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Zink LM, Delbarre E, Eberl HC, Keilhauer EC, Bönisch C, Pünzeler S, Bartkuhn M, Collas P, Mann M, Hake SB. H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements. Nucleic Acids Res 2017; 45:5691-5706. [PMID: 28334823 PMCID: PMC5449609 DOI: 10.1093/nar/gkx131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/14/2017] [Indexed: 01/07/2023] Open
Abstract
Histone chaperones prevent promiscuous histone interactions before chromatin assembly. They guarantee faithful deposition of canonical histones and functionally specialized histone variants into chromatin in a spatial- and temporally-restricted manner. Here, we identify the binding partners of the primate-specific and H3.3-related histone variant H3.Y using several quantitative mass spectrometry approaches, and biochemical and cell biological assays. We find the HIRA, but not the DAXX/ATRX, complex to recognize H3.Y, explaining its presence in transcriptionally active euchromatic regions. Accordingly, H3.Y nucleosomes are enriched in the transcription-promoting FACT complex and depleted of repressive post-translational histone modifications. H3.Y mutational gain-of-function screens reveal an unexpected combinatorial amino acid sequence requirement for histone H3.3 interaction with DAXX but not HIRA, and for H3.3 recruitment to PML nuclear bodies. We demonstrate the importance and necessity of specific H3.3 core and C-terminal amino acids in discriminating between distinct chaperone complexes. Further, chromatin immunoprecipitation sequencing experiments reveal that in contrast to euchromatic HIRA-dependent deposition sites, human DAXX/ATRX-dependent regions of histone H3 variant incorporation are enriched in heterochromatic H3K9me3 and simple repeat sequences. These data demonstrate that H3.Y's unique amino acids allow a functional distinction between HIRA and DAXX binding and its consequent deposition into open chromatin.
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Affiliation(s)
- Lisa-Maria Zink
- Department of Molecular Biology, BioMedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Erwan Delbarre
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - H Christian Eberl
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Clemens Bönisch
- Department of Molecular Biology, BioMedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Sebastian Pünzeler
- Department of Molecular Biology, BioMedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany.,Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany
| | - Sandra B Hake
- Department of Molecular Biology, BioMedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany.,Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany
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Bönisch C, Irmler M, Brachthäuser L, Neff F, Bamberger MT, Marschall S, Hrabě de Angelis M, Beckers J. Dexamethasone treatment alters insulin, leptin, and adiponectin levels in male mice as observed in DIO but does not lead to alterations of metabolic phenotypes in the offspring. Mamm Genome 2015; 27:17-28. [PMID: 26662513 PMCID: PMC4731435 DOI: 10.1007/s00335-015-9616-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 11/23/2015] [Indexed: 12/26/2022]
Abstract
Epigenetic inheritance (EI) of metabolic phenotypes via the paternal lineage has been shown in rodent models of diet-induced obesity (DIO). However, the factors involved in soma-to-germline information transfer remain elusive. Here, we address the role of alterations in insulin, leptin, and adiponectin levels for EI of metabolic phenotypes by treating C57BL/6NTac male mice (F0) with the synthetic glucocorticoid dexamethasone and generating offspring (F1) either by in vitro fertilization or by natural fecundation. Dexamethasone treatment slightly alters F0 body composition by increasing fat mass and decreasing lean mass, and significantly improves glucose tolerance. Moreover, it increases insulin and leptin levels and reduces adiponectin levels in F0 fathers as observed in mouse models of DIO. However, these paternal changes of metabolic hormones do not alter metabolic parameters, such as body weight, body composition and glucose homeostasis in male and female F1 mice even when these are challenged with a high-fat diet. Accordingly, sperm transcriptomes are not altered by dexamethasone treatment. Our results suggest that neither increased glucocorticoid, insulin, and leptin levels, nor decreased adiponectin levels in fathers are sufficient to confer soma-to-germline information transfer in EI of obesity via the paternal lineage.
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Affiliation(s)
- Clemens Bönisch
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Irmler
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Laura Brachthäuser
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Institute of Pathology, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Frauke Neff
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Institute of Pathology, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Mareike T Bamberger
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Susan Marschall
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Chair of Experimental Genetics, Technische Universität München, 85354, Freising, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Chair of Experimental Genetics, Technische Universität München, 85354, Freising, Germany.
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.
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Horsch M, Aguilar-Pimentel JA, Bönisch C, Côme C, Kolster-Fog C, Jensen KT, Lund AH, Lee I, Grossman LI, Sinkler C, Hüttemann M, Bohn E, Fuchs H, Ollert M, Gailus-Durner V, Hrabĕ de Angelis M, Beckers J. Cox4i2, Ifit2, and Prdm11 Mutant Mice: Effective Selection of Genes Predisposing to an Altered Airway Inflammatory Response from a Large Compendium of Mutant Mouse Lines. PLoS One 2015; 10:e0134503. [PMID: 26263558 PMCID: PMC4532500 DOI: 10.1371/journal.pone.0134503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/09/2015] [Indexed: 11/19/2022] Open
Abstract
We established a selection strategy to identify new models for an altered airway inflammatory response from a large compendium of mutant mouse lines that were systemically phenotyped in the German Mouse Clinic (GMC). As selection criteria we included published gene functional data, as well as immunological and transcriptome data from GMC phenotyping screens under standard conditions. Applying these criteria we identified a few from several hundred mutant mouse lines and further characterized the Cox4i2tm1Hutt, Ifit2tm1.1Ebsb, and Prdm11tm1.1ahl lines following ovalbumin (OVA) sensitization and repeated OVA airway challenge. Challenged Prdm11tm1.1ahl mice exhibited changes in B cell counts, CD4+ T cell counts, and in the number of neutrophils in bronchoalveolar lavages, whereas challenged Ifit2tm1.1Ebsb mice displayed alterations in plasma IgE, IgG1, IgG3, and IgM levels compared to the challenged wild type littermates. In contrast, challenged Cox4i2tm1Hutt mutant mice did not show alterations in the humoral or cellular immune response compared to challenged wild type mice. Transcriptome analyses from lungs of the challenged mutant mouse lines showed extensive changes in gene expression in Prdm11tm1.1ahl mice. Functional annotations of regulated genes of all three mutant mouse lines were primarily related to inflammation and airway smooth muscle (ASM) remodeling. We were thus able to define an effective selection strategy to identify new candidate genes for the predisposition to an altered airway inflammatory response under OVA challenge conditions. Similar selection strategies may be used for the analysis of additional genotype – envirotype interactions for other diseases.
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Affiliation(s)
- Marion Horsch
- Helmholtz Zentrum München GmbH, German Mouse Clinic, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Juan Antonio Aguilar-Pimentel
- Helmholtz Zentrum München GmbH, German Mouse Clinic, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
- Department of Dermatology and Allergy, TUM and Clinical Research Division of Molecular and Clinical Allergotoxicology, Munich, Germany
| | - Clemens Bönisch
- Helmholtz Zentrum München GmbH, German Mouse Clinic, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Christophe Côme
- Biotech Research and Innovation Centre, Lund Group, University of Copenhagen, Ole Maaloes vej 5, DK-2200 Copenhagen, Denmark
| | - Cathrine Kolster-Fog
- Biotech Research and Innovation Centre, Lund Group, University of Copenhagen, Ole Maaloes vej 5, DK-2200 Copenhagen, Denmark
| | - Klaus T. Jensen
- Biotech Research and Innovation Centre, Lund Group, University of Copenhagen, Ole Maaloes vej 5, DK-2200 Copenhagen, Denmark
| | - Anders H. Lund
- Biotech Research and Innovation Centre, Lund Group, University of Copenhagen, Ole Maaloes vej 5, DK-2200 Copenhagen, Denmark
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do, 330–714, Republic of Korea
| | - Lawrence I. Grossman
- Wayne State University, Center for Molecular Medicine and Genetics, 540 E. Canfield Avenue, Detroit, Michigan 48201, United States of America
| | - Christopher Sinkler
- Wayne State University, Center for Molecular Medicine and Genetics, 540 E. Canfield Avenue, Detroit, Michigan 48201, United States of America
| | - Maik Hüttemann
- Wayne State University, Center for Molecular Medicine and Genetics, 540 E. Canfield Avenue, Detroit, Michigan 48201, United States of America
| | - Erwin Bohn
- Universitätsklinikum Tübingen, Institut für Medizinische Mikrobiologie, Elfriede-Aulhorn-Strasse 6, D-72076 Tübingen, Germany
| | - Helmut Fuchs
- Helmholtz Zentrum München GmbH, German Mouse Clinic, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Markus Ollert
- Center of Allergy and Environment Munich (ZAUM), Technische Universität München, Munich, Germany
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg and Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark
| | - Valérie Gailus-Durner
- Helmholtz Zentrum München GmbH, German Mouse Clinic, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Martin Hrabĕ de Angelis
- Helmholtz Zentrum München GmbH, German Mouse Clinic, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
- Technische Universität München, Chair of Experimental Genetics, D-85354 Freising, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
| | - Johannes Beckers
- Helmholtz Zentrum München GmbH, German Mouse Clinic, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
- Technische Universität München, Chair of Experimental Genetics, D-85354 Freising, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- * E-mail:
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Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, Bönisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A. The histone variant H2A.Bbd is enriched at sites of DNA synthesis. Nucleic Acids Res 2014; 42:6405-20. [PMID: 24753410 PMCID: PMC4041467 DOI: 10.1093/nar/gku303] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 01/04/2023] Open
Abstract
Histone variants play an important role in shaping the mammalian epigenome and their aberrant expression is frequently observed in several types of cancer. However, the mechanisms that mediate their function and the composition of the variant-containing chromatin are still largely unknown. A proteomic interrogation of chromatin containing the different H2A variants macroH2A.1.2, H2A.Bbd and H2A revealed a strikingly different protein composition. Gene ontology analysis reveals a strong enrichment of splicing factors as well as components of the mammalian replisome in H2A.Bbd-containing chromatin. We find H2A.Bbd localizing transiently to sites of DNA synthesis during S-phase and during DNA repair. Cells that express H2A.Bbd have a shortened S-phase and are more susceptible to DNA damage, two phenotypes that are also observed in human Hodgkin's lymphoma cells that aberrantly express this variant. Based on our experiments we conclude that H2A.Bbd is targeted to newly synthesized DNA during replication and DNA repair. The transient incorporation of H2A.Bbd may be due to the intrinsic instability of nucleosomes carrying this variant or a faster chromatin loading. This potentially leads to a disturbance of the existing chromatin structure, which may have effects on cell cycle regulation and DNA damage sensitivity.
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Affiliation(s)
- Viola Sansoni
- Munich Center of Integrated Protein Science, Ludwig Maximilians University of Munich, 80336 Munich, Germany
| | | | - Malini Rajan
- Technische Universität Darmstadt Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Andreas Schmidt
- Munich Center of Integrated Protein Science, Ludwig Maximilians University of Munich, 80336 Munich, Germany
| | - Clemens Bönisch
- Adolf-Butenandt Institute, Ludwig Maximilians University of Munich, 80336 Munich, Germany
| | - Andreas W Thomae
- Munich Center of Integrated Protein Science, Ludwig Maximilians University of Munich, 80336 Munich, Germany
| | - Martin S Staege
- Department of Pediatrics, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany
| | - Sandra B Hake
- Munich Center of Integrated Protein Science, Ludwig Maximilians University of Munich, 80336 Munich, Germany Adolf-Butenandt Institute, Ludwig Maximilians University of Munich, 80336 Munich, Germany
| | - M Cristina Cardoso
- Technische Universität Darmstadt Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Axel Imhof
- Munich Center of Integrated Protein Science, Ludwig Maximilians University of Munich, 80336 Munich, Germany Adolf-Butenandt Institute, Ludwig Maximilians University of Munich, 80336 Munich, Germany
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García-Giménez JL, Òlaso G, Hake SB, Bönisch C, Wiedemann SM, Markovic J, Dasí F, Gimeno A, Pérez-Quilis C, Palacios O, Capdevila M, Viña J, Pallardó FV. Histone h3 glutathionylation in proliferating mammalian cells destabilizes nucleosomal structure. Antioxid Redox Signal 2013; 19:1305-20. [PMID: 23541030 PMCID: PMC3791047 DOI: 10.1089/ars.2012.5021] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
AIMS Here we report that chromatin, the complex and dynamic eukaryotic DNA packaging structure, is able to sense cellular redox changes. Histone H3, the only nucleosomal protein that possesses cysteine(s), can be modified by glutathione (GSH). RESULTS Using Biotin labeled glutathione ethyl ester (BioGEE) treatment of nucleosomes in vitro, we show that GSH, the most abundant antioxidant in mammals, binds to histone H3. BioGEE treatment of NIH3T3 cells indicates that glutathionylation of H3 is maximal in fast proliferating cells, correlating well with enhanced levels of H3 glutathionylation in different tumor cell lines. Furthermore, glutathionylation of H3 in vivo decreases in livers from aged SAMP8 and C57BL/6J mice. We demonstrate biochemically and by mass spectrometry that histone variants H3.2/H3.3 are glutathionylated on their cysteine residue 110. Furthermore, circular dichroism, thermal denaturation of reconstituted nucleosomes, and molecular modeling indicate that glutathionylation of histone H3 produces structural changes affecting nucleosomal stability. INNOVATION We characterize the implications of histone H3 glutathionylation in cell physiology and the modulation of core histone proteins structure affected by this modification. CONCLUSION Histone H3 senses cellular redox changes through glutathionylation of Cys, which increases during cell proliferation and decreases during aging. Glutathionylation of histone H3 affects nucleosome stability structure leading to a more open chromatin structure.
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Abstract
In eukaryotes, DNA is organized together with histones and non-histone proteins into a highly complex nucleoprotein structure called chromatin, with the nucleosome as its monomeric subunit. Various interconnected mechanisms regulate DNA accessibility, including replacement of canonical histones with specialized histone variants. Histone variant incorporation can lead to profound chromatin structure alterations thereby influencing a multitude of biological processes ranging from transcriptional regulation to genome stability. Among core histones, the H2A family exhibits highest sequence divergence, resulting in the largest number of variants known. Strikingly, H2A variants differ mostly in their C-terminus, including the docking domain, strategically placed at the DNA entry/exit site and implicated in interactions with the (H3–H4)2-tetramer within the nucleosome and in the L1 loop, the interaction interface of H2A–H2B dimers. Moreover, the acidic patch, important for internucleosomal contacts and higher-order chromatin structure, is altered between different H2A variants. Consequently, H2A variant incorporation has the potential to strongly regulate DNA organization on several levels resulting in meaningful biological output. Here, we review experimental evidence pinpointing towards outstanding roles of these highly variable regions of H2A family members, docking domain, L1 loop and acidic patch, and close by discussing their influence on nucleosome and higher-order chromatin structure and stability.
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Affiliation(s)
- Clemens Bönisch
- Department of Molecular Biology, Center for Integrated Protein Science Munich, Adolf-Butenandt-Institute, Ludwig-Maximilians-University Munich, 80336 Munich, Germany.
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Ratnakumar K, Duarte LF, LeRoy G, Hasson D, Smeets D, Vardabasso C, Bönisch C, Zeng T, Xiang B, Zhang DY, Li H, Wang X, Hake SB, Schermelleh L, Garcia BA, Bernstein E. ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression. Genes Dev 2012; 26:433-8. [PMID: 22391447 DOI: 10.1101/gad.179416.111] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The histone variant macroH2A generally associates with transcriptionally inert chromatin; however, the factors that regulate its chromatin incorporation remain elusive. Here, we identify the SWI/SNF helicase ATRX (α-thalassemia/MR, X-linked) as a novel macroH2A-interacting protein. Unlike its role in assisting H3.3 chromatin deposition, ATRX acts as a negative regulator of macroH2A's chromatin association. In human erythroleukemic cells deficient for ATRX, macroH2A accumulates at the HBA gene cluster on the subtelomere of chromosome 16, coinciding with the loss of α-globin expression. Collectively, our results implicate deregulation of macroH2A's distribution as a contributing factor to the α-thalassemia phenotype of ATRX syndrome.
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Affiliation(s)
- Kajan Ratnakumar
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
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Bönisch C, Schneider K, Pünzeler S, Wiedemann SM, Bielmeier C, Bocola M, Eberl HC, Kuegel W, Neumann J, Kremmer E, Leonhardt H, Mann M, Michaelis J, Schermelleh L, Hake SB. H2A.Z.2.2 is an alternatively spliced histone H2A.Z variant that causes severe nucleosome destabilization. Nucleic Acids Res 2012; 40:5951-64. [PMID: 22467210 PMCID: PMC3401452 DOI: 10.1093/nar/gks267] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The histone variant H2A.Z has been implicated in many biological processes, such as gene regulation and genome stability. Here, we present the identification of H2A.Z.2.2 (Z.2.2), a novel alternatively spliced variant of histone H2A.Z and provide a comprehensive characterization of its expression and chromatin incorporation properties. Z.2.2 mRNA is found in all human cell lines and tissues with highest levels in brain. We show the proper splicing and in vivo existence of this variant protein in humans. Furthermore, we demonstrate the binding of Z.2.2 to H2A.Z-specific TIP60 and SRCAP chaperone complexes and its active replication-independent deposition into chromatin. Strikingly, various independent in vivo and in vitro analyses, such as biochemical fractionation, comparative FRAP studies of GFP-tagged H2A variants, size exclusion chromatography and single molecule FRET, in combination with in silico molecular dynamics simulations, consistently demonstrate that Z.2.2 causes major structural changes and significantly destabilizes nucleosomes. Analyses of deletion mutants and chimeric proteins pinpoint this property to its unique C-terminus. Our findings enrich the list of known human variants by an unusual protein belonging to the H2A.Z family that leads to the least stable nucleosome known to date.
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Affiliation(s)
- Clemens Bönisch
- Department of Molecular Biology, Adolf-Butenandt-Institute, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
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Müller-Taubenberger A, Bönisch C, Fürbringer M, Wittek F, Hake SB. The histone methyltransferase Dot1 is required for DNA damage repair and proper development in Dictyostelium. Biochem Biophys Res Commun 2010; 404:1016-22. [PMID: 21187070 DOI: 10.1016/j.bbrc.2010.12.101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 12/20/2010] [Indexed: 10/18/2022]
Abstract
Posttranslational histone modifications play an important role in modulating gene expression and chromatin structure. Here we report the identification of histone H3K79 dimethylation in the simple eukaryote Dictyostelium discoideum. We have deleted the D. discoideum Dot1/KMT4 homologue and demonstrate that it is the sole enzyme responsible for histone H3K79me2. Cells lacking Dot1 are reduced in growth and delayed in development, but do not show apparent changes in cell cycle regulation. Furthermore, our results indicate that Dot1 contributes to UV damage resistance and DNA repair in D. discoideum. In summary, the data support the view that the machinery controlling the setting of histone marks is evolutionary highly conserved and provide evidence that D. discoideum is a suitable model system to analyze these modifications and their functions during development and differentiation.
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Affiliation(s)
- Annette Müller-Taubenberger
- Institute for Anatomy and Cell Biology, Schillerstr. 42, Ludwig Maximilians University of Munich, 80336 Munich, Germany.
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Wiedemann SM, Mildner SN, Bönisch C, Israel L, Maiser A, Matheisl S, Straub T, Merkl R, Leonhardt H, Kremmer E, Schermelleh L, Hake SB. Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. ACTA ACUST UNITED AC 2010; 190:777-91. [PMID: 20819935 PMCID: PMC2935562 DOI: 10.1083/jcb.201002043] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The expression of a new histone variant H3.Y increases during cellular stress to regulate cell cycle progression and gene expression. Nucleosomal incorporation of specialized histone variants is an important mechanism to generate different functional chromatin states. Here, we describe the identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. Their messenger RNAs are found in certain human cell lines, in addition to several normal and malignant human tissues. In keeping with their primate specificity, H3.X and H3.Y are detected in different brain regions. Transgenic H3.X and H3.Y proteins are stably incorporated into chromatin in a similar fashion to the known H3 variants. Importantly, we demonstrate biochemically and by mass spectrometry that endogenous H3.Y protein exists in vivo, and that stress stimuli, such as starvation and cellular density, increase the abundance of H3.Y-expressing cells. Global transcriptome analysis revealed that knockdown of H3.Y affects cell growth and leads to changes in the expression of many genes involved in cell cycle control. Thus, H3.Y is a novel histone variant involved in the regulation of cellular responses to outside stimuli.
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Affiliation(s)
- Sonja M Wiedemann
- Adolf-Butenandt-Institute, Department of Molecular Biology, Ludwig Maximilians University of Munich, 80336 Munich, Germany
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11
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Abstract
Many phenotypic changes of eukaryotic cells due to changes in gene expression depend on alterations in chromatin structure. Processes involved in the alteration of chromatin are diverse and include post-translational modifications of histone proteins, incorporation of specific histone variants, methylation of DNA and ATP-dependent chromatin remodeling. Interconnected with these processes are the localization of chromatin domains within the nuclear architecture and the appearance of various classes of noncoding regulatory RNAs. Recent experiments underscore the role of these processes in influencing diverse biological functions. However, the evidence to date implies the importance of an interplay of all these chromatin-changing functions, generating an epigenetic regulatory circuit that is still not well understood.
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Affiliation(s)
- Clemens Bönisch
- Adolf-Butenandt-Institute & Center for Integrated Protein Science Munich (CIPSM), Department of Molecular Biology, Ludwig-Maximilians University, Schillerstr. 44, 80336 Munich, Germany.
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12
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Bönisch C, Temme C, Moritz B, Wahle E. Degradation of hsp70 and other mRNAs in Drosophila via the 5' 3' pathway and its regulation by heat shock. J Biol Chem 2007; 282:21818-28. [PMID: 17545151 DOI: 10.1074/jbc.m702998200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Two general pathways of mRNA decay have been characterized in yeast. Both start with deadenylation. The major pathway then proceeds via cap hydrolysis and 5'-exonucleolytic degradation whereas the minor pathway consists of 3'-exonucleolytic decay followed by hydrolysis of the remaining cap structure. In higher eukaryotes, these pathways of mRNA decay are believed to be conserved but have not been well characterized. We have investigated the decay of the hsp70 mRNA in Drosophila Schneider cells. As shown by the use of reporter constructs, rapid deadenylation of this mRNA is directed by its 3'-untranslated region. The main deadenylase is the CCR4.NOT complex; the PAN nuclease makes a lesser contribution. Heat shock prevents deadenylation not only of the hsp70 but also of bulk mRNA. A completely deadenylated capped hsp70 mRNA decay intermediate accumulates transiently and is degraded via cap hydrolysis and 5'-decay. Thus, decapping is a slow step in the degradation pathway. Cap hydrolysis is also inhibited during heat shock. Degradation of reporter RNAs from the 3'-end became detectable only upon inhibition of 5'-decay and thus represents a minor decay pathway. Because two reporter RNAs and at least two endogenous mRNAs were degraded primarily from the 5'-end with cap hydrolysis as a slow step, this pathway appears to be of general importance for mRNA decay in Drosophila.
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Affiliation(s)
- Clemens Bönisch
- Institute of Biochemistry and Biotechnology, University of Halle, Kurt-Mothes-Strasse 3, Halle, Germany
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