151
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Palczewski MB, Petraitis H, Thomas DD. Nitric oxide is an epigenetic regulator of histone post-translational modifications in cancer. CURRENT OPINION IN PHYSIOLOGY 2019. [DOI: 10.1016/j.cophys.2019.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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152
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The histone chaperoning pathway: from ribosome to nucleosome. Essays Biochem 2019; 63:29-43. [PMID: 31015382 PMCID: PMC6484783 DOI: 10.1042/ebc20180055] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022]
Abstract
Nucleosomes represent the fundamental repeating unit of eukaryotic DNA, and comprise eight core histones around which DNA is wrapped in nearly two superhelical turns. Histones do not have the intrinsic ability to form nucleosomes; rather, they require an extensive repertoire of interacting proteins collectively known as ‘histone chaperones’. At a fundamental level, it is believed that histone chaperones guide the assembly of nucleosomes through preventing non-productive charge-based aggregates between the basic histones and acidic cellular components. At a broader level, histone chaperones influence almost all aspects of chromatin biology, regulating histone supply and demand, governing histone variant deposition, maintaining functional chromatin domains and being co-factors for histone post-translational modifications, to name a few. In this essay we review recent structural insights into histone-chaperone interactions, explore evidence for the existence of a histone chaperoning ‘pathway’ and reconcile how such histone-chaperone interactions may function thermodynamically to assemble nucleosomes and maintain chromatin homeostasis.
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153
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Biochemical characterization of the placeholder nucleosome for DNA hypomethylation maintenance. Biochem Biophys Rep 2019; 18:100634. [PMID: 31008378 PMCID: PMC6458450 DOI: 10.1016/j.bbrep.2019.100634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/23/2022] Open
Abstract
DNA methylation functions as a prominent epigenetic mark, and its patterns are transmitted to the genomes of offspring. The nucleosome containing the histone H2A.Z variant and histone H3K4 mono-methylation acts as a “placeholder” nucleosome for DNA hypomethylation maintenance in zebrafish embryonic cells. However, the mechanism by which DNA methylation is deterred by the placeholder nucleosome is poorly understood. In the present study, we reconstituted the placeholder nucleosome containing histones H2A.Z and H3 with the Lys4 mono-methylation. The thermal stability assay revealed that the placeholder nucleosome is less stable than the canonical nucleosome. Nuclease susceptibility assays suggested that the nucleosomal DNA ends of the placeholder nucleosome are more accessible than those of the canonical nucleosome. These characteristics of the placeholder nucleosome are quite similar to those of the H2A.Z nucleosome without H3K4 methylation. Importantly, the linker histone H1, which is reportedly involved in the recruitment of DNA methyltransferases, efficiently binds to all of the placeholder, H2A.Z, and canonical nucleosomes. Therefore, the characteristics of the H2A.Z nucleosome are conserved in the placeholder nucleosome without synergistic effects on the H3K4 mono-methylation. The placeholder nucleosome containing H2A.Z and H3K4me1 was reconstituted in vitro. The placeholder nucleosome has similar characteristics to the H2A.Z nucleosome. H3K4me1 may not affect the stability and structure of the placeholder nucleosome.
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154
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Histone stress: an unexplored source of chromosomal instability in cancer? Curr Genet 2019; 65:1081-1088. [DOI: 10.1007/s00294-019-00967-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 01/24/2023]
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155
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Bosselut R. Control of Intra-Thymic αβ T Cell Selection and Maturation by H3K27 Methylation and Demethylation. Front Immunol 2019; 10:688. [PMID: 31001282 PMCID: PMC6456692 DOI: 10.3389/fimmu.2019.00688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/13/2019] [Indexed: 12/25/2022] Open
Abstract
In addition to transcription factor binding, the dynamics of DNA modifications (methylation) and chromatin structure are essential contributors to the control of transcription in eukaryotes. Research in the past few years has emphasized the importance of histone H3 methylation at lysine 27 for lineage specific gene repression, demonstrated that deposition of this mark at specific genes is subject to differentiation-induced changes during development, and identified enzymatic activities, methyl transferases and demethylases, that control these changes. The present review discusses the importance of these mechanisms during intrathymic αβ T cell selection and late differentiation.
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Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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156
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Histone variant macroH2A: from chromatin deposition to molecular function. Essays Biochem 2019; 63:59-74. [DOI: 10.1042/ebc20180062] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/01/2023]
Abstract
Abstract
The eukaryotic genome is regulated in the context of chromatin. Specialized histones, known as histone variants, incorporate into chromatin to replace their canonical counterparts and represent an important layer of regulation to diversify the structural characteristics and functional outputs of chromatin. MacroH2A is an unusual histone variant with a bulky C-terminal non-histone domain that distinguishes it from all other histones. It is a critical player in stabilizing differentiated cell identity by posing as a barrier to somatic cell reprogramming toward pluripotency and acts as a tumor suppressor in a wide range of cancers. MacroH2A histones are generally regarded as repressive variants that are enriched at the inactive X chromosome (Xi) and broad domains across autosomal chromatin. Recent studies have shed light on to how macroH2A influences transcriptional outputs within distinct genomic contexts and revealed new intriguing molecular functions of macroH2A variants beyond transcriptional regulation. Furthermore, the mechanisms of its mysterious chromatin deposition are beginning to be unraveled, facilitating our understanding of its complex regulation of genome function.
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157
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Klein CB. Emerging confluences of epigenetics and DNA repair in cancer and disease. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2019; 780:11-14. [PMID: 31395354 DOI: 10.1016/j.mrrev.2019.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Catherine B Klein
- Department of Environmental Medicine, NYU School of Medicine, 341 East 25 Street, New York, NY, 10010, United States.
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158
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Clouaire T, Legube G. A Snapshot on the Cis Chromatin Response to DNA Double-Strand Breaks. Trends Genet 2019; 35:330-345. [PMID: 30898334 DOI: 10.1016/j.tig.2019.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 12/11/2022]
Abstract
In eukaryotes, detection and repair of DNA double-strand breaks (DSBs) operate within chromatin, an incredibly complex structure that tightly packages and regulates DNA metabolism. Chromatin participates in the repair of these lesions at multiple steps, from detection to genomic sequence recovery and chromatin is itself extensively modified during the repair process. In recent years, new methodologies and dedicated techniques have expanded the experimental toolbox, opening up a new era granting the high-resolution analysis of chromatin modifications at annotated DSBs in a genome-wide manner. A complex picture is starting to emerge whereby chromatin is altered at various scales around DSBs, in a manner that relates to the repair pathway used, hence defining a 'repair histone code'. Here, we review the recent advances regarding our knowledge of the chromatin landscape induced in cis around DSBs, with an emphasis on histone post-translational modifications and histone variants.
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Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.
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159
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The Roles of Human DNA Methyltransferases and Their Isoforms in Shaping the Epigenome. Genes (Basel) 2019; 10:genes10020172. [PMID: 30813436 PMCID: PMC6409524 DOI: 10.3390/genes10020172] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/16/2019] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
A DNA sequence is the hard copy of the human genome and it is a driving force in determining the physiological processes in an organism. Concurrently, the chemical modification of the genome and its related histone proteins is dynamically involved in regulating physiological processes and diseases, which overall constitutes the epigenome network. Among the various forms of epigenetic modifications, DNA methylation at the C-5 position of cytosine in the cytosine–guanine (CpG) dinucleotide is one of the most well studied epigenetic modifications. DNA methyltransferases (DNMTs) are a family of enzymes involved in generating and maintaining CpG methylation across the genome. In mammalian systems, DNA methylation is performed by DNMT1 and DNMT3s (DNMT3A and 3B). DNMT1 is predominantly involved in the maintenance of DNA methylation during cell division, while DNMT3s are involved in establishing de novo cytosine methylation and maintenance in both embryonic and somatic cells. In general, all DNMTs require accessory proteins, such as ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domain 1 (UHRF1) or DNMT3-like (DNMT3L), for their biological function. This review mainly focuses on the role of DNMT3B and its isoforms in de novo methylation and maintenance of DNA methylation, especially with respect to their role as an accessory protein.
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160
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Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA. Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition. Epigenetics Chromatin 2019; 12:11. [PMID: 30736855 PMCID: PMC6368739 DOI: 10.1186/s13072-019-0256-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/23/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Epithelial to mesenchymal transition (EMT) plays a crucial role in cancer propagation. It can be orchestrated by the activation of multiple signaling pathways, which have been found to be highly coordinated with many epigenetic regulators. Although the mechanism of EMT has been studied over decades, cross talk between signaling and epigenetic regulation is not fully understood. RESULTS Here, we present a time-resolved multi-omics strategy, which featured the identification of the correlation between protein changes (proteome), signaling pathways (phosphoproteome) and chromatin modulation (histone modifications) dynamics during TGF-β-induced EMT. Our data revealed that Erk signaling was activated in 5-min stimulation and structural proteins involved in cytoskeleton rearrangement were regulated after 1-day treatment, constituting a detailed map of systematic changes. The comprehensive profiling of histone post-translational modifications identified H3K27me3 as the most significantly up-regulated mark. We thus speculated and confirmed that a combined inhibition of Erk signaling and Ezh2 (H3K27me3 methyltransferase) was more effective in blocking EMT progress than individual inhibitions. CONCLUSIONS In summary, our data provided a more detailed map of cross talk between signaling pathway and chromatin regulation comparing to previous EMT studies. Our findings point to a promising therapeutic strategy for EMT-related diseases by combining Erk inhibitor (singling pathway) and Ezh2 inhibitor (epigenetic regulation).
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Affiliation(s)
- Congcong Lu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katarzyna Kulej
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Karen Ross
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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161
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van Emmerik CL, van Ingen H. Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 110:1-19. [PMID: 30803691 DOI: 10.1016/j.pnmrs.2019.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 05/09/2023]
Abstract
NMR is an essential technique for obtaining information at atomic resolution on the structure, motions and interactions of biomolecules. Here, we review the contribution of NMR to our understanding of the fundamental unit of chromatin: the nucleosome. Nucleosomes compact the genome by wrapping the DNA around a protein core, the histone octamer, thereby protecting genomic integrity. Crucially, the imposed barrier also allows strict regulation of gene expression, DNA replication and DNA repair processes through an intricate system of histone and DNA modifications and a wide range of interactions between nucleosomes and chromatin factors. In this review, we describe how NMR has contributed to deciphering the molecular basis of nucleosome function. Starting from pioneering studies in the 1960s using natural abundance NMR studies, we focus on the progress in sample preparation and NMR methodology that has allowed high-resolution studies on the nucleosome and its subunits. We summarize the results and approaches of state-of-the-art NMR studies on nucleosomal DNA, histone complexes, nucleosomes and nucleosomal arrays. These studies highlight the particular strength of NMR in studying nucleosome dynamics and nucleosome-protein interactions. Finally, we look ahead to exciting new possibilities that will be afforded by on-going developments in solution and solid-state NMR. By increasing both the depth and breadth of nucleosome NMR studies, it will be possible to offer a unique perspective on the dynamic landscape of nucleosomes and its interacting proteins.
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Affiliation(s)
- Clara L van Emmerik
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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162
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Bowerman S, Hickok RJ, Wereszczynski J. Unique Dynamics in Asymmetric macroH2A-H2A Hybrid Nucleosomes Result in Increased Complex Stability. J Phys Chem B 2019; 123:419-427. [PMID: 30557018 DOI: 10.1021/acs.jpcb.8b10668] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The fundamental unit of eukaryotic chromatin is the nucleosome core particle, a protein/DNA complex that binds ∼147 base pairs of DNA to a histone octamer. These histones-H3, H4, H2A, H2B-form the nucleosome core through a stacked interaction in which two H2A-H2B dimers flank the (H3-H4)2 tetramer. In vivo, genetic accessibility can be modulated by the substitution of canonical histones with variant proteins that contain the same structural motif but a different amino acid sequence, such as the transcriptional repression-associated macroH2A variant. Previously, Chakravarthy and Luger published a crystal study that showed that H2A substitution is not necessarily required of both H2A moieties, but that in vitro recombination of nucleosomes in the presence of both macroH2A and H2A histone folds results in a hybrid macroH2A-H2A nucleosome with one dimer of each type. Here, we present molecular dynamics simulations of this hybrid construct and compare the results to our previous study on homogeneous H2A- and macroH2A-containing nucleosomes. We find that the hybrid contains a unique set of dynamics that stabilize the interactions between protein constituents and create an altogether more stable nucleosome, both in terms of protein-DNA and protein-protein binding. While dimer-tetramer interactions are asymmetric, as the difference in moieties would suggest, we observe that it is the canonical dimer that is pulled further into the nucleosome core, resulting in more secure dimer-tetramer bonds and a more stable histone core, and we also find significantly more interaction between the dimer subunits. Together, these models provide evidence for hybrid H2A-macroH2A nucleosome formation being not only possible but actually energetically more favorable than a homogeneous construct, with dynamics that are unique from their homogeneous H2A or macroH2A nucleosome counterparts. These effects of hybrid substitution likely propagate into higher-order chromatin structures to hinder transcriptional activity.
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Affiliation(s)
- Samuel Bowerman
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Robert J Hickok
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
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163
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Shindo Y, Amodeo AA. Dynamics of Free and Chromatin-Bound Histone H3 during Early Embryogenesis. Curr Biol 2019; 29:359-366.e4. [DOI: 10.1016/j.cub.2018.12.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/29/2018] [Accepted: 12/13/2018] [Indexed: 11/27/2022]
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164
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van Eijk P, Nandi SP, Yu S, Bennett M, Leadbitter M, Teng Y, Reed SH. Nucleosome remodeling at origins of global genome-nucleotide excision repair occurs at the boundaries of higher-order chromatin structure. Genome Res 2018; 29:74-84. [PMID: 30552104 PMCID: PMC6314166 DOI: 10.1101/gr.237198.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/07/2018] [Indexed: 11/24/2022]
Abstract
Repair of UV-induced DNA damage requires chromatin remodeling. How repair is initiated in chromatin remains largely unknown. We recently demonstrated that global genome–nucleotide excision repair (GG-NER) in chromatin is organized into domains in relation to open reading frames. Here, we define these domains, identifying the genomic locations from which repair is initiated. By examining DNA damage–induced changes in the linear structure of nucleosomes at these sites, we demonstrate how chromatin remodeling is initiated during GG-NER. In undamaged cells, we show that the GG-NER complex occupies chromatin, establishing the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBSs). We demonstrate that these sites are frequently located at genomic boundaries that delineate chromosomally interacting domains (CIDs). These boundaries define domains of higher-order nucleosome–nucleosome interaction. We demonstrate that initiation of GG-NER in chromatin is accompanied by the disruption of dynamic nucleosomes that flank GCBSs by the GG-NER complex.
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Affiliation(s)
- Patrick van Eijk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Shuvro Prokash Nandi
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Shirong Yu
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Mark Bennett
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Matthew Leadbitter
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Yumin Teng
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Simon H Reed
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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165
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Bachu M, Tamura T, Chen C, Narain A, Nehru V, Sarai N, Ghosh SB, Ghosh A, Kavarthapu R, Dufau ML, Ozato K. A versatile mouse model of epitope-tagged histone H3.3 to study epigenome dynamics. J Biol Chem 2018; 294:1904-1914. [PMID: 30552116 DOI: 10.1074/jbc.ra118.005550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/09/2018] [Indexed: 12/26/2022] Open
Abstract
The variant histone H3.3 is incorporated into the genome in a transcription-dependent manner. This histone is thus thought to play a role in epigenetic regulation. However, our understanding of how H3.3 controls gene expression and epigenome landscape has remained incomplete. This is partly because precise localization of H3.3 in the genome has been difficult to decipher particularly for cells in vivo To circumvent this difficulty, we generated knockin mice, by homologous recombination, to replace both of the two H3.3 loci (H3f3a and H3f3b) with the hemagglutinin-tagged H3.3 cDNA cassette, which also contained a GFP gene. We show here that the hemagglutinin-tagged H3.3 and GFP are expressed in the majority of cells in all adult tissues tested. ChIP-seq data, combined with RNA-seq, revealed a striking correlation between the level of transcripts and that of H3.3 accumulation in expressed genes. Finally, we demonstrate that H3.3 deposition is markedly enhanced upon stimulation by interferon on interferon-stimulated genes, highlighting transcription-coupled H3.3 dynamics. Together, these H3.3 knockin mice serve as a useful experimental model to study epigenome regulation in development and in various adult cells in vivo.
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Affiliation(s)
| | - Tomohiko Tamura
- From the Division of Developmental Biology and.,the Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Chao Chen
- From the Division of Developmental Biology and
| | | | | | | | | | - Anu Ghosh
- From the Division of Developmental Biology and
| | - Raghuveer Kavarthapu
- the Section on Molecular Endocrinology, NICHD, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Maria L Dufau
- the Section on Molecular Endocrinology, NICHD, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Keiko Ozato
- From the Division of Developmental Biology and
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166
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Willhoft O, Ghoneim M, Lin CL, Chua EYD, Wilkinson M, Chaban Y, Ayala R, McCormack EA, Ocloo L, Rueda DS, Wigley DB. Structure and dynamics of the yeast SWR1-nucleosome complex. Science 2018; 362:362/6411/eaat7716. [PMID: 30309918 DOI: 10.1126/science.aat7716] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022]
Abstract
The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo-electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution reveals details of the intricate interactions between components of the SWR1 complex and its nucleosome substrate. Interactions between the Swr1 motor domains and the DNA wrap at superhelical location 2 distort the DNA, causing a bulge with concomitant translocation of the DNA by one base pair, coupled to conformational changes of the histone core. Furthermore, partial unwrapping of the DNA from the histone core takes place upon binding of nucleosomes to SWR1 complex. The unwrapping, as monitored by single-molecule data, is stabilized and has its dynamics altered by adenosine triphosphate binding but does not require hydrolysis.
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Affiliation(s)
- Oliver Willhoft
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Mohamed Ghoneim
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London W12 0NN, UK.,Molecular Virology, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Chia-Liang Lin
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Eugene Y D Chua
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Martin Wilkinson
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Yuriy Chaban
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Rafael Ayala
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Elizabeth A McCormack
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Lorraine Ocloo
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - David S Rueda
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London W12 0NN, UK. .,Molecular Virology, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Dale B Wigley
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
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167
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Jiang H, Xu S, Chen Y, Li H, Tian L, Zhou H, Zhao Z, Yang C, Zhong Z, Cai G, Su D. The structural basis of human Spt16 N-terminal domain interaction with histone (H3-H4) 2 tetramer. Biochem Biophys Res Commun 2018; 508:864-870. [PMID: 30528735 DOI: 10.1016/j.bbrc.2018.11.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 11/21/2018] [Indexed: 02/05/2023]
Abstract
FACT (Facilitates Chromatin Transactions) is a heterodimeric protein complex involved in RNA polymerase II transcription elongation, playing essential roles in chromatin remodeling during transcription, replication, and DNA damage repair. The FACT subunit hSpt16 is essential for nucleosome reorganization. The N-terminal domain of hSpt16 (hSpt16-NTD) was recently described as a histone (H3-H4)2-binding domain; however, its mode of interaction remains unknown. In this study, we solved the structure of hSpt16-NTD437 at 2.19 Å and found that a long-disordered region (hSpt16-LDR), after the main body of hSpt16-NTD, is a novel histone-binding motif. Furthermore, hSpt16-LDR interaction with (H3-H4)2 is H3 N-terminal tail-independent. Therefore, Spt16-NTD is a histone H3-H4-specific binding domain with a distinct mechanism of interaction between histones and histone chaperones.
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Affiliation(s)
- Hua Jiang
- State Key Lab of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Sidan Xu
- State Key Lab of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Yiping Chen
- State Key Lab of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Huiyan Li
- State Key Lab of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Lu Tian
- State Key Lab of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Hongying Zhou
- Department of Human Anatomy, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, PR China
| | - Zhiwei Zhao
- Department of Human Anatomy, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, PR China
| | - Cheng Yang
- Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, PR China
| | - Zhihui Zhong
- Laboratory of Nonhuman Primate Disease Modeling Research, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China
| | - Guocai Cai
- Department of Cardiovascular Medicine, The Third Hospital of MianYang (Sichuan Mental Health Center), Sichuan, 621000, PR China
| | - Dan Su
- State Key Lab of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China.
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168
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Sauer PV, Gu Y, Liu WH, Mattiroli F, Panne D, Luger K, Churchill MEA. Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1. Nucleic Acids Res 2018; 46:9907-9917. [PMID: 30239791 PMCID: PMC6212844 DOI: 10.1093/nar/gky823] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/15/2018] [Indexed: 02/03/2023] Open
Abstract
Eukaryotic chromatin is a highly dynamic structure with essential roles in virtually all DNA-dependent cellular processes. Nucleosomes are a barrier to DNA access, and during DNA replication, they are disassembled ahead of the replication machinery (the replisome) and reassembled following its passage. The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3-H4 directly onto newly synthesized DNA. Therefore, CAF-1 is important for the establishment and propagation of chromatin structure. The molecular mechanism by which CAF-1 mediates H3-H4 deposition has remained unclear. However, recent studies have revealed new insights into the architecture and stoichiometry of the trimeric CAF-1 complex and how it interacts with and deposits H3-H4 onto substrate DNA. The CAF-1 trimer binds to a single H3-H4 dimer, which induces a conformational rearrangement in CAF-1 promoting its interaction with substrate DNA. Two CAF-1•H3-H4 complexes co-associate on nucleosome-free DNA depositing (H3-H4)2 tetramers in the first step of nucleosome assembly. Here, we review the progress made in our understanding of CAF-1 structure, mechanism of action, and how CAF-1 contributes to chromatin dynamics during DNA replication.
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Affiliation(s)
- Paul V Sauer
- European Molecular Biology Laboratory, 38042 Grenoble, France
| | - Yajie Gu
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Wallace H Liu
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Daniel Panne
- European Molecular Biology Laboratory, 38042 Grenoble, France,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Karolin Luger
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Mair EA Churchill
- Department of Pharmacology and Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA,To whom correspondence should be addressed. Tel: +1 303 724 3670;
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169
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Maxouri S, Taraviras S, Lygerou Z. Visualizing the dynamics of histone variants in the S-phase nucleus. Genome Biol 2018; 19:182. [PMID: 30382897 PMCID: PMC6211500 DOI: 10.1186/s13059-018-1556-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Histone variants constitute a fundamental feature of the epigenome. However, their dynamics during normal and challenged DNA replication and their distribution in the three-dimensional space of the nucleus remain poorly characterized. A recent study employed stochastic optical reconstruction microscopy (STORM) to obtain a high-resolution view of the spatial distribution of H3 histone variants in the nucleus and related this to the timing of DNA replication.
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Affiliation(s)
- Stella Maxouri
- Laboratory of Biology, School of Medicine, University of Patras, Patras, Greece
| | - Stavros Taraviras
- Laboratory of Physiology, School of Medicine, University of Patras, Patras, Greece
| | - Zoi Lygerou
- Laboratory of Biology, School of Medicine, University of Patras, Patras, Greece.
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170
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Stafford JM, Lee CH, Voigt P, Descostes N, Saldaña-Meyer R, Yu JR, Leroy G, Oksuz O, Chapman JR, Suarez F, Modrek AS, Bayin NS, Placantonakis DG, Karajannis MA, Snuderl M, Ueberheide B, Reinberg D. Multiple modes of PRC2 inhibition elicit global chromatin alterations in H3K27M pediatric glioma. SCIENCE ADVANCES 2018; 4:eaau5935. [PMID: 30402543 PMCID: PMC6209383 DOI: 10.1126/sciadv.aau5935] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/27/2018] [Indexed: 05/17/2023]
Abstract
A methionine substitution at lysine-27 on histone H3 variants (H3K27M) characterizes ~80% of diffuse intrinsic pontine gliomas (DIPG) and inhibits polycomb repressive complex 2 (PRC2) in a dominant-negative fashion. Yet, the mechanisms for this inhibition and abnormal epigenomic landscape have not been resolved. Using quantitative proteomics, we discovered that robust PRC2 inhibition requires levels of H3K27M greatly exceeding those of PRC2, seen in DIPG. While PRC2 inhibition requires interaction with H3K27M, we found that this interaction on chromatin is transient, with PRC2 largely being released from H3K27M. Unexpectedly, inhibition persisted even after PRC2 dissociated from H3K27M-containing chromatin, suggesting a lasting impact on PRC2. Furthermore, allosterically activated PRC2 is particularly sensitive to H3K27M, leading to the failure to spread H3K27me from PRC2 recruitment sites and consequently abrogating PRC2's ability to establish H3K27me2-3 repressive chromatin domains. In turn, levels of polycomb antagonists such as H3K36me2 are elevated, suggesting a more global, downstream effect on the epigenome. Together, these findings reveal the conditions required for H3K27M-mediated PRC2 inhibition and reconcile seemingly paradoxical effects of H3K27M on PRC2 recruitment and activity.
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Affiliation(s)
- James M. Stafford
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Philipp Voigt
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ricardo Saldaña-Meyer
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Gary Leroy
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ozgur Oksuz
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Fernando Suarez
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Pediatrics, NYUSoM, New York, NY, USA
| | - Aram S. Modrek
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Neurosurgery, NYUSoM, New York, NY, USA
| | - N. Sumru Bayin
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Neurosurgery, NYUSoM, New York, NY, USA
| | - Dimitris G. Placantonakis
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Neurosurgery, NYUSoM, New York, NY, USA
- Kimmel Center for Stem Cell Biology, NYUSoM, New York, NY, USA
- Neuroscience Institute, NYUSoM, New York, NY, USA
| | - Matthias A. Karajannis
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Pediatrics, NYUSoM, New York, NY, USA
| | - Matija Snuderl
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Pathology, Division of Neuropathology, NYUSoM, New York, NY, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Proteomics Laboratory, NYUSoM, New York, NY, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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171
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Clouaire T, Rocher V, Lashgari A, Arnould C, Aguirrebengoa M, Biernacka A, Skrzypczak M, Aymard F, Fongang B, Dojer N, Iacovoni JS, Rowicka M, Ginalski K, Côté J, Legube G. Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures. Mol Cell 2018; 72:250-262.e6. [PMID: 30270107 PMCID: PMC6202423 DOI: 10.1016/j.molcel.2018.08.020] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/13/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
Double-strand breaks (DSBs) are extremely detrimental DNA lesions that can lead to cancer-driving mutations and translocations. Non-homologous end joining (NHEJ) and homologous recombination (HR) represent the two main repair pathways operating in the context of chromatin to ensure genome stability. Despite extensive efforts, our knowledge of DSB-induced chromatin still remains fragmented. Here, we describe the distribution of 20 chromatin features at multiple DSBs spread throughout the human genome using ChIP-seq. We provide the most comprehensive picture of the chromatin landscape set up at DSBs and identify NHEJ- and HR-specific chromatin events. This study revealed the existence of a DSB-induced monoubiquitination-to-acetylation switch on histone H2B lysine 120, likely mediated by the SAGA complex, as well as higher-order signaling at HR-repaired DSBs whereby histone H1 is evicted while ubiquitin and 53BP1 accumulate over the entire γH2AX domains. DSB-chromatin landscape and HR/NHEJ chromatin signatures uncovered by ChIP-seq H2BK120 undergoes a switch from ubiquitination to acetylation at a local scale H1 is removed and ubiquitin accumulates on entire γH2AX domains, mainly at HR DSB 53BP1 spreads over megabase-sized domains, mostly in G1 at HR-prone DSBs
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Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France.
| | - Vincent Rocher
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Anahita Lashgari
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Coline Arnould
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Marion Aguirrebengoa
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Anna Biernacka
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - François Aymard
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Bernard Fongang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA
| | - Norbert Dojer
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA; Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Jason S Iacovoni
- Bioinformatic Plateau I2MC, INSERM and University of Toulouse, Toulouse 31062, France
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France.
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172
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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173
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Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in Caenorhabditis elegans. Genetics 2018; 210:969-982. [PMID: 30217796 PMCID: PMC6218224 DOI: 10.1534/genetics.118.301353] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/04/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic information contributes to proper gene expression and development, and can be transmitted not only through mitotic divisions but also from parents to progeny. We investigated the roles in epigenetic inheritance of MES-4 and MET-1, the two Caenorhabditis elegans enzymes that methylate H3K36 (histone H3 Lys 36). Mass spectrometry analysis confirmed immunostaining results showing that both MES-4 and MET-1 catalyze H3K36me3. In the adult germline, MES-4 is enriched in the distal mitotic zone and MET-1 is enriched in the meiotic pachytene zone. Embryos inherit H3K36me3-marked chromosomes from both the oocyte and sperm, and a maternal load of MES-4 and MET-1. Maternal MES-4 quickly associates with sperm chromosomes; that association requires that the sperm chromosomes bear H3K36me3, suggesting that MES-4 is recruited to chromosomes by preexisting H3K36me3. In embryos that inherit H3K36me3-positive oocyte chromosomes and H3K36me3-negative sperm chromosomes, MES-4 and H3K36me3 are maintained on only a subset of chromosomes until at least the 32-cell stage, likely because MES-4 propagates H3K36me3 on regions of the genome with preexisting H3K36me3. In embryos lacking MES-4, H3K36me3 levels on chromosomes drop precipitously postfertilization. In contrast to the relatively high levels of MES-4 in early-stage embryos, MET-1 levels are low at early stages and start increasing by the ∼26-cell stage, consistent with expression from the zygotic genome. Our findings support the model that MET-1 mediates transcription-coupled H3K36me3 in the parental germline and transcriptionally active embryos, and that MES-4 transmits an epigenetic memory of H3K36me3 across generations and through early embryo cell divisions by maintaining inherited patterns of H3K36me3.
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174
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Interaction of positive coactivator 4 with histone 3.3 protein is essential for transcriptional activation of the luteinizing hormone receptor gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:971-981. [PMID: 30496042 DOI: 10.1016/j.bbagrm.2018.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 11/23/2022]
Abstract
The luteinizing hormone receptor (LHR) is essential for sexual development and reproduction in mammals. We have established that Sp1 has a central role in derepression of LHR gene transcription induced by Trichostatin A (TSA) in MCF7 cells. Moreover, the co-activator PC4 which associates directly with Sp1 at the LHR promoter is essential for TSA-mediated LHR transcription. This study explores interactions of PC4 with histone proteins, which presumably triggers chromatin modifications during LHR transcriptional activation. TSA treatment of MCF7 cells expressing PC4-Flag protein induces acetylation of histone 3 (H3) and immunoprecipitation (IP) studies revealed its interaction with PC4-Flag protein. MS/MS analysis of the protein complex obtained after IP from TSA treated samples detected H3.3 acetylated at K9, K14, K18, K23 and K27 as a PC4 interacting protein. The association of PC4 with H3.3 was corroborated by IP and re-ChIP using H3.3 antibody. Similarly, IP and re-ChIP showed association of PC4 with H3 acetylated protein. Knockdown of PC4 in MCF7 cells reduced H3.3 enrichment, H3 acetylation at the Lys sites and LHR promoter activity in TSA treated cells despite an increase in H3 and H3.3 protein induced by TSA, linking PC4 to H3 acetylation and LHR transcription. Depletion of H3.3 A/B in MCF7 cells impair chromatin accessibility and enrichment of Pol II and TFIIB at the LHR promoter and its activation, resulting in marked reduction of LHR gene expression. Together, these findings point to the critical role of PC4 and its association with acetylated H3.3 in TSA-induced LHR gene transcription.
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175
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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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176
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Azad GK, Swagatika S, Kumawat M, Kumawat R, Tomar RS. Modifying Chromatin by Histone Tail Clipping. J Mol Biol 2018; 430:3051-3067. [DOI: 10.1016/j.jmb.2018.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/15/2022]
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177
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Au-Yeung N, Horvath CM. Histone H2A.Z Suppression of Interferon-Stimulated Transcription and Antiviral Immunity Is Modulated by GCN5 and BRD2. iScience 2018; 6:68-82. [PMID: 30240626 PMCID: PMC6137307 DOI: 10.1016/j.isci.2018.07.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/27/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Type I interferon (IFN)-stimulated gene (ISG) expression requires interaction between a transcription factor complex, ISGF3, and target gene promoters to initiate transcription and protection against infection. To uncover chromatin regulatory features of this antiviral immune response, IFN-induced nucleosome and histone dynamics of human ISG loci were examined. ISGF3 recruitment after IFN stimulation was accompanied by nucleosome reorganization at promoters and gene bodies. IFN stimulation induced loss of core histones H2B, H3, and H4, as well as H2A.Z at ISG promoters. A strong correlation was found between H2A.Z occupancy and ISGF3 target sites, and IFN-stimulated H2A.Z removal requires STAT1, STAT2, and IRF9. Neither INO80 nor SWI/SNF participate in IFN-driven H2A.Z eviction, but GCN5 and BRD2 are required. Interference with H2A.Z expression enhanced ISGF3 recruitment to ISG promoters, ISG mRNA expression, and IFN-stimulated antiviral immunity. This indicates that H2A.Z nucleosomes at ISG promoters restrict optimal ISGF3 engagement and modulate the biological response to IFN.
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Affiliation(s)
- Nancy Au-Yeung
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Curt M Horvath
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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178
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Lai X, Verhage L, Hugouvieux V, Zubieta C. Pioneer Factors in Animals and Plants-Colonizing Chromatin for Gene Regulation. Molecules 2018; 23:E1914. [PMID: 30065231 PMCID: PMC6222629 DOI: 10.3390/molecules23081914] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 01/08/2023] Open
Abstract
Unlike most transcription factors (TF), pioneer TFs have a specialized role in binding closed regions of chromatin and initiating the subsequent opening of these regions. Thus, pioneer TFs are key factors in gene regulation with critical roles in developmental transitions, including organ biogenesis, tissue development, and cellular differentiation. These developmental events involve some major reprogramming of gene expression patterns, specifically the opening and closing of distinct chromatin regions. Here, we discuss how pioneer TFs are identified using biochemical and genome-wide techniques. What is known about pioneer TFs from animals and plants is reviewed, with a focus on the strategies used by pioneer factors in different organisms. Finally, the different molecular mechanisms pioneer factors used are discussed, highlighting the roles that tertiary and quaternary structures play in nucleosome-compatible DNA-binding.
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Affiliation(s)
- Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG, 38000 Grenoble, France.
| | - Leonie Verhage
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG, 38000 Grenoble, France.
| | - Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG, 38000 Grenoble, France.
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG, 38000 Grenoble, France.
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179
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Regulation of Mammalian DNA Replication via the Ubiquitin-Proteasome System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:421-454. [PMID: 29357069 DOI: 10.1007/978-981-10-6955-0_19] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Proper regulation of DNA replication ensures the faithful transmission of genetic material essential for optimal cellular and organismal physiology. Central to this regulation is the activity of a set of enzymes that induce or reverse posttranslational modifications of various proteins critical for the initiation, progression, and termination of DNA replication. This is particularly important when DNA replication proceeds in cancer cells with elevated rates of genomic instability and increased proliferative capacities. Here, we describe how DNA replication in mammalian cells is regulated via the activity of the ubiquitin-proteasome system as well as the consequence of derailed ubiquitylation signaling involved in this important cellular activity.
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180
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Shastrula PK, Lund PJ, Garcia BA, Janicki SM. Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms. J Biol Chem 2018; 293:12360-12377. [PMID: 29921582 DOI: 10.1074/jbc.ra118.001845] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/30/2018] [Indexed: 01/26/2023] Open
Abstract
The histone H3 variant H3.3 is a highly conserved and dynamic regulator of chromatin organization. Therefore, fully elucidating its nucleosome incorporation mechanisms is essential to understanding its functions in epigenetic inheritance. We previously identified the RNase P protein subunit, Rpp29, as a repressor of H3.3 chromatin assembly. Here, we use a biochemical assay to show that Rpp29 interacts with H3.3 through a sequence element in its own N terminus, and we identify a novel interaction with histone H2B at an adjacent site. The fact that archaeal Rpp29 does not include this N-terminal region suggests that it evolved to regulate eukaryote-specific functions. Oncogenic H3.3 mutations alter the H3.3-Rpp29 interaction, which suggests that they could dysregulate Rpp29 function in chromatin assembly. We also used KNS42 cells, an H3.3(G34V) pediatric high-grade glioma cell line, to show that Rpp29 1) represses H3.3 incorporation into transcriptionally active protein-coding, rRNA, and tRNA genes; 2) represses mRNA, protein expression, and antisense RNA; and 3) represses euchromatic post-translational modifications (PTMs) and promotes heterochromatic PTM deposition (i.e. histone H3 Lys-9 trimethylation (H3K9me3) and H3.1/2/3K27me3). Notably, we also found that K27me2 is increased and K36me1 decreased on H3.3(G34V), which suggests that Gly-34 mutations dysregulate Lys-27 and Lys-36 methylation in cis The fact that Rpp29 represses H3.3 chromatin assembly and sense and antisense RNA and promotes H3K9me3 and H3K27me3 suggests that Rpp29 regulates H3.3-mediated epigenetic mechanisms by processing a transcribed signal that recruits H3.3 to its incorporation sites.
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Affiliation(s)
- Prashanth Krishna Shastrula
- From the Wistar Institute, Philadelphia, Pennsylvania 19104.,the Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania 19104, and
| | - Peder J Lund
- the Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Benjamin A Garcia
- the Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Susan M Janicki
- From the Wistar Institute, Philadelphia, Pennsylvania 19104,
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181
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Gómez-Zambrano Á, Crevillén P, Franco-Zorrilla JM, López JA, Moreno-Romero J, Roszak P, Santos-González J, Jurado S, Vázquez J, Köhler C, Solano R, Piñeiro M, Jarillo JA. Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes. MOLECULAR PLANT 2018; 11:815-832. [PMID: 29604400 DOI: 10.1016/j.molp.2018.03.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 05/07/2023]
Abstract
Deposition of the H2A.Z histone variant by the SWR1 complex (SWR1-C) in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWR1-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWR1-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo-lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and reproductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses transcription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWR1-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.
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Affiliation(s)
- Ángeles Gómez-Zambrano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - José M Franco-Zorrilla
- Plant Molecular Genetics Department and Genomics Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Juan A López
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75652, Sweden
| | - Pawel Roszak
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75652, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75652, Sweden
| | - Silvia Jurado
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Jesús Vázquez
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75652, Sweden
| | - Roberto Solano
- Plant Molecular Genetics Department and Genomics Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain.
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182
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Rasheed Z, Altorbag AA, Al-Bossier AS, Alnasser NA, Alkharraz OS, Altuwayjiri KM, Alobaid AS, Alsaif AK, Alanazi YH, Alghidani BA, Alduayji MA, Bu Mozah AA, Alsuhaibani SA. Protective potential of thymoquinone against peroxynitrite induced modifications in histone H2A: In vitro studies. Int J Biol Macromol 2018; 112:169-174. [DOI: 10.1016/j.ijbiomac.2018.01.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/20/2018] [Accepted: 01/23/2018] [Indexed: 12/14/2022]
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183
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Cheung P, Vallania F, Warsinske HC, Donato M, Schaffert S, Chang SE, Dvorak M, Dekker CL, Davis MM, Utz PJ, Khatri P, Kuo AJ. Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging. Cell 2018; 173:1385-1397.e14. [PMID: 29706550 PMCID: PMC5984186 DOI: 10.1016/j.cell.2018.03.079] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/27/2018] [Accepted: 03/28/2018] [Indexed: 12/17/2022]
Abstract
Post-translational modifications of histone proteins and exchanges of histone variants of chromatin are central to the regulation of nearly all DNA-templated biological processes. However, the degree and variability of chromatin modifications in specific human immune cells remain largely unknown. Here, we employ a highly multiplexed mass cytometry analysis to profile the global levels of a broad array of chromatin modifications in primary human immune cells at the single-cell level. Our data reveal markedly different cell-type- and hematopoietic-lineage-specific chromatin modification patterns. Differential analysis between younger and older adults shows that aging is associated with increased heterogeneity between individuals and elevated cell-to-cell variability in chromatin modifications. Analysis of a twin cohort unveils heritability of chromatin modifications and demonstrates that aging-related chromatin alterations are predominantly driven by non-heritable influences. Together, we present a powerful platform for chromatin and immunology research. Our discoveries highlight the profound impacts of aging on chromatin modifications.
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Affiliation(s)
- Peggie Cheung
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Francesco Vallania
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hayley C Warsinske
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Schaffert
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Alex J Kuo
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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184
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Champroux A, Cocquet J, Henry-Berger J, Drevet JR, Kocer A. A Decade of Exploring the Mammalian Sperm Epigenome: Paternal Epigenetic and Transgenerational Inheritance. Front Cell Dev Biol 2018; 6:50. [PMID: 29868581 PMCID: PMC5962689 DOI: 10.3389/fcell.2018.00050] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/18/2018] [Indexed: 12/12/2022] Open
Abstract
The past decade has seen a tremendous increase in interest and progress in the field of sperm epigenetics. Studies have shown that chromatin regulation during male germline development is multiple and complex, and that the spermatozoon possesses a unique epigenome. Its DNA methylation profile, DNA-associated proteins, nucleo-protamine distribution pattern and non-coding RNA set up a unique epigenetic landscape which is delivered, along with its haploid genome, to the oocyte upon fertilization, and therefore can contribute to embryogenesis and to the offspring health. An emerging body of compelling data demonstrates that environmental exposures and paternal lifestyle can change the sperm epigenome and, consequently, may affect both the embryonic developmental program and the health of future generations. This short review will attempt to provide an overview of what is currently known about sperm epigenome and the existence of transgenerational epigenetic inheritance of paternally acquired traits that may contribute to the offspring phenotype.
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Affiliation(s)
- Alexandre Champroux
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julie Cocquet
- INSERM U1016, Institut Cochin, Centre National de la Recherche Scientifique UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Joëlle Henry-Berger
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Joël R. Drevet
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ayhan Kocer
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
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185
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Ordu O, Kremser L, Lusser A, Dekker NH. Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics. J Chem Phys 2018; 148:123323. [PMID: 29604863 DOI: 10.1063/1.5009100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in eukaryotes. Their role in DNA compaction comes with regulatory functions that impact essential genomic processes such as replication, transcription, and repair. The assembly of nucleosomes obeys a precise pathway in which tetramers of histones H3 and H4 bind to the DNA first to form tetrasomes, and two dimers of histones H2A and H2B are subsequently incorporated to complete the complex. As viable intermediates, we previously showed that tetrasomes can spontaneously flip between a left-handed and right-handed conformation of DNA-wrapping. To pinpoint the underlying mechanism, here we investigated the role of the H3-H3 interface for tetramer flexibility in the flipping process at the single-molecule level. Using freely orbiting magnetic tweezers, we studied the assembly and structural dynamics of individual tetrasomes modified at the cysteines close to this interaction interface by iodoacetamide (IA) in real time. While such modification did not affect the structural properties of the tetrasomes, it caused a 3-fold change in their flipping kinetics. The results indicate that the IA-modification enhances the conformational plasticity of tetrasomes. Our findings suggest that subnucleosomal dynamics may be employed by chromatin as an intrinsic and adjustable mechanism to regulate DNA supercoiling.
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Affiliation(s)
- Orkide Ordu
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H Dekker
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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186
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Molaro A, Young JM, Malik HS. Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. Genome Res 2018; 28:460-473. [PMID: 29549088 PMCID: PMC5880237 DOI: 10.1101/gr.229799.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022]
Abstract
Eukaryotic genomes must accomplish both compact packaging for genome stability and inheritance, as well as accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3, and H4) and by deploying histone variants with specialized chromatin functions. Some histone variants are conserved across all eukaryotes, whereas others are lineage-specific. Here, we performed detailed phylogenomic analyses of “short H2A histone” variants found in mammalian genomes. We discovered a previously undescribed typically-sized H2A variant in monotremes and marsupials, H2A.R, which may represent the common ancestor of the short H2As. We also discovered a novel class of short H2A histone variants in eutherian mammals, H2A.Q. We show that short H2A variants arose on the X Chromosome in the common ancestor of all eutherian mammals and diverged into four evolutionarily distinct clades: H2A.B, H2A.L, H2A.P, and H2A.Q. However, the repertoires of short histone H2A variants vary extensively among eutherian mammals due to lineage-specific gains and losses. Finally, we show that all four short H2As are subject to accelerated rates of protein evolution relative to both canonical and other variant H2A proteins including H2A.R. Our analyses reveal that short H2As are a unique class of testis-restricted histone variants displaying an unprecedented evolutionary dynamism. Based on their X-Chromosomal localization, genetic turnover, and testis-specific expression, we hypothesize that short H2A variants may participate in genetic conflicts involving sex chromosomes during reproduction.
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Affiliation(s)
- Antoine Molaro
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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187
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Baretti M, Azad NS. The role of epigenetic therapies in colorectal cancer. Curr Probl Cancer 2018; 42:530-547. [PMID: 29625794 DOI: 10.1016/j.currproblcancer.2018.03.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/21/2018] [Accepted: 03/08/2018] [Indexed: 12/14/2022]
Abstract
Although developments in the diagnosis and therapy of colorectal cancer (CRC) have been made in the last decade, much work remains to be done as it remains the second leading cause of cancer death. It is now well established that epigenetic events, together with genetic alterations, are key events in initiation and progression of CRC. Epigenetics refers to heritable alterations in gene expression that do not involve changes in the DNA sequence. These alterations include DNA methylation, histone alterations, chromatin remodelers, and noncoding RNAs. In CRC, aberrations in epigenome may also involve in the development of drug resistance to conventional drugs such as 5-fluorouracil, oxaliplatin, and irinotecan. Thus, it has been suggested that combined therapies with epigenetic agents may reverse drug resistance. In this regard, DNA methyltransferase inhibitors and histone deacetylase inhibitors have been extensively investigated in CRC. The aim of this review is to provide a brief overview of the preclinical data that represent a proof of principle for the employment of epigenetic agents in CRC with a focus on the advantages of combinatorial therapy over single-drug treatment. We will also critically discuss the results and limitations of initial clinical experiences of epigenetic-based therapy in CRC and summarize ongoing clinical trials. Nevertheless, since recent translational research suggest that epigenetic modulators play a key role in augmenting immunogenicity of the tumor microenvironment and in restoring immune recognition, we will also highlight the recent developments of combinations strategies of immunotherapies and epigenetic therapies in CRC, summarizing preclinical, and clinical data to signify this evolving and promising field for CRC treatment.
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Affiliation(s)
- Marina Baretti
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University.
| | - Nilofer Saba Azad
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University
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188
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Hoghoughi N, Barral S, Vargas A, Rousseaux S, Khochbin S. Histone variants: essential actors in male genome programming. J Biochem 2018; 163:97-103. [PMID: 29165574 DOI: 10.1093/jb/mvx079] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/13/2017] [Indexed: 02/03/2023] Open
Abstract
Prior to its transmission to the offspring, the male genome has to be tightly compacted. A genome-scale histone eviction and the subsequent repackaging of DNA by protamines (Prms) direct this essential genome condensation step. The requirement for male germ cells to undergo such a dramatic and unique genome reorganization explains why these cells express the largest number of histone variants, including many testis-specific ones. Indeed, an open chromatin, nucleosome instability and a facilitated process of histone disassembly are direct consequences of the presence of these histone variants in the chromatin of male germ cells. These histone-induced changes in chromatin first control a stage-specific gene expression program and then directly mediate the histone-to-Prm transition process. This review aims at summarizing and discussing a series of recent functional studies of male germ cell histone variants with a focus on their impact on the process of histone eviction and male genome compaction.
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Affiliation(s)
- Naghmeh Hoghoughi
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| | - Sophie Barral
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| | - Alexandra Vargas
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| | - Sophie Rousseaux
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| | - Saadi Khochbin
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
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189
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Catarino RR, Stark A. Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev 2018; 32:202-223. [PMID: 29491135 PMCID: PMC5859963 DOI: 10.1101/gad.310367.117] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enhancers are important genomic regulatory elements directing cell type-specific transcription. They assume a key role during development and disease, and their identification and functional characterization have long been the focus of scientific interest. The advent of next-generation sequencing and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based genome editing has revolutionized the means by which we study enhancer biology. In this review, we cover recent developments in the prediction of enhancers based on chromatin characteristics and their identification by functional reporter assays and endogenous DNA perturbations. We discuss that the two latter approaches provide different and complementary insights, especially in assessing enhancer sufficiency and necessity for transcription activation. Furthermore, we discuss recent insights into mechanistic aspects of enhancer function, including findings about cofactor requirements and the role of post-translational histone modifications such as monomethylation of histone H3 Lys4 (H3K4me1). Finally, we survey how these approaches advance our understanding of transcription regulation with respect to promoter specificity and transcriptional bursting and provide an outlook covering open questions and promising developments.
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Affiliation(s)
- Rui R Catarino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
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190
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Zinchenko A, Berezhnoy NV, Wang S, Rosencrans WM, Korolev N, van der Maarel JR, Nordenskiöld L. Single-molecule compaction of megabase-long chromatin molecules by multivalent cations. Nucleic Acids Res 2018; 46:635-649. [PMID: 29145649 PMCID: PMC5778610 DOI: 10.1093/nar/gkx1135] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 10/18/2017] [Accepted: 10/29/2017] [Indexed: 11/21/2022] Open
Abstract
To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo. Variation of HO loading revealed a number of unique features related to the efficiency of chromatin compaction by multivalent cations, the mechanism of compaction, and the character of partly compact chromatin structures. The observations may be relevant for how DNA accessibility in chromatin is maintained. Compaction of saturated chromatin, in turn, is accompanied by an intra-chain segregation at the level of single chromatin molecules, suggesting an intriguing scenario of selective activation/deactivation of DNA as a result of chromatin fiber heterogeneity due to the nucleosome positioning. We suggest that this chromatin, reconstituted on megabase-long DNA because of its large size, is a useful model of eukaryotic chromatin.
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Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Sai Wang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - William M Rosencrans
- Department of Physics and Astronomy, Colgate University, Hamilton, NY 13346, USA
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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191
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Zhang K, Wang H, Rajput SK, Folger JK, Smith GW. Characterization of H3.3 and HIRA expression and function in bovine early embryos. Mol Reprod Dev 2018; 85:106-116. [PMID: 29232016 DOI: 10.1002/mrd.22939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/01/2017] [Indexed: 01/20/2023]
Abstract
Histone variant H3.3 is encoded by two distinct genes, H3F3A and H3F3B, that are closely associated with actively transcribed genes. H3.3 replacement is continuous and essential for maintaining correct chromatin structure during mouse oogenesis. Upon fertilization, H3.3 is incorporated to parental chromatin, and is required for blastocyst formation in mice. The H3.3 exchange process is facilitated by the chaperone HIRA, particularly during zygote development. We previously demonstrated that H3.3 is required for bovine early embryonic development; here, we explored the mechanisms of its functional requirement. H3F3A mRNA abundance is stable whereas H3F3B and HIRA mRNA are relatively dynamic during early embryonic development. H3F3B mRNA quantity is also considerably higher than H3F3A. Immunofluorescence analysis revealed an even distribution of H3.3 between paternal and maternal pronuclei in zygotes, and subsequent stage-specific localization of H3.3 in early bovine embryos. Knockdown of H3.3 by targeting both H3F3A and H3F3B dramatically decreased the expression of NANOG (a pluripotency marker) and CTGF (Connective tissue growth factor; a trophectoderm marker) in bovine blastocysts. Additionally, we noted that Histone H3 lysine 36 dimethylation and linker Histone H1 abundance is reduced in H3.3-deficient embryos, which was similar to effects following knockdown of CHD1 (Chromodomain helicase DNA-binding protein 1). By contrast, no difference was observed in the abundance of Histone H3 lysine 4 trimethylation, Histone H3 lysine 9 dimethylation, or Splicing factor 3 B1. Collectively, these results established that H3.3 is required for correct epigenetic modifications and H1 deposition, dysregulation of which likely mediate the poor development in H3.3-deficient embryos.
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Affiliation(s)
- Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Dairy Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Laboratory of Mammalian Reproductive Biology and Genomics, Michigan State University, East Lansing, Michigan
- Department of Animal Science, Michigan State University, East Lansing, Michigan
| | - Han Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sandeep K Rajput
- Laboratory of Mammalian Reproductive Biology and Genomics, Michigan State University, East Lansing, Michigan
- Department of Animal Science, Michigan State University, East Lansing, Michigan
| | - Joseph K Folger
- Laboratory of Mammalian Reproductive Biology and Genomics, Michigan State University, East Lansing, Michigan
- Department of Animal Science, Michigan State University, East Lansing, Michigan
| | - George W Smith
- Laboratory of Mammalian Reproductive Biology and Genomics, Michigan State University, East Lansing, Michigan
- Department of Animal Science, Michigan State University, East Lansing, Michigan
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192
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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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193
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Leung JWC, Emery LE, Miller KM. CRISPR/Cas9 Gene Editing of Human Histone H2A Variant H2AX and MacroH2A. Methods Mol Biol 2018; 1832:255-269. [PMID: 30073532 DOI: 10.1007/978-1-4939-8663-7_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Histone H2A variants play important roles in maintaining the integrity of the genome. For example, the histone variant H2AX is phosphorylated on Ser139 (called γH2AX) at DNA double-strand breaks (DSB) and serves as a signal for the initiation of downstream DNA damage response (DDR) factor recruitment and DNA repair activities within damaged chromatin. For decades, genetic studies in human cells involving DNA damage signaling and repair factors have relied mostly on either knockdown by RNA interference (i.e., shRNA and siRNA) or the use of mouse embryonic fibroblasts derived from knockout (KO) mice. Recent advances in gene editing using ZNF nuclease, TALEN, and CRISPR/Cas9 have allowed the generation of human KO cell lines, allowing genetic models for studying the DDR, including histone H2A variants in human cells. Here, we describe a detailed protocol for generating and verifying KO of H2AX and macroH2A histone H2A variants using CRISPR/Cas9 gene editing in human cancer cell lines. This protocol allows the use and development of genetic systems in human cells to study histone variants and their functions, including within the DDR.
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Affiliation(s)
- Justin W C Leung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Radiation Oncology, Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Lara E Emery
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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194
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Ferdous MM, Bao Y, Vinciotti V, Liu X, Wilson P. Predicting gene expression from genome wide protein binding profiles. Neurocomputing 2018. [DOI: 10.1016/j.neucom.2017.09.094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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195
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Penke TJR, McKay DJ, Strahl BD, Matera AG, Duronio RJ. Functional Redundancy of Variant and Canonical Histone H3 Lysine 9 Modification in Drosophila. Genetics 2018; 208:229-244. [PMID: 29133298 PMCID: PMC5753860 DOI: 10.1534/genetics.117.300480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/10/2017] [Indexed: 01/07/2023] Open
Abstract
Histone post-translational modifications (PTMs) and differential incorporation of variant and canonical histones into chromatin are central modes of epigenetic regulation. Despite similar protein sequences, histone variants are enriched for different suites of PTMs compared to their canonical counterparts. For example, variant histone H3.3 occurs primarily in transcribed regions and is enriched for "active" histone PTMs like Lys9 acetylation (H3.3K9ac), whereas the canonical histone H3 is enriched for Lys9 methylation (H3K9me), which is found in transcriptionally silent heterochromatin. To determine the functions of K9 modification on variant vs. canonical H3, we compared the phenotypes caused by engineering H3.3K9R and H3K9R mutant genotypes in Drosophila melanogaster Whereas most H3.3K9R , and a small number of H3K9R , mutant animals are capable of completing development and do not have substantially altered protein-coding transcriptomes, all H3.3K9R H3K9R combined mutants die soon after embryogenesis and display decreased expression of genes enriched for K9ac. These data suggest that the role of K9ac in gene activation during development can be provided by either H3 or H3.3. Conversely, we found that H3.3K9 is methylated at telomeric transposons and that this mark contributes to repressive chromatin architecture, supporting a role for H3.3 in heterochromatin that is distinct from that of H3. Thus, our genetic and molecular analyses demonstrate that K9 modification of variant and canonical H3 have overlapping roles in development and transcriptional regulation, though to differing extents in euchromatin and heterochromatin.
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Affiliation(s)
- Taylor J R Penke
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Genetics, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, North Carolina 27599
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Genetics, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, North Carolina 27599
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Genetics, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, North Carolina 27599
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196
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Serra-Cardona A, Zhang Z. Replication-Coupled Nucleosome Assembly in the Passage of Epigenetic Information and Cell Identity. Trends Biochem Sci 2017; 43:136-148. [PMID: 29292063 DOI: 10.1016/j.tibs.2017.12.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 12/31/2022]
Abstract
During S phase, replicated DNA must be assembled into nucleosomes using both newly synthesized and parental histones in a process that is tightly coupled to DNA replication. This DNA replication-coupled process is regulated by multitude of histone chaperones as well as by histone-modifying enzymes. In recent years novel insights into nucleosome assembly of new H3-H4 tetramers have been gained through studies on the classical histone chaperone CAF-1 and the identification of novel factors involved in this process. Moreover, in vitro reconstitution of chromatin replication has shed light on nucleosome assembly of parental H3-H4, a process that remains elusive. Finally, recent studies have revealed that the replication-coupled nucleosome assembly is important for the determination and maintenance of cell fate in multicellular organisms.
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Affiliation(s)
- Albert Serra-Cardona
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA.
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197
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Nyamugenda E, Cox AB, Pierce JB, Banning RC, Huynh ML, May C, Marshall S, Turkal CE, Duina AA. Charged residues on the side of the nucleosome contribute to normal Spt16-gene interactions in budding yeast. Epigenetics 2017; 13:1-7. [PMID: 29271283 DOI: 10.1080/15592294.2017.1418132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Previous work in Saccharomyces cerevisiae identified three residues located in close proximity to each other on the side of the nucleosome whose integrity is required for proper association of the Spt16 component of the FACT complex across transcribed genes. In an effort to gain further insights into the parameters that control Spt16 interactions with genes in vivo, we tested the effects of additional histone mutants on Spt16 occupancy across two constitutively transcribed genes. These studies revealed that mutations in several charged residues in the vicinity of the three residues originally identified as important for Spt16-gene interactions also significantly perturb normal association of Spt16 across genes. Based on these and our previous findings, we propose that the charge landscape across the region encompassed by these residues, which we refer to as the Influences Spt16-Gene Interactions or ISGI region, is an important contributor to proper Spt16-gene interactions in vivo.
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Affiliation(s)
| | - A Brandon Cox
- a Biology Department , Hendrix College , Conway , AR 72032
| | - Jacob B Pierce
- a Biology Department , Hendrix College , Conway , AR 72032
| | - Ryan C Banning
- a Biology Department , Hendrix College , Conway , AR 72032
| | | | - Catey May
- a Biology Department , Hendrix College , Conway , AR 72032
| | - Sarah Marshall
- a Biology Department , Hendrix College , Conway , AR 72032
| | | | - Andrea A Duina
- a Biology Department , Hendrix College , Conway , AR 72032
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198
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Morozov VM, Giovinazzi S, Ishov AM. CENP-B protects centromere chromatin integrity by facilitating histone deposition via the H3.3-specific chaperone Daxx. Epigenetics Chromatin 2017; 10:63. [PMID: 29273057 PMCID: PMC5741900 DOI: 10.1186/s13072-017-0164-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/24/2017] [Indexed: 12/27/2022] Open
Abstract
Background The main chromatin unit, the nucleosome, can be modulated by the incorporation of histone variants that, in combination with posttranslational histones modifications, determine epigenetics properties of chromatin. Understanding the mechanism that creates a histone variants landscape at different genomic elements is expected to elevate our comprehension of chromatin assembly and function. The Daxx chaperone deposits transcription-associated histone H3.3 at centromeres, but mechanism of centromere-specific Daxx targeting remains unclear. Results In this study, we identified an unexpected function of the constitutive centromeric protein CENP-B that serves as a “beacon” for H3.3 incorporation. CENP-B depletion reduces Daxx association and H3.3 incorporation at centromeres. Daxx/CENP-B interaction and Daxx centromeric association are SUMO dependent and requires SIMs of Daxx. Depletion of SUMO-2, but not SUMO-1, decreases Daxx/CENP-B interaction and reduces centromeric accumulation of Daxx and H3.3, demonstrating distinct functions of SUMO paralogs in H3.3 chaperoning. Finally, disruption of CENP-B/Daxx-dependent H3.3 pathway deregulates heterochromatin marks H3K9me3, ATRX and HP1α at centromeres and elevates chromosome instability. Conclusion The demonstrated roles of CENP-B and SUMO-2 in H3.3 loading reveal a novel mechanism controlling chromatin maintenance and genome stability. Given that CENP-B is the only centromere protein that binds centromere-specific DNA elements, our study provides a new link between centromere DNA and unique epigenetic landscape of centromere chromatin. Electronic supplementary material The online version of this article (10.1186/s13072-017-0164-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Viacheslav M Morozov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA
| | - Serena Giovinazzi
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA.,Division of Food Safety, Florida Department of Agriculture and Consumer Services, Tallahassee, FL, USA
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA.
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199
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Shaping Chromatin in the Nucleus: The Bricks and the Architects. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:1-14. [PMID: 29208640 DOI: 10.1101/sqb.2017.82.033753] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromatin organization in the nucleus provides a vast repertoire of information in addition to that encoded genetically. Understanding how this organization impacts genome stability and influences cell fate and tumorigenesis is an area of rapid progress. Considering the nucleosome, the fundamental unit of chromatin structure, the study of histone variants (the bricks) and their selective loading by histone chaperones (the architects) is particularly informative. Here, we report recent advances in understanding how relationships between histone variants and their chaperones contribute to tumorigenesis using cell lines and Xenopus development as model systems. In addition to their role in histone deposition, we also document interactions between histone chaperones and other chromatin factors that govern higher-order structure and control DNA metabolism. We highlight how a fine-tuned assembly line of bricks (H3.3 and CENP-A) and architects (HIRA, HJURP, and DAXX) is key in adaptation to developmental and pathological changes. An example of this conceptual advance is the exquisite sensitivity displayed by p53-null tumor cells to modulation of HJURP, the histone chaperone for CENP-A (CenH3 variant). We discuss how these findings open avenues for novel therapeutic paradigms in cancer care.
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200
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Resetting the Yeast Epigenome with Human Nucleosomes. Cell 2017; 171:1508-1519.e13. [PMID: 29198523 DOI: 10.1016/j.cell.2017.10.043] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/11/2017] [Accepted: 10/24/2017] [Indexed: 01/23/2023]
Abstract
Humans and yeast are separated by a billion years of evolution, yet their conserved histones retain central roles in gene regulation. Here, we "reset" yeast to use core human nucleosomes in lieu of their own (a rare event taking 20 days), which initially only worked with variant H3.1. The cells adapt by acquiring suppressor mutations in cell-division genes or by acquiring certain aneuploid states. Converting five histone residues to their yeast counterparts restored robust growth. We reveal that humanized nucleosomes are positioned according to endogenous yeast DNA sequence and chromatin-remodeling network, as judged by a yeast-like nucleosome repeat length. However, human nucleosomes have higher DNA occupancy, globally reduce RNA content, and slow adaptation to new conditions by delaying chromatin remodeling. These humanized yeasts (including H3.3) pose fundamental new questions about how chromatin is linked to many cell processes and provide a platform to study histone variants via yeast epigenome reprogramming.
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