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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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2
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Azizan S, Selvarajah SA, Tang J, Jeninga MD, Schulz D, Pareek K, Herr T, Day KP, De Koning-Ward TF, Petter M, Duffy MF. The P. falciparum alternative histones Pf H2A.Z and Pf H2B.Z are dynamically acetylated and antagonized by PfSir2 histone deacetylases at heterochromatin boundaries. mBio 2023; 14:e0201423. [PMID: 37882786 PMCID: PMC10746207 DOI: 10.1128/mbio.02014-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The malaria parasite Plasmodium falciparum relies on variant expression of members of multi-gene families as a strategy for environmental adaptation to promote parasite survival and pathogenesis. These genes are located in transcriptionally silenced DNA regions. A limited number of these genes escape gene silencing, and switching between them confers variant fitness on parasite progeny. Here, we show that PfSir2 histone deacetylases antagonize DNA-interacting acetylated alternative histones at the boundaries between active and silent DNA. This finding implicates acetylated alternative histones in the mechanism regulating P. falciparum variant gene silencing and thus malaria pathogenesis. This work also revealed that acetylation of alternative histones at promoters is dynamically associated with promoter activity across the genome, implicating acetylation of alternative histones in gene regulation genome wide. Understanding mechanisms of gene regulation in P. falciparum may aid in the development of new therapeutic strategies for malaria, which killed 619,000 people in 2021.
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Affiliation(s)
- Suffian Azizan
- School of BioSciences, The University of Melbourne, Melbourne, Australia
- Bio21 Institute, Parkville, Victoria, Australia
| | - Shamista A. Selvarajah
- School of BioSciences, The University of Melbourne, Melbourne, Australia
- Bio21 Institute, Parkville, Victoria, Australia
| | - Jingyi Tang
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Australia
| | - Myriam D. Jeninga
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | | | - Kapil Pareek
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Tamara Herr
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Karen P. Day
- Bio21 Institute, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tania F. De Koning-Ward
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Australia
| | - Michaela Petter
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Michael F. Duffy
- Bio21 Institute, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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3
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Abstract
Nearly three-fourths of all eukaryotic DNA is occupied by nucleosomes, protein-DNA complexes comprising octameric histone core proteins and ∼150 base pairs of DNA. In addition to acting as a DNA compaction vehicle, the dynamics of nucleosomes regulate the DNA site accessibility for the nonhistone proteins, thereby controlling regulatory processes involved in determining the cell identity and cell fate. Here, we propose an analytical framework to analyze the role of nucleosome dynamics on the target search process of transcription factors through a simple discrete-state stochastic description of the search process. By considering the experimentally determined kinetic rates associated with protein and nucleosome dynamics as the only inputs, we estimate the target search time of a protein via first-passage probability calculations separately during nucleosome breathing and sliding dynamics. Although both the nucleosome dynamics permit transient access to the DNA sites that are otherwise occluded by the histone proteins, our result suggests substantial differences between the protein search mechanism on a nucleosome performing breathing and sliding dynamics. Furthermore, we identify the molecular factors that influence the search efficiency and demonstrate how these factors together portray a highly dynamic landscape of gene regulation. Our analytical results are validated using extensive Monte Carlo simulations.
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Affiliation(s)
- Sujeet Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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4
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Mechetin GV, Zharkov DO. DNA Damage Response and Repair in Boron Neutron Capture Therapy. Genes (Basel) 2023; 14:127. [PMID: 36672868 PMCID: PMC9859301 DOI: 10.3390/genes14010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Boron neutron capture therapy (BNCT) is an approach to the radiotherapy of solid tumors that was first outlined in the 1930s but has attracted considerable attention recently with the advent of a new generation of neutron sources. In BNCT, tumor cells accumulate 10B atoms that react with epithermal neutrons, producing energetic α particles and 7Li atoms that damage the cell's genome. The damage inflicted by BNCT appears not to be easily repairable and is thus lethal for the cell; however, the molecular events underlying the action of BNCT remain largely unaddressed. In this review, the chemistry of DNA damage during BNCT is outlined, the major mechanisms of DNA break sensing and repair are summarized, and the specifics of the repair of BNCT-induced DNA lesions are discussed.
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Affiliation(s)
- Grigory V. Mechetin
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
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5
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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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6
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Nucleosome assembly and disassembly pathways in vitro. PLoS One 2022; 17:e0267382. [PMID: 35830437 PMCID: PMC9278766 DOI: 10.1371/journal.pone.0267382] [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: 12/13/2021] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Structural fluctuations of nucleosomes modulate the access to internal DNA in eukaryotic cells; clearly characterisation of this fundamental process is crucial to understanding gene regulation. Here we apply PhAST (Photochemical Analysis of Structural Transitions) to monitor at a base pair level, structural alterations induced all along the DNA upon histone binding or release. By offering the first reliable, detailed comparison of nucleosome assembly and disassembly in vitro, we reveal similarities and differences between the two processes. We identify multiple, sequential intermediate states characterised by specific PhAST signals whose localisation and amplitude reflect asymmetries of DNA/histone interactions with respect to the nucleosome pseudo dyad. These asymmetries involve not only the DNA extremities but also regions close to the pseudo dyad. Localisations of asymmetries develop in a consistent manner during both assembly and disassembly processes; they primarily reflect the DNA sequence effect on the efficiency of DNA-histone binding. More unexpectedly, the amplitude component of PhAST signals not only evolves as a function of intermediate states but does so differently between assembly and disassembly pathways. Our observation of differences between assembly and disassembly opens up new avenues to define the role of the DNA sequence in processes underlying the regulation of gene expression. Overall, we provide new insights into how the intrinsic properties of DNA are integrated into a holistic mechanism that controls chromatin structure.
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Histone variants H3.3 and H2A.Z/H3.3 facilitate excision of uracil from nucleosome core particles. DNA Repair (Amst) 2022; 116:103355. [PMID: 35717761 PMCID: PMC9262417 DOI: 10.1016/j.dnarep.2022.103355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022]
Abstract
At the most fundamental level of chromatin organization, DNA is packaged as nucleosome core particles (NCPs) where DNA is wound around a core of histone proteins. This ubiquitous sequestration of DNA within NCPs presents a significant barrier to many biological processes, including DNA repair. We previously demonstrated that histone variants from the H2A family facilitate excision of uracil (U) lesions by DNA base excision repair (BER) glycosylases. Here, we consider how the histone variant H3.3 and double-variant H2A.Z/H3.3 modulate the BER enzymes uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase (SMUG1). Using an NCP model system with U:G base pairs at a wide variety of geometric positions we generate the global repair profile for both glycosylases. Enhanced excision of U by UDG and SMUG1 is observed with the H3.3 variant. We demonstrate that these H3.3-containing NCPs form two species: (1) octasomes, which contain the full complement of eight histone proteins and (2) hexasomes which are sub-nucleosomal particles that contain six histones. Both the octasome and hexasome species facilitate excision activity of UDG and SMUG1, with the largest impacts observed at sterically-occluded lesion sites and in terminal regions of DNA of the hexasome that do not closely interact with histones. For the double-variant H2A.Z/H3.3 NCPs, which exist as octasomes, the global repair profile reveals that UDG but not SMUG1 has increased U excision activity. The enhanced glycosylase activity reveals potential functions for these histone variants to facilitate BER in packaged DNA and contributes to our understanding of DNA repair in chromatin and its significance regarding mutagenesis and genomic integrity.
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Yang Y, Zhang L, Xiong C, Chen J, Wang L, Wen Z, Yu J, Chen P, Xu Y, Jin J, Cai Y, Li G. HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs. Nucleic Acids Res 2022; 50:191-206. [PMID: 34893908 PMCID: PMC8754660 DOI: 10.1093/nar/gkab1221] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 12/21/2022] Open
Abstract
Histone variants have been implicated in regulating chromatin dynamics and genome functions. Previously, we have shown that histone variant H3.3 actively marks enhancers and cooperates with H2A.Z at promoters to prime the genes into a poised state in mouse embryonic stem cells (mESCs). However, how these two important histone variants collaboratively function in this process still remains elusive. In this study, we found that depletion of different components of HIRA complex, a specific chaperone of H3.3, results in significant decreases of H2A.Z enrichment at genome scale. In addition, CUT&Tag data revealed a genomic colocalization between HIRA complex and SRCAP complex. In vivo and in vitro biochemical assays verified that HIRA complex could interact with SRCAP complex through the Hira subunit. Furthermore, our chromatin accessibility and transcription analyses demonstrated that HIRA complex contributed to preset a defined chromatin feature around TSS region for poising gene transcription. In summary, our results unveiled that while regulating the H3.3 incorporation in the regulatory regions, HIRA complex also collaborates with SRCAP to deposit H2A.Z onto the promoters, which cooperatively determines the transcriptional potential of the poised genes in mESCs.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liwei Zhang
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaoyang Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- National Engineering Laboratory for AIDS Vaccine, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yong Cai
- School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- National Engineering Laboratory for AIDS Vaccine, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing, China
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9
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Liu C, Zhao J, Li G. Preparation and Characterization of Chromatin Templates for Histone Methylation Assays. Methods Mol Biol 2022; 2529:91-107. [PMID: 35733011 DOI: 10.1007/978-1-0716-2481-4_4] [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] [Indexed: 06/15/2023]
Abstract
In eukaryotic cells, chromatin plays an important role in gene regulation by controlling the access of the transcription machinery to DNA. In this chapter, we will describe methods for generating different chromatin templates to investigate the impact of histone variants and chromatin structure on histone methyltransferase activities. For this purpose, we take Polycomb Repressive Complex 2 (PRC2) as an example and investigate how its activity on H3K27me3 is regulated by the histone variants H3.3 and H2A.Z and higher-order chromatin structure.
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Affiliation(s)
- Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jicheng Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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10
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Lewis TS, Sokolova V, Jung H, Ng H, Tan D. Structural basis of chromatin regulation by histone variant H2A.Z. Nucleic Acids Res 2021; 49:11379-11391. [PMID: 34643712 PMCID: PMC8565303 DOI: 10.1093/nar/gkab907] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023] Open
Abstract
The importance of histone variant H2A.Z in transcription regulation has been well established, yet its mechanism-of-action remains enigmatic. Conflicting evidence exists in support of both an activating and a repressive role of H2A.Z in transcription. Here we report cryo-electron microscopy (cryo-EM) structures of nucleosomes and chromatin fibers containing H2A.Z and those containing canonical H2A. The structures show that H2A.Z incorporation results in substantial structural changes in both nucleosome and chromatin fiber. While H2A.Z increases the mobility of DNA terminus in nucleosomes, it simultaneously enables nucleosome arrays to form a more regular and condensed chromatin fiber. We also demonstrated that H2A.Z’s ability to enhance nucleosomal DNA mobility is largely attributed to its characteristic shorter C-terminus. Our study provides the structural basis for H2A.Z-mediated chromatin regulation, showing that the increase flexibility of the DNA termini in H2A.Z nucleosomes is central to its dual-functions in chromatin regulation and in transcription.
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Affiliation(s)
- Tyler S Lewis
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY 11794, USA
| | - Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY 11794, USA
| | - Harry Jung
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY 11794, USA
| | - Honkit Ng
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY 11794, USA.,Cryo Electron Microscopy Resource Center, Rockefeller University; New York, NY 10065, USA
| | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY 11794, USA
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11
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Colino-Sanguino Y, Clark SJ, Valdes-Mora F. The H2A.Z-nuclesome code in mammals: emerging functions. Trends Genet 2021; 38:273-289. [PMID: 34702577 DOI: 10.1016/j.tig.2021.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022]
Abstract
H2A.Z is a histone variant that provides specific structural and docking-side properties to the nucleosome, resulting in diverse and specialised molecular and cellular functions. In this review, we discuss the latest studies uncovering new functional aspects of mammalian H2A.Z in gene transcription, including pausing and elongation of RNA polymerase II (RNAPII) and enhancer activity; DNA repair; DNA replication; and 3D chromatin structure. We also review the recently described role of H2A.Z in embryonic development, cell differentiation, neurodevelopment, and brain function. In conclusion, our cumulative knowledge of H2A.Z over the past 40 years, in combination with the implementation of novel molecular technologies, is unravelling an unexpected and complex role of histone variants in gene regulation and disease.
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Affiliation(s)
- Yolanda Colino-Sanguino
- Cancer Epigenetics Biology and Therapeutics, Precision Medicine Theme, Children's Cancer Institute, Sydney, NSW, Australia; School of Children and Women Health, University of NSW Sydney, Sydney, NSW, Australia.
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Fatima Valdes-Mora
- Cancer Epigenetics Biology and Therapeutics, Precision Medicine Theme, Children's Cancer Institute, Sydney, NSW, Australia; School of Children and Women Health, University of NSW Sydney, Sydney, NSW, Australia.
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12
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Chanou A, Hamperl S. Single-Molecule Techniques to Study Chromatin. Front Cell Dev Biol 2021; 9:699771. [PMID: 34291054 PMCID: PMC8287188 DOI: 10.3389/fcell.2021.699771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Besides the basic organization in nucleosome core particles (NCPs), eukaryotic chromatin is further packed through interactions with numerous protein complexes including transcription factors, chromatin remodeling and modifying enzymes. This nucleoprotein complex provides the template for many important biological processes, such as DNA replication, transcription, and DNA repair. Thus, to understand the molecular basis of these DNA transactions, it is critical to define individual changes of the chromatin structure at precise genomic regions where these machineries assemble and drive biological reactions. Single-molecule approaches provide the only possible solution to overcome the heterogenous nature of chromatin and monitor the behavior of individual chromatin transactions in real-time. In this review, we will give an overview of currently available single-molecule methods to obtain mechanistic insights into nucleosome positioning, histone modifications and DNA replication and transcription analysis-previously unattainable with population-based assays.
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Affiliation(s)
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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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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Dai L, Xiao X, Pan L, Shi L, Xu N, Zhang Z, Feng X, Ma L, Dou S, Wang P, Zhu B, Li W, Zhou Z. Recognition of the inherently unstable H2A nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange. Cell Rep 2021; 35:109183. [PMID: 34038732 DOI: 10.1016/j.celrep.2021.109183] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/29/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022] Open
Abstract
The multisubunit chromatin remodeler SWR1/SRCAP/p400 replaces the nucleosomal H2A-H2B dimer with the free-form H2A.Z-H2B dimer, but the mechanism governing the unidirectional H2A-to-H2A.Z exchange remains elusive. Here, we perform single-molecule force spectroscopy to dissect the disassembly/reassembly processes of the H2A nucleosome and H2A.Z nucleosome. We find that the N-terminal 1-135 residues of yeast SWR1 complex protein 2 (previously termed Swc2-Z) facilitate the disassembly of nucleosomes containing H2A but not H2A.Z. The Swc2-mediated nucleosome disassembly/reassembly requires the inherently unstable H2A nucleosome, whose instability is conferred by three H2A α2-helical residues, Gly47, Pro49, and Ile63, as they selectively weaken the structural rigidity of the H2A-H2B dimer. It also requires Swc2-ZN (residues 1-37) that directly anchors to the H2A nucleosome and functions in the SWR1-catalyzed H2A.Z replacement in vitro and yeast H2A.Z deposition in vivo. Our findings provide mechanistic insights into how the SWR1 complex discriminates between the H2A nucleosome and H2A.Z nucleosome, establishing a simple paradigm for the governance of unidirectional H2A.Z exchange.
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Affiliation(s)
- Linchang Dai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Pan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liuxin Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuoxing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China.
| | - Zheng Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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17
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Marr LT, Ocampo J, Clark DJ, Hayes JJ. Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes. Epigenetics Chromatin 2021; 14:5. [PMID: 33430969 PMCID: PMC7802155 DOI: 10.1186/s13072-020-00381-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/28/2020] [Indexed: 01/09/2023] Open
Abstract
Background The vast majority of methods available to characterize genome-wide chromatin structure exploit differences in DNA accessibility to nucleases or chemical crosslinking. We developed a novel method to gauge genome-wide accessibility of histone protein surfaces within nucleosomes by assessing reactivity of engineered cysteine residues with a thiol-specific reagent, biotin-maleimide (BM). Results Yeast nuclei were obtained from cells expressing the histone mutant H2B S116C, in which a cysteine resides near the center of the external flat protein surface of the nucleosome. BM modification revealed that nucleosomes are generally equivalently accessible throughout the S. cerevisiae genome, including heterochromatic regions, suggesting limited, higher-order chromatin structures in which this surface is obstructed by tight nucleosome packing. However, we find that nucleosomes within 500 bp of transcription start sites exhibit the greatest range of accessibility, which correlates with the density of chromatin remodelers. Interestingly, accessibility is not well correlated with RNA polymerase density and thus the level of gene expression. We also investigated the accessibility of cysteine mutations designed to detect exposure of histone surfaces internal to the nucleosome thought to be accessible in actively transcribed genes: H3 102, is at the H2A–H2B dimer/H3–H4 tetramer interface, and H3 A110C, resides at the H3–H3 interface. However, in contrast to the external surface site, we find that neither of these internal sites were found to be appreciably exposed. Conclusions Overall, our finding that nucleosomes surfaces within S. cerevisiae chromatin are equivalently accessible genome-wide is consistent with a globally uncompacted chromatin structure lacking substantial higher-order organization. However, we find modest differences in accessibility that correlate with chromatin remodelers but not transcription, suggesting chromatin poised for transcription is more accessible than actively transcribed or intergenic regions. In contrast, we find that two internal sites remain inaccessible, suggesting that such non-canonical nucleosome species generated during transcription are rapidly and efficiently converted to canonical nucleosome structure and thus not widely present in native chromatin.
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Affiliation(s)
- Luke T Marr
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI-CONICET), C1428ADN, Buenos Aires, Argentina
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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18
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Edwards GB, Muthurajan UM, Bowerman S, Luger K. Analytical Ultracentrifugation (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of Biological Macromolecules. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2020; 133:e131. [PMID: 33351266 PMCID: PMC7781197 DOI: 10.1002/cpmb.131] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The biochemical and biophysical investigation of proteins, nucleic acids, and the assemblies that they form yields essential information to understand complex systems. Analytical ultracentrifugation (AUC) represents a broadly applicable and information-rich method for investigating macromolecular characteristics such as size, shape, stoichiometry, and binding properties, all in the true solution-state environment that is lacking in most orthogonal methods. Despite this, AUC remains underutilized relative to its capabilities and potential in the fields of biochemistry and molecular biology. Although there has been a rapid development of computing power and AUC analysis tools in this millennium, fewer advancements have occurred in development of new applications of the technique, leaving these powerful instruments underappreciated and underused in many research institutes. With AUC previously limited to absorbance and Rayleigh interference optics, the addition of fluorescence detection systems has greatly enhanced the applicability of AUC to macromolecular systems that are traditionally difficult to characterize. This overview provides a resource for novices, highlighting the potential of AUC and encouraging its use in their research, as well as for current users, who may benefit from our experience. We discuss the strengths of fluorescence-detected AUC and demonstrate the power of even simple AUC experiments to answer practical and fundamental questions about biophysical properties of macromolecular assemblies. We address the development and utility of AUC, explore experimental design considerations, present case studies investigating properties of biological macromolecules that are of common interest to researchers, and review popular analysis approaches. © 2020 The Authors.
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Affiliation(s)
| | - Uma M. Muthurajan
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
| | - Samuel Bowerman
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
- Howard Hughes Medical InstituteUniversity of Colorado BoulderBoulderColorado
| | - Karolin Luger
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
- Howard Hughes Medical InstituteUniversity of Colorado BoulderBoulderColorado
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19
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Jing Y, Ding D, Tian G, Kwan KCJ, Liu Z, Ishibashi T, Li XD. Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility. Nucleic Acids Res 2020; 48:9538-9549. [PMID: 32766790 PMCID: PMC7515725 DOI: 10.1093/nar/gkaa663] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and function in chromatin remain poorly understood. Here, we utilized an expressed protein ligation (EPL) strategy to synthesize histone H4 with site-specific succinylation at K77 residue (H4K77succ), an evolutionarily conserved succinylation site at the nucleosomal DNA-histone interface. We then assembled mononucleosomes with the semisynthetic H4K77succ in vitro. We demonstrated that this succinylation impacts nucleosome dynamics and promotes DNA unwrapping from the histone surface, which allows proteins such as transcription factors to rapidly access buried regions of the nucleosomal DNA. In budding yeast, a lysine-to-glutamic acid mutation, which mimics Ksucc, at the H4K77 site reduced nucleosome stability and led to defects in DNA damage repair and telomere silencing in vivo. Our findings revealed this uncharacterized histone modification has important roles in nucleosome and chromatin dynamics.
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dongbo Ding
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ka Chun Jonathan Kwan
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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20
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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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21
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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22
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Creighton SD, Stefanelli G, Reda A, Zovkic IB. Epigenetic Mechanisms of Learning and Memory: Implications for Aging. Int J Mol Sci 2020; 21:E6918. [PMID: 32967185 PMCID: PMC7554829 DOI: 10.3390/ijms21186918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
The neuronal epigenome is highly sensitive to external events and its function is vital for producing stable behavioral outcomes, such as the formation of long-lasting memories. The importance of epigenetic regulation in memory is now well established and growing evidence points to altered epigenome function in the aging brain as a contributing factor to age-related memory decline. In this review, we first summarize the typical role of epigenetic factors in memory processing in a healthy young brain, then discuss the aspects of this system that are altered with aging. There is general agreement that many epigenetic marks are modified with aging, but there are still substantial inconsistencies in the precise nature of these changes and their link with memory decline. Here, we discuss the potential source of age-related changes in the epigenome and their implications for therapeutic intervention in age-related cognitive decline.
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Affiliation(s)
- Samantha D. Creighton
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
| | - Gilda Stefanelli
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
| | - Anas Reda
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada;
| | - Iva B. Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada;
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23
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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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24
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Abstract
Chromatin is a highly dynamic structure that closely relates with gene expression in eukaryotes. ATP-dependent chromatin remodelling, histone post-translational modification and DNA methylation are the main ways that mediate such plasticity. The histone variant H2A.Z is frequently encountered in eukaryotes, and can be deposited or removed from nucleosomes by chromatin remodelling complex SWR1 or INO80, respectively, leading to altered chromatin state. H2A.Z has been found to be involved in a diverse range of biological processes, including genome stability, DNA repair and transcriptional regulation. Due to their formidable production of secondary metabolites, filamentous fungi play outstanding roles in pharmaceutical production, food safety and agriculture. During the last few years, chromatin structural changes were proven to be a key factor associated with secondary metabolism in fungi. However, studies on the function of H2A.Z are scarce. Here, we summarize current knowledge of H2A.Z functions with a focus on filamentous fungi. We propose that H2A.Z is a potential target involved in the regulation of secondary metabolite biosynthesis by fungi.
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25
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Retureau R, Foloppe N, Elbahnsi A, Oguey C, Hartmann B. A dynamic view of DNA structure within the nucleosome: Biological implications. J Struct Biol 2020; 211:107511. [PMID: 32311461 DOI: 10.1016/j.jsb.2020.107511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
Most of eukaryotic cellular DNA is packed in nucleosome core particles (NCPs), in which the DNA (DNANCP) is wrapped around histones. The influence of this organization on the intrinsic local dynamics of DNA is largely unknown, in particular because capturing such information from experiments remains notoriously challenging. Given the importance of dynamical properties in DNA functions, we addressed this issue using CHARMM36 MD simulations of a nucleosome containing the NCP positioning 601 sequence and four related free dodecamers. Comparison between DNANCP and free DNA reveals a limited impact of the dense DNA-histone interface on correlated motions of dinucleotide constituents and on fluctuations of inter base pair parameters. A characteristic feature intimately associated with the DNANCP super-helical path is a set of structural periodicities that includes a marked alternation of regions enriched in backbone BI and BII conformers. This observation led to uncover a convincing correspondence between the sequence effect on BI/BII propensities in both DNANCP and free DNA, strengthening the idea that the histone preference for particular DNA sequences relies on those intrinsic structural properties. These results offer for the first time a detailed view of the DNA dynamical behavior within NCP. They show in particular that the DNANCP dynamics is substantial enough to preserve the ability to structurally adjust to external proteins, for instance remodelers. Also, fresh structural arguments highlight the relevance of relationships between DNA sequence and structural properties for NCP formation. Overall, our work offers a more rational framework to approach the functional, biological roles of NCP.
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Affiliation(s)
- Romain Retureau
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | | | - Ahmad Elbahnsi
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France; LPTM, UMR8089, CNRS, CY Cergy Paris Université, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Christophe Oguey
- LPTM, UMR8089, CNRS, CY Cergy Paris Université, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Brigitte Hartmann
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France.
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26
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Lei B, Berger F. H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity. PLANT COMMUNICATIONS 2020; 1:100015. [PMID: 33404536 PMCID: PMC7747964 DOI: 10.1016/j.xplc.2019.100015] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/13/2019] [Accepted: 12/11/2019] [Indexed: 05/16/2023]
Abstract
The eukaryotic nucleosome prevents access to the genome. Convergently evolving histone isoforms, also called histone variants, form diverse families that are enriched over distinct features of plant genomes. Among the diverse families of plant histone variants, H2A.Z exclusively marks genes. Here we review recent research progress on the genome-wide distribution patterns and deposition of H2A.Z in plants as well as its association with histone modifications and roles in plant chromatin regulation. We also discuss some hypotheses that explain the different findings about the roles of H2A.Z in plants.
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27
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Chen Z, Gabizon R, Brown AI, Lee A, Song A, Díaz-Celis C, Kaplan CD, Koslover EF, Yao T, Bustamante C. High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier. eLife 2019; 8:48281. [PMID: 31364986 PMCID: PMC6744274 DOI: 10.7554/elife.48281] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/30/2019] [Indexed: 12/16/2022] Open
Abstract
Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression.
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Affiliation(s)
- Zhijie Chen
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Ronen Gabizon
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
| | - Aidan I Brown
- Department of Physics, University of California, San Diego, San Diego, United States
| | - Antony Lee
- Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Aixin Song
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - César Díaz-Celis
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Elena F Koslover
- Department of Physics, University of California, San Diego, San Diego, United States
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Carlos Bustamante
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States.,Jason L Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, United States.,Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, United States
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28
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Structural insights into the ability of nucleoplasmin to assemble and chaperone histone octamers for DNA deposition. Sci Rep 2019; 9:9487. [PMID: 31263230 PMCID: PMC6602930 DOI: 10.1038/s41598-019-45726-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/12/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleoplasmin (NP) is a pentameric histone chaperone that regulates the condensation state of chromatin in different cellular processes. We focus here on the interaction of NP with the histone octamer, showing that NP could bind sequentially the histone components to assemble an octamer-like particle, and crosslinked octamers with high affinity. The three-dimensional reconstruction of the NP/octamer complex generated by single-particle cryoelectron microscopy, revealed that several intrinsically disordered tail domains of two NP pentamers, facing each other through their distal face, encage the histone octamer in a nucleosome-like conformation and prevent its dissociation. Formation of this complex depended on post-translational modification and exposure of the acidic tract at the tail domain of NP. Finally, NP was capable of transferring the histone octamers to DNA in vitro, assembling nucleosomes. This activity may have biological relevance for processes in which the histone octamer must be rapidly removed from or deposited onto the DNA.
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29
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Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
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Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
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30
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Singh RK, Fan J, Gioacchini N, Watanabe S, Bilsel O, Peterson CL. Transient Kinetic Analysis of SWR1C-Catalyzed H2A.Z Deposition Unravels the Impact of Nucleosome Dynamics and the Asymmetry of Histone Exchange. Cell Rep 2019; 27:374-386.e4. [PMID: 30970243 PMCID: PMC6545893 DOI: 10.1016/j.celrep.2019.03.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 01/20/2019] [Accepted: 03/08/2019] [Indexed: 12/16/2022] Open
Abstract
The SWR1C chromatin remodeling enzyme catalyzes ATP-dependent replacement of nucleosomal H2A with the H2A.Z variant, regulating key DNA-mediated processes such as transcription and DNA repair. Here, we investigate the transient kinetic mechanism of the histone exchange reaction, employing ensemble FRET, fluorescence correlation spectroscopy (FCS), and the steady-state kinetics of ATP hydrolysis. Our studies indicate that SWR1C modulates nucleosome dynamics on both the millisecond and microsecond timescales, poising the nucleosome for the dimer exchange reaction. The transient kinetic analysis of the remodeling reaction performed under single turnover conditions unraveled a striking asymmetry in the ATP-dependent replacement of nucleosomal dimers, promoted by localized DNA unwrapping. Taken together, our transient kinetic studies identify intermediates and provide crucial insights into the SWR1C-catalyzed dimer exchange reaction and shed light on how the mechanics of H2A.Z deposition might contribute to transcriptional regulation in vivo.
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Affiliation(s)
- Raushan K Singh
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jiayl Fan
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan Gioacchini
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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31
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Zhou K, Gaullier G, Luger K. Nucleosome structure and dynamics are coming of age. Nat Struct Mol Biol 2018; 26:3-13. [PMID: 30532059 DOI: 10.1038/s41594-018-0166-x] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Since the first high-resolution structure of the nucleosome was reported in 1997, the available information on chromatin structure has increased very rapidly. Here, we review insights derived from cutting-edge biophysical and structural approaches applied to the study of nucleosome dynamics and nucleosome-binding factors, with a focus on the experimental advances driving the research. In addition, we highlight emerging challenges in nucleosome structural biology.
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Affiliation(s)
- Keda Zhou
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Guillaume Gaullier
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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32
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High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes. Nat Commun 2018; 9:4628. [PMID: 30401903 PMCID: PMC6219519 DOI: 10.1038/s41467-018-06758-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/17/2018] [Indexed: 11/08/2022] Open
Abstract
Nucleosomes play a dual role in compacting the genome and regulating the access to DNA. To unravel the underlying mechanism, we study fluorescently labeled mononucleosomes by multi-parameter FRET measurements and characterize their structural and dynamic heterogeneity upon NaCl-induced destabilization. Species-selective fluorescence lifetime analysis and dynamic photon distribution analysis reveal intermediates during nucleosome opening and lead to a coherent structural and kinetic model. In dynamic octasomes and hexasomes the interface between the H2A-H2B dimers and the (H3-H4)2 tetramer opens asymmetrically by an angle of ≈20° on a 50 and 15 µs time scale, respectively. This is followed by a slower stepwise release of the dimers coupled with DNA unwrapping. A mutation (H2A-R81A) at the interface between H2A and H3 facilitates initial opening, confirming the central role of the dimer:tetramer interface for nucleosome stability. Partially opened states such as those described here might serve as convenient nucleation sites for DNA-recognizing proteins.
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33
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Osakabe A, Lorković ZJ, Kobayashi W, Tachiwana H, Yelagandula R, Kurumizaka H, Berger F. Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility. Nucleic Acids Res 2018; 46:7675-7685. [PMID: 29945241 PMCID: PMC6125630 DOI: 10.1093/nar/gky540] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, variants of core histone H2A are selectively incorporated in distinct functional domains of chromatin and are distinguished by conserved sequences of their C-terminal tail, the L1 loop and the docking domain, suggesting that each variant confers specific properties to the nucleosome. Chromatin of flowering plants contains four types of H2A variants, which biochemical properties have not been characterized. We report that in contrast with animals, in Arabidopsis thaliana H2A variants define only four major types of homotypic nucleosomes containing exclusively H2A, H2A.Z, H2A.X or H2A.W. In vitro assays show that the L1 loop and the docking domain confer distinct stability of the nucleosome. In vivo and in vitro assays suggest that the L1 loop and the docking domain cooperate with the C-terminal tail to regulate chromatin accessibility. Based on these findings we conclude that the type of H2A variant in the nucleosome impacts on its interaction with DNA and propose that H2A variants regulate the dynamics of chromatin accessibility. In plants, the predominance of homotypic nucleosomes with specific physical properties and their specific localization to distinct domains suggest that H2A variants play a dominant role in chromatin dynamics and function.
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Affiliation(s)
- Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wataru Kobayashi
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Ramesh Yelagandula
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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34
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Dhar S, Gursoy-Yuzugullu O, Parasuram R, Price BD. The tale of a tail: histone H4 acetylation and the repair of DNA breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0284. [PMID: 28847821 DOI: 10.1098/rstb.2016.0284] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2017] [Indexed: 02/06/2023] Open
Abstract
The ability of cells to detect and repair DNA double-strand breaks (DSBs) within the complex architecture of the genome requires co-ordination between the DNA repair machinery and chromatin remodelling complexes. This co-ordination is essential to process damaged chromatin and create open chromatin structures which are required for repair. Initially, there is a PARP-dependent recruitment of repressors, including HP1 and several H3K9 methyltransferases, and exchange of histone H2A.Z by the NuA4-Tip60 complex. This creates repressive chromatin at the DSB in which the tail of histone H4 is bound to the acidic patch on the nucleosome surface. These repressor complexes are then removed, allowing rapid acetylation of the H4 tail by Tip60. H4 acetylation blocks interaction between the H4 tail and the acidic patch on adjacent nucleosomes, decreasing inter-nucleosomal interactions and creating open chromatin. Further, the H4 tail is now free to recruit proteins such as 53BP1 to DSBs, a process modulated by H4 acetylation, and provides binding sites for bromodomain proteins, including ZMYND8 and BRD4, which are important for DSB repair. Here, we will discuss how the H4 tail functions as a dynamic hub that can be programmed through acetylation to alter chromatin packing and recruit repair proteins to the break site.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Surbhi Dhar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02132, USA
| | - Ozge Gursoy-Yuzugullu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02132, USA
| | - Ramya Parasuram
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02132, USA
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02132, USA
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35
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Jing Y, Liu Z, Tian G, Bao X, Ishibashi T, Li XD. Site-Specific Installation of Succinyl Lysine Analog into Histones Reveals the Effect of H2BK34 Succinylation on Nucleosome Dynamics. Cell Chem Biol 2018; 25:166-174.e7. [DOI: 10.1016/j.chembiol.2017.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/19/2017] [Accepted: 11/14/2017] [Indexed: 11/25/2022]
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36
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Elbahnsi A, Retureau R, Baaden M, Hartmann B, Oguey C. Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution. J Chem Theory Comput 2018; 14:1045-1058. [DOI: 10.1021/acs.jctc.7b00936] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ahmad Elbahnsi
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
- LPTM,
UMR 8089, CNRS, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Romain Retureau
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
| | - Marc Baaden
- Laboratoire
de Biochimie Théorique, CNRS, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Brigitte Hartmann
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
| | - Christophe Oguey
- LPTM,
UMR 8089, CNRS, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
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37
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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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38
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Oncogenic potential of histone-variant H2A.Z.1 and its regulatory role in cell cycle and epithelial-mesenchymal transition in liver cancer. Oncotarget 2017; 7:11412-23. [PMID: 26863632 PMCID: PMC4905482 DOI: 10.18632/oncotarget.7194] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/23/2016] [Indexed: 12/28/2022] Open
Abstract
H2A.Z is a highly conserved H2A variant, and two distinct H2A.Z isoforms, H2A.Z.1 and H2A.Z.2, have been identified as products of two non-allelic genes, H2AFZ and H2AFV. H2A.Z has been reported to be overexpressed in breast, prostate and bladder cancers, but most studies did not clearly distinguish between isoforms. One recent study reported a unique role for the H2A.Z isoform H2A.Z.2 as a driver of malignant melanoma. Here we first report that H2A.Z.1 plays a pivotal role in the liver tumorigenesis by selectively regulating key molecules in cell cycle and epithelial-mesenchymal transition (EMT). H2AFZ expression was significantly overexpressed in a large cohort of hepatocellular carcinoma (HCC) patients, and high expression of H2AFZ was significantly associated with their poor prognosis. H2A.Z.1 overexpression was demonstrated in a subset of human HCC and cell lines. H2A.Z.1 knockdown suppressed HCC cell growth by transcriptional deregulation of cell cycle proteins and caused apoptotic cell death of HCC cells. We also observed that H2A.Z.1 knockdown reduced the metastatic potential of HCC cells by selectively modulating epithelial-mesenchymal transition regulatory proteins such as E-cadherin and fibronectin. In addition, H2A.Z.1 knockdown reduced the in vivo tumor growth rate in a mouse xenograft model. In conclusion, our findings suggest the oncogenic potential of H2A.Z.1 in liver tumorigenesis and that it plays established role in accelerating cell cycle transition and EMT during hepatocarcinogenesis. This makes H2A.Z.1 a promising target in liver cancer therapy.
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39
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Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H. Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A. Open Biol 2017; 6:rsob.160127. [PMID: 27358293 PMCID: PMC4929947 DOI: 10.1098/rsob.160127] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/06/2016] [Indexed: 12/13/2022] Open
Abstract
H2A.Z is incorporated into nucleosomes located around transcription start sites and functions as an epigenetic regulator for the transcription of certain genes. During transcriptional regulation, the heterotypic H2A.Z/H2A nucleosome containing one each of H2A.Z and H2A is formed. However, previous homotypic H2A.Z nucleosome structures suggested that the L1 loop region of H2A.Z would sterically clash with the corresponding region of canonical H2A in the heterotypic nucleosome. To resolve this issue, we determined the crystal structures of heterotypic H2A.Z/H2A nucleosomes. In the H2A.Z/H2A nucleosome structure, the H2A.Z L1 loop structure was drastically altered without any structural changes of the canonical H2A L1 loop, thus avoiding the steric clash. Unexpectedly, the heterotypic H2A.Z/H2A nucleosome is more stable than the homotypic H2A.Z nucleosome. These data suggested that the flexible character of the H2A.Z L1 loop plays an essential role in forming the stable heterotypic H2A.Z/H2A nucleosome.
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Affiliation(s)
- Naoki Horikoshi
- Research Institute for Science and Engineering, 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, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroyuki Taguchi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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40
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Lehmann K, Zhang R, Schwarz N, Gansen A, Mücke N, Langowski J, Toth K. Effects of charge-modifying mutations in histone H2A α3-domain on nucleosome stability assessed by single-pair FRET and MD simulations. Sci Rep 2017; 7:13303. [PMID: 29038501 PMCID: PMC5643395 DOI: 10.1038/s41598-017-13416-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/21/2017] [Indexed: 01/01/2023] Open
Abstract
Nucleosomes are important for chromatin compaction and gene regulation; their integrity depends crucially on the structural properties of the histone tails. Recent all-atom molecular dynamics simulations revealed that removal of the N-terminal tails of histone H3, known to destabilize nucleosomes, causes a rearrangement of two arginines of histone H2A, namely R81 and R88 by altering the electrostatic environment of the H2A α3 domain. Whether this rearrangement is the cause or the effect of decreased stability, is unclear. Here, we emulate the altered electrostatic environment that was found after H3 tail clipping through charge-modifying mutations to decouple its impact on intranucleosomal interactions from that of the histone tails. Förster resonance energy transfer experiments on recombinant nucleosomes and all-atom molecular dynamics simulations reveal a compensatory role of those amino acids in nucleosome stability. The simulations indicate a weakened interface between H2A-H2B dimers and the (H3-H4)2 tetramer, as well as between dimers and DNA. These findings agree with the experimental observations of position and charge dependent decreased nucleosome stability induced by the introduced mutations. This work highlights the importance of the H2A α3 domain and suggests allosteric effects between this domain and the outer DNA gyre as well as the H3 N-terminal tail.
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Affiliation(s)
- Kathrin Lehmann
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, D-69120, Germany.
| | - Ruihan Zhang
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, D-69120, Germany.,Key laboratory of medicinal chemistry for natural resources, Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Nathalie Schwarz
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, D-69120, Germany
| | - Alexander Gansen
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, D-69120, Germany
| | - Norbert Mücke
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, D-69120, Germany
| | - Jörg Langowski
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, D-69120, Germany
| | - Katalin Toth
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, D-69120, Germany.
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41
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Cortijo S, Charoensawan V, Brestovitsky A, Buning R, Ravarani C, Rhodes D, van Noort J, Jaeger KE, Wigge PA. Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. MOLECULAR PLANT 2017; 10:1258-1273. [PMID: 28893714 PMCID: PMC6175055 DOI: 10.1016/j.molp.2017.08.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/21/2017] [Accepted: 08/24/2017] [Indexed: 05/18/2023]
Abstract
Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade of Arabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.
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Affiliation(s)
- Sandra Cortijo
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Varodom Charoensawan
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi District, Bangkok 10400, Thailand; Integrative Computational BioScience (ICBS) Center, Mahidol University, 999 Phuttamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
| | - Anna Brestovitsky
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Ruth Buning
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Charles Ravarani
- Medical Research Council Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniela Rhodes
- Medical Research Council Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Structural Biology, Nanyang Technical University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Katja E Jaeger
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Philip A Wigge
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
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42
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Safina A, Cheney P, Pal M, Brodsky L, Ivanov A, Kirsanov K, Lesovaya E, Naberezhnov D, Nesher E, Koman I, Wang D, Wang J, Yakubovskaya M, Winkler D, Gurova K. FACT is a sensor of DNA torsional stress in eukaryotic cells. Nucleic Acids Res 2017; 45:1925-1945. [PMID: 28082391 PMCID: PMC5389579 DOI: 10.1093/nar/gkw1366] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/29/2016] [Indexed: 02/01/2023] Open
Abstract
Transitions of B-DNA to alternative DNA structures (ADS) can be triggered by negative torsional strain, which occurs during replication and transcription, and may lead to genomic instability. However, how ADS are recognized in cells is unclear. We found that the binding of candidate anticancer drug, curaxin, to cellular DNA results in uncoiling of nucleosomal DNA, accumulation of negative supercoiling and conversion of multiple regions of genomic DNA into left-handed Z-form. Histone chaperone FACT binds rapidly to the same regions via the SSRP1 subunit in curaxin-treated cells. In vitro binding of purified SSRP1 or its isolated CID domain to a methylated DNA fragment containing alternating purine/pyrimidines, which is prone to Z-DNA transition, is much stronger than to other types of DNA. We propose that FACT can recognize and bind Z-DNA or DNA in transition from a B to Z form. Binding of FACT to these genomic regions triggers a p53 response. Furthermore, FACT has been shown to bind to other types of ADS through a different structural domain, which also leads to p53 activation. Thus, we propose that FACT acts as a sensor of ADS formation in cells. Recognition of ADS by FACT followed by a p53 response may explain the role of FACT in DNA damage prevention.
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Affiliation(s)
- Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Peter Cheney
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Mahadeb Pal
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Leonid Brodsky
- Department of Evolutionary & Environmental Biology, Tauber Bioinformatics Research Center, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Alexander Ivanov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Kirill Kirsanov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Ekaterina Lesovaya
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia.,I.P. Pavlov Ryazan State Medical University, Ryazan, Russia
| | - Denis Naberezhnov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Elimelech Nesher
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA.,Department of Molecular Biology, Ariel University, Ariel 40700, Israel
| | - Igor Koman
- Department of Molecular Biology, Ariel University, Ariel 40700, Israel
| | - Dan Wang
- Department of Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Jianming Wang
- Department of Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Marianna Yakubovskaya
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Duane Winkler
- Department of Molecular and Cell Biology, University of Texas at Dallas, 800 W. Campbell Rd., Richardson, TX 75080, USA
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
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43
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Gibson MD, Brehove M, Luo Y, North J, Poirier MG. Methods for Investigating DNA Accessibility with Single Nucleosomes. Methods Enzymol 2017; 581:379-415. [PMID: 27793287 DOI: 10.1016/bs.mie.2016.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleosomes are the fundamental organizing unit of all eukaryotic genomes. Understanding how proteins gain access to DNA-binding sites located within nucleosomes is important for understanding DNA processing including transcription, replication, and repair. Single-molecule total internal reflection fluorescence (smTIRF) microscopy measurements can provide key insight into how proteins gain and maintain access to DNA sites within nucleosomes. Here, we describe methods for smTIRF experiments including the preparation of fluorophore-labeled nucleosomes, the smTIRF system, data acquisition, analysis, and controls. These methods are presented for investigating transcription factor binding within nucleosomes. However, they are applicable for investigating the binding of any site-specific DNA-binding protein within nucleosomes.
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Affiliation(s)
- M D Gibson
- The Ohio State University, Columbus, OH, United States
| | - M Brehove
- The Ohio State University, Columbus, OH, United States
| | - Y Luo
- The Ohio State University, Columbus, OH, United States
| | - J North
- The Ohio State University, Columbus, OH, United States
| | - M G Poirier
- The Ohio State University, Columbus, OH, United States.
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44
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Chakraborty K, Loverde SM. Asymmetric breathing motions of nucleosomal DNA and the role of histone tails. J Chem Phys 2017; 147:065101. [DOI: 10.1063/1.4997573] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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45
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INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers. Nat Commun 2017; 8:15616. [PMID: 28604691 PMCID: PMC5472786 DOI: 10.1038/ncomms15616] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
ATP-dependent chromatin remodellers modulate nucleosome dynamics by mobilizing or disassembling nucleosomes, as well as altering nucleosome composition. These chromatin remodellers generally function by translocating along nucleosomal DNA at the H3–H4 interface of nucleosomes. Here we show that, unlike other remodellers, INO80 translocates along DNA at the H2A–H2B interface of nucleosomes and persistently displaces DNA from the surface of H2A–H2B. DNA translocation and DNA torsional strain created near the entry site of nucleosomes by INO80 promotes both the mobilization of nucleosomes and the selective exchange of H2A.Z–H2B dimers out of nucleosomes and replacement by H2A–H2B dimers without any additional histone chaperones. We find that INO80 translocates and mobilizes H2A.Z-containing nucleosomes more efficiently than those containing H2A, partially accounting for the preference of INO80 to replace H2A.Z with H2A. Our data suggest that INO80 has a mechanism for dimer exchange that is distinct from other chromatin remodellers including its paralogue SWR1. Chromatin remodellers usually mobilize or disassemble nucleosomes by translocating along the nucleosomal DNA at the H3-H4 interface. Here, the authors provide evidence chromatin remodeller INO80 translocates along DNA at the H2A-H2B interface and displaces DNA from the surface of H2A-H2B.
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46
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Eckstein M, Eleazer R, Rea M, Fondufe-Mittendorf Y. Epigenomic reprogramming in inorganic arsenic-mediated gene expression patterns during carcinogenesis. REVIEWS ON ENVIRONMENTAL HEALTH 2017; 32:93-103. [PMID: 27701139 DOI: 10.1515/reveh-2016-0025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/08/2016] [Indexed: 05/22/2023]
Abstract
Arsenic is a ubiquitous metalloid that is not mutagenic but is carcinogenic. The mechanism(s) by which arsenic causes cancer remain unknown. To date, several mechanisms have been proposed, including the arsenic-induced generation of reactive oxygen species (ROS). However, it is also becoming evident that inorganic arsenic (iAs) may exert its carcinogenic effects by changing the epigenome, and thereby modifying chromatin structure and dynamics. These epigenetic changes alter the accessibility of gene regulatory factors to DNA, resulting in specific changes in gene expression both at the levels of transcription initiation and gene splicing. In this review, we discuss recent literature reports describing epigenetic changes induced by iAs exposure and the possible epigenetic mechanisms underlying these changes.
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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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Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. Proc Natl Acad Sci U S A 2016; 114:334-339. [PMID: 28028239 DOI: 10.1073/pnas.1611118114] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nucleosome core particle (NCP) is the basic structural unit for genome packaging in eukaryotic cells and consists of DNA wound around a core of eight histone proteins. DNA access is modulated through dynamic processes of NCP disassembly. Partly disassembled structures, such as the hexasome (containing six histones) and the tetrasome (four histones), are important for transcription regulation in vivo. However, the pathways for their formation have been difficult to characterize. We combine time-resolved (TR) small-angle X-ray scattering and TR-FRET to correlate changes in the DNA conformations with composition of the histone core during salt-induced disassembly of canonical NCPs. We find that H2A-H2B histone dimers are released sequentially, with the first dimer being released after the DNA has formed an asymmetrically unwrapped, teardrop-shape DNA structure. This finding suggests that the octasome-to-hexasome transition is guided by the asymmetric unwrapping of the DNA. The link between DNA structure and histone composition suggests a potential mechanism for the action of proteins that alter nucleosome configurations such as histone chaperones and chromatin remodeling complexes.
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49
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Kim J, Wei S, Lee J, Yue H, Lee TH. Single-Molecule Observation Reveals Spontaneous Protein Dynamics in the Nucleosome. J Phys Chem B 2016; 120:8925-31. [PMID: 27487198 PMCID: PMC5436049 DOI: 10.1021/acs.jpcb.6b06235] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Structural dynamics of a protein molecule is often critical to its function. Single-molecule methods provide efficient ways to investigate protein dynamics, although it is very challenging to achieve a millisecond or higher temporal resolution. Here we report spontaneous structural dynamics of the histone protein core in the nucleosome based on a single-molecule method that can reveal submillisecond dynamics by combining maximum likelihood estimation and fluorescence correlation spectroscopy. The nucleosome, comprising ∼147 bp DNA and an octameric histone protein core consisting of H2A, H2B, H3, and H4, is the fundamental packing unit of the eukaryotic genome. The nucleosome imposes a physical barrier that should be overcome during various DNA-templated processes. Structural fluctuation of the nucleosome in the histone core has been hypothesized to be required for nucleosome disassembly but has yet to be directly probed. Our results indicate that at 100 mM NaCl the histone H2A-H2B dimer dissociates from the histone core transiently once every 3.6 ± 0.6 ms and returns to its position within 2.0 ± 0.3 ms. We also found that the motion is facilitated upon H3K56 acetylation and inhibited upon replacing H2A with H2A.Z. These results provide the first direct examples of how a localized post-translational modification or an epigenetic variation affects the kinetic and thermodynamic stabilities of a macromolecular protein complex, which may directly contribute to its functions.
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Affiliation(s)
- Jongseong Kim
- Molecular Imaging and Neurovascular Research (MINER) Laboratory, Department of Neurology, Dongguk University Ilsan Hospital, Goyang 10326, The Republic of Korea
| | - Sijie Wei
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jaehyoun Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Hongjun Yue
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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50
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A Quantitative Characterization of Nucleoplasmin/Histone Complexes Reveals Chaperone Versatility. Sci Rep 2016; 6:32114. [PMID: 27558753 PMCID: PMC4997359 DOI: 10.1038/srep32114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/02/2016] [Indexed: 01/29/2023] Open
Abstract
Nucleoplasmin (NP) is an abundant histone chaperone in vertebrate oocytes and embryos involved in storing and releasing maternal histones to establish and maintain the zygotic epigenome. NP has been considered a H2A-H2B histone chaperone, and recently it has been shown that it can also interact with H3-H4. However, its interaction with different types of histones has not been quantitatively studied so far. We show here that NP binds H2A-H2B, H3-H4 and linker histones with Kd values in the subnanomolar range, forming different complexes. Post-translational modifications of NP regulate exposure of the polyGlu tract at the disordered distal face of the protein and induce an increase in chaperone affinity for all histones. The relative affinity of NP for H2A-H2B and linker histones and the fact that they interact with the distal face of the chaperone could explain their competition for chaperone binding, a relevant process in NP-mediated sperm chromatin remodelling during fertilization. Our data show that NP binds H3-H4 tetramers in a nucleosomal conformation and dimers, transferring them to DNA to form disomes and tetrasomes. This finding might be relevant to elucidate the role of NP in chromatin disassembly and assembly during replication and transcription.
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