histones H3 and H4 would preferentially bind RNA, provided they were in an octameric complex with H2A and H2B. In transcription studies with T7 RNA polymerase, H3 and H4 were transferred to the nascent RNA, provided the template was linear. If the DNA was topologically restrained, which is a condition that more closely maintains transcription-induced stresses, H3 and H4 would not release. Histones H3 and H4 would be released from this template when H2A and H2B were present, a release that was enhanced by the presence of nucleosome assembly protein-1 (NAP1). Since a small quantity of H2A and H2B is sufficient to facilitate this transfer, it is proposed that H2A and H2B function to repeatedly shuttle H3 and H4 from the template DNA to the RNA. Cross-linked histones (dimethylsuberimidate-cross-linked octamer) were reconstituted into nucleosomes and found to be transferred to the RNA at the same frequency as un-cross-linked histones, an indication that such large complexes can be released during transcription. Transcription was carried out in the presence of Escherichia coli topoisomerase I so that positive coils would accumulate on the DNA. Histones H3 and H4 would again not be transferred from this DNA, unless H2A and H2B were present. In this instance, however, when NAP1 was present, the shuttling of H3 and H4 to the RNA caused a significant depletion of H2A and H2B from the positively coiled DNA. These results are discussed with regard to current models for transcription through nucleosomes.
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Affiliation(s)
- Vladislav Levchenko
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
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22
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What happens to nucleosomes during transcription? ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39017-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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23
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Chromatin structure and dynamics: a historical perspective. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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24
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Sánchez MA, Velasco L, Palacián E. Structure-function relationships in nucleosomal arrays containing linker histone H5. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1628:177-85. [PMID: 12932830 DOI: 10.1016/s0167-4781(03)00141-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To study the structural and functional changes accompanying the integration of histone H5 into the nucleosome structure, linear DNA species have been employed with a terminal promoter for bacteriophage T7 RNA polymerase followed by tandem repeats of a 207-bp nucleosome positioning sequence. The oligonucleosomes assembled from 12-repeat DNA and saturating amounts of core histone octamer plus histone H5 are compacted, in the presence of 1 mM free magnesium ions, to the level of the 30-nm fiber. Under these ionic conditions the efficiency in RNA synthesis and the size distribution of RNA chains obtained with this template are the same as those corresponding to the template without H5, indicating that the 30-nm fiber stabilized by H5 does not impair RNA elongation. Therefore, under our experimental conditions, incorporation of one molecule of histone H5 per nucleosome does not affect elongation of RNA even when a folded structure is produced. However, elongation is inhibited by binding of an excess of H5.
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Affiliation(s)
- Miguel A Sánchez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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25
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Hizume K, Yoshimura SH, Maruyama H, Kim J, Wada H, Takeyasu K. Chromatin reconstitution: development of a salt-dialysis method monitored by nano-technology. ARCHIVES OF HISTOLOGY AND CYTOLOGY 2002; 65:405-13. [PMID: 12680456 DOI: 10.1679/aohc.65.405] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The regulation of DNA replication and transcription is achieved by dynamic structural changes of chromatin in which a series of proteins will acquire accessibility to specific regions of the DNA strand. A combination of biochemistry and nano-technology is essential to address questions regarding the structural basis for such macromolecular mechanisms. In the present study, we established an efficient salt-dialysis method of chromatin reconstitution and employed atomic force microscopy (AFM) as a single-molecule-imaging technique, to monitor the efficiency of the reconstitution. At first, the reconstitution efficiency with short DNA molecules of several kilo-base pairs was low, although the salt dialysis yielded a "beads-on-a-string" structure of oligonucleosomes with each nucleosome trapping 158+/-27 bp DNA. However, the efficiency for nucleosome formation became higher when longer DNA molecules with a super-helical constraint were used. A statistical analysis of the obtained AFM images identified a first-order relationship between the efficiency of the reconstitution and the length of the super-coiled DNA used. A high efficiency of approximately 290 bp/nucleosome that is close to the in vivo situation was obtained with a approximately 100 kbp template DNA. This enabled the structure-function studies of long chromatin molecules under well-defined conditions.
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Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Kyoto University Graduate School of Biostudies, Kyoto, Japan
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26
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Morales P, Rouviere-Yaniv J, Dreyfus M. The histone-like protein HU does not obstruct movement of T7 RNA polymerase in Escherichia coli cells but stimulates its activity. J Bacteriol 2002; 184:1565-70. [PMID: 11872707 PMCID: PMC134870 DOI: 10.1128/jb.184.6.1565-1570.2002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In vivo, RNA polymerases (RNAPs) do not transcribe naked DNA but do transcribe protein-associated DNA. Studies with the model enzyme T7 RNAP have shown that, in eukaryotic cells or in vitro, nucleosomes can inhibit both transcription initiation and elongation. We examine here whether the presence of HU, one of the major histone-like proteins in Escherichia coli cells (the genuine milieu for T7 RNAP) affects its activity. An engineered lac operon fused to the T7 late promoter was introduced into the chromosome of T7 RNAP-producing strains that either overexpress HU or lack it. The flows of RNAP that enter and exit this operon were compared with regard to the content of HU. We found that the fraction of T7 RNAP molecules that do not reach the end of the lac operon (ca. 15%) is the same whether the host cells overexpressed HU or lacked it: thus, the enzyme either freely displaces HU or transcribes through it. However, in these cells, the transcript yield was increased when HU is overexpressed and decreased in the hup mutants, presumably reflecting changes in DNA supercoiling. Thus, in contrast to eukaryotic nucleosomes, HU does not impair T7 RNAP activity but has a stimulatory effect. Finally, our results suggest that HU can also influence mRNA stability in vivo.
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Affiliation(s)
- Pilar Morales
- Laboratoire de Physiologie Bactérienne (CNRS, UPR 9073), Institut de Biologie Physico-Chimique, 75005 Paris, France
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27
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Tomschik M, Karymov MA, Zlatanova J, Leuba SH. The archaeal histone-fold protein HMf organizes DNA into bona fide chromatin fibers. Structure 2001; 9:1201-11. [PMID: 11738046 DOI: 10.1016/s0969-2126(01)00682-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The discovery of histone-like proteins in Archaea urged studies into the possible organization of archaeal genomes in chromatin. Despite recent advances, a variety of structural questions remain unanswered. RESULTS We have used the atomic force microscope (AFM) with traditional nuclease digestion assays to compare the structure of nucleoprotein complexes reconstituted from tandemly repeated eukaryal nucleosome-positioning sequences and histone octamers, H3/H4 tetramers, and the histone-fold archaeal protein HMf. The data unequivocally show that HMf reconstitutes are indeed organized as chromatin fibers, morphologically indistinguishable from their eukaryal counterparts. The nuclease digestion patterns revealed a clear pattern of protection at regular intervals, again similar to the patterns observed with eukaryal chromatin fibers. In addition, we studied HMf reconstitutes on mononucleosome-sized DNA fragments and observed a great degree of similarity in the internal organization of these particles and those organized by H3/H4 tetramers. A difference in stability was observed at the level of mono-, di-, and triparticles between the HMf particles and canonical octamer-containing nucleosomes. CONCLUSIONS The in vitro reconstituted HMf-nucleoprotein complexes can be considered as bona fide chromatin structures. The differences in stability at the monoparticle level should be due to structural differences between HMf and core histone H3/H4 tetramers, i.e., to the complete absence in HMf of histone tails beyond the histone fold. We speculate that the existence of core histone tails in eukaryotes may provide a greater stability to nucleosomal particles and also provide the additional ability of chromatin structure to regulate DNA function in eukaryotic cells by posttranslational histone tail modifications.
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Affiliation(s)
- M Tomschik
- Physical Molecular Biology, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, 41 Library Drive, Room B507, MSC 5055, Bethesda, MD 20892, USA
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28
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Shirakawa H, Herrera JE, Bustin M, Postnikov Y. Targeting of high mobility group-14/-17 proteins in chromatin is independent of DNA sequence. J Biol Chem 2000; 275:37937-44. [PMID: 10973947 DOI: 10.1074/jbc.m000989200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromosomal proteins high mobility group (HMG)-14 and HMG-17 are nucleosomal-binding proteins that unfold the chromatin fiber and enhance transcription from chromatin templates. Their intracellular organization is dynamic and related to both cell cycle and transcription. Here we examine possible mechanisms for targeting HMG-14/-17 to specific regions in chromatin. Chromatin immunoprecipitation assays indicate that HMG-17 protein is not preferentially associated with chromatin regions containing transcriptionally active genes, or any type of specific DNA. We used a modification of the random amplified polymorphic DNA method to analyze DNA in various HMG-14/-17.nucleosome complexes. We found that although HMG-14 or HMG-17 proteins preferentially associate with core particles in which the DNA has a low frequency of CG dinucleotides, the genome does not contain consensus sequences that serve as specific targeting sites for the binding of either HMG-14 or HMG-17 proteins to nucleosomes. We used size exclusion and ion exchange chromatography to demonstrate that nuclei contain a large portion of HMG-17 associated with other proteins in a multiprotein complex. We suggest that these complexes regulate the dynamic organization of HMG-14/-17 in the nucleus and serve to target the proteins to specific sites in chromatin.
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Affiliation(s)
- H Shirakawa
- Protein Section, Division of Basic Sciences, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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29
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Morales V, Richard-Foy H. Role of histone N-terminal tails and their acetylation in nucleosome dynamics. Mol Cell Biol 2000; 20:7230-7. [PMID: 10982840 PMCID: PMC86277 DOI: 10.1128/mcb.20.19.7230-7237.2000] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Histone N-terminal tails are central to the processes that modulate nucleosome structure and function. We have studied the contribution of core histone tails to the structure of a single nucleosome and to a histone (H3-H4)(2) tetrameric particle assembled on a topologically constrained DNA minicircle. The effect of histone tail cleavage and histone tail acetylation on the structure of the nucleoprotein particle was investigated by analyzing the DNA topoisomer equilibrium after relaxation of DNA torsional stress by topoisomerase I. Removal of the H3 and H4 N-terminal tails, as well as their acetylation, provoked a dramatic change in the linking-number difference of the (H3-H4)(2) tetrameric particle, with a release of up to 70% of the negative supercoiling previously constrained by this structure. The (H3-H4)(2) tetramers containing tailless or hyperacetylated histones showed a striking preference for relaxed DNA over negatively supercoiled DNA. This argues in favor of a change in tetramer structure that constrains less DNA and adopts a relaxed flat conformation instead of its left-handed conformation within the nucleosome. In contrast neither removal or hyperacetylation of H3 and H4 tails nor removal or hyperacetylation of H2A and H2B N-terminal tails affected the nucleosome structure. This indicates that the globular domain of H2A and H2B is sufficient to stabilize the tailless or the hyperacetylated (H3-H4)(2) tetramer in a left-handed superhelix conformation. These results suggest that the effect of histone tail acetylation that facilitates transcription may be mediated via transient formation of an (H3-H4)(2) tetrameric particle that could adopt an open structure only when H3 and/or H4 tails are hyperacetylated.
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Affiliation(s)
- V Morales
- Laboratoire de Biologie Moléculaire Eucaryote, Institut de Biologie Cellulaire et de Génétique du Centre National de la Recherche Scientifique, 31062 Toulouse, France
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30
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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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31
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ten Heggeler-Bordier B, Muller S, Monestier M, Wahli W. An immuno-electron microscopical analysis of transcribing multinucleosomal templates: what happens to the histones? J Mol Biol 2000; 299:853-8. [PMID: 10843841 DOI: 10.1006/jmbi.2000.3790] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Immuno-electron microscopy was used to visualize the structure of reconstituted chromatin after in vitro transcription by purified T7 RNA polymerase. T7 RNA polymerase disrupts the nucleosomal structure in the transcribed region. This disruption is not influenced by the template, linear or supercoiled, and the presence or absence of nucleosomal positioning sequences in the transcribed region. In this study, we used monoclonal autoantibodies reacting with the nucleosome core particles and epitopes within several regions of the four different core histones. Some of the residues recognized by the autoantibodies are accessible on the surface of the nucleosomes and some are more internal and therefore less exposed at the surface. We show that the loss of the nucleosomal configuration during transcription is due to the loss of histone/DNA binding and that at least part of the histones are transferred to the nascent RNA chains. Consequently, after in vitro transcription by T7 RNA polymerase, the nucleosomal template does not conserve its original configuration, and no interaction of antigen/antibodies is observed anymore in the region that has been transcribed. Therefore, we conclude that in our in vitro transcription assay, nucleosomes are detached from the template, and not simply unfolded with histones remaining attached to the DNA.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Autoantibodies/immunology
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA, Superhelical/ultrastructure
- DNA-Binding Proteins/immunology
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/ultrastructure
- DNA-Directed RNA Polymerases/metabolism
- Epitopes/immunology
- Histones/immunology
- Histones/metabolism
- Histones/ultrastructure
- Mice
- Microscopy, Immunoelectron
- Molecular Conformation
- Nucleosomes/chemistry
- Nucleosomes/genetics
- Nucleosomes/metabolism
- Nucleosomes/ultrastructure
- Plasmids/chemistry
- Plasmids/genetics
- Plasmids/metabolism
- Plasmids/ultrastructure
- Protein Binding
- RNA, Ribosomal, 5S/biosynthesis
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- RNA, Ribosomal, 5S/ultrastructure
- RNA-Binding Proteins/immunology
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/ultrastructure
- Templates, Genetic
- Transcription, Genetic/genetics
- Viral Proteins
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32
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Vestner B, Waldmann T, Gruss C. Histone octamer dissociation is not required for in vitro replication of simian virus 40 minichromosomes. J Biol Chem 2000; 275:8190-5. [PMID: 10713143 DOI: 10.1074/jbc.275.11.8190] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication of chromosomal templates requires the passage of the replication machinery through nucleosomally organized DNA. To gain further insights into these processes we have used chromatin that was reconstituted with dimethyl suberimidate-cross-linked histone octamers as template in the SV40 in vitro replication system. By supercoiling analysis we found that cross-linked histone octamers were reconstituted with the same kinetic and efficiency as control octamers. Minichromosomes with cross-linked nucleosomes were completely replicated, although the efficiency of replication was lower compared with control chromatin. Analysis of the chromatin structure of the replicated DNA revealed that the cross-linked octamer is transferred to the daughter strands. Thus, our data imply that histone octamer dissociation is not a prerequisite for the passage of the replication machinery and the transfer of the parental nucleosomes.
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Affiliation(s)
- B Vestner
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Federal Republic of Germany
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33
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Peng HF, Jackson V. In vitro studies on the maintenance of transcription-induced stress by histones and polyamines. J Biol Chem 2000; 275:657-68. [PMID: 10617664 DOI: 10.1074/jbc.275.1.657] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Several factors were evaluated to determine their role in facilitating the presence of transcription-induced stresses in a circular DNA. Transcription was done with T7 RNA polymerase in the presence of E. coli topoisomerase I and closed circular DNA. Positive stress was observed in hypotonic conditions or when one of the polyamines, spermidine or spermine, were present. Polycations such as polylysine, polyarginine, histone H1, histones H2A-H2B, and protamine were observed to induce minimal positive stress. It is known that polyamines influence DNA structure by causing both self-association and sequence-specific structural alterations (polyamine-induced localized bending). Experimental evidence indicates that the likely cause of the positive stress is the induced bending. In order to evaluate protein-mediated bending, transcription was done on nucleosomes. A minimum of three nucleosomes on a DNA of 6055 bp was sufficient to generate very high levels of positive stress. Histones H3-H4 in the absence of H2A-H2B were responsible for this effect. Since these histones by themselves are able to maintain negative coils on DNA, it is concluded that protein-mediated bending is yet another mechanism for placing rotational restriction on DNA. The bending of DNA by either polyamines or histones is an effective mechanism for promoting transcription-induced stresses at physiological ionic strength.
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Affiliation(s)
- H F Peng
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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34
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Chirinos M, Hernández F, Palacián E. Transcription of DNA templates associated with histone (H3 x H4)(2) tetramers. Arch Biochem Biophys 1999; 370:222-30. [PMID: 10510281 DOI: 10.1006/abbi.1999.1392] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate the in vitro transcription by bacteriophage T7 RNA polymerase of oligonucleosomes lacking histone H2A x H2B dimers, templates were assembled from histone (H3 x H4)(2) tetramers with and without the complementary amount of H2A x H2B dimers and two different DNA species: pGEMEX-1, devoid of nucleosome positioning sequences, and T7-207-18, which contains downstream from the promoter 18 tandem repeats of a 207-bp positioning sequence. Assembly with core histone octamers affects pGEMEX-1 transcription mainly at the initiation level, while T7-207-18 is almost exclusively inhibited at the level of elongation. With both DNA templates and under different salt conditions, RNA synthesis is much more efficient on oligonucleosomes containing only (H3 x H4)(2) tetramers than on those with whole histone octamers. Under conditions promoting a low transcription rate, it is unambiguously shown with pGEMEX-1 that the block to initiation due to the presence of core histone octamers is substantially removed when (H3 x H4)(2) is substituted for the whole octamer. With T7-207-18, under assay conditions allowing transcription of the whole coding region of the naked DNA, analysis of the transcription products indicates that RNA elongation on the template containing (H3 x H4)(2) tetramers takes place as easily as on free DNA, in contrast with the significant inhibition observed in the presence of whole histone octamers.
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Affiliation(s)
- M Chirinos
- Centro de Biología Molecular "Severo Ochoa,", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
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35
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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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36
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Sato MH, Ura K, Hohmura KI, Tokumasu F, Yoshimura SH, Hanaoka F, Takeyasu K. Atomic force microscopy sees nucleosome positioning and histone H1-induced compaction in reconstituted chromatin. FEBS Lett 1999; 452:267-71. [PMID: 10386604 DOI: 10.1016/s0014-5793(99)00644-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We addressed the question of how nuclear histones and DNA interact and form a nucleosome structure by applying atomic force microscopy to an in vitro reconstituted chromatin system. The molecular images obtained by atomic force microscopy demonstrated that oligonucleosomes reconstituted with purified core histones and DNA yielded a 'beads on a string' structure with each nucleosome trapping 158 +/- 27 bp DNA. When dinucleosomes were assembled on a DNA fragment containing two tandem repeats of the positioning sequence of the Xenopus 5S RNA gene, two nucleosomes were located around each positioning sequence. The spacing of the nucleosomes fluctuated in the absence of salt and the nucleosomes were stabilized around the range of the positioning signals in the presence of 50 mM NaCl. An addition of histone H1 to the system resulted in a tight compaction of the dinucleosomal structure.
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Affiliation(s)
- M H Sato
- Department of Natural Environmental Sciences, Faculty of Integrated Human Studies, Kyoto University, Japan
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37
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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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38
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Navarro M, Cross GA, Wirtz E. Trypanosoma brucei variant surface glycoprotein regulation involves coupled activation/inactivation and chromatin remodeling of expression sites. EMBO J 1999; 18:2265-72. [PMID: 10205179 PMCID: PMC1171309 DOI: 10.1093/emboj/18.8.2265] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Trypanosoma brucei is an extracellular protozoan parasite that cycles between mammalian hosts and the tsetse vector. In bloodstream-form trypanosomes, only one variant surface glycoprotein gene (VSG) expression site (ES) is active at any time. Transcriptional switching between ESs results in antigenic variation. No VSG is transcribed in the insect procyclic stage. We have used bacteriophage T7 RNA polymerase (T7RNAP) to study the transcriptional accessibility of ES chromatin in vivo. We show that T7RNAP-mediated transcription from chromosomally integrated T7 promoters is repressed along the entire length of the ES in the procyclic form, but not in the bloodstream form, suggesting that the accessible chromatin of inactive bloodstream-form ESs is remodeled upon differentiation to yield a structure that is no longer permissive for T7RNAP-mediated transcription. In the bloodstream form, replacing the active ES promoter with a T7 promoter, which is incapable of sustaining high-level transcription of the entire ES, prompts an ES switch. These data suggest two distinct mechanisms for ES regulation: a chromatin-mediated developmental silencing of the ES in the procyclic form and a rapid coupled mechanism for ES activation and inactivation in the bloodstream form.
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Affiliation(s)
- M Navarro
- Laboratory of Molecular Parasitology, The Rockefeller University (Box 185), 1230 York Avenue, New York, NY 10021-6399, USA
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39
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Chakravarti D, Ogryzko V, Kao HY, Nash A, Chen H, Nakatani Y, Evans RM. A viral mechanism for inhibition of p300 and PCAF acetyltransferase activity. Cell 1999; 96:393-403. [PMID: 10025405 DOI: 10.1016/s0092-8674(00)80552-8] [Citation(s) in RCA: 283] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Nucleosomal histone modification is believed to be a critical step in the activation of RNA polymerase II-dependent transcription. p300/CBP and PCAF histone acetyltransferases (HATs) are coactivators for several transcription factors, including nuclear hormone receptors, p53, and Stat1alpha, and participate in transcription by forming an activation complex and by promoting histone acetylation. The adenoviral E1A oncoprotein represses transcriptional signaling by binding to p300/CBP and displacing PCAF and p/CIP proteins from the complex. Here, we show that E1A directly represses the HAT activity of both p300/CBP and PCAF in vitro and p300-dependent transcription in vivo. Additionally, E1A inhibits nucleosomal histone modifications by the PCAF complex and blocks p53 acetylation. These results demonstrate the modulation of HAT activity as a novel mechanism of transcriptional regulation.
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Affiliation(s)
- D Chakravarti
- Gene Expression Laboratory, The Salk Institute for Biological Sciences, La Jolla, California 92037, USA
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40
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Schiltz RL, Mizzen CA, Vassilev A, Cook RG, Allis CD, Nakatani Y. Overlapping but distinct patterns of histone acetylation by the human coactivators p300 and PCAF within nucleosomal substrates. J Biol Chem 1999; 274:1189-92. [PMID: 9880483 DOI: 10.1074/jbc.274.3.1189] [Citation(s) in RCA: 324] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A number of transcriptional coactivators possess intrinsic histone acetylase activity, providing a direct link between hyperacetylated chromatin and transcriptional activation. We have determined the core histone residues acetylated in vitro by recombinant p300 and PCAF within mononucleosomes. p300 specifically acetylates all sites of histones H2A and H2B known to be acetylated in bulk chromatin in vivo but preferentially acetylates lysines 14 and 18 of histone H3 and lysines 5 and 8 of histone H4. PCAF primarily acetylates lysine 14 of H3 but also less efficiently acetylates lysine 8 of H4. PCAF in its native form, which is present in a stable multimeric protein complex lacking p300/CBP, primarily acetylates H3 to a monoacetylated form, suggesting that PCAF-associated polypeptides do not alter the substrate specificity. These distinct patterns of acetylation by the p300 and PCAF may contribute to their differential roles in transcriptional regulation.
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Affiliation(s)
- R L Schiltz
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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41
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Wirtz E, Hoek M, Cross GA. Regulated processive transcription of chromatin by T7 RNA polymerase in Trypanosoma brucei. Nucleic Acids Res 1998; 26:4626-34. [PMID: 9753730 PMCID: PMC147901 DOI: 10.1093/nar/26.20.4626] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Inability of T7 RNA polymerase to processively transcribe higher eukaryotic chromatin is interpreted as a correlate of its reported inhibition by nucleosomes on reconstituted templates in vitro . We used chromosomally integrated reporter cassettes to examine features of T7 transcription in a lower eukaryotic system. Luciferase reporters were targeted to rDNA in transgenic Trypanosoma brucei stably expressing the phage polymerase. Because trypanosome mRNAs are capped by RNA splicing in trans , T7 transcription could be gauged by luciferase activity. In contrast to findings from higher eukaryotes, T7 transcription is vigorous and processive on chromatin templates in T.brucei , surpassing levels achieved with endogenous promoters, including those recruiting RNA polymerase I. This may be a reflection of intrinsic differences in chromatin structure between differently evolved eukaryotes or of an integration site that is exceptionally permissive for T7 transcription due to a local accessible chromatin conformation. T7 transcription could be manipulated to achieve different levels of constitutive expression, through the use of promoter mutations. Moreover, T7 initiation could be regulated by the prokaryotic Tet repressor and elongation halted by T7 terminator sequences. We have exploited these features to construct a robust inducible expression system, whose utility potentially extends to other trans -splicing organisms.
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Affiliation(s)
- E Wirtz
- Laboratory of Molecular Parasitology, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399, USA
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42
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Hernández F, López-Alarcón L, Puerta C, Palacián E. Transcriptional inhibitory role of the tail domains of histone (H3 x H4)2 tetramers. Arch Biochem Biophys 1998; 358:98-103. [PMID: 9750170 DOI: 10.1006/abbi.1998.0850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Histone-DNA templates for bacteriophage T7 RNA polymerase were assembled from a plasmid containing a promoter and a terminator for this polymerase, (H3 x H4)2 tetramers deprived of their tail domains, and H2A x H2B dimers. Histone (H3 x H4)2 tetramers lacking their terminal domains were obtained from trypsin-digested nucleosomal cores. The oligonucleosomal templates containing (H3 x H4)2 tetramers lacking their tail domains, like the control templates with intact core histone octamers, protect approximately 146 base pairs of DNA against micrococcal nuclease digestion. The transcriptional inhibition caused by the association of DNA with core histone octamers is significantly reduced upon elimination of the tail domains of the (H3 x H4)2 tetramers. Apparently, the terminal domains of (H3 x H4)2 must be present to block transcription efficiently. These results show the important inhibitory role played by the tail domains of the histone (H3 x H4)2 tetramers, suggesting the involvement of these regions in transcriptional regulation.
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Affiliation(s)
- F Hernández
- Consejo Superior de Investigaciones, Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
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43
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Wolffe AP, Kurumizaka H. The nucleosome: a powerful regulator of transcription. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1998; 61:379-422. [PMID: 9752726 DOI: 10.1016/s0079-6603(08)60832-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nucleosomes provide the architectural framework for transcription. Histones, DNA elements, and transcription factors are organized into precise regulatory complexes. Positioned nucleosomes can facilitate or impede the transcription process. These structures are dynamic, reflecting the capacity of chromatin to adopt different functional states. Histones are mobile with respect to DNA sequence. Individual histone domains are targeted for posttranslational modifications. Histone acetylation promotes transcription factor access to nucleosomal DNA and relieves inhibitory effects on transcriptional initiation and elongation. The nucleosomal infrastructure emerges as powerful contributor to the regulation of gene activity.
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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, USA
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44
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Ogryzko VV, Kotani T, Zhang X, Schiltz RL, Howard T, Yang XJ, Howard BH, Qin J, Nakatani Y. Histone-like TAFs within the PCAF histone acetylase complex. Cell 1998; 94:35-44. [PMID: 9674425 DOI: 10.1016/s0092-8674(00)81219-2] [Citation(s) in RCA: 445] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PCAF histone acetylase plays a role in regulation of transcription, cell cycle progression, and differentiation. Here, we show that PCAF is found in a complex consisting of more than 20 distinct polypeptides. Strikingly, some polypeptides are identical to TBP-associated factors (TAFs), which are subunits of TFIID. Like TFIID, histone fold-containing factors are present within the PCAF complex. The histone H3- and H2B-like subunits within the PCAF complex are identical to those within TFIID, namely, hTAF(II)31 and hTAF(II)20/15, respectively. The PCAF complex has a novel histone H4-like subunit with similarity to hTAF(II)80 that interacts with the histone H3-like domain of hTAF(II)31. Moreover, the PCAF complex has a novel subunit with WD40 repeats having a similarity to hTAF(II)100.
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Affiliation(s)
- V V Ogryzko
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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45
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Chirinos M, Hernández F, Palacián E. Repressive effect on oligonucleosome transcription of the core histone tail domains. Biochemistry 1998; 37:7251-9. [PMID: 9585538 DOI: 10.1021/bi9729817] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Histone-DNA templates for bacteriophage T7 RNA polymerase were assembled from histone octamers and three different DNA species, two circular (pGEMEX-1 and pT207-18) and one linear (T7-207-18). pGEMEX is devoid of nucleosome positioning sequences, while in pT207-18 and T7-207-18 the region downstream of the promoter contains 18 tandem repeats of a 207 bp positioning sequence derived from the 5S RNA gene of the sea urchin Lytechinus variegatus. Elimination of the histone tails in the assembled oligonucleosomes by trypsin digestion is accompanied, in all three DNA species, by substantial increases in transcription efficiency, assayed at different KCl and MgCl2 concentrations, after allowing for the aggregation observed under certain conditions. In the absence of KCl and at low MgCl2 concentration, the presence of 2 mM spermidine causes substantial aggregation of the intact oligonucleosomes but has a much smaller effect on those trypsin digested. The untreated histone-DNA templates, assembled on pGEMEX-1 and T7-207-18, give transcription products significantly shorter than those obtained with the corresponding free DNA. With oligonucleosome templates lacking histone tails, the transcripts have an average length intermediate between those corresponding to free DNA and intact histone-DNA, which indicates a partial elimination of the elongation restrictions imposed by intact histone octamers. The absence of histone terminal domains facilitates both transcriptional initiation and elongation. Apparently, the interaction of the histone tails with DNA at the nucleosomal level is responsible, at least in part, for their repressive effect on transcription.
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Affiliation(s)
- M Chirinos
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Spain
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46
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Wong J, Li Q, Levi BZ, Shi YB, Wolffe AP. Structural and functional features of a specific nucleosome containing a recognition element for the thyroid hormone receptor. EMBO J 1997; 16:7130-45. [PMID: 9384590 PMCID: PMC1170314 DOI: 10.1093/emboj/16.23.7130] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Xenopus thyroid hormone receptor betaA (TRbetaA) gene contains an important thyroid hormone response element (TRE) that is assembled into a positioned nucleosome. We determine the translational position of the nucleosome containing the TRE and the rotational positioning of the double helix with respect to the histone surface. Histone H1 is incorporated into the nucleosome leading to an asymmetric protection to micrococcal nuclease cleavage of linker DNA relative to the nucleosome core. Histone H1 association is without significant consequence for the binding of the heterodimer of thyroid hormone receptor and 9-cis retinoic acid receptor (TR/RXR) to nucleosomal DNA in vitro, or for the regulation of TRbetaA gene transcription following microinjection into the oocyte nucleus. Small alterations of 3 and 6 bp in the translational positioning of the TRE in chromatin are also without effect on the transcriptional activity of the TRbetaA gene, whereas a small change in the rotational position of the TRE (3 bp) relative to the histone surface significantly reduces the binding of TR/RXR to the nucleosome and decreases transcriptional activation directed by TR/RXR. Our results indicate that the specific architecture of the nucleosome containing the TRE may have regulatory significance for expression of the TRbetaA gene.
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Affiliation(s)
- J Wong
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, NIH, Building 18T, Room 106, Bethesda, MD 20892-5431, USA
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47
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Peng HF, Jackson V. Measurement of the frequency of histone displacement during the in vitro transcription of nucleosomes: RNA is a competitor for these histones. Biochemistry 1997; 36:12371-82. [PMID: 9315878 DOI: 10.1021/bi971046g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Transcription through tandemly arranged nucleosomes was studied to determine the frequency at which the nucleosomes would disrupt and cause displacement of the associated histones to a competitor DNA. In order to more effectively preserve topological effects, the template that was used in the in vitro transcription system was a large covalently, closed circular plasmid (8.9 kb). The plasmid contained two promoters for T7 RNA polymerase, each separated by 4.4 kb, and transcription was done in the presence of topoisomerase I at physiological ionic strength. Nucleosome disruption was observed at an approximate frequency of 1 in 4 nucleosomes such that after several rounds of transcription on the plasmid 80% of the nucleosomes were disrupted. Unexpectedly, all four histones were found associated with the RNA rather than the competitor DNA. The histones bound the competitor DNA only after removal of the RNA by RNase A treatment. By analyzing the topological state of the competitor DNA, it was observed that the majority of the histones that were displaced from the RNA were able to re-form nucleosomes. Additional experiments were done to determine the reasons for the preferential binding of histones to the newly synthesized RNA. It was found that the large molecular weight RNA binds histones with an approximate 100-fold greater affinity relative to DNA when at physiological ionic strength. Within the cell, this high-affinity binding would be expected to require cellular mechanisms to regulate the interaction of RNA with histones. The relatively high frequency of displacement of all four histones during transcription is higher than what is observed in vivo and suggests that additional factors are needed to regulate this displacement. These observations are discussed and compared with previous studies that have examined the process of transcription through nucleosomes.
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Affiliation(s)
- H F Peng
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee 53226, USA
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48
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Abstract
Ternary complexes of DNA-dependent RNA polymerase with its DNA template and nascent transcript are central intermediates in transcription. In recent years, several unusual biochemical reactions have been discovered that affect the progression of RNA polymerase in ternary complexes through various transcription units. These reactions can be signaled intrinsically, by nucleic acid sequences and the RNA polymerase, or extrinsically, by protein or other regulatory factors. These factors can affect any of these processes, including promoter proximal and promoter distal pausing in both prokaryotes and eukaryotes, and therefore play a central role in regulation of gene expression. In eukaryotic systems, at least two of these factors appear to be related to cellular transformation and human cancers. New models for the structure of ternary complexes, and for the mechanism by which they move along DNA, provide plausible explanations for novel biochemical reactions that have been observed. These models predict that RNA polymerase moves along DNA without the constant possibility of dissociation and consequent termination. A further prediction of these models is that the polymerase can move in a discontinuous or inchworm-like manner. Many direct predictions of these models have been confirmed. However, one feature of RNA chain elongation not predicted by the model is that the DNA sequence can determine whether the enzyme moves discontinuously or monotonically. In at least two cases, the encounter between the RNA polymerase and a DNA block to elongation appears to specifically induce a discontinuous mode of synthesis. These findings provide important new insights into the RNA chain elongation process and offer the prospect of understanding many significant biological regulatory systems at the molecular level.
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Affiliation(s)
- S M Uptain
- Department of Molecular and Cell Biology, University of California at Berkeley 94720, USA.
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49
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Godde JS, Kass SU, Hirst MC, Wolffe AP. Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter. J Biol Chem 1996; 271:24325-8. [PMID: 8798682 DOI: 10.1074/jbc.271.40.24325] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Expansion and methylation of CGG repeat sequences is associated with Fragile X syndrome in humans. We have examined the consequences of CGG repeat expansion and methylation for nucleosome assembly and positioning on the Fragile X Mental Retardation gene 1 (FMR1) gene. Short unmethylated CGG repeats are not particularly favored in terms of affinity for the histone octamer or for positioning of the reconstituted nucleosome. However, upon methylation their affinity for the histone octamer increases and a highly positioned nucleosome assembles with the repeat sequences found adjacent to the nucleosomal dyad. Expansion of these CGG repeats abolishes the preferential nucleosome assembly due to methylation. Thus, the expansion and methylation of these triplet repeats can alter the functional organization of chromatin, which may contribute to alterations in the expression of the FMR1 gene and the disease phenotype.
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Affiliation(s)
- J S Godde
- Laboratory of Molecular Embryology, NICHHD, National Institutes of Health, Bethesda, Maryland 20892-5430, USA
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50
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Abstract
Expansion of CTG repeat sequences is associated with several human genetic diseases. We have examined the consequences of CTG repeat expansion for nucleosome assembly and positioning. Short CTG repeats are found within the most favored DNA sequences yet defined for nucleosome assembly. We find that as few as six CTG repeats will facilitate nucleosome assembly to a similar extent as the 50 or more repeats found in disease genes. Thus an increase in nucleosome stability on expansion of existing triplet repeats is unlikely to explain the acquisition of the disease phenotype. However, the CTG repeat sequence is efficiently wrapped around the histone octamer, preferring to associate with histones at the nucleosomal dyad. Thus short segments CTG repeat sequence will facilitate the assembly of a stable positioned nucleosome which might contribute to the expansion phenomenon and the functional organization of chromatin.
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Affiliation(s)
- J S Godde
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-2710, USA
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