1
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Mojica EA, Kültz D. A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms. J Proteome Res 2023. [PMID: 37624673 DOI: 10.1021/acs.jproteome.3c00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Histone post-translational modifications (PTMs) are epigenetic marks that play a critical role in the expression and maintenance of DNA, but they remain largely uninvestigated in nonmodel organisms due to technical challenges. To begin alleviating this issue, we developed a workflow for histone PTM analysis in Mozambique tilapia (Oreochromis mossambicus), being a widespread and environmentally hardy fish, using mass spectrometry methods. By incorporating multiple protein digestion methods into the preparation of each sample, we reliably quantified 214 biologically relevant histone PTMs. All of these histone PTMs, collectively referred to as the global histone PTM landscape, were characterized in the gills, kidney, and testes of this fish. By comparing the global histone PTM landscape between the three tissues, we found that 91.59% of histone PTMs were tissue-dependent. The workflow and tools for histone PTM analysis described in this study are now publicly available and enable comprehensive investigation into the influence of environmental stress on histone PTMs in nonmodel organisms. Given the functionality and flexibility of histone PTMs, we anticipate that the study of histone PTMs in ecologically relevant contexts will provide ground-breaking insights into comparative physiology and evolution.
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Affiliation(s)
- Elizabeth A Mojica
- Department of Animal Sciences, University of California - Davis, One Shields Avenue, Meyer Hall, Davis, California 95616, United States
| | - Dietmar Kültz
- Department of Animal Sciences, University of California - Davis, One Shields Avenue, Meyer Hall, Davis, California 95616, United States
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2
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Barrientos-Moreno M, Maya-Miles D, Murillo-Pineda M, Fontalva S, Pérez-Alegre M, Andujar E, Prado F. Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects. Sci Rep 2023; 13:11397. [PMID: 37452085 PMCID: PMC10349138 DOI: 10.1038/s41598-023-38280-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Genome duplication occurs through the coordinated action of DNA replication and nucleosome assembly at replication forks. Defective nucleosome assembly causes DNA lesions by fork breakage that need to be repaired. In addition, it causes a loss of chromatin integrity. These chromatin alterations can be restored, even though the mechanisms are unknown. Here, we show that the process of chromatin restoration can deal with highly severe chromatin defects induced by the absence of the chaperones CAF1 and Rtt106 or a strong reduction in the pool of available histones, and that this process can be followed by analyzing the topoisomer distribution of the 2µ plasmid. Using this assay, we demonstrate that chromatin restoration is slow and independent of checkpoint activation, whereas it requires the action of transcription and the FACT complex. Therefore, cells are able to "repair" not only DNA lesions but also chromatin alterations associated with defective nucleosome assembly.
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Affiliation(s)
- Marta Barrientos-Moreno
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Douglas Maya-Miles
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Marina Murillo-Pineda
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Sara Fontalva
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Mónica Pérez-Alegre
- Genomic Unit, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Eloísa Andujar
- Genomic Unit, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Félix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain.
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3
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Abstract
Organisms mount the cellular stress response whenever environmental parameters exceed the range that is conducive to maintaining homeostasis. This response is critical for survival in emergency situations because it protects macromolecular integrity and, therefore, cell/organismal function. From an evolutionary perspective, the cellular stress response counteracts severe stress by accelerating adaptation via a process called stress-induced evolution. In this Review, we summarize five key physiological mechanisms of stress-induced evolution. Namely, these are stress-induced changes in: (1) mutation rates, (2) histone post-translational modifications, (3) DNA methylation, (4) chromoanagenesis and (5) transposable element activity. Through each of these mechanisms, organisms rapidly generate heritable phenotypes that may be adaptive, maladaptive or neutral in specific contexts. Regardless of their consequences to individual fitness, these mechanisms produce phenotypic variation at the population level. Because variation fuels natural selection, the physiological mechanisms of stress-induced evolution increase the likelihood that populations can avoid extirpation and instead adapt under the stress of new environmental conditions.
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Affiliation(s)
- Elizabeth A Mojica
- Department of Animal Science, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
| | - Dietmar Kültz
- Department of Animal Science, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
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4
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Abstract
The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin. The resulting structures modulate essential nuclear processes such as transcription, replication, and repair to facilitate or impede their multi-step progression and these contribute to dynamic modification of the 3D-genome organization. It is generally accepted that protein–protein and protein–DNA interactions form the basis of 3D-genome organization. However, the constant generation of mechanical forces, torques, and other stresses produced by various proteins translocating along DNA could be playing a larger role in genome organization than currently appreciated. Clearly, a thorough understanding of the mechanical determinants imposed by DNA transactions on the 3D organization of the genome is required. We provide here an overview of our current knowledge and highlight the importance of DNA and chromatin mechanics in gene expression.
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Affiliation(s)
- Rajiv Kumar Jha
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - Fedor Kouzine
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
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5
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Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Is There a Histone Code for Cellular Quiescence? Front Cell Dev Biol 2021; 9:739780. [PMID: 34778253 PMCID: PMC8586460 DOI: 10.3389/fcell.2021.739780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022] Open
Abstract
Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
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Affiliation(s)
- Kenya Bonitto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kirthana Sarathy
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kaiser Atai
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mithun Mitra
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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6
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Duprey A, Groisman EA. The regulation of DNA supercoiling across evolution. Protein Sci 2021; 30:2042-2056. [PMID: 34398513 PMCID: PMC8442966 DOI: 10.1002/pro.4171] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 11/11/2022]
Abstract
DNA supercoiling controls a variety of cellular processes, including transcription, recombination, chromosome replication, and segregation, across all domains of life. As a physical property, DNA supercoiling alters the double helix structure by under- or over-winding it. Intriguingly, the evolution of DNA supercoiling reveals both similarities and differences in its properties and regulation across the three domains of life. Whereas all organisms exhibit local, constrained DNA supercoiling, only bacteria and archaea exhibit unconstrained global supercoiling. DNA supercoiling emerges naturally from certain cellular processes and can also be changed by enzymes called topoisomerases. While structurally and mechanistically distinct, topoisomerases that dissipate excessive supercoils exist in all domains of life. By contrast, topoisomerases that introduce positive or negative supercoils exist only in bacteria and archaea. The abundance of topoisomerases is also transcriptionally and post-transcriptionally regulated in domain-specific ways. Nucleoid-associated proteins, metabolites, and physicochemical factors influence DNA supercoiling by acting on the DNA itself or by impacting the activity of topoisomerases. Overall, the unique strategies that organisms have evolved to regulate DNA supercoiling hold significant therapeutic potential, such as bactericidal agents that target bacteria-specific processes or anticancer drugs that hinder abnormal DNA replication by acting on eukaryotic topoisomerases specialized in this process. The investigation of DNA supercoiling therefore reveals general principles, conserved mechanisms, and kingdom-specific variations relevant to a wide range of biological questions.
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Affiliation(s)
- Alexandre Duprey
- Department of Microbial PathogenesisYale School of MedicineNew HavenConnecticutUSA
| | - Eduardo A. Groisman
- Department of Microbial PathogenesisYale School of MedicineNew HavenConnecticutUSA
- Yale Microbial Sciences InstituteWest HavenConnecticutUSA
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7
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Lloyd JT, McLaughlin K, Lubula MY, Gay JC, Dest A, Gao C, Phillips M, Tonelli M, Cornilescu G, Marunde MR, Evans CM, Boyson SP, Carlson S, Keogh MC, Markley JL, Frietze S, Glass KC. Structural Insights into the Recognition of Mono- and Diacetylated Histones by the ATAD2B Bromodomain. J Med Chem 2020; 63:12799-12813. [PMID: 33084328 DOI: 10.1021/acs.jmedchem.0c01178] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bromodomains exhibit preferences for specific patterns of post-translational modifications on core and variant histone proteins. We examined the ligand specificity of the ATAD2B bromodomain and compared it to its closely related paralogue in ATAD2. We show that the ATAD2B bromodomain recognizes mono- and diacetyllysine modifications on histones H4 and H2A. A structure-function approach was used to identify key residues in the acetyllysine-binding pocket that dictate the molecular recognition process, and we examined the binding of an ATAD2 bromodomain inhibitor by ATAD2B. Our analysis demonstrated that critical contacts required for bromodomain inhibitor coordination are conserved between the ATAD2/B bromodomains, with many residues playing a dual role in acetyllysine recognition. We further characterized an alternative splice variant of ATAD2B that results in a loss of function. Our results outline the structural and functional features of the ATAD2B bromodomain and identify a novel mechanism regulating the interaction of the ATAD2B protein with chromatin.
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Affiliation(s)
- Jonathan T Lloyd
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Kyle McLaughlin
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Mulu Y Lubula
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Jamie C Gay
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Andrea Dest
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Margaret Phillips
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Chiara M Evans
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Samuel P Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | | | - John L Markley
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Karen C Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
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8
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Marrocco J, Einhorn NR, McEwen BS. Environmental epigenetics of sex differences in the brain. HANDBOOK OF CLINICAL NEUROLOGY 2020; 175:209-220. [PMID: 33008526 DOI: 10.1016/b978-0-444-64123-6.00015-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Experiences throughout the life course lead to unique phenotypes even among those with the same genotype. Genotype sets the substrate on which physiologic processes, which communicate with the brain, mediate the effects of life experiences via epigenetics. Epigenetics modify the expression of genes in the brain and body in response to circulating hormones and other mediators, which are activated to facilitate survival responses through a process called allostasis. Epigenetic signatures can even be inherited, resulting in transgenerational effects. This chapter addresses epigenetics in the context of sex differences, discussing the intersection between genetics and gonadal hormones and their effect in the brain at discrete developmental periods.
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Affiliation(s)
- Jordan Marrocco
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, Rockefeller University, New York, NY, United States.
| | - Nathan R Einhorn
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, Rockefeller University, New York, NY, United States
| | - Bruce S McEwen
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, Rockefeller University, New York, NY, United States
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9
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Tafessu A, Banaszynski LA. Establishment and function of chromatin modification at enhancers. Open Biol 2020; 10:200255. [PMID: 33050790 PMCID: PMC7653351 DOI: 10.1098/rsob.200255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
How a single genome can give rise to distinct cell types remains a fundamental question in biology. Mammals are able to specify and maintain hundreds of cell fates by selectively activating unique subsets of their genome. This is achieved, in part, by enhancers-genetic elements that can increase transcription of both nearby and distal genes. Enhancers can be identified by their unique chromatin signature, including transcription factor binding and the enrichment of specific histone post-translational modifications, histone variants, and chromatin-associated cofactors. How each of these chromatin features contributes to enhancer function remains an area of intense study. In this review, we provide an overview of enhancer-associated chromatin states, and the proteins and enzymes involved in their establishment. We discuss recent insights into the effects of the enhancer chromatin state on ongoing transcription versus their role in the establishment of new transcription programmes, such as those that occur developmentally. Finally, we highlight the role of enhancer chromatin in new conceptual advances in gene regulation such as condensate formation.
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Affiliation(s)
| | - Laura A. Banaszynski
- UT Southwestern Medical Center, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390-8511, USA
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10
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Kantidze OL, Razin SV. Weak interactions in higher-order chromatin organization. Nucleic Acids Res 2020; 48:4614-4626. [PMID: 32313950 PMCID: PMC7229822 DOI: 10.1093/nar/gkaa261] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein-protein and protein-DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.
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Affiliation(s)
- Omar L Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
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11
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Audugé N, Padilla-Parra S, Tramier M, Borghi N, Coppey-Moisan M. Chromatin condensation fluctuations rather than steady-state predict chromatin accessibility. Nucleic Acids Res 2020; 47:6184-6194. [PMID: 31081027 PMCID: PMC6614833 DOI: 10.1093/nar/gkz373] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/24/2019] [Accepted: 05/07/2019] [Indexed: 01/16/2023] Open
Abstract
Chromatin accessibility to protein factors is critical for genome activities. However, the dynamic properties of chromatin higher-order structures that regulate its accessibility are poorly understood. Here, we took advantage of the microenvironment sensitivity of the fluorescence lifetime of EGFP-H4 histone incorporated in chromatin to map in the nucleus of live cells the dynamics of chromatin condensation and its direct interaction with a tail acetylation recognition domain (the double bromodomain module of human TAFII250, dBD). We reveal chromatin condensation fluctuations supported by mechanisms fundamentally distinct from that of condensation. Fluctuations are spontaneous, yet their amplitudes are affected by their sub-nuclear localization and by distinct and competing mechanisms dependent on histone acetylation, ATP and both. Moreover, we show that accessibility of acetylated histone H4 to dBD is not restricted by chromatin condensation nor predicted by acetylation, rather, it is predicted by chromatin condensation fluctuations.
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Affiliation(s)
- Nicolas Audugé
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
| | - Sergi Padilla-Parra
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
| | - Marc Tramier
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
| | - Nicolas Borghi
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
| | - Maïté Coppey-Moisan
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
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12
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Reynolds DA, Yoo MJ, Dixson DL, Ross C. Exposure to the Florida red tide dinoflagellate, Karenia brevis, and its associated brevetoxins induces ecophysiological and proteomic alterations in Porites astreoides. PLoS One 2020; 15:e0228414. [PMID: 32032360 PMCID: PMC7006924 DOI: 10.1371/journal.pone.0228414] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/14/2020] [Indexed: 01/27/2023] Open
Abstract
As reef-building corals are increasingly being exposed to persistent threats that operate on both regional and global scales, there is a pressing need to better understand the complex processes that diminish coral populations. This study investigated the impacts of the Florida red tide dinoflagellate Karenia brevis and associated brevetoxins on selected facets of coral biology using Porites astreoides as a model system. When provided with choice assays, P. astreoides larvae were shown to actively avoid seawater containing red tide (5×105 cells L-1–7.6×106 cells L-1) or purified brevetoxins (0.018 μg mL-1 brevetoxin-2 and 0.0018 μg mL-1 brevetoxin-3). However, forced exposure to similar treatments induced time-dependent physiological and behavioral changes that were captured by PAM fluorometry and settlement and survival assays, respectively. Adult fragments of P. astreoides exposed to red tide or associated brevetoxins displayed signs of proteomic alterations that were characterized by the use of an iTRAQ-based quantitative proteomic analysis. The novel use of this technique with P. astreoides demonstrated that protein regulation was highly contingent upon biological versus chemical treatment (i.e. live K. brevis vs. solely brevetoxin exposure) and that several broad pathways associated with cell stress were affected including redox homeostasis, protein folding, energy metabolism and reactive oxygen species production. The results herein provide new insight into the ecology, behavior and sublethal stress of reef-building corals in response to K. brevis exposure and underscore the importance of recognizing the potential of red tide to act as a regional stressor to these important foundation species.
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Affiliation(s)
- David A. Reynolds
- Department of Biology, University of North Florida, Jacksonville, Florida, United States of America
| | - Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, United States of America
| | - Danielle L. Dixson
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, United States of America
| | - Cliff Ross
- Department of Biology, University of North Florida, Jacksonville, Florida, United States of America
- * E-mail:
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13
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Ando H, Horibata Y, Aoyama C, Shimizu H, Shinohara Y, Yamashita S, Sugimoto H. Side-chain oxysterols suppress the transcription of CTP: Phosphoethanolamine cytidylyltransferase and 3-hydroxy-3-methylglutaryl-CoA reductase by inhibiting the interaction of p300 and NF-Y, and H3K27 acetylation. J Steroid Biochem Mol Biol 2019; 195:105482. [PMID: 31580889 DOI: 10.1016/j.jsbmb.2019.105482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/10/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
Abstract
CTP: phosphoethanolamine cytidylyltransferase (Pcyt2) is the rate-limiting enzyme in mammalian phosphatidylethanolamine (PE) biosynthesis. Previously, we reported that increasedPcyt2 mRNA levels after serum starvation are suppressed by 25-hydroxycholesterol (HC) (25-HC), and that nuclear factor-Y (NF-Y) is involved in the inhibitory effects. Transcription of Hmgcr, which encodes 3-hydroxy-3-methylglutaryl-CoA reductase, is suppressed in the same manner. However, no typical sterol regulatory element (SRE) was detected in the Pcyt2 promoter. We were therefore interested in the effect of 25-HC on the modification of histones and thus treated cells with histone acetyltransferase inhibitor (anacardic acid) or histone deacetylase inhibitor (trichostatin A). The suppressive effect of 25-HC on Pcyt2 and Hmgcr mRNA transcription was ameliorated by trichostatin A. Anacardic acid, 25-HC and 24(S)-HC suppressed their transcription by inhibiting H3K27 acetylation in their promoters as evaluated by chromatin immunoprecipitation (ChIP) assays. 27-HC, 22(S)-HC and 22(R)-HC also suppressed their transcription, but 7α-HC, 7β-HC, the synthetic LXR agonist T0901317 and cholesterol did not. Furthermore, 25-HC inhibited p300 recruitment to the Pcyt2 and Hmgcr promoters, and suppressed H3K27 acetylation. 25-HC in the medium was easily conducted into cells. Based on these results, we concluded that 25-HC (and other side-chain oxysterols) in the medium was easily transferred into cells, suppressed H3K27 acetylation via p300 recruitment on the NF-Y complex in the Pcyt2 and Hmgcr promoters, and then suppressed transcription of these genes although LXR is not involved.
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Affiliation(s)
- Hiromi Ando
- Department of Biochemistry, Dokkyo Medical University School of Medicine, Mibu 321-0293, Japan
| | - Yasuhiro Horibata
- Department of Biochemistry, Dokkyo Medical University School of Medicine, Mibu 321-0293, Japan
| | - Chieko Aoyama
- Department of Biochemistry, Dokkyo Medical University School of Medicine, Mibu 321-0293, Japan
| | - Hiroaki Shimizu
- Department of Biochemistry, Dokkyo Medical University School of Medicine, Mibu 321-0293, Japan
| | - Yasutake Shinohara
- Department of Biochemistry, Dokkyo Medical University School of Medicine, Mibu 321-0293, Japan
| | - Satoko Yamashita
- Department of Biochemistry, Dokkyo Medical University School of Medicine, Mibu 321-0293, Japan
| | - Hiroyuki Sugimoto
- Department of Biochemistry, Dokkyo Medical University School of Medicine, Mibu 321-0293, Japan.
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14
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Ming J, Wu S, You T, Wang X, Yu C, Luo P, Zhang A, Pan X. Histone Deacetylation in the Promoter of p16 Is Involved in Fluoride-Induced Human Osteoblast Activation via the Inhibition of Sp1 Binding. Biol Trace Elem Res 2019; 188:373-383. [PMID: 29931577 DOI: 10.1007/s12011-018-1413-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/07/2018] [Indexed: 01/22/2023]
Abstract
Chronic fluorosis is a systemic condition which principally manifests as defects in the skeleton and teeth. Skeletal fluorosis is characterized by aberrant proliferation and activation of osteoblasts, however, the underlying mechanisms of osteoblast activation induced by fluoride are not fully understood. Therefore, we investigated the pathogenic mechanism of human primary osteoblast proliferation and activation in relation to histone acetylation of the promoter p16, a well-known cell cycle regulation-related gene. The results showed that sodium fluoride (NaF) induced deacetylation and decreased expression of the p16 gene via inhibition of specificity protein 1 (Sp1) binding to its response element, which accounts for NaF increasing cell viability and promoting proliferation in human primary osteoblasts. These results reveal the regulatory mechanism of histone acetylation of the p16 gene on osteoblast activation in skeletal fluorosis.
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Affiliation(s)
- Juan Ming
- Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Shouli Wu
- Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Tongzhao You
- Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Xilan Wang
- Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Chun Yu
- Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Peng Luo
- Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Aihua Zhang
- Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Xueli Pan
- Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, China.
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China.
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15
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Bennett SA, Tanaz R, Cobos SN, Torrente MP. Epigenetics in amyotrophic lateral sclerosis: a role for histone post-translational modifications in neurodegenerative disease. Transl Res 2019; 204:19-30. [PMID: 30391475 PMCID: PMC6331271 DOI: 10.1016/j.trsl.2018.10.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/26/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is the third most common adult onset neurodegenerative disorder worldwide. It is generally characterized by progressive paralysis starting at the limbs ultimately leading to death caused by respiratory failure. There is no cure and current treatments fail to slow the progression of the disease. As such, new treatment options are desperately needed. Epigenetic targets are an attractive possibility because they are reversible. Epigenetics refers to heritable changes in gene expression unrelated to changes in DNA sequence. Three main epigenetic mechanisms include the methylation of DNA, microRNAs and the post-translational modification of histone proteins. Histone modifications occur in many amino acid residues and include phosphorylation, acetylation, methylation as well as other chemical moieties. Recent evidence points to a possible role for epigenetic mechanisms in the etiology of ALS. Here, we review recent advances linking ALS and epigenetics, with a strong focus on histone modifications. Both local and global changes in histone modification profiles are associated with ALS drawing attention to potential targets for future diagnostic and treatment approaches.
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Affiliation(s)
- Seth A Bennett
- Department of Chemistry, Brooklyn College, Brooklyn, NewYork; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York
| | - Royena Tanaz
- Department of Chemistry, Brooklyn College, Brooklyn, NewYork
| | - Samantha N Cobos
- Department of Chemistry, Brooklyn College, Brooklyn, NewYork; Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016
| | - Mariana P Torrente
- Department of Chemistry, Brooklyn College, Brooklyn, NewYork; Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, New York.
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16
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Beayno A, El Hayek S, Noufi P, Tarabay Y, Shamseddeen W. The Role of Epigenetics in Addiction: Clinical Overview and Recent Updates. Methods Mol Biol 2019; 2011:609-631. [PMID: 31273724 DOI: 10.1007/978-1-4939-9554-7_35] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Addiction is an international public health problem. It is a polygenic disorder best understood by accounting for the interplay between genetic and environmental factors. A recent way of perceiving this interaction is through epigenetics, which help grasp the neurobiological changes that occur in addiction and explain its relapsing-remitting nature. It is now known that every cell has a different way of expressing its phenotype, despite a universal DNA sequence. This is particularly true in the central nervous system where environmental factors influence this expression. Three major epigenetic processes have been found to participate in the perpetuation of addiction by changing the state of the chromatin and the degree of gene transcription: histone acetylation and methylation, DNA methylation, and noncoding RNAs. In the animal model literature, substantial evidence exists about the role of these epigenetic changes in the different phases of substance use disorders. This book chapter is a non-systematic literature review of the recent publications tackling the topic of epigenetics in addiction. Even though this evidence remains scarce and relatively poorly systematized, it is a promising foundation for future research of molecules that target specific brain regions and their functions to address core behavioral changes seen in addiction.
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Affiliation(s)
- Antoine Beayno
- Department of Psychiatry, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Samer El Hayek
- Department of Psychiatry, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Paul Noufi
- Department of Psychiatry, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Yara Tarabay
- Faculty of Pedagogy, Lebanese University, New Rawda, Lebanon.,Faculty of Natural and Applied Sciences, Notre Dame University, Louaize, Lebanon
| | - Wael Shamseddeen
- Department of Psychiatry, Faculty of Medicine, American University of Beirut, Beirut, Lebanon. .,Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA.
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17
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Intracellular nucleosomes constrain a DNA linking number difference of -1.26 that reconciles the Lk paradox. Nat Commun 2018; 9:3989. [PMID: 30266901 PMCID: PMC6162219 DOI: 10.1038/s41467-018-06547-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/11/2018] [Indexed: 02/07/2023] Open
Abstract
The interplay between chromatin structure and DNA topology is a fundamental, yet elusive, regulator of genome activities. A paradigmatic case is the “linking number paradox” of nucleosomal DNA, which refers to the incongruence between the near two left-handed superhelical turns of DNA around the histone octamer and the DNA linking number difference (∆Lk) stabilized by individual nucleosomes, which has been experimentally estimated to be about −1.0. Here, we analyze the DNA topology of a library of mononucleosomes inserted into small circular minichromosomes to determine the average ∆Lk restrained by individual nucleosomes in vivo. Our results indicate that most nucleosomes stabilize about −1.26 units of ∆Lk. This value balances the twist (∆Tw ≈ + 0.2) and writhe (∆Wr ≈ −1.5) deformations of nucleosomal DNA in terms of the equation ∆Lk = ∆Tw + ∆Wr. Our finding reconciles the existing discrepancy between theoretical and observed measurement of the ΔLk constrained by nucleosomes. There had been an enduring discrepancy between theoretical and observed measurement of the DNA linking number (∆Lk) constrained by nucleosomes. Here the authors provide measurements of the ∆Lk constrained by individual nucleosomes in native chromatin that reconcile this discrepancy.
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18
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Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes. Genome Res 2018; 28:1494-1507. [PMID: 30154222 PMCID: PMC6169895 DOI: 10.1101/gr.237180.118] [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: 03/16/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022]
Abstract
Polycomb group (PcG) proteins are transcriptional repressors that play important roles in regulating gene expression during animal development. In vitro experiments have shown that PcG protein complexes can compact chromatin to limit the activity of chromatin remodeling enzymes and access of the transcriptional machinery to DNA. In fitting with these ideas, gene promoters associated with PcG proteins have been reported to be less accessible than other gene promoters. However, it remains largely untested in vivo whether PcG proteins define chromatin accessibility or other chromatin features. To address this important question, we examine the chromatin accessibility and nucleosome landscape at PcG protein-bound promoters in mouse embryonic stem cells using the assay for transposase accessible chromatin (ATAC)-seq. Combined with genetic ablation strategies, we unexpectedly discover that although PcG protein-occupied gene promoters exhibit reduced accessibility, this does not rely on PcG proteins. Instead, the Polycomb repressive complex 1 (PRC1) appears to play a unique role in driving elevated nucleosome occupancy and decreased nucleosomal spacing in Polycomb chromatin domains. Our new genome-scale observations argue, in contrast to the prevailing view, that PcG proteins do not significantly affect chromatin accessibility and highlight an underappreciated complexity in the relationship between chromatin accessibility, the nucleosome landscape, and PcG-mediated transcriptional repression.
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19
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Takesue H, Hirota T, Tachimura M, Tokashiki A, Ieiri I. Nucleosome Positioning and Gene Regulation of the SGLT2 Gene in the Renal Proximal Tubular Epithelial Cells. Mol Pharmacol 2018; 94:953-962. [DOI: 10.1124/mol.118.111807] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/27/2018] [Indexed: 11/22/2022] Open
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20
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Evidence for the implication of the histone code in building the genome structure. Biosystems 2018; 164:49-59. [DOI: 10.1016/j.biosystems.2017.11.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
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21
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Zhang C, Zhai Z, Tang M, Cheng Z, Li T, Wang H, Zhu WG. Quantitative proteome-based systematic identification of SIRT7 substrates. Proteomics 2017; 17. [PMID: 28556401 DOI: 10.1002/pmic.201600395] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 12/22/2022]
Abstract
SIRT7 is a class III histone deacetylase that is involved in numerous cellular processes. Only six substrates of SIRT7 have been reported thus far, so we aimed to systematically identify SIRT7 substrates using stable-isotope labeling with amino acids in cell culture (SILAC) coupled with quantitative mass spectrometry (MS). Using SIRT7+/+ and SIRT7-/- mouse embryonic fibroblasts as our model system, we identified and quantified 1493 acetylation sites in 789 proteins, of which 261 acetylation sites in 176 proteins showed ≥2-fold change in acetylation state between SIRT7-/- and SIRT7+/+ cells. These proteins were considered putative SIRT7 substrates and were carried forward for further analysis. We then validated the predictive efficiency of the SILAC-MS experiment by assessing substrate acetylation status in vitro in six predicted proteins. We also performed a bioinformatic analysis of the MS data, which indicated that many of the putative protein substrates were involved in metabolic processes. Finally, we expanded our list of candidate substrates by performing a bioinformatics-based prediction analysis of putative SIRT7 substrates, using our list of putative substrates as a positive training set, and again validated a subset of the proteins in vitro. In summary, we have generated a comprehensive list of SIRT7 candidate substrates.
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Affiliation(s)
- Chaohua Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P. R. China
| | - Zichao Zhai
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P. R. China
| | - Ming Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P. R. China.,Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, P. R. China
| | - Zhongyi Cheng
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou, P. R. China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P. R. China
| | - Haiying Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P. R. China
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P. R. China.,Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, P. R. China.,Peking University-Tsinghua University Center for Life Sciences, Beijing, P. R. China
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22
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Guo Z, Lv L, Liu D, Fu B. Effects of trichostatin A on pig SCNT blastocyst formation rate and cell number: A meta-analysis. Res Vet Sci 2017; 117:161-166. [PMID: 29277014 DOI: 10.1016/j.rvsc.2017.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/20/2017] [Accepted: 12/17/2017] [Indexed: 12/21/2022]
Abstract
Although somatic cell nuclear transfer (SCNT) can be used to create transgenic pigs for human xenotransplantation, low efficiency limits its use. Trichostatin A (TSA) promotes SCNT embryo development, but whether TSA modifies SCNT blastocyst numbers is unclear. Thus, there is an urgent need to understand whether TSA modifies the rate and number of embryos that grow from oocytes to blastocysts in culture and what types of cell signaling pathways may be involved. Thus, we identified 63 reports, of which 13 are included in this meta-analysis. Data show that TSA significantly increased the SCNT blastocyst formation rate, but did not change blastocyst cell number. Due to study heterogeneity (I2>50%), we hypothesized that donor cells were of different backgrounds so we analyzed two donor cell subgroups: fetal and adult fibroblasts. Analysis of the fetal fibroblast subgroups showed no heterogeneity, but the adult fibroblast subgroups were heterogeneous, suggesting epigenetic reprogramming of fetal fibroblasts by TSA. Adult fibroblast heterogeneity may be complex and reprogramming by TSA is more difficult. Thus, TSA fibroblasts reprogramming is the source of heterogeneity in this meta-analysis. More work is needed to better understand how TSA influences SCNT pig embryonic development, and histone deacetylase inhibitors can be assessed with respect to SCNT pig embryos. Finally, efforts in epigenetic research may improve SCNT pig embryo outcomes.
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Affiliation(s)
- Zhenhua Guo
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Animal Husbandry Research Institute, Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, No. 368 Xuefu Road, Harbin 150086, PR China; Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation, Ministry of Agriculture, No. 2 Yuanmingyuanxi Road, Beijing 100193, PR China
| | - Lei Lv
- Wood Science Research Institute of Heilongjiang Academy of Forestry, No. 134 Haping Road, Harbin 150080, PR China
| | - Di Liu
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Animal Husbandry Research Institute, Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, No. 368 Xuefu Road, Harbin 150086, PR China.
| | - Bo Fu
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Animal Husbandry Research Institute, Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, No. 368 Xuefu Road, Harbin 150086, PR China
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23
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Nikitina T, Norouzi D, Grigoryev SA, Zhurkin VB. DNA topology in chromatin is defined by nucleosome spacing. SCIENCE ADVANCES 2017; 3:e1700957. [PMID: 29098179 PMCID: PMC5659657 DOI: 10.1126/sciadv.1700957] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/27/2017] [Indexed: 06/07/2023]
Abstract
In eukaryotic nucleosomes, DNA makes ~1.7 superhelical turns around histone octamer. However, there is a long-standing discrepancy between the nucleosome core structure determined by x-ray crystallography and measurements of DNA topology in circular minichromosomes, indicating that there is only ~1.0 superhelical turn per nucleosome. Although several theoretical assumptions were put forward to explain this paradox by conformational variability of the nucleosome linker, none was tested experimentally. We analyzed topological properties of DNA in circular nucleosome arrays with precisely positioned nucleosomes. Using topological electrophoretic assays and electron microscopy, we demonstrate that the DNA linking number per nucleosome strongly depends on the nucleosome spacing and varies from -1.4 to -0.9. For the predominant {10n + 5} class of nucleosome repeats found in native chromatin, our results are consistent with the DNA topology observed earlier. Thus, we reconcile the topological properties of nucleosome arrays with nucleosome core structure and provide a simple explanation for the DNA topology in native chromatin with variable DNA linker length. Topological polymorphism of the chromatin fibers described here may reflect a more general tendency of chromosomal domains containing active or repressed genes to acquire different nucleosome spacing to retain topologically distinct higher-order structures.
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Affiliation(s)
- Tatiana Nikitina
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davood Norouzi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergei A. Grigoryev
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Victor B. Zhurkin
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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24
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Cheng-Sánchez I, García-Ruiz C, Guerrero-Vásquez GA, Sarabia F. An Olefin Cross-Metathesis Approach to Depudecin and Stereoisomeric Analogues. J Org Chem 2017; 82:4744-4757. [PMID: 28397496 DOI: 10.1021/acs.joc.7b00424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new total synthesis of the natural product (-)-depudecin, a unique and unexplored histone deacetylase (HDAC) inhibitor, is reported. A key feature of the synthesis is the utilization of an olefin cross-metathesis strategy, which provides for an efficient and improved access to natural depudecin, compared with our previous linear synthesis. Featured by its brevity and convergency, our developed synthetic strategy was applied to the preparation of the 10-epi derivative and the enantiomer of depudecin, which represent interesting stereoisomeric analogues for structure-activity relationship studies.
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Affiliation(s)
- Iván Cheng-Sánchez
- Department of Organic Chemistry, Faculty of Sciences, University of Malaga , Campus de Teatinos s/n, 29071, Malaga, Spain
| | - Cristina García-Ruiz
- Department of Organic Chemistry, Faculty of Sciences, University of Malaga , Campus de Teatinos s/n, 29071, Malaga, Spain
| | - Guillermo A Guerrero-Vásquez
- Department of Organic Chemistry, Faculty of Sciences, University of Malaga , Campus de Teatinos s/n, 29071, Malaga, Spain
| | - Francisco Sarabia
- Department of Organic Chemistry, Faculty of Sciences, University of Malaga , Campus de Teatinos s/n, 29071, Malaga, Spain
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25
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Vlijm R, Kim SH, De Zwart PL, Dalal Y, Dekker C. The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes. NANOSCALE 2017; 9:1862-1870. [PMID: 28094382 PMCID: PMC7959483 DOI: 10.1039/c6nr06245h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness of the DNA wrapping around the nucleosome core is intrinsically ambidextrous, and depends on the pre-assembly supercoiling state of the DNA, i.e., it is not uniquely determined by the octameric histone core. Nucleosomes assembled onto negatively supercoiled DNA are found to exhibit a left-handed conformation, whereas assembly onto positively supercoiled DNA results in right-handed nucleosomes. This intrinsic flexibility to adopt both chiralities is observed both for canonical H3 nucleosomes, and for centromere-specific variant CENP-A nucleosomes. These data support recent advances suggesting an intrinsic adaptability of the nucleosome, and provide insights into how nucleosomes might rapidly re-assemble after cellular processes that generate positive supercoiling in vivo.
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Affiliation(s)
- R Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - S H Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - P L De Zwart
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - Y Dalal
- Chromatin Structure and Epigenetic Mechanisms Unit, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - C Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
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26
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Bi X, Ren Y, Kath M. Proliferating cell nuclear antigen (PCNA) contributes to the high-order structure and stability of heterochromatin in Saccharomyces cerevisiae. Chromosome Res 2016; 25:89-100. [PMID: 27987109 DOI: 10.1007/s10577-016-9540-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 11/29/2016] [Accepted: 12/02/2016] [Indexed: 10/20/2022]
Abstract
Heterochromatin plays important roles in the structure, maintenance, and function of the eukaryotic genome. It is associated with special histone modifications and specialized non-histone proteins and assumes a more compact structure than euchromatin. Genes embedded in heterochromatin are generally transcriptionally silent. It was found previously that several mutations of proliferating cell nuclear antigen (PCNA), a DNA replication processivity factor, reduce transcriptional silencing at heterochromatin loci in Saccharomyces cerevisiae. However, the notion that PCNA plays a role in transcriptional silencing was recently questioned because of a potential problem concerning the silencing assays used in prior studies. To determine if PCNA is a bona fide contributor to heterochromatin-mediated transcriptional silencing, we examined the effects of PCNA mutations on heterochromatin structure. We found evidence implicating PCNA in the maintenance of the high-order structure and stability of heterochromatin, which indicates a role of DNA replication in heterochromatin maintenance.
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Affiliation(s)
- Xin Bi
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
| | - Yue Ren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Morgan Kath
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
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27
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Tomar JS, Peddinti RK. A. baumannii histone acetyl transferase Hpa2: optimization of homology modeling, analysis of protein-protein interaction and virtual screening. J Biomol Struct Dyn 2016; 35:1115-1126. [PMID: 27125865 DOI: 10.1080/07391102.2016.1172025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the current scenario, widespread multidrug resistivity in ESKAPE pathogens demands identification of novel drug targets to keep their infections at bay. For this purpose, we have identified a novel target Hpa2 of A. baumannii, a member of GNAT superfamily of HATs. But due to sequence identity of equal or less than 35%, the correct sequence alignment and construction of 3D monomeric and dimeric models of Hpa2 having optimal structural parameters is a troublesome task. To circumvent these problems, we have designed an easy and optimized protocol for Hpa2 monomer modeling, and for generation of dimeric Hpa2 model using data-driven protein-protein docking experiment. Improvement in the structural features of generated model is an onerous process and generally achieved by paying time and computational cost. Herein, it is achieved by reconciliation of FoldX commands which takes less time in execution. Evaluations performed to validate structural parameters and stability of monomeric and dimeric Hpa2 attests to its quality. Analysis of interfacial residues, energy terms and RMSD values indicated a clear correlation between experimental and theoretical interface properties of the dimers, corroborating to the regime used for Hpa2 dimer generation. Structural information from the refined models was used for virtual screening of substrate-derived library and polyamines to achieve a new platform for developing A. baumannii inhibitory molecules. Molecules showing preferential binding at the dimer interface could be used as allosteric inhibitors. Binding of polyamines with model illustrated the same binding pattern as described experimentally in case of yeast Hpa2.
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Affiliation(s)
- Jyoti Singh Tomar
- a Department of Chemistry , Indian Institute of Technology Roorkee , Roorkee 247667 , Uttarakhand , India
| | - Rama Krishna Peddinti
- a Department of Chemistry , Indian Institute of Technology Roorkee , Roorkee 247667 , Uttarakhand , India
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28
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Plagg B, Ehrlich D, Kniewallner KM, Marksteiner J, Humpel C. Increased Acetylation of Histone H4 at Lysine 12 (H4K12) in Monocytes of Transgenic Alzheimer's Mice and in Human Patients. Curr Alzheimer Res 2016; 12:752-60. [PMID: 26159193 DOI: 10.2174/1567205012666150710114256] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/30/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is a neurodegenerative disorder characterized by amyloid-β (Aβ) plaque formation, tau pathology, neurodegeneration and inflammatory processes. Monocytes are involved in inflammation in AD and are recruited to the diseased brain. Recently it has been shown that aberrant epigenetic processes including acetylation are associated with the development of AD. The aim of the present study was to examine acetylation of histone H4 at lysine 12 (H4K12) in monocytes in two transgenic AD mouse models (the triple transgenic 3xTg and a model overexpressing amyloid-precursor protein APP with the Swedish-Dutch-Iowa mutations), and to compare with monocytes isolated from human patients with mild cognitive impairment (MCI) and AD. METHODS Mouse and human monocytes were selectively isolated with a positive (PluriSelect) respectively with a negative selection method (Miltenyi). Histones were extracted and acetylation of H4K12 was analyzed by a quantification fluorometric kit. Moreover, monocyte cytokine release was measured and cell death analyzed by FACS using incorporation of 7-AAD. RESULTS Our data show a significant increase of monocytic H4K12 acetylation in both transgenic AD mouse models early during development of the plaque deposition in the brain. In line with these data we found significantly elevated acetylation of H4K12 in human patients with MCI but not in patients with AD. Further we observed that the monocytes of AD mice and of AD patients were significantly more vulnerable to cell damage (as seen by 7-AAD incorporation in FACS analysis) and displayed an enhanced release of pro-inflammatory cytokines (MIP2 and TNFα). CONCLUSION Our findings indicate that epigenetic changes in peripheral monocytes are an early event in AD-pathology. Thus H4K12 acetylation may be considered as a novel biomarker for early changes in AD development.
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Affiliation(s)
| | | | | | | | - Christian Humpel
- Department of Psychiatry and Psychotherapy, Anichstr. 35, A-6020 Innsbruck, Austria.
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Zhang F, Huang Q, Yan J, Chen Z. Histone Acetylation Induced Transformation of B-DNA to Z-DNA in Cells Probed through FT-IR Spectroscopy. Anal Chem 2016; 88:4179-82. [DOI: 10.1021/acs.analchem.6b00400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fengqiu Zhang
- Institute
of Technical Biology and Agriculture Engineering, Hefei Institutes
of Physical Science, Key Laboratory
of Ion-beam Bioengineering, Chinese Academy of Sciences, Hefei, China
- School of Nuclear Science and Technology, University of Science & Technology of China, Hefei, China
- Henan
Key Laboratory of Ion-beam Bioengineering, School of Physical Engineering, Zhengzhou University, Zhengzhou, China
| | - Qing Huang
- Institute
of Technical Biology and Agriculture Engineering, Hefei Institutes
of Physical Science, Key Laboratory
of Ion-beam Bioengineering, Chinese Academy of Sciences, Hefei, China
- School of Nuclear Science and Technology, University of Science & Technology of China, Hefei, China
| | - Jingwen Yan
- Institute
of Technical Biology and Agriculture Engineering, Hefei Institutes
of Physical Science, Key Laboratory
of Ion-beam Bioengineering, Chinese Academy of Sciences, Hefei, China
| | - Zhu Chen
- Institute
of Technical Biology and Agriculture Engineering, Hefei Institutes
of Physical Science, Key Laboratory
of Ion-beam Bioengineering, Chinese Academy of Sciences, Hefei, China
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30
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Norouzi D, Zhurkin VB. Topological polymorphism of the two-start chromatin fiber. Biophys J 2016; 108:2591-2600. [PMID: 25992737 DOI: 10.1016/j.bpj.2015.04.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/07/2015] [Accepted: 04/15/2015] [Indexed: 12/16/2022] Open
Abstract
Specific details concerning the spatial organization of nucleosomes in 30 nm fibers remain unknown. To investigate this, we analyzed all stereochemically possible configurations of two-start nucleosome fibers with short DNA linkers L = 13-37 bp (nucleosome repeat length (NRL) = 160-184 bp). Four superhelical parameters-inclination of nucleosomes, twist, rise, and diameter-uniquely describe a regular symmetric fiber. The energy of a fiber is defined as the sum of four terms: elastic energy of the linker DNA, steric repulsion, electrostatics, and a phenomenological (H4 tail-acidic patch) interaction between two stacked nucleosomes. By optimizing the fiber energy with respect to the superhelical parameters, we found two types of topological transition in fibers (associated with the change in inclination angle): one caused by an abrupt 360° change in the linker DNA twisting (change in the DNA linking number, ΔLk = 1), and another caused by overcrossing of the linkers (ΔLk = 2). To the best of our knowledge, this topological polymorphism of the two-start fibers was not reported in the computations published earlier. Importantly, the optimal configurations of the fibers with linkers L = 10n and 10n + 5 bp are characterized by different values of the DNA linking number-that is, they are topologically different. Our results are consistent with experimental observations, such as the inclination 60° to 70° (the angle between the nucleosomal disks and the fiber axis), helical rise, diameter, and left-handedness of the fibers. In addition, we make several testable predictions, among them different degrees of DNA supercoiling in fibers with L = 10n and 10n + 5 bp, different flexibility of the two types of fibers, and a correlation between the local NRL and the level of transcription in different parts of the yeast genome.
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Affiliation(s)
- Davood Norouzi
- Laboratory of Cell Biology, National Cancer Institute NIH, Bethesda, Maryland
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute NIH, Bethesda, Maryland.
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31
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Krajewski WA. Mobilization of hyperacetylated mononucleosomes by purified yeast ISW2 in vitro. Arch Biochem Biophys 2015; 591:1-6. [PMID: 26692330 DOI: 10.1016/j.abb.2015.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/02/2015] [Accepted: 12/10/2015] [Indexed: 11/26/2022]
Abstract
Catalytic activity of ISWI chromatin remodelers, which regulate nucleosome positioning on the DNA, depends on interactions of the putative acidic patch in ISWI helicase domain with the N-termini of nucleosomal H4--such, that removal of H4 termini abolishes ISWI remodeling. Acetylation of H4 termini is also known to disrupt H4 interactions with acidic protein surfaces, and thus, histone acetylation could potentially impede ISWI functions. Since active chromatin in vivo is hyperacetylated, it is important to clarify if ISWI activities can function on the in vivo hyperacetylated nucleosomes. We evaluated if purified yeast ISW2 can act on mononucleosomes in which all four core histones are highly acetylated. Mononucleosomes were assembled using purified histones from mammalian CV1 cells grown in the presence of deacetylase inhibitor Trichostatin A (TSA). The CV1 cell line is characterized by fast kinetic of accumulation of highly acetylated histone isoforms in response to TSA treatment. However, such 'native' histone hyperacetylation had no apparent effects on the nucleosome remodeling propensities, suggesting that histone hyperacetylation does not necessarily block ISWI functions and that ISWI enzymes can function on active chromatin as well.
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Affiliation(s)
- Wladyslaw A Krajewski
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, 119334, Russia.
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32
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Experience Modulates the Effects of Histone Deacetylase Inhibitors on Gene and Protein Expression in the Hippocampus: Impaired Plasticity in Aging. J Neurosci 2015; 35:11729-42. [PMID: 26290249 DOI: 10.1523/jneurosci.4339-14.2015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED The therapeutic potential of histone deacetylase inhibitor (HDACi) treatment has attracted considerable attention in the emerging area of cognitive neuroepigenetics. The possibility that ongoing cognitive experience importantly regulates the cell biological effects of HDACi administration, however, has not been systematically examined. In an initial experiment addressing this issue, we tested whether water maze training influences the gene expression response to acute systemic HDACi administration in the young adult rat hippocampus. Training powerfully modulated the response to HDACi treatment, increasing the total number of genes regulated to nearly 3000, including many not typically linked to neural plasticity, compared with <300 following HDACi administration alone. Although water maze training itself also regulated nearly 1800 genes, the specific mRNAs, gene networks, and biological pathways involved were largely distinct when the same experience was provided together with HDACi administration. Next, we tested whether the synaptic protein response to HDACi treatment is similarly dependent on recent cognitive experience, and whether this plasticity is altered in aged rats with memory impairment. Whereas synaptic protein labeling in the young hippocampus was selectively increased when HDACi administration was provided in conjunction with water maze training, combined treatment had no effect on synaptic proteins in the aged hippocampus. Our findings indicate that ongoing experience potently regulates the molecular consequences of HDACi treatment and that the interaction of recent cognitive experience with histone acetylation dynamics is disrupted in the aged hippocampus. SIGNIFICANCE STATEMENT The possibility that interventions targeting epigenetic regulation could be effective in treating a range of neurodegenerative disorders has attracted considerable interest. Here we demonstrate in the rat hippocampus that ongoing experience powerfully modifies the molecular response to one such intervention, histone deacetylase inhibitor (HDACi) administration. A single learning episode dramatically shifts the gene expression profile induced by acute HDACi treatment, yielding a qualitatively distinct hippocampal transcriptome compared with the influence of behavioral training alone. The downstream synaptic protein response to HDACi administration is similarly experience-dependent, and we report that this plasticity is disrupted in the aged hippocampus. The findings highlight that accommodating the modulatory influence of ongoing experience represents a challenge for therapeutic development in the area of cognitive neuroepigenetics.
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Norouzi D, Katebi A, Cui F, Zhurkin VB. Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription. AIMS BIOPHYSICS 2015; 2:613-629. [PMID: 28133628 PMCID: PMC5271602 DOI: 10.3934/biophy.2015.4.613] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10–70 bp (nucleosome repeat length NRL = 157–217 bp). In our model, the energy of a fiber is a sum of the elastic energy of the linker DNA, steric repulsion, electrostatics, and the H4 tail-acidic patch interaction between two stacked nucleosomes. We found two families of energetically feasible conformations of the fibers—one observed earlier, and the other novel. The fibers from the two families are characterized by different DNA linking numbers—that is, they are topologically different. Remarkably, the optimal geometry of a fiber and its topology depend on the linker length: the fibers with linkers L = 10n and 10n + 5 bp have DNA linking numbers per nucleosome ΔLk ≈ −1.5 and −1.0, respectively. In other words, the level of DNA supercoiling is directly related to the length of the inter-nucleosome linker in the chromatin fiber (and therefore, to NRL). We hypothesize that this topological polymorphism of chromatin fibers may play a role in the process of transcription, which is known to generate different levels of DNA supercoiling upstream and downstream from RNA polymerase. A genome-wide analysis of the NRL distribution in active and silent yeast genes yielded results consistent with this assumption.
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Affiliation(s)
- Davood Norouzi
- Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA
| | - Ataur Katebi
- Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA
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34
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García-Ruiz C, Cheng-Sánchez I, Sarabia F. Stereoselective Total Synthesis of (-)-Depudecin. Org Lett 2015; 17:5558-61. [PMID: 26517569 DOI: 10.1021/acs.orglett.5b02697] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The total synthesis of the natural product depudecin, an antiangiogenic microbial polyketide with inhibitory activity against histone deacetylases, is reported. Characterized by a highly oxidized 11-carbon chain containing two epoxides conjugated through a trans-disubstituted olefin, its total synthesis was efficiently accomplished by a novel asymmetric methodology of epoxide formation based on a new class of chiral sulfonium salts, allowing for the construction of the oxirane rings in an efficient and stereoselective fashion.
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Affiliation(s)
- Cristina García-Ruiz
- Department of Organic Chemistry, Faculty of Sciences, University of Málaga , Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Iván Cheng-Sánchez
- Department of Organic Chemistry, Faculty of Sciences, University of Málaga , Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Francisco Sarabia
- Department of Organic Chemistry, Faculty of Sciences, University of Málaga , Campus de Teatinos s/n, 29071 Málaga, Spain
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35
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Banerjee S, Rakshit T, Sett S, Mukhopadhyay R. Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, As Revealed by Single Molecule Atomic Force Spectroscopy. J Phys Chem B 2015; 119:13278-87. [PMID: 26419288 DOI: 10.1021/acs.jpcb.5b07795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
One of the important properties of the transcriptional coactivator p300 is histone acetyltransferase (HAT) activity that enables p300 to influence chromatin action via histone modulation. p300 can exert its HAT action upon the other nuclear proteins too--one notable example being the transcription-factor-like protein HMGB1, which functions also as a cytokine, and whose accumulation in the cytoplasm, as a response to tissue damage, is triggered by its acetylation. Hitherto, no information on the structure and stability of the complexes between full-length p300 (p300FL) (300 kDa) and the histone/HMGB1 proteins are available, probably due to the presence of unstructured regions within p300FL that makes it difficult to be crystallized. Herein, we have adopted the high-resolution atomic force microscopy (AFM) approach, which allows molecularly resolved three-dimensional contour mapping of a protein molecule of any size and structure. From the off-rate and activation barrier values, obtained using single molecule dynamic force spectroscopy, the biochemical proposition of preferential binding of p300FL to histone H3, compared to the octameric histone, can be validated. Importantly, from the energy landscape of the dissociation events, a model for the p300-histone and the p300-HMGB1 dynamic complexes that HAT forms, can be proposed. The lower unbinding forces of the complexes observed in acetylating conditions, compared to those observed in non-acetylating conditions, indicate that upon acetylation, p300 tends to weakly associate, probably as an outcome of charge alterations on the histone/HMGB1 surface and/or acetylation-induced conformational changes. To our knowledge, for the first time, a single molecule level treatment of the interactions of HAT, where the full-length protein is considered, is being reported.
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Affiliation(s)
- S Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - T Rakshit
- Department of Biological Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - S Sett
- Department of Biological Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - R Mukhopadhyay
- Department of Biological Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
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36
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Noor Z, Afzal N, Rashid S. Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays. PLoS One 2015; 10:e0139588. [PMID: 26431201 PMCID: PMC4592208 DOI: 10.1371/journal.pone.0139588] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/15/2015] [Indexed: 12/20/2022] Open
Abstract
Histone deacetylases (HDAC) are metal-dependent enzymes and considered as important targets for cell functioning. Particularly, higher expression of class I HDACs is common in the onset of multiple malignancies which results in deregulation of many target genes involved in cell growth, differentiation and survival. Although substantial attempts have been made to control the irregular functioning of HDACs by employing various inhibitors with high sensitivity towards transformed cells, limited success has been achieved in epigenetic cancer therapy. Here in this study, we used ligand-based pharmacophore and 2-dimensional quantitative structure activity relationship (QSAR) modeling approaches for targeting class I HDAC isoforms. Pharmacophore models were generated by taking into account the known IC50 values and experimental energy scores with extensive validations. The QSAR model having an external R2 value of 0.93 was employed for virtual screening of compound libraries. 10 potential lead compounds (C1-C10) were short-listed having strong binding affinities for HDACs, out of which 2 compounds (C8 and C9) were able to interact with all members of class I HDACs. The potential binding modes of HDAC2 and HDAC8 to C8 were explored through molecular dynamics simulations. Overall, bioactivity and ligand efficiency (binding energy/non-hydrogen atoms) profiles suggested that proposed hits may be more effective inhibitors for cancer therapy.
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Affiliation(s)
- Zainab Noor
- National Center for Bioinformatics, Quaid I Azam University, Islamabad, Pakistan
| | - Noreen Afzal
- National Center for Bioinformatics, Quaid I Azam University, Islamabad, Pakistan
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid I Azam University, Islamabad, Pakistan
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37
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Benevento M, Tonge PD, Puri MC, Nagy A, Heck AJ, Munoz J. Fluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics. Proteomics 2015; 15:3219-31. [DOI: 10.1002/pmic.201500031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/16/2015] [Accepted: 06/15/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Marco Benevento
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht The Netherlands
- Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Peter D. Tonge
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; TO Canada
| | - Mira C. Puri
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; TO Canada
- Department of Medical Biophysics; University of Toronto; TO Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; TO Canada
- Department of Obstetrics and Gynaecology; University of Toronto; TO Canada
- Institute of Medical Science; University of Toronto; TO Canada
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht The Netherlands
- Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Javier Munoz
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht The Netherlands
- Netherlands Proteomics Centre; Utrecht The Netherlands
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Kalda A, Zharkovsky A. Epigenetic Mechanisms of Psychostimulant-Induced Addiction. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 120:85-105. [PMID: 26070754 DOI: 10.1016/bs.irn.2015.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Psychostimulant-induced addiction involves potentially life-long behavioral abnormalities that are caused by repeated exposure to a drug of abuse in vulnerable individuals. The persistence of these behavioral changes suggests that long-lasting alterations in gene expression, particularly within the brain's reward regions, may contribute significantly to the addiction phenotype. An increasing number of works over the past decade have demonstrated the important role of epigenetic regulatory events in mediating the lasting effects of drugs of abuse (including psychostimulants, such as cocaine and amphetamine) in animal models of drug addiction. In this review, we have introduced the importance of epigenetic processes in regulating gene expression and have described the role that dynamic epigenetic changes may play in psychostimulant-induced addiction via long-lasting transcriptional changes following repeated drug exposure. We overviewed the evidence showing that repeated exposure to psychostimulants induces three major modes of epigenetic regulation within the brain's reward regions-histone modification, DNA methylation, and noncoding RNAs. In several instances, it has been possible to demonstrate directly the contribution of these epigenetic changes to psychostimulant-related behavioral abnormalities. Studies of epigenetics may also help to determine the role environmental factors play in an individual's vulnerability to addiction. Further studies are required to validate these epigenetic changes in human addiction and to evaluate the possibility of developing new diagnostic tests and more effective treatments for addiction syndromes.
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Affiliation(s)
- Anti Kalda
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
| | - Alexander Zharkovsky
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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39
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Histone deacetylase inhibitors in hematological malignancies and solid tumors. Arch Pharm Res 2015; 38:933-49. [PMID: 25653088 DOI: 10.1007/s12272-015-0571-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/28/2015] [Indexed: 01/23/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are emerging as promising anticancer drugs. Because aberrant activity and expression of HDACs have been implicated in various cancer types, a wide range of HDAC inhibitors are being investigated as anticancer agents. Furthermore, due to the demonstrable anticancer activity in both in vitro and in vivo studies, numerous HDAC inhibitors have undergone a rapid phase of clinical development in various cancer types, either as a monotherapy or in combination with other anticancer agents. Although preclinical trials show that HDAC inhibitors have a variety of biological effects across multiple pathways, including regulation of gene expression, inducing apoptosis and cell cycle arrest, inhibiting angiogenesis, and regulation of DNA damage and repair, the mechanism by which the clinical activity is mediated remains unclear. Understanding the mechanisms of anticancer activity of HDAC inhibitors is essential not only for rational drug design for targeted therapies, but for the design of optimized clinical protocols. This paper describes the links between HDACs and cancer, and the underlying mechanisms of action of HDAC inhibitors against hematological malignancies and solid tumors. Further, this review presents the clinical outcomes of vorinostat, romidepsin, and belinostat, which are approved by the United States Food and Drug Administration for the treatment of lymphomas.
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40
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Bi X. Heterochromatin structure: lessons from the budding yeast. IUBMB Life 2014; 66:657-66. [PMID: 25355678 DOI: 10.1002/iub.1322] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 10/12/2014] [Accepted: 10/14/2014] [Indexed: 12/28/2022]
Abstract
The eukaryotic genome can be roughly divided into euchromatin and heterochromatin domains that are structurally and functionally distinct. Heterochromatin is characterized by its high compactness and its inhibitory effect on DNA transactions such as gene expression. Formation of heterochromatin involves special histone modifications and the recruitment and spread of silencing complexes and causes changes in the primary and higher order structures of chromatin. The past two decades have seen dramatic advances in dissecting the molecular aspects of heterochromatin because of the identification of the histone code for heterochromatin as well as its writers and erasers (histone-modifying enzymes) and readers (silencing factors recognizing histone modifications). How heterochromatic histone modifications and silencing factors contribute to the special primary and higher order structures of heterochromatin has begun to be understood. The budding yeast Saccharomyces cerevisiae has long been used as a model organism for heterochromatin studies. Results from these studies have contributed significantly to the elucidation of the general principles governing the formation, maintenance, and function of heterochromatin. This review is focused on investigations into the structural aspects of heterochromatin in S. cerevisiae. Current understanding of other aspects of heterochromatin including how it promotes gene silencing and its epigenetic inheritance is briefly summarized.
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Affiliation(s)
- Xin Bi
- Department of Biology, University of Rochester, Rochester, NY, USA
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41
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Turan S, Qiao J, Madden S, Benham C, Kotz M, Schambach A, Bode J. Expanding Flp-RMCE options: the potential of Recombinase Mediated Twin-Site Targeting (RMTT). Gene 2014; 546:135-44. [DOI: 10.1016/j.gene.2014.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/02/2014] [Indexed: 01/02/2023]
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42
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Kim YZ. Altered histone modifications in gliomas. Brain Tumor Res Treat 2014; 2:7-21. [PMID: 24926467 PMCID: PMC4049557 DOI: 10.14791/btrt.2014.2.1.7] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/16/2014] [Accepted: 03/21/2014] [Indexed: 12/24/2022] Open
Abstract
Gliomas are the most frequently occurring primary brain tumors in adults. Although they exist in different malignant stages, including histologically benign forms and highly aggressive states, most gliomas are clinically challenging for neuro-oncologists because of their infiltrative growth patterns and inherent relapse tendency with increased malignancy. Once this disease reaches the glioblastoma multiforme stage, the prognosis of patients is dismal: median survival time is 15 months. Extensive genetic analyses of glial tumors have revealed a variety of deregulated genetic pathways involved in DNA repair, apoptosis, cell migration/adhesion, and cell cycle. Recently, it has become evident that epigenetic alterations may also be an important factor for glioma genesis. Of epigenetic marks, histone modification is a key mark that regulates gene expression and thus modulates a wide range of cellular processes. In this review, I discuss the neuro-oncological significance of altered histone modifications and modifiers in glioma patients while briefly overviewing the biological roles of histone modifications.
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Affiliation(s)
- Young Zoon Kim
- Division of Neuro-Oncology, Department of Neurosurgery, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
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43
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Li C, Xu J, Li J, Li Q, Yang H. Involvement of Arabidopsis Histone Acetyltransferase HAC Family Genes in the Ethylene Signaling Pathway. ACTA ACUST UNITED AC 2014; 55:426-35. [DOI: 10.1093/pcp/pct180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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44
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Gilbert N, Allan J. Supercoiling in DNA and chromatin. Curr Opin Genet Dev 2013; 25:15-21. [PMID: 24584092 PMCID: PMC4042020 DOI: 10.1016/j.gde.2013.10.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 01/20/2023]
Abstract
Supercoiling is a fundamental property of DNA and chromatin. It is modulated by polymerase and topoisomerase activities and, through regulated constraint, by DNA/chromatin binding proteins. As a non-covalent and elusive topological modification, supercoiling has proved intractable to research despite being a crucial regulator of nuclear structure and function. Recent studies have improved our understanding of the formation, regulation and organisation of supercoiling domains in vivo, and reinforce the prospect that the propagation of supercoiling can influence local and global chromatin structure. However, to further our understanding the development of new experimental tools and models are required to better dissect the mechanics of this key topological regulator.
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Affiliation(s)
- Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK.
| | - James Allan
- Institute of Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, UK.
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45
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Abstract
A number of pharmacological agents are currently available for the induction of the fetal hemoglobin (Hb F) to treat the patients with sickle cell disease and beta-thalassemia. In the present review, we summarized the investigation and development of these Hb F-inducing agents and introduced histone deacetylase inhibitors as the new strategy to induce Hb F to treat the hemoglobin disorders
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Affiliation(s)
- Hua Cao
- Division of Medical Genetics, University of Washington, Seattle 98195, USA.
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Vandermeers F, Neelature Sriramareddy S, Costa C, Hubaux R, Cosse JP, Willems L. The role of epigenetics in malignant pleural mesothelioma. Lung Cancer 2013; 81:311-318. [PMID: 23790315 DOI: 10.1016/j.lungcan.2013.05.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/18/2013] [Accepted: 05/22/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Fabian Vandermeers
- Molecular and Cellular Epigenetics (GIGA-Cancer) and Molecular Biology (GxABT), University of Liège (ULg), Liège, Belgium
| | - Sathya Neelature Sriramareddy
- Molecular and Cellular Epigenetics (GIGA-Cancer) and Molecular Biology (GxABT), University of Liège (ULg), Liège, Belgium
| | - Chrisostome Costa
- Molecular and Cellular Epigenetics (GIGA-Cancer) and Molecular Biology (GxABT), University of Liège (ULg), Liège, Belgium
| | - Roland Hubaux
- Molecular and Cellular Epigenetics (GIGA-Cancer) and Molecular Biology (GxABT), University of Liège (ULg), Liège, Belgium
| | - Jean-Philippe Cosse
- Molecular and Cellular Epigenetics (GIGA-Cancer) and Molecular Biology (GxABT), University of Liège (ULg), Liège, Belgium
| | - Luc Willems
- Molecular and Cellular Epigenetics (GIGA-Cancer) and Molecular Biology (GxABT), University of Liège (ULg), Liège, Belgium.
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Nuclear factor κB-dependent histone acetylation is specifically involved in persistent forms of memory. J Neurosci 2013; 33:7603-14. [PMID: 23616565 DOI: 10.1523/jneurosci.4181-12.2013] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Memory consolidation requires gene expression regulation by transcription factors, which eventually may induce chromatin modifications as histone acetylation. This mechanism is regulated by histone acetylases and deacetylases. It is not yet clear whether memory consolidation always recruits histone acetylation or it is only engaged in more persistent memories. To address this question, we used different strength of training for novel object recognition task in mice. Only strong training induced a long-lasting memory and an increase in hippocampal histone H3 acetylation. Histone acetylase inhibition in the hippocampus during consolidation impaired memory persistence, whereas histone deacetylase inhibition caused weak memory to persist. Nuclear factor κB (NF-κB) transcription factor inhibition impaired memory persistence and, concomitantly, reduced the general level of H3 acetylation. Accordingly, we found an important increase in H3 acetylation at a specific NF-κB-regulated promoter region of the Camk2d gene, which was reversed by NF-kB inhibition. These results show for the first time that histone acetylation is a specific molecular signature of enduring memories.
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Shimahara H, Hirano T, Ohya K, Matsuta S, Seeram SS, Tate SI. Nucleosome structural changes induced by binding of non-histone chromosomal proteins HMGN1 and HMGN2. FEBS Open Bio 2013; 3:184-91. [PMID: 23772392 PMCID: PMC3668530 DOI: 10.1016/j.fob.2013.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 01/07/2023] Open
Abstract
Interactions between the nucleosome and the non-histone chromosomal proteins (HMGN1 and HMGN2) were studied by circular dichroism (CD) spectroscopy to elucidate structural changes in the nucleosome induced by HMGN binding. Unlike previous studies that used a nucleosome extracted from living cells, in this study we utilized a nucleosome reconstituted from unmodified recombinant histones synthesized in Escherichia coli and a 189-bp synthetic DNA fragment harboring a nucleosome positioning sequence. This DNA fragment consists of 5′-TATAAACGCC-3′ repeats that has a high affinity to the histone octamer. A nucleosome containing a unique octamer-binding sequence at a specific location on the DNA was produced at sufficiently high yield for spectroscopic analysis. CD data have indicated that both HMGN1 and HMGN2 can increase the winding angle of the nucleosome DNA, but the extent of the structural changes induced by these proteins differs significantly. This suggests HMGN1 and HMGN2 would have different abilities to facilitate nucleosome remodeling. A nucleosome was reconstituted from recombinant histones and a synthetic DNA. Nucleosomes were produced at sufficiently high yield for spectroscopic analysis. A nucleosome with and without HMGN proteins was analyzed using CD spectroscopy. CD data indicate that HMGN proteins increase the winding angle of the nucleosome DNA. HMGN1 and HMGN2 may have different abilities to facilitate nucleosome remodeling.
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Key Words
- CD
- CD, circular dichroism
- HMG, high mobility group
- HMGN
- HMGN1 HMGN2, non-histone chromosomal proteins
- IPTG, isopropyl-β-d-galactopyranoside
- LB, Luria–Bertani
- MNase, micrococcal nuclease
- NMR, nuclear magnetic resonance
- Nucleosome
- PCR, polymerase chain reaction
- RP-HPLC, reverse phase high performance liquid chromatography
- Reconstitution
- SDS–PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis
- Unmodified recombinant histones
- phH2A, phH2B, phH3, and phH4, vectors for the gene expression of all four recombinant human core histones H2A, H2B, H3, and H4, respectively
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Affiliation(s)
- Hideto Shimahara
- Corresponding author. Tel.: +81 761 51 1478; fax: +81 761 51 1455.
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Giudice FS, Pinto DS, Nör JE, Squarize CH, Castilho RM. Inhibition of histone deacetylase impacts cancer stem cells and induces epithelial-mesenchyme transition of head and neck cancer. PLoS One 2013; 8:e58672. [PMID: 23527004 PMCID: PMC3603970 DOI: 10.1371/journal.pone.0058672] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/05/2013] [Indexed: 12/30/2022] Open
Abstract
The genome is organized and packed into the nucleus through interactions with core histone proteins. Emerging evidence suggests that tumors are highly responsive to epigenetic alterations that induce chromatin-based events and dynamically influence tumor behavior. We examined chromatin organization in head and neck squamous cell carcinoma (HNSCC) using acetylation levels of histone 3 as a marker of chromatin compaction. Compared to control oral keratinocytes, we found that HNSCC cells are hypoacetylated and that microenvironmental cues (e.g., microvasculature endothelial cells) induce tumor acetylation. Furthermore, we found that chemical inhibition of histone deacetylases (HDAC) reduces the number of cancer stem cells (CSC) and inhibits clonogenic sphere formation. Paradoxically, inhibition of HDAC also induced epithelial-mesenchymal transition (EMT) in HNSCC cells, accumulation of BMI-1, an oncogene associated with tumor aggressiveness, and expression of the vimentin mesenchymal marker. Importantly, we observed co-expression of vimentin and acetylated histone 3 at the invasion front of human HNSCC tumor tissues. Collectively, these findings suggest that environmental cues, such as endothelial cell-secreted factors, modulate tumor plasticity by limiting the population of CSC and inducing EMT. Therefore, inhibition of HDAC may constitute a novel strategy to disrupt the population of CSC in head and neck tumors to create a homogeneous population of cancer cells with biologically defined signatures and predictable behavior.
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Affiliation(s)
- Fernanda S. Giudice
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Decio S. Pinto
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Jacques E. Nör
- Department of Cariology, Restorative Sciences and Endodontics, School of Dentistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
| | - Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
- * E-mail:
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A Multidisciplinary Approach to Learning and Memory in the Crab Neohelice (Chasmagnathus) granulata. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/b978-0-12-415823-8.00026-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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