1
|
Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB. PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex. Nat Commun 2018; 9:4300. [PMID: 30327463 PMCID: PMC6191444 DOI: 10.1038/s41467-018-06665-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 02/09/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022] Open
Abstract
Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.
Collapse
Affiliation(s)
- Stephanie Link
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Ramona M M Spitzer
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Moritz C Völker-Albert
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Coriolis Pharma, Fraunhoferstr. 18B, 82152, Planegg, Germany
| | - Thomas Burgold
- Wellcome Trust - MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sebastian Pünzeler
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Coparion GmbH & Co. KG, Charles-de-Gaulle-Platz 1d, 50679, Cologne, Germany
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Ida Lindström
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Andrea Nist
- Genomics Core Facility, Philipps-University Marburg, 35043, Marburg, Germany
| | - Catherine Regnard
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Philipps-University Marburg, 35043, Marburg, Germany
- Institute for Molecular Oncology, Philipps-University Marburg, 35043, Marburg, Germany
| | - Brian Hendrich
- Wellcome Trust - MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Axel Imhof
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany
| | - 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
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany.
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Pünzeler S, Link S, Wagner G, Keilhauer EC, Kronbeck N, Spitzer RM, Leidescher S, Markaki Y, Mentele E, Regnard C, Schneider K, Takahashi D, Kusakabe M, Vardabasso C, Zink LM, Straub T, Bernstein E, Harata M, Leonhardt H, Mann M, Rupp RA, Hake SB. Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation. EMBO J 2017. [PMID: 28645917 DOI: 10.15252/embj.201695757] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome-wide mapping reveals that PWWP2A binds selectively to H2A.Z-containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C-terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in Xenopus results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.
Collapse
Affiliation(s)
- Sebastian Pünzeler
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Stephanie Link
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gabriele Wagner
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nina Kronbeck
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ramona Mm Spitzer
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Susanne Leidescher
- Department of Biology, Biozentrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Yolanda Markaki
- Department of Biology, Biozentrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Edith Mentele
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Catherine Regnard
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Katrin Schneider
- Department of Biology, Biozentrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Daisuke Takahashi
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku Sendai, Japan
| | - Masayuki Kusakabe
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku Sendai, Japan
| | - Chiara Vardabasso
- Department of Oncological Sciences and Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa M Zink
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tobias Straub
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Emily Bernstein
- Department of Oncological Sciences and Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku Sendai, Japan
| | - Heinrich Leonhardt
- Department of Biology, Biozentrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Ralph Aw Rupp
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Sandra B Hake
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany .,Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| |
Collapse
|
4
|
Vardabasso C, Gaspar-Maia A, Hasson D, Pünzeler S, Valle-Garcia D, Straub T, Keilhauer EC, Strub T, Dong J, Panda T, Chung CY, Yao JL, Singh R, Segura MF, Fontanals-Cirera B, Verma A, Mann M, Hernando E, Hake SB, Bernstein E. Histone Variant H2A.Z.2 Mediates Proliferation and Drug Sensitivity of Malignant Melanoma. Mol Cell 2015; 59:75-88. [PMID: 26051178 DOI: 10.1016/j.molcel.2015.05.009] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/24/2015] [Accepted: 04/30/2015] [Indexed: 01/19/2023]
Abstract
Histone variants are emerging as key regulatory molecules in cancer. We report a unique role for the H2A.Z isoform H2A.Z.2 as a driver of malignant melanoma. H2A.Z.2 is highly expressed in metastatic melanoma, correlates with decreased patient survival, and is required for cellular proliferation. Our integrated genomic analyses reveal that H2A.Z.2 controls the transcriptional output of E2F target genes in melanoma cells. These genes are highly expressed and display a distinct signature of H2A.Z occupancy. We identify BRD2 as an H2A.Z-interacting protein, levels of which are also elevated in melanoma. We further demonstrate that H2A.Z.2-regulated genes are bound by BRD2 and E2F1 in an H2A.Z.2-dependent manner. Importantly, H2A.Z.2 deficiency sensitizes melanoma cells to chemotherapy and targeted therapies. Collectively, our findings implicate H2A.Z.2 as a mediator of cell proliferation and drug sensitivity in malignant melanoma, holding translational potential for novel therapeutic strategies.
Collapse
Affiliation(s)
- Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexandre Gaspar-Maia
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sebastian Pünzeler
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany
| | - David Valle-Garcia
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Molecular Genetics Department, Institute for Cellular Physiology, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Tobias Straub
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Thomas Strub
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taniya Panda
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi-Yeh Chung
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan L Yao
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel F Segura
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Barbara Fontanals-Cirera
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Amit Verma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Eva Hernando
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Sandra B Hake
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany.
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
5
|
Jack APM, Bussemer S, Hahn M, Pünzeler S, Snyder M, Wells M, Csankovszki G, Solovei I, Schotta G, Hake SB. H3K56me3 is a novel, conserved heterochromatic mark that largely but not completely overlaps with H3K9me3 in both regulation and localization. PLoS One 2013; 8:e51765. [PMID: 23451023 PMCID: PMC3579866 DOI: 10.1371/journal.pone.0051765] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [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: 08/01/2012] [Accepted: 11/07/2012] [Indexed: 11/18/2022] Open
Abstract
Histone lysine (K) methylation has been shown to play a fundamental role in modulating chromatin architecture and regulation of gene expression. Here we report on the identification of histone H3K56, located at the pivotal, nucleosome DNA entry/exit point, as a novel methylation site that is evolutionary conserved. We identify trimethylation of H3K56 (H3K56me3) as a modification that is present during all cell cycle phases, with the exception of S-phase, where it is underrepresented on chromatin. H3K56me3 is a novel heterochromatin mark, since it is enriched at pericentromeres but not telomeres and is thereby similar, but not identical, to the localization of H3K9me3 and H4K20me3. Possibly due to H3 sequence similarities, Suv39h enzymes, responsible for trimethylation of H3K9, also affect methylation of H3K56. Similarly, we demonstrate that trimethylation of H3K56 is removed by members of the JMJD2 family of demethylases that also target H3K9me3. Furthermore, we identify and characterize mouse mJmjd2E and its human homolog hKDM4L as novel, functionally active enzymes that catalyze the removal of two methyl groups from trimethylated H3K9 and K56. H3K56me3 is also found in C. elegans, where it co-localizes with H3K9me3 in most, but not all, tissues. Taken together, our findings raise interesting questions regarding how methylation of H3K9 and H3K56 is regulated in different organisms and their functional roles in heterochromatin formation and/or maintenance.
Collapse
Affiliation(s)
- Antonia P. M. Jack
- Center for Integrated Protein Science Munich (CIPSM) at the Adolf-Butenandt-Institute, Department of Molecular Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Silva Bussemer
- Center for Integrated Protein Science Munich (CIPSM) at the Adolf-Butenandt-Institute, Department of Molecular Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Matthias Hahn
- Center for Integrated Protein Science Munich (CIPSM) at the Adolf-Butenandt-Institute, Department of Molecular Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sebastian Pünzeler
- Center for Integrated Protein Science Munich (CIPSM) at the Adolf-Butenandt-Institute, Department of Molecular Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Martha Snyder
- Department of MCDB, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael Wells
- Department of MCDB, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gyorgyi Csankovszki
- Department of MCDB, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Irina Solovei
- LMU Biozentrum, Department of Biology II, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Gunnar Schotta
- Center for Integrated Protein Science Munich (CIPSM) at the Adolf-Butenandt-Institute, Department of Molecular Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sandra B. Hake
- Center for Integrated Protein Science Munich (CIPSM) at the Adolf-Butenandt-Institute, Department of Molecular Biology, Ludwig-Maximilians-University Munich, Munich, Germany
- * E-mail:
| |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- Clemens Bönisch
- Department of Molecular Biology, Adolf-Butenandt-Institute, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|