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Nozawa H, Nagae F, Ogihara S, Hirano R, Yamazaki H, Iizuka R, Akatsu M, Kujirai T, Takada S, Kurumizaka H, Uemura S. Nucleosomal DNA unwinding pathway through canonical and non-canonical histone disassembly. Commun Biol 2024; 7:1144. [PMID: 39277674 PMCID: PMC11401932 DOI: 10.1038/s42003-024-06856-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 09/05/2024] [Indexed: 09/17/2024] Open
Abstract
The nucleosome including H2A.B, a mammalian-specific H2A variant, plays pivotal roles in spermatogenesis, embryogenesis, and oncogenesis, indicating unique involvement in transcriptional regulation distinct from canonical H2A nucleosomes. Despite its significance, the exact regulatory mechanism remains elusive. This study utilized solid-state nanopores to investigate DNA unwinding dynamics, applying local force between DNA and histones. Comparative analysis of canonical H2A and H2A.B nucleosomes demonstrated that the H2A.B variant required a lower voltage for complete DNA unwinding. Furthermore, synchronization analysis and molecular dynamics simulations indicate that the H2A.B variant rapidly unwinds DNA, causing the H2A-H2B dimer to dissociate from DNA immediately upon disassembly of the histone octamer. In contrast, canonical H2A nucleosomes unwind DNA at a slower rate, suggesting that the H2A-H2B dimer undergoes a state of stacking at the pore. These findings suggest that nucleosomal DNA in the H2A.B nucleosomes undergoes a DNA unwinding process involving histone octamer disassembly distinct from that of canonical H2A nucleosomes, enabling smoother unwinding. The integrated approach of MD simulations and nanopore measurements is expected to evolve into a versatile tool for studying molecular interactions, not only within nucleosomes but also through the forced dissociation of DNA-protein complexes.
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Affiliation(s)
- Hikaru Nozawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Fritz Nagae
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Satoshi Ogihara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rina Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hirohito Yamazaki
- Top Runner Incubation Center for Academia-Industry Fusion, Nagaoka University of Technology, Nagaoka, Niigata, Japan
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Munetaka Akatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hitoshi Kurumizaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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2
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Ouararhni K, Mietton F, Sabir JSM, Ibrahim A, Molla A, Albheyri RS, Zari AT, Bahieldin A, Menoni H, Bronner C, Dimitrov S, Hamiche A. Identification of a novel DNA oxidative damage repair pathway, requiring the ubiquitination of the histone variant macroH2A1.1. BMC Biol 2024; 22:188. [PMID: 39218869 PMCID: PMC11368025 DOI: 10.1186/s12915-024-01987-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 08/18/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The histone variant macroH2A (mH2A), the most deviant variant, is about threefold larger than the conventional histone H2A and consists of a histone H2A-like domain fused to a large Non-Histone Region responsible for recruiting PARP-1 to chromatin. The available data suggest that the histone variant mH2A participates in the regulation of transcription, maintenance of heterochromatin, NAD+ metabolism, and double-strand DNA repair. RESULTS Here, we describe a novel function of mH2A, namely its implication in DNA oxidative damage repair through PARP-1. The depletion of mH2A affected both repair and cell survival after the induction of oxidative lesions in DNA. PARP-1 formed a specific complex with mH2A nucleosomes in vivo. The mH2A nucleosome-associated PARP-1 is inactive. Upon oxidative damage, mH2A is ubiquitinated, PARP-1 is released from the mH2A nucleosomal complex, and is activated. The in vivo-induced ubiquitination of mH2A, in the absence of any oxidative damage, was sufficient for the release of PARP-1. However, no release of PARP-1 was observed upon treatment of the cells with either the DNA alkylating agent MMS or doxorubicin. CONCLUSIONS Our data identify a novel pathway for the repair of DNA oxidative lesions, requiring the ubiquitination of mH2A for the release of PARP-1 from chromatin and its activation.
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Affiliation(s)
- Khalid Ouararhni
- Département de Génomique Fonctionnelle Et Cancer, Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), Université de Strasbourg/CNRS/INSERM, Equipe Labellisée La Ligue Nationale Contre Le Cancer, 67404, Illkirch Cedex, France
| | - Flore Mietton
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000, Grenoble, France
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulkhaleg Ibrahim
- Département de Génomique Fonctionnelle Et Cancer, Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), Université de Strasbourg/CNRS/INSERM, Equipe Labellisée La Ligue Nationale Contre Le Cancer, 67404, Illkirch Cedex, France
- National Research Centre for Tropical and Transboundary Diseases (NRCTTD), Alzentan, 99316, Libya
| | - Annie Molla
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000, Grenoble, France
| | - Raed S Albheyri
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ali T Zari
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hervé Menoni
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000, Grenoble, France
| | - Christian Bronner
- Département de Génomique Fonctionnelle Et Cancer, Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), Université de Strasbourg/CNRS/INSERM, Equipe Labellisée La Ligue Nationale Contre Le Cancer, 67404, Illkirch Cedex, France
| | - Stefan Dimitrov
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000, Grenoble, France.
- Institute of Molecular Biology Roumen Tsanev, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Ali Hamiche
- Département de Génomique Fonctionnelle Et Cancer, Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), Université de Strasbourg/CNRS/INSERM, Equipe Labellisée La Ligue Nationale Contre Le Cancer, 67404, Illkirch Cedex, France.
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3
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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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4
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Lai PM, Chan KM. Roles of Histone H2A Variants in Cancer Development, Prognosis, and Treatment. Int J Mol Sci 2024; 25:3144. [PMID: 38542118 PMCID: PMC10969971 DOI: 10.3390/ijms25063144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 07/16/2024] Open
Abstract
Histones are nuclear proteins essential for packaging genomic DNA and epigenetic gene regulation. Paralogs that can substitute core histones (H2A, H2B, H3, and H4), named histone variants, are constitutively expressed in a replication-independent manner throughout the cell cycle. With specific chaperones, they can be incorporated to chromatin to modify nucleosome stability by modulating interactions with nucleosomal DNA. This allows the regulation of essential fundamental cellular processes for instance, DNA damage repair, chromosomal segregation, and transcriptional regulation. Among all the histone families, histone H2A family has the largest number of histone variants reported to date. Each H2A variant has multiple functions apart from their primary role and some, even be further specialized to perform additional tasks in distinct lineages, such as testis specific shortH2A (sH2A). In the past decades, the discoveries of genetic alterations and mutations in genes encoding H2A variants in cancer had revealed variants' potentiality in driving carcinogenesis. In addition, there is growing evidence that H2A variants may act as novel prognostic indicators or biomarkers for both early cancer detection and therapeutic treatments. Nevertheless, no studies have ever concluded all identified variants in a single report. Here, in this review, we summarize the respective functions for all the 19 mammalian H2A variants and their roles in cancer biology whilst potentiality being used in clinical setting.
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Affiliation(s)
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China;
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5
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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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6
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Karam G, Molaro A. Casting histone variants during mammalian reproduction. Chromosoma 2023:10.1007/s00412-023-00803-9. [PMID: 37347315 PMCID: PMC10356639 DOI: 10.1007/s00412-023-00803-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
Abstract
During mammalian reproduction, germ cell chromatin packaging is key to prepare parental genomes for fertilization and to initiate embryonic development. While chromatin modifications such as DNA methylation and histone post-translational modifications are well known to carry regulatory information, histone variants have received less attention in this context. Histone variants alter the stability, structure and function of nucleosomes and, as such, contribute to chromatin organization in germ cells. Here, we review histone variants expression dynamics during the production of male and female germ cells, and what is currently known about their parent-of-origin effects during reproduction. Finally, we discuss the apparent conundrum behind these important functions and their recent evolutionary diversification.
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Affiliation(s)
- Germaine Karam
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Antoine Molaro
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
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7
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The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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8
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Sokolova V, Sarkar S, Tan D. Histone variants and chromatin structure, update of advances. Comput Struct Biotechnol J 2022; 21:299-311. [PMID: 36582440 PMCID: PMC9764139 DOI: 10.1016/j.csbj.2022.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Histone proteins are highly conserved among all eukaryotes. They have two important functions in the cell: to package the genomic DNA and to regulate gene accessibility. Fundamental to these functions is the ability of histone proteins to interact with DNA and to form the nucleoprotein complex called chromatin. One of the mechanisms the cells use to regulate chromatin and gene expression is through replacing canonical histones with their variants at specific loci to achieve functional consequence. Recent cryo-electron microscope (cryo-EM) studies of chromatin containing histone variants reveal new details that shed light on how variant-specific features influence the structures and functions of chromatin. In this article, we review the current state of knowledge on histone variants biochemistry and discuss the implication of these new structural information on histone variant biology and their functions in transcription.
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9
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Takizawa Y, Kurumizaka H. Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194851. [PMID: 35952957 DOI: 10.1016/j.bbagrm.2022.194851] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Chromatin is a dynamic molecular complex composed of DNA and proteins that package the DNA in the nucleus of eukaryotic cells. The basic structural unit of chromatin is the nucleosome core particle, composed of ~150 base pairs of genomic DNA wrapped around a histone octamer containing two copies each of four histones, H2A, H2B, H3, and H4. Individual nucleosome core particles are connected by short linker DNAs, forming a nucleosome array known as a beads-on-a-string fiber. Higher-order structures of chromatin are closely linked to nuclear events such as replication, transcription, recombination, and repair. Recently, a variety of chromatin structures have been determined by single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), and their structural details have provided clues about the chromatin architecture functions in the cell. In this review, we highlight recent cryo-EM structural studies of a fundamental chromatin unit to clarify the functions of chromatin.
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Affiliation(s)
- Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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10
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Maree JP, Tvardovskiy A, Ravnsborg T, Jensen ON, Rudenko G, Patterton HG. Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A. Nucleic Acids Res 2022; 50:9705-9723. [PMID: 36095123 PMCID: PMC9508842 DOI: 10.1093/nar/gkac759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/09/2022] [Accepted: 08/30/2022] [Indexed: 11/12/2022] Open
Abstract
Trypanosomes diverged from the main eukaryotic lineage about 600 million years ago, and display some unusual genomic and epigenetic properties that provide valuable insight into the early processes employed by eukaryotic ancestors to regulate chromatin-mediated functions. We analysed Trypanosoma brucei core histones by high mass accuracy middle-down mass spectrometry to map core histone post-translational modifications (PTMs) and elucidate cis-histone combinatorial PTMs (cPTMs). T. brucei histones are heavily modified and display intricate cPTMs patterns, with numerous hypermodified cPTMs that could contribute to the formation of non-repressive euchromatic states. The Trypanosoma brucei H2A C-terminal tail is hyperacetylated, containing up to five acetylated lysine residues. MNase-ChIP-seq revealed a striking enrichment of hyperacetylated H2A at Pol II transcription start regions, and showed that H2A histones that are hyperacetylated in different combinations localised to different genomic regions, suggesting distinct epigenetic functions. Our genomics and proteomics data provide insight into the complex epigenetic mechanisms used by this parasite to regulate a genome that lacks the transcriptional control mechanisms found in later-branched eukaryotes. The findings further demonstrate the complexity of epigenetic mechanisms that were probably shared with the last eukaryotic common ancestor.
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Affiliation(s)
- Johannes P Maree
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Tina Ravnsborg
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Gloria Rudenko
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Hugh-G Patterton
- Center for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7600, South Africa
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11
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Herchenröther A, Wunderlich TM, Lan J, Hake SB. Spotlight on histone H2A variants: From B to X to Z. Semin Cell Dev Biol 2022; 135:3-12. [PMID: 35365397 DOI: 10.1016/j.semcdb.2022.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 12/30/2022]
Abstract
Chromatin, the functional organization of DNA with histone proteins in eukaryotic nuclei, is the tightly-regulated template for several biological processes, such as transcription, replication, DNA damage repair, chromosome stability and sister chromatid segregation. In order to achieve a reversible control of local chromatin structure and DNA accessibility, various interconnected mechanisms have evolved. One of such processes includes the deposition of functionally-diverse variants of histone proteins into nucleosomes, the building blocks of chromatin. Among core histones, the family of H2A histone variants exhibits the largest number of members and highest sequence-divergence. In this short review, we report and discuss recent discoveries concerning the biological functions of the animal histone variants H2A.B, H2A.X and H2A.Z and how dysregulation or mutation of the latter impacts the development of disease.
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Affiliation(s)
| | - Tim M Wunderlich
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany
| | - Jie Lan
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany.
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12
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Phillips EO, Gunjan A. Histone Variants: The Unsung Guardians of the Genome. DNA Repair (Amst) 2022; 112:103301. [DOI: 10.1016/j.dnarep.2022.103301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/01/2022] [Accepted: 02/12/2022] [Indexed: 12/15/2022]
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13
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Nodelman IM, Patel A, Levendosky RF, Bowman GD. Reconstitution and Purification of Nucleosomes with Recombinant Histones and Purified DNA. ACTA ACUST UNITED AC 2021; 133:e130. [PMID: 33305911 DOI: 10.1002/cpmb.130] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleosomes are substrates for a broad range of factors, including those involved in transcription or chromosome maintenance/reorganization and enzymes that covalently modify histones. Given the heterogeneous nature of nucleosomes in vivo (i.e., varying histone composition, post-translational modifications, DNA sequence register), understanding the specificity and activities of chromatin-interacting factors has required in vitro studies using well-defined nucleosome substrates. Here, we provide detailed methods for large-scale PCR preparation of DNA, assembly of nucleosomes from purified DNA and histones, and purification of DNA and mononucleosomes. Such production of well-defined nucleosomes for biochemical and biophysical studies is key for studying numerous proteins and protein complexes that bind and/or alter nucleosomes and for revealing inherent characteristics of nucleosomes. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Large-scale PCR amplification of DNA Basic Protocol 2: DNA and nucleosome purification using a Bio-Rad Mini Prep Cell/Prep Cell Basic Protocol 3: Nucleosome reconstitution via linear gradient salt dialysis.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Ashok Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.,Present address: Catalent Cell and Gene Therapy, Baltimore, Maryland
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
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14
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Ohno M, Ando T, Priest DG, Taniguchi Y. Hi-CO: 3D genome structure analysis with nucleosome resolution. Nat Protoc 2021; 16:3439-3469. [PMID: 34050337 DOI: 10.1038/s41596-021-00543-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 03/23/2021] [Indexed: 01/03/2023]
Abstract
The nucleosome is the basic organizational unit of the genome. The folding structure of nucleosomes is closely related to genome functions, and has been reported to be in dynamic interplay with binding of various nuclear proteins to genomic loci. Here, we describe our high-throughput chromosome conformation capture with nucleosome orientation (Hi-CO) technology to derive 3D nucleosome positions with their orientations at every genomic locus in the nucleus. This technology consists of an experimental procedure for nucleosome proximity analysis and a computational procedure for 3D modeling. The experimental procedure is based on an improved method of high-throughput chromosome conformation capture (Hi-C) analysis. Whereas conventional Hi-C allows spatial proximity analysis among genomic loci with 1-10 kbp resolution, our Hi-CO allows proximity analysis among DNA entry or exit points at every nucleosome locus. This analysis is realized by carrying out ligations among the entry/exit points in every nucleosome in a micrococcal-nuclease-fragmented genome, and by quantifying frequencies of ligation products with next-generation sequencing. Our protocol has enabled this analysis by cleanly excluding unwanted non-ligation products that are abundant owing to the frequent genome fragmentation by micrococcal nuclease. The computational procedure is based on simulated annealing-molecular dynamics, which allows determination of optimized 3D positions and orientations of every nucleosome that satisfies the proximity ligation data sufficiently well. Typically, examination of the Saccharomyces cerevisiae genome with 130 million sequencing reads facilitates analysis of a total of 66,360 nucleosome loci with 6.8 nm resolution. The technique requires 2-3 weeks for sequencing library preparation and 2 weeks for simulation.
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Affiliation(s)
- Masae Ohno
- Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Tadashi Ando
- Laboratory for Biomolecular Function Simulation, Quantitative Biology Center, RIKEN, Kobe, Japan.,Department of Applied Electronics, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, Japan
| | - David G Priest
- Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Yuichi Taniguchi
- Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan. .,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan. .,Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
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15
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Cole L, Kurscheid S, Nekrasov M, Domaschenz R, Vera DL, Dennis JH, Tremethick DJ. Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells. Nat Commun 2021; 12:2524. [PMID: 33953180 PMCID: PMC8100287 DOI: 10.1038/s41467-021-22688-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/25/2021] [Indexed: 01/02/2023] Open
Abstract
Chromatin accessibility of a promoter is fundamental in regulating transcriptional activity. The histone variant H2A.Z has been shown to contribute to this regulation, but its role has remained poorly understood. Here, we prepare high-depth maps of the position and accessibility of H2A.Z-containing nucleosomes for all human Pol II promoters in epithelial, mesenchymal and isogenic cancer cell lines. We find that, in contrast to the prevailing model, many different types of active and inactive promoter structures are observed that differ in their nucleosome organization and sensitivity to MNase digestion. Key aspects of an active chromatin structure include positioned H2A.Z MNase resistant nucleosomes upstream or downstream of the TSS, and a MNase sensitive nucleosome at the TSS. Furthermore, the loss of H2A.Z leads to a dramatic increase in the accessibility of transcription factor binding sites. Collectively, these results suggest that H2A.Z has multiple and distinct roles in regulating gene expression dependent upon its location in a promoter.
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Affiliation(s)
- Lauren Cole
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | - Sebastian Kurscheid
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Maxim Nekrasov
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Renae Domaschenz
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Daniel L Vera
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Dennis
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA.
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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16
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Abstract
Eukaryotic nucleosomes organize chromatin by wrapping 147 bp of DNA around a histone core particle comprising two molecules each of histone H2A, H2B, H3 and H4. The DNA entering and exiting the particle may be bound by the linker histone H1. Whereas deposition of bulk histones is confined to S-phase, paralogs of the common histones, known as histone variants, are available to carry out functions throughout the cell cycle and accumulate in post-mitotic cells. Histone variants confer different structural properties on nucleosomes by wrapping more or less DNA or by altering nucleosome stability. They carry out specialized functions in DNA repair, chromosome segregation and regulation of transcription initiation, or perform tissue-specific roles. In this Cell Science at a Glance article and the accompanying poster, we briefly examine new insights into histone origins and discuss variants from each of the histone families, focusing on how structural differences may alter their functions. Summary: Histone variants change the structural properties of nucleosomes by wrapping more or less DNA, altering nucleosome stability or carrying out specialized functions.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
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17
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Kohestani H, Wereszczynski J. Effects of H2A.B incorporation on nucleosome structures and dynamics. Biophys J 2021; 120:1498-1509. [PMID: 33609493 DOI: 10.1016/j.bpj.2021.01.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/31/2020] [Accepted: 01/12/2021] [Indexed: 01/20/2023] Open
Abstract
The H2A.B histone variant is an epigenetic regulator involved in transcriptional upregulation, DNA synthesis, and splicing that functions by replacing the canonical H2A histone in the nucleosome core particle. Introduction of H2A.B results in less compact nucleosome states with increased DNA unwinding and accessibility at the nucleosomal entry and exit sites. Despite being well characterized experimentally, the molecular mechanisms by which H2A.B incorporation alters nucleosome stability and dynamics remain poorly understood. To study the molecular mechanisms of H2A.B, we have performed a series of conventional and enhanced sampling molecular dynamics simulation of H2A.B- and canonical H2A-containing nucleosomes. Results of conventional simulations show that H2A.B weakens protein-protein and protein-DNA interactions at specific locations throughout the nucleosome. These weakened interactions result in significantly more DNA opening from both the entry and exit sites in enhanced sampling simulations. Furthermore, free energy profiles show that H2A.B-containing nucleosomes have significantly broader free wells and that H2A.B allows for sampling of states with increased DNA breathing, which are shown to be stable on the hundreds of nanoseconds timescale with further conventional simulations. Together, our results show the molecular mechanisms by which H2A.B creates less compacted nucleosome states as a means of increasing genetic accessibility and gene transcription.
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Affiliation(s)
- Havva Kohestani
- Department of Biology, Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Jeff Wereszczynski
- Department of Physics, Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois.
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18
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Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome. Commun Biol 2021; 4:191. [PMID: 33580188 PMCID: PMC7881002 DOI: 10.1038/s42003-021-01707-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/11/2021] [Indexed: 01/07/2023] Open
Abstract
H2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate "open conformation", in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome.
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19
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Nucleosome Positioning and Spacing: From Mechanism to Function. J Mol Biol 2021; 433:166847. [PMID: 33539878 DOI: 10.1016/j.jmb.2021.166847] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023]
Abstract
Eukaryotes associate their genomes with histone proteins, forming nucleosome particles. Nucleosomes regulate and protect the genetic information. They often assemble into evenly spaced arrays of nucleosomes. These regular nucleosome arrays cover significant portions of the genome, in particular over genes. The presence of these evenly spaced nucleosome arrays is highly conserved throughout the entire eukaryotic domain. Here, we review the mechanisms behind the establishment of this primary structure of chromatin with special emphasis on the biogenesis of evenly spaced nucleosome arrays. We highlight the roles that transcription, nucleosome remodelers, DNA sequence, and histone density play towards the formation of evenly spaced nucleosome arrays and summarize our current understanding of their cellular functions. We end with key unanswered questions that remain to be explored to obtain an in-depth understanding of the biogenesis and function of the nucleosome landscape.
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20
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Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J. Short H2A histone variants are expressed in cancer. Nat Commun 2021; 12:490. [PMID: 33473122 PMCID: PMC7817690 DOI: 10.1038/s41467-020-20707-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
Short H2A (sH2A) histone variants are primarily expressed in the testes of placental mammals. Their incorporation into chromatin is associated with nucleosome destabilization and modulation of alternate splicing. Here, we show that sH2As innately possess features similar to recurrent oncohistone mutations associated with nucleosome instability. Through analyses of existing cancer genomics datasets, we find aberrant sH2A upregulation in a broad array of cancers, which manifest splicing patterns consistent with global nucleosome destabilization. We posit that short H2As are a class of "ready-made" oncohistones, whose inappropriate expression contributes to chromatin dysfunction in cancer.
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Affiliation(s)
- Guo-Liang Chew
- The Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Marie Bleakley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Harmit S Malik
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Antoine Molaro
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Genetics, Reproduction and Development (GReD) Institute, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Jay Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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21
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Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu P, Zhou Z. Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2. EMBO J 2021; 40:e105907. [PMID: 33073403 PMCID: PMC7780145 DOI: 10.15252/embj.2020105907] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 01/03/2023] Open
Abstract
Nucleosomes are dynamic entities with wide-ranging compositional variations. Human histone variants H2A.B and H2A.Z.2.2 play critical roles in multiple biological processes by forming unstable nucleosomes and open chromatin structures, but how H2A.B and H2A.Z.2.2 confer these dynamic features to nucleosomes remains unclear. Here, we report cryo-EM structures of nucleosome core particles containing human H2A.B (H2A.B-NCP) at atomic resolution, identifying large-scale structural rearrangements in the histone octamer in H2A.B-NCP. H2A.B-NCP compacts approximately 103 bp of DNA wrapping around the core histones in approximately 1.2 left-handed superhelical turns, in sharp contrast to canonical nucleosome encompassing approximately 1.7 turns of DNA. Micrococcal nuclease digestion assay reveals that nineteen H2A.B-specific residues, including a ROF ("regulating-octamer-folding") sequence of six consecutive residues, are responsible for loosening of H2A.B-NCPs. Unlike H2A.B-NCP, the H2A.Z.2.2-containing nucleosome (Z.2.2-NCP) adopts a less-extended structure and compacts around 125 bp of DNA. Further investigation uncovers a crucial role for the H2A.Z.2.2-specific ROF in both H2A.Z.2.2-NCP opening and SWR1-dependent histone replacement. Taken together, these first high-resolution structure of unstable nucleosomes induced by histone H2A variants elucidate specific functions of H2A.B and H2A.Z.2.2 in enhancing chromatin dynamics.
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Affiliation(s)
- Min Zhou
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Linchang Dai
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Chengmin Li
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Liuxin Shi
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan Huang
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhenqian Guo
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Fei Wu
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ping Zhu
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zheng Zhou
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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22
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Molaro A, Wood AJ, Janssens D, Kindelay SM, Eickbush MT, Wu S, Singh P, Muller CH, Henikoff S, Malik HS. Biparental contributions of the H2A.B histone variant control embryonic development in mice. PLoS Biol 2020; 18:e3001001. [PMID: 33362208 PMCID: PMC7757805 DOI: 10.1371/journal.pbio.3001001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
Histone variants expand chromatin functions in eukaryote genomes. H2A.B genes are testis-expressed short histone H2A variants that arose in placental mammals. Their biological functions remain largely unknown. To investigate their function, we generated a knockout (KO) model that disrupts all 3 H2A.B genes in mice. We show that H2A.B KO males have globally altered chromatin structure in postmeiotic germ cells. Yet, they do not show impaired spermatogenesis or testis function. Instead, we find that H2A.B plays a crucial role postfertilization. Crosses between H2A.B KO males and females yield embryos with lower viability and reduced size. Using a series of genetic crosses that separate parental and zygotic contributions, we show that the H2A.B status of both the father and mother, but not of the zygote, affects embryonic viability and growth during gestation. We conclude that H2A.B is a novel parental-effect gene, establishing a role for short H2A histone variants in mammalian development. We posit that parental antagonism over embryonic growth drove the origin and ongoing diversification of short histone H2A variants in placental mammals.
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Affiliation(s)
- Antoine Molaro
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Anna J. Wood
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Derek Janssens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Selina M. Kindelay
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael T. Eickbush
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Steven Wu
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Priti Singh
- Comparative Medicine, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Charles H. Muller
- Male Fertility Laboratory, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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23
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Kurumizaka H, Kujirai T, Takizawa Y. Contributions of Histone Variants in Nucleosome Structure and Function. J Mol Biol 2020; 433:166678. [PMID: 33065110 DOI: 10.1016/j.jmb.2020.10.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 11/19/2022]
Abstract
Chromatin compacts genomic DNA in eukaryotes. The primary chromatin unit is the nucleosome core particle, composed of four pairs of the core histones, H2A, H2B, H3, and H4, and 145-147 base pairs of DNA. Since replication, recombination, repair, and transcription take place in chromatin, the structure and dynamics of the nucleosome must be versatile. These nucleosome characteristics underlie the epigenetic regulation of genomic DNA. In higher eukaryotes, many histone variants have been identified as non-allelic isoforms, which confer nucleosome diversity. In this article, we review the manifold types of nucleosomes produced by histone variants, which play important roles in the epigenetic regulation of chromatin.
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Affiliation(s)
- Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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24
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Martire S, Banaszynski LA. The roles of histone variants in fine-tuning chromatin organization and function. Nat Rev Mol Cell Biol 2020; 21:522-541. [PMID: 32665685 PMCID: PMC8245300 DOI: 10.1038/s41580-020-0262-8] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Histones serve to both package and organize DNA within the nucleus. In addition to histone post-translational modification and chromatin remodelling complexes, histone variants contribute to the complexity of epigenetic regulation of the genome. Histone variants are characterized by a distinct protein sequence and a selection of designated chaperone systems and chromatin remodelling complexes that regulate their localization in the genome. In addition, histone variants can be enriched with specific post-translational modifications, which in turn can provide a scaffold for recruitment of variant-specific interacting proteins to chromatin. Thus, through these properties, histone variants have the capacity to endow specific regions of chromatin with unique character and function in a regulated manner. In this Review, we provide an overview of recent advances in our understanding of the contribution of histone variants to chromatin function in mammalian systems. First, we discuss new molecular insights into chaperone-mediated histone variant deposition. Next, we discuss mechanisms by which histone variants influence chromatin properties such as nucleosome stability and the local chromatin environment both through histone variant sequence-specific effects and through their role in recruiting different chromatin-associated complexes. Finally, we focus on histone variant function in the context of both embryonic development and human disease, specifically developmental syndromes and cancer.
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Affiliation(s)
- Sara Martire
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Laura A Banaszynski
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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25
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Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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26
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Sato S, Tanaka N, Arimura Y, Kujirai T, Kurumizaka H. The N-terminal and C-terminal halves of histone H2A.Z independently function in nucleosome positioning and stability. Genes Cells 2020; 25:538-546. [PMID: 32500630 PMCID: PMC7496805 DOI: 10.1111/gtc.12791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 01/21/2023]
Abstract
Nucleosome positioning and stability affect gene regulation in eukaryotic chromatin. Histone H2A.Z is an evolutionally conserved histone variant that forms mobile and unstable nucleosomes in vivo and in vitro. In the present study, we reconstituted nucleosomes containing human H2A.Z.1 mutants, in which the N‐terminal or C‐terminal half of H2A.Z.1 was replaced by the corresponding canonical H2A region. We found that the N‐terminal portion of H2A.Z.1 is involved in flexible nucleosome positioning, whereas the C‐terminal portion leads to weak H2A.Z.1‐H2B association in the nucleosome. These results indicate that the N‐terminal and C‐terminal portions are independently responsible for the H2A.Z.1 nucleosome characteristics.
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Affiliation(s)
- Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Naoki Tanaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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27
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Peng J, Yuan C, Hua X, Zhang Z. Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures. Epigenetics Chromatin 2020; 13:28. [PMID: 32664941 PMCID: PMC7362417 DOI: 10.1186/s13072-020-00351-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 07/09/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND H2A.B, the most divergent histone variant of H2A, can significantly modulate nucleosome and chromatin structures. However, the related structural details and the underlying mechanism remain elusive to date. In this work, we built atomic models of the H2A.B-containing nucleosome core particle (NCP), chromatosome, and chromatin fiber. Multiscale modeling including all-atom molecular dynamics and coarse-grained simulations were then carried out for these systems. RESULTS It is found that sequence differences at the C-terminal tail, the docking domain, and the L2 loop, between H2A.B and H2A are directly responsible for the DNA unwrapping in the H2A.B NCP, whereas the N-terminus of H2A.B may somewhat compensate for the aforementioned unwrapping effect. The assembly of the H2A.B NCP is more difficult than that of the H2A NCP. H2A.B may also modulate the interactions of H1 with both the NCP and the linker DNA and could further affect the higher-order structure of the chromatin fiber. CONCLUSIONS The results agree with the experimental results and may shed new light on the biological function of H2A.B. Multiscale modeling may be a valuable tool for investigating structure and dynamics of the nucleosome and the chromatin induced by various histone variants.
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Affiliation(s)
- Junhui Peng
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, National Science Center for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Chuang Yuan
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, National Science Center for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
| | - Xinfan Hua
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, National Science Center for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
| | - Zhiyong Zhang
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, National Science Center for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.
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28
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Short Histone H2A Variants: Small in Stature but not in Function. Cells 2020; 9:cells9040867. [PMID: 32252453 PMCID: PMC7226823 DOI: 10.3390/cells9040867] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/19/2022] Open
Abstract
The dynamic packaging of DNA into chromatin regulates all aspects of genome function by altering the accessibility of DNA and by providing docking pads to proteins that copy, repair and express the genome. Different epigenetic-based mechanisms have been described that alter the way DNA is organised into chromatin, but one fundamental mechanism alters the biochemical composition of a nucleosome by substituting one or more of the core histones with their variant forms. Of the core histones, the largest number of histone variants belong to the H2A class. The most divergent class is the designated “short H2A variants” (H2A.B, H2A.L, H2A.P and H2A.Q), so termed because they lack a H2A C-terminal tail. These histone variants appeared late in evolution in eutherian mammals and are lineage-specific, being expressed in the testis (and, in the case of H2A.B, also in the brain). To date, most information about the function of these peculiar histone variants has come from studies on the H2A.B and H2A.L family in mice. In this review, we describe their unique protein characteristics, their impact on chromatin structure, and their known functions plus other possible, even non-chromatin, roles in an attempt to understand why these peculiar histone variants evolved in the first place.
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29
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RNA-Guided Genomic Localization of H2A.L.2 Histone Variant. Cells 2020; 9:cells9020474. [PMID: 32085641 PMCID: PMC7072763 DOI: 10.3390/cells9020474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 12/22/2022] Open
Abstract
The molecular basis of residual histone retention after the nearly genome-wide histone-to-protamine replacement during late spermatogenesis is a critical and open question. Our previous investigations showed that in postmeiotic male germ cells, the genome-scale incorporation of histone variants TH2B-H2A.L.2 allows a controlled replacement of histones by protamines to occur. Here, we highlight the intrinsic ability of H2A.L.2 to specifically target the pericentric regions of the genome and discuss why pericentric heterochromatin is a privileged site of histone retention in mature spermatozoa. We observed that the intranuclear localization of H2A.L.2 is controlled by its ability to bind RNA, as well as by an interplay between its RNA-binding activity and its tropism for pericentric heterochromatin. We identify the H2A.L.2 RNA-binding domain and demonstrate that in somatic cells, the replacement of H2A.L.2 RNA-binding motif enhances and stabilizes its pericentric localization, while the forced expression of RNA increases its homogenous nuclear distribution. Based on these data, we propose that the specific accumulation of RNA on pericentric regions combined with H2A.L.2 tropism for these regions are responsible for stabilizing H2A.L.2 on these regions in mature spermatozoa. This situation would favor histone retention on pericentric heterochromatin.
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30
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Tanaka H, Sato S, Koyama M, Kujirai T, Kurumizaka H. Biochemical and structural analyses of the nucleosome containing human histone H2A.J. J Biochem 2019; 167:419-427. [DOI: 10.1093/jb/mvz109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/24/2019] [Indexed: 02/02/2023] Open
Abstract
Abstract
Histone H2A.J, a histone H2A variant conserved in mammals, may function in the expression of genes related to inflammation and cell proliferation. In the present study, we purified the human histone H2A.J variant and found that H2A.J is efficiently incorporated into the nucleosome in vitro. H2A.J formed the stable nucleosome, which accommodated the DNA ends. Mutations in the H2A.J-specific residues did not affect the nucleosome stability, although the mutation of the H2A.J Ala40 residue, which is conserved in some members of the canonical H2A class, reduced the nucleosome stability. Consistently, the crystal structure of the H2A.J nucleosome revealed that the H2A.J-specific residues, including the Ala40 residue, did not affect the nucleosome structure. These results provide basic information for understanding the function of the H2A.J nucleosome.
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Affiliation(s)
- Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masako Koyama
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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31
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Yao F, Yu P, Li Y, Yuan X, Li Z, Zhang T, Liu F, Wang Y, Wang Y, Li D, Ma B, Shu C, Kong W, Zhou B, Wang L. Histone Variant H2A.Z Is Required for the Maintenance of Smooth Muscle Cell Identity as Revealed by Single-Cell Transcriptomics. Circulation 2019; 138:2274-2288. [PMID: 29871976 DOI: 10.1161/circulationaha.117.033114] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Histone variants endow chromatin with specific structures, and play essential roles in development and diseases. However, little is known about their roles in controlling cell identity in vascular diseases. METHODS Given the cell heterogeneity in atherosclerotic lesions, we applied single-cell RNA-Sequencing to analyze diseased human arteries, and identified histone variant H2A.Z as a key histone signature to maintain vascular smooth muscle cell (VSMC) identity. RESULTS We show that H2A.Z occupies genomic regions near VSMC marker genes, and its occupancy is decreased in VSMCs undergoing dedifferentiation. Mechanistically, H2A.Z occupancy preferentially promotes nucleosome turnover, and facilitates the recruitment of SMAD3 and MED1, thereby activating VSMC marker gene expression. In addition, H2A.Z expression is dramatically reduced at both mRNA and protein levels in diseased human vascular tissues compared to those in normal arteries. Notably, in vivo overexpression of H2A.Z rescues injury-induced loss of VSMC identity and neointima formation. CONCLUSIONS Together, our data introduce dynamic occupancy of a histone variant as a novel regulatory basis contributing to cell fate decisions, and imply H2A.Z as a potential intervention node for vascular diseases.
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Affiliation(s)
- Fang Yao
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Peng Yu
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Yue Li
- Department of Cardiac Surgery, Air Force General Hospital of People's Liberation Army, Beijing, China (Y.L.)
| | - Xinli Yuan
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Zheng Li
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Tao Zhang
- Department of Vascular Surgery, Peking University People's Hospital, Beijing, China (T.Z.)
| | - Fei Liu
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Yingbao Wang
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing.,Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China (Y.W., B.M., W.K.)
| | | | - Dandan Li
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Baihui Ma
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China (Y.W., B.M., W.K.)
| | - Chang Shu
- Department of Cardiovascular Surgery (C.S.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Wei Kong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China (Y.W., B.M., W.K.)
| | - Bingying Zhou
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Li Wang
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases (F.Y., P.Y., X.Y., Z.L., F.L., Y.W., D.L., B.Z., L.W.), Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
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32
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Abstract
Repair of damaged DNA plays a crucial role in maintaining genomic integrity and normal cell function. The base excision repair (BER) pathway is primarily responsible for removing modified nucleobases that would otherwise cause deleterious and mutagenic consequences and lead to disease. The BER process is initiated by a DNA glycosylase, which recognizes and excises the target nucleobase lesion, and is completed via downstream enzymes acting in a well-coordinated manner. A majority of our current understanding about how BER enzymes function comes from in vitro studies using free duplex DNA as a simplified model. In eukaryotes, however, BER is challenged by the packaging of genomic DNA into chromatin. The fundamental structural repeating unit of chromatin is the nucleosome, which presents a more complex substrate context than free duplex DNA for repair. In this chapter, we discuss how BER enzymes, particularly glycosylases, engage in the context of packaged DNA with insights obtained from both in vivo and in vitro studies. Furthermore, we review factors and mechanisms that can modify chromatin architecture and/or influence DNA accessibility to BER machinery, such as the geometric location of the damage site, nucleosomal DNA unwrapping, histone post-translational modifications, histone variant incorporation, and chromatin remodeling.
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Affiliation(s)
- Chuxuan Li
- Department of Chemistry, Brown University, Providence, RI, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, United States.
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33
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Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo. Biochem Biophys Res Commun 2019; 515:719-724. [DOI: 10.1016/j.bbrc.2019.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/02/2019] [Indexed: 11/20/2022]
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34
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The dynamics and regulation of chromatin remodeling during spermiogenesis. Gene 2019; 706:201-210. [DOI: 10.1016/j.gene.2019.05.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/06/2023]
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35
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Wang T, Chuffart F, Bourova-Flin E, Wang J, Mi J, Rousseaux S, Khochbin S. Histone variants: critical determinants in tumour heterogeneity. Front Med 2019; 13:289-297. [PMID: 30280307 DOI: 10.1007/s11684-018-0667-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/02/2018] [Indexed: 12/25/2022]
Abstract
Malignant cell transformation could be considered as a series of cell reprogramming events driven by oncogenic transcription factors and upstream signalling pathways. Chromatin plasticity and dynamics are critical determinants in the control of cell reprograming. An increase in chromatin dynamics could therefore constitute an essential step in driving oncogenesis and in generating tumour cell heterogeneity, which is indispensable for the selection of aggressive properties, including the ability of cells to disseminate and acquire resistance to treatments. Histone supply and dosage, as well as histone variants, are the best-known regulators of chromatin dynamics. By facilitating cell reprogramming, histone under-dosage and histone variants should also be crucial in cell transformation and tumour metastasis. Here we summarize and discuss our knowledge of the role of histone supply and histone variants in chromatin dynamics and their ability to enhance oncogenic cell reprogramming and tumour heterogeneity.
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Affiliation(s)
- Tao Wang
- CNRS UMR 5309, Inserm, U1209, University of Grenoble Alpes, Institute for Advanced Biosciences, 38706, Grenoble, France.,State Key Laboratory for Medical Genomics and Department of Hematology, Shanghai Institute of Hematology, Collaborative Innovation Center of Systems Biomedicine, Pôle Sino-Français des Sciences du Vivant et Genomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Florent Chuffart
- CNRS UMR 5309, Inserm, U1209, University of Grenoble Alpes, Institute for Advanced Biosciences, 38706, Grenoble, France
| | - Ekaterina Bourova-Flin
- CNRS UMR 5309, Inserm, U1209, University of Grenoble Alpes, Institute for Advanced Biosciences, 38706, Grenoble, France
| | - Jin Wang
- State Key Laboratory for Medical Genomics and Department of Hematology, Shanghai Institute of Hematology, Collaborative Innovation Center of Systems Biomedicine, Pôle Sino-Français des Sciences du Vivant et Genomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianqing Mi
- State Key Laboratory for Medical Genomics and Department of Hematology, Shanghai Institute of Hematology, Collaborative Innovation Center of Systems Biomedicine, Pôle Sino-Français des Sciences du Vivant et Genomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Sophie Rousseaux
- CNRS UMR 5309, Inserm, U1209, University of Grenoble Alpes, Institute for Advanced Biosciences, 38706, Grenoble, France
| | - Saadi Khochbin
- CNRS UMR 5309, Inserm, U1209, University of Grenoble Alpes, Institute for Advanced Biosciences, 38706, Grenoble, France.
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36
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Pritchard AL. The Role of Histone Variants in Cancer. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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37
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Rodriguez Y, Duan M, Wyrick JJ, Smerdon MJ. A cassette of basic amino acids in histone H2B regulates nucleosome dynamics and access to DNA damage. J Biol Chem 2018; 293:7376-7386. [PMID: 29588367 PMCID: PMC5949990 DOI: 10.1074/jbc.ra117.000358] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/12/2018] [Indexed: 12/25/2022] Open
Abstract
Nucleosome dynamics, such as spontaneous DNA unwrapping, are postulated to have a critical role in regulating the access of DNA repair machinery to DNA lesions within nucleosomes. However, the specific histone domains that regulate nucleosome dynamics and the impact of such changes in intrinsic nucleosome dynamics on DNA repair are not well understood. Previous studies identified a highly conserved region in the N-terminal tail of histone H2B known as the histone H2Brepression (or HBR) domain, which has a significant influence on gene expression, chromatin assembly, and DNA damage formation and repair. However, the molecular mechanism(s) that may account for these observations are limited. In this study, we characterized the stability and dynamics of ΔHBR mutant nucleosome core particles (NCPs) in vitro by restriction enzyme accessibility (REA), FRET, and temperature-induced sliding of histone octamers. Our results indicate that ΔHBR-NCPs are more dynamic, with a larger steady-state fraction of the NCP population occupying the unwrapped state than for WT-NCPs. Additionally, ΔHBR-histone octamers are more susceptible to temperature-induced sliding on DNA than WT histone octamers. Furthermore, we show that the activity of base excision repair enzymes at uracil lesions and single nucleotide gaps is enhanced in a site-specific manner in ΔHBR-NCPs. This enhanced activity correlates well with regions exhibiting increased DNA unwrapping. Finally, removal of the HBR domain is not sufficient to completely alleviate the structural constraints imposed by histone octamers on the activity of base excision repair enzymes.
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Affiliation(s)
- Yesenia Rodriguez
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520
| | - Mingrui Duan
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520
| | - John J Wyrick
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520; Center for Reproductive Biology, Washington State University, Pullman, Washington 99164-7520
| | - Michael J Smerdon
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520.
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38
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Molaro A, Young JM, Malik HS. Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. Genome Res 2018; 28:460-473. [PMID: 29549088 PMCID: PMC5880237 DOI: 10.1101/gr.229799.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022]
Abstract
Eukaryotic genomes must accomplish both compact packaging for genome stability and inheritance, as well as accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3, and H4) and by deploying histone variants with specialized chromatin functions. Some histone variants are conserved across all eukaryotes, whereas others are lineage-specific. Here, we performed detailed phylogenomic analyses of “short H2A histone” variants found in mammalian genomes. We discovered a previously undescribed typically-sized H2A variant in monotremes and marsupials, H2A.R, which may represent the common ancestor of the short H2As. We also discovered a novel class of short H2A histone variants in eutherian mammals, H2A.Q. We show that short H2A variants arose on the X Chromosome in the common ancestor of all eutherian mammals and diverged into four evolutionarily distinct clades: H2A.B, H2A.L, H2A.P, and H2A.Q. However, the repertoires of short histone H2A variants vary extensively among eutherian mammals due to lineage-specific gains and losses. Finally, we show that all four short H2As are subject to accelerated rates of protein evolution relative to both canonical and other variant H2A proteins including H2A.R. Our analyses reveal that short H2As are a unique class of testis-restricted histone variants displaying an unprecedented evolutionary dynamism. Based on their X-Chromosomal localization, genetic turnover, and testis-specific expression, we hypothesize that short H2A variants may participate in genetic conflicts involving sex chromosomes during reproduction.
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Affiliation(s)
- Antoine Molaro
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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39
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Giebler M, Staege MS, Blauschmidt S, Ohm LI, Kraus M, Würl P, Taubert H, Greither T. Elevated HERV-K Expression in Soft Tissue Sarcoma Is Associated with Worsened Relapse-Free Survival. Front Microbiol 2018; 9:211. [PMID: 29487589 PMCID: PMC5816752 DOI: 10.3389/fmicb.2018.00211] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/30/2018] [Indexed: 01/22/2023] Open
Abstract
A wide variety of endogenous retroviral sequences has been demonstrated in the human genome so far, divided into several different families according to the sequence homology to viral strains. While increased expression of human endogenous retrovirus (HERV) elements has already been linked to unfavorable prognosis in hepatocellular carcinoma, breast cancer, and ovarian carcinoma yet less is known about the impact of the expression of different HERV elements on sarcomagenesis in general as well as the outcome of soft tissue sarcoma (STS) patients. Therefore, in this study the association between expression of HERV-K and HERV-F and the clinicopathological characteristics in a cohort of STSs as well as the patients’ prognosis was evaluated. HERV-K and HERV-F expression was assessed by quantitative real-time PCR in 120 patient specimens. HERV-K and HERV-F expression was significantly correlated (rS = 0.5; p = 6.4 × 10-9; Spearman’s rank bivariate correlation). Also, tumor diameter exhibited a significant negative association to HERV-K and HERV-F expression. Levels of several hypoxia-related RNAs like HIF-1α and miR-210 showed a significant positive correlation with both HERV-K and HERV-F expression. Although in survival analyses no impact of HERV expression on disease-specific survival could be detected, patients with elevated HERV-K expression had a significantly shorter relapse-free survival (p = 0.014, log-rank analysis). In conclusion, we provide evidence for the first time that the increased expression of HERV-K in tumors is associated with STS patients’ prognosis.
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Affiliation(s)
- Maria Giebler
- Center for Reproductive Medicine and Andrology, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Martin S Staege
- Department of Pediatrics I, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Sindy Blauschmidt
- Center for Reproductive Medicine and Andrology, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Lea I Ohm
- Department of Pediatrics I, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Matthias Kraus
- Center for Reproductive Medicine and Andrology, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Peter Würl
- Department of General, Visceral and Thoracic Surgery, Städtische Klinikum Dessau, Dessau-Roßlau, Germany
| | - Helge Taubert
- Division Molecular Urology, Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Greither
- Center for Reproductive Medicine and Andrology, Martin Luther University of Halle-Wittenberg, Halle, Germany
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40
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Kujirai T, Arimura Y, Fujita R, Horikoshi N, Machida S, Kurumizaka H. Methods for Preparing Nucleosomes Containing Histone Variants. Methods Mol Biol 2018; 1832:3-20. [PMID: 30073519 DOI: 10.1007/978-1-4939-8663-7_1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Histone variants are key epigenetic players that regulate transcription, repair, replication, and recombination of genomic DNA. Histone variant incorporation into nucleosomes induces structural diversity of nucleosomes, consequently leading to the structural versatility of chromatin. Such chromatin diversity created by histone variants may play a central role in the epigenetic regulation of genes. Each histone variant possesses specific biochemical and physical characteristics, and thus the preparation methods are complicated. Here, we introduce the methods for the purification of human histone variants as recombinant proteins, and describe the preparation methods for histone complexes and nucleosomes containing various histone variants. We also describe the detailed method for the preparation of heterotypic nucleosomes, which may function in certain biological phenomena. These methods are useful for biochemical, structural, and biophysical studies.
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Affiliation(s)
- Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, 162-8480, Tokyo, Japan
| | - Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, 162-8480, Tokyo, Japan
| | - Risa Fujita
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, 162-8480, Tokyo, Japan
| | - Naoki Horikoshi
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, 162-8480, Tokyo, Japan
| | - Shinichi Machida
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, 162-8480, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan.
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, 162-8480, Tokyo, Japan.
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41
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Quénet D. Histone Variants and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:1-39. [DOI: 10.1016/bs.ircmb.2017.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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42
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Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H. Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8. Biochemistry 2017; 56:2184-2196. [DOI: 10.1021/acs.biochem.6b01098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroyuki Taguchi
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yan Xie
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Horikoshi
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Koichi Sato
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasuhiro Arimura
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Akihisa Osakabe
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Tomoya Kujirai
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Takeshi Iwasaki
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuichiro Semba
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Taro Tachibana
- Department of Bioengineering, Graduate
School of Engineering, Osaka City University, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Hiroshi Kimura
- Cell Biology Unit,
Institute of
Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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43
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Barral S, Morozumi Y, Tanaka H, Montellier E, Govin J, de Dieuleveult M, Charbonnier G, Couté Y, Puthier D, Buchou T, Boussouar F, Urahama T, Fenaille F, Curtet S, Héry P, Fernandez-Nunez N, Shiota H, Gérard M, Rousseaux S, Kurumizaka H, Khochbin S. Histone Variant H2A.L.2 Guides Transition Protein-Dependent Protamine Assembly in Male Germ Cells. Mol Cell 2017; 66:89-101.e8. [PMID: 28366643 DOI: 10.1016/j.molcel.2017.02.025] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/03/2017] [Accepted: 02/24/2017] [Indexed: 01/10/2023]
Abstract
Histone replacement by transition proteins (TPs) and protamines (Prms) constitutes an essential step for the successful production of functional male gametes, yet nothing is known on the underlying functional interplay between histones, TPs, and Prms. Here, by studying spermatogenesis in the absence of a spermatid-specific histone variant, H2A.L.2, we discover a fundamental mechanism involved in the transformation of nucleosomes into nucleoprotamines. H2A.L.2 is synthesized at the same time as TPs and enables their loading onto the nucleosomes. TPs do not displace histones but rather drive the recruitment and processing of Prms, which are themselves responsible for histone eviction. Altogether, the incorporation of H2A.L.2 initiates and orchestrates a series of successive transitional states that ultimately shift to the fully compacted genome of the mature spermatozoa. Hence, the current view of histone-to-nucleoprotamine transition should be revisited and include an additional step with H2A.L.2 assembly prior to the action of TPs and Prms.
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MESH Headings
- Animals
- COS Cells
- Chlorocebus aethiops
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Computational Biology
- Databases, Genetic
- Fertility
- Gene Expression Regulation, Developmental
- Genetic Predisposition to Disease
- Genome
- Histones/deficiency
- Histones/genetics
- Histones/metabolism
- Infertility, Male/genetics
- Infertility, Male/metabolism
- Infertility, Male/pathology
- Infertility, Male/physiopathology
- Male
- Mice, 129 Strain
- Mice, Knockout
- Nucleosomes/genetics
- Nucleosomes/metabolism
- Phenotype
- Protamines/metabolism
- Spermatogenesis/genetics
- Spermatozoa/metabolism
- Spermatozoa/pathology
- Transfection
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Affiliation(s)
- Sophie Barral
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Yuichi Morozumi
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France; Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroki Tanaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Emilie Montellier
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Jérôme Govin
- Université Grenoble Alpes, Inserm U1038, CEA, BIG-BGE, Grenoble 38000, France
| | - Maud de Dieuleveult
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Guillaume Charbonnier
- TGML, platform IbiSA, Aix Marseille Univ, Inserm U1090, TAGC, Marseille 13288, France
| | - Yohann Couté
- Université Grenoble Alpes, Inserm U1038, CEA, BIG-BGE, Grenoble 38000, France
| | - Denis Puthier
- TGML, platform IbiSA, Aix Marseille Univ, Inserm U1090, TAGC, Marseille 13288, France
| | - Thierry Buchou
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Fayçal Boussouar
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Takashi Urahama
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - François Fenaille
- Laboratoire d'Etude du Métabolisme des Médicaments, DSV/iBiTec-S/SPI, CEA Saclay, Gif-sur-Yvette 91191 Cedex, France
| | - Sandrine Curtet
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Patrick Héry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | | | - Hitoshi Shiota
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Matthieu Gérard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Sophie Rousseaux
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Saadi Khochbin
- CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38700, France.
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44
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Soboleva TA, Parker BJ, Nekrasov M, Hart-Smith G, Tay YJ, Tng WQ, Wilkins M, Ryan D, Tremethick DJ. A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B. PLoS Genet 2017; 13:e1006633. [PMID: 28234895 PMCID: PMC5345878 DOI: 10.1371/journal.pgen.1006633] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/10/2017] [Accepted: 02/14/2017] [Indexed: 01/08/2023] Open
Abstract
The replacement of histone H2A with its variant forms is critical for regulating all aspects of genome organisation and function. The histone variant H2A.B appeared late in evolution and is most highly expressed in the testis followed by the brain in mammals. This raises the question of what new function(s) H2A.B might impart to chromatin in these important tissues. We have immunoprecipitated the mouse orthologue of H2A.B, H2A.B.3 (H2A.Lap1), from testis chromatin and found this variant to be associated with RNA processing factors and RNA Polymerase (Pol) II. Most interestingly, many of these interactions with H2A.B.3 (Sf3b155, Spt6, DDX39A and RNA Pol II) were inhibited by the presence of endogenous RNA. This histone variant can bind to RNA directly in vitro and in vivo, and associates with mRNA at intron—exon boundaries. This suggests that the ability of H2A.B to bind to RNA negatively regulates its capacity to bind to these factors (Sf3b155, Spt6, DDX39A and RNA Pol II). Unexpectedly, H2A.B.3 forms highly decompacted nuclear subdomains of active chromatin that co-localizes with splicing speckles in male germ cells. H2A.B.3 ChIP-Seq experiments revealed a unique chromatin organization at active genes being not only enriched at the transcription start site (TSS), but also at the beginning of the gene body (but being excluded from the +1 nucleosome) compared to the end of the gene. We also uncover a general histone variant replacement process whereby H2A.B.3 replaces H2A.Z at intron-exon boundaries in the testis and the brain, which positively correlates with expression and exon inclusion. Taken together, we propose that a special mechanism of splicing may occur in the testis and brain whereby H2A.B.3 recruits RNA processing factors from splicing speckles to active genes following its replacement of H2A.Z. The substitution of core histones with their non-allelic variant forms plays a particular important role in regulating chromatin function because they can directly alter the structure of chromatin, and provide new protein interaction interfaces for the recruitment of proteins involved in gene expression. Despite being discovered over a decade ago, the function of H2A.B, a variant of the H2A class, in its proper physiological context (being expressed in the testis and the brain) is unknown. We provide strong evidence that H2A.B has a role in the processing of RNA. It is found in the gene body of an active gene, directly interacts with RNA polymerase II and splicing factors and is located in the nucleus at distinct regions enriched with RNA processing factors (splicing speckles). Most significantly, we show that H2A.B can directly bind to RNA both in vitro and in germ cells. Therefore, H2A.B has the novel ability to bind to both RNA and DNA (as well as proteins) thus directly linking chromatin structure with the function of RNA. Taken together, this suggests that a special mechanism of splicing may operate in the testis and brain.
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Affiliation(s)
- Tatiana A. Soboleva
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Brian J. Parker
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Maxim Nekrasov
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Gene Hart-Smith
- NSW Systems Biology Initiative, University of New South Wales, Sydney, Australia
| | - Ying Jin Tay
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Wei-Quan Tng
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Marc Wilkins
- NSW Systems Biology Initiative, University of New South Wales, Sydney, Australia
| | - Daniel Ryan
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David J. Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- * E-mail:
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45
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Cauchy P, Koch F, Andrau JC. Two possible modes of pioneering associated with combinations of H2A.Z and p300/CBP at nucleosome-occupied enhancers. Transcription 2017; 8:179-184. [PMID: 28301306 DOI: 10.1080/21541264.2017.1291395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pioneer transcription factors are defined by their ability to bind nucleosome-occupied regions. Here, we discuss the properties of nucleosomes bound by pioneers at enhancer regions. We describe how select pioneers bind nucleosome-occupied or -depleted enhancer sites. Importantly, by revisiting and expanding existing data sets, we show differential H2A.Z and p300/CBP association at bound enhancers, highlighting two possible pioneering modes.
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Affiliation(s)
- Pierre Cauchy
- a Max Planck Institute of Immunobiology and Epigenetics , Department of Cellular and Molecular Immunology , Freiburg im Breisgau , Germany
| | - Frederic Koch
- b Max Planck Institute for Molecular Genetics , Department of Developmental Genetics , Berlin , Germany
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46
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Buschbeck M, Hake SB. Variants of core histones and their roles in cell fate decisions, development and cancer. Nat Rev Mol Cell Biol 2017; 18:299-314. [DOI: 10.1038/nrm.2016.166] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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47
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Kujirai T, Horikoshi N, Xie Y, Taguchi H, Kurumizaka H. Identification of the amino acid residues responsible for stable nucleosome formation by histone H3.Y. Nucleus 2017; 8:239-248. [PMID: 28118111 DOI: 10.1080/19491034.2016.1277303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Histone H3.Y is conserved among primates. We previously reported that exogenously produced H3.Y accumulates around transcription start sites, suggesting that it may play a role in transcription regulation. The H3.Y nucleosome forms a relaxed chromatin conformation with flexible DNA ends. The H3.Y-specific Lys42 residue is partly responsible for enhancing the flexibility of the nucleosomal DNA. To our surprise, we found that H3.Y stably associates with chromatin and nucleosomes in vivo and in vitro. However, the H3.Y residues responsible for its stable nucleosome incorporation have not been identified yet. In the present study, we performed comprehensive mutational analyses of H3.Y, and determined that the H3.Y C-terminal region including amino acid residues 124-135 is responsible for its stable association with DNA. Among the H3.Y C-terminal residues, the H3.Y Met124 residue significantly contributed to the stable DNA association with the H3.Y-H4 tetramer. The H3.Y M124I mutation substantially reduced the H3.Y-H4 association in the nucleosome. In contrast, the H3.Y K42R mutation affected the nucleosome stability less, although it contributes to the flexible DNA ends of the nucleosome. Therefore, these H3.Y-specific residues, Lys42 and Met124, play different and specific roles in nucleosomal DNA relaxation and stable nucleosome formation, respectively, in chromatin.
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Affiliation(s)
- Tomoya Kujirai
- a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan
| | - Naoki Horikoshi
- b Research Institute for Science and Engineering , Shinjuku-ku, Tokyo , Japan
| | - Yan Xie
- a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan
| | - Hiroyuki Taguchi
- a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan
| | - Hitoshi Kurumizaka
- a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan.,b Research Institute for Science and Engineering , Shinjuku-ku, Tokyo , Japan.,c Institute for Medical-oriented Structural Biology , Waseda University , Shinjuku-ku, Tokyo , Japan
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48
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El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones. Epigenetics Chromatin 2017; 10:2. [PMID: 28096900 PMCID: PMC5223428 DOI: 10.1186/s13072-016-0109-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants. RESULTS We propose two proteomics-oriented manually curated databases for mouse and human histone variants. We manually curated >1700 gene, transcript and protein entries to produce a non-redundant list of 83 mouse and 85 human histones. These entries were annotated in accordance with the current nomenclature and unified with the "HistoneDB2.0 with Variants" database. This resource is provided in a format that can be directly read by programs used for mass spectrometry data interpretation. In addition, it was used to interpret mass spectrometry data acquired on histones extracted from mouse testis. Several histone variants, which had so far only been inferred by homology or detected at the RNA level, were detected by mass spectrometry, confirming the existence of their protein form. CONCLUSIONS Mouse and human histone entries were collected from different databases and subsequently curated to produce a non-redundant protein-centric resource, MS_HistoneDB. It is dedicated to the proteomic study of histones in mouse and human and will hopefully facilitate the identification and functional study of histone variants.
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Affiliation(s)
- Sara El Kennani
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Annie Adrait
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Saadi Khochbin
- CNRS UMR 5309 INSERM U1209, Institute of Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Christophe Bruley
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Delphine Pflieger
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Jérôme Govin
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
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49
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Levendosky RF, Sabantsev A, Deindl S, Bowman GD. The Chd1 chromatin remodeler shifts hexasomes unidirectionally. eLife 2016; 5. [PMID: 28032848 PMCID: PMC5226652 DOI: 10.7554/elife.21356] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/28/2016] [Indexed: 12/27/2022] Open
Abstract
Despite their canonical two-fold symmetry, nucleosomes in biological contexts are often asymmetric: functionalized with post-translational modifications (PTMs), substituted with histone variants, and even lacking H2A/H2B dimers. Here we show that the Widom 601 nucleosome positioning sequence can produce hexasomes in a specific orientation on DNA, providing a useful tool for interrogating chromatin enzymes and allowing for the generation of nucleosomes with precisely defined asymmetry. Using this methodology, we demonstrate that the Chd1 chromatin remodeler from Saccharomyces cerevisiae requires H2A/H2B on the entry side for sliding, and thus, unlike the back-and-forth sliding observed for nucleosomes, Chd1 shifts hexasomes unidirectionally. Chd1 takes part in chromatin reorganization surrounding transcribing RNA polymerase II (Pol II), and using asymmetric nucleosomes we show that ubiquitin-conjugated H2B on the entry side stimulates nucleosome sliding by Chd1. We speculate that biased nucleosome and hexasome sliding due to asymmetry contributes to the packing of arrays observed in vivo. DOI:http://dx.doi.org/10.7554/eLife.21356.001
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Affiliation(s)
- Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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50
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Talbert PB, Henikoff S. Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 2016; 18:115-126. [PMID: 27924075 DOI: 10.1038/nrm.2016.148] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most histones are assembled into nucleosomes behind the replication fork to package newly synthesized DNA. By contrast, histone variants, which are encoded by separate genes, are typically incorporated throughout the cell cycle. Histone variants can profoundly change chromatin properties, which in turn affect DNA replication and repair, transcription, and chromosome packaging and segregation. Recent advances in the study of histone replacement have elucidated the dynamic processes by which particular histone variants become substrates of histone chaperones, ATP-dependent chromatin remodellers and histone-modifying enzymes. Here, we review histone variant dynamics and the effects of replacing DNA synthesis-coupled histones with their replication-independent variants on the chromatin landscape.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
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