1
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Zhang S, Meng Y, Zhou L, Qiu L, Wang H, Su D, Zhang B, Chan K, Han J. Targeting epigenetic regulators for inflammation: Mechanisms and intervention therapy. MedComm (Beijing) 2022; 3:e173. [PMID: 36176733 PMCID: PMC9477794 DOI: 10.1002/mco2.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 11/11/2022] Open
Abstract
Emerging evidence indicates that resolution of inflammation is a critical and dynamic endogenous process for host tissues defending against external invasive pathogens or internal tissue injury. It has long been known that autoimmune diseases and chronic inflammatory disorders are characterized by dysregulated immune responses, leading to excessive and uncontrol tissue inflammation. The dysregulation of epigenetic alterations including DNA methylation, posttranslational modifications to histone proteins, and noncoding RNA expression has been implicated in a host of inflammatory disorders and the immune system. The inflammatory response is considered as a critical trigger of epigenetic alterations that in turn intercede inflammatory actions. Thus, understanding the molecular mechanism that dictates the outcome of targeting epigenetic regulators for inflammatory disease is required for inflammation resolution. In this article, we elucidate the critical role of the nuclear factor‐κB signaling pathway, JAK/STAT signaling pathway, and the NLRP3 inflammasome in chronic inflammatory diseases. And we formulate the relationship between inflammation, coronavirus disease 2019, and human cancers. Additionally, we review the mechanism of epigenetic modifications involved in inflammation and innate immune cells. All that matters is that we propose and discuss the rejuvenation potential of interventions that target epigenetic regulators and regulatory mechanisms for chronic inflammation‐associated diseases to improve therapeutic outcomes.
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Affiliation(s)
- Su Zhang
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Yang Meng
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Lian Zhou
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Lei Qiu
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Heping Wang
- Department of Neurosurgery Tongji Hospital of Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Dan Su
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Bo Zhang
- Laboratory of Cancer Epigenetics and Genomics Department of Gastrointestinal Surgery Frontiers Science Center for Disease‐Related Molecular Network West China Hospital Sichuan University Chengdu China
| | - Kui‐Ming Chan
- Department of Biomedical Sciences City University of Hong Kong Hong Kong China
| | - Junhong Han
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
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2
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Genome-Wide Identification and Spatial Expression Analysis of Histone Modification Gene Families in the Rubber Dandelion Taraxacum kok-saghyz. PLANTS 2022; 11:plants11162077. [PMID: 36015381 PMCID: PMC9415798 DOI: 10.3390/plants11162077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022]
Abstract
Taraxacum kok-saghyz (Tks), also known as the Russian dandelion, is a recognized alternative source of natural rubber quite comparable, for quality and use, to the one obtained from the so-called rubber tree, Hevea brasiliensis. In addition to that, Tks roots produce several other compounds, including inulin, whose use in pharmaceutical and dietary products is quite extensive. Histone-modifying genes (HMGs) catalyze a series of post-translational modifications that affect chromatin organization and conformation, which, in turn, regulate many downstream processes, including gene expression. In this study, we present the first analysis of HMGs in Tks. Altogether, we identified 154 putative Tks homologs: 60 HMTs, 34 HDMs, 42 HATs, and 18 HDACs. Interestingly, whilst most of the classes showed similar numbers in other plant species, including M. truncatula and A. thaliana, HATs and HMT-PRMTs were indeed more abundant in Tks. Composition and structure analysis of Tks HMG proteins showed, for some classes, the presence of novel domains, suggesting a divergence from the canonical HMG model. The analysis of publicly available transcriptome datasets, combined with spatial expression of different developmental tissues, allowed us to identify several HMGs with a putative role in metabolite biosynthesis. Overall, our work describes HMG genomic organization and sets the premises for the functional characterization of epigenetic modifications in rubber-producing plants.
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3
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Yu X, Li M, Guo C, Wu Y, Zhao L, Shi Q, Song J, Song B. Therapeutic Targeting of Cancer: Epigenetic Homeostasis. Front Oncol 2021; 11:747022. [PMID: 34765551 PMCID: PMC8576334 DOI: 10.3389/fonc.2021.747022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
A large number of studies have revealed that epigenetics plays an important role in cancer development. However, the currently-developed epigenetic drugs cannot achieve a stable curative effect. Thus, it may be necessary to redefine the role of epigenetics in cancer development. It has been shown that embryonic development and tumor development share significant similarities in terms of biological behavior and molecular expression patterns, and epigenetics may be the link between them. Cell differentiation is likely a manifestation of epigenetic homeostasis at the cellular level. In this article, we introduced the importance of epigenetic homeostasis in cancer development and analyzed the shortcomings of current epigenetic treatment regimens. Understanding the dynamic process of epigenetic homeostasis in organ development can help us characterize cancer according to its differentiation stages, explore new targets for cancer treatment, and improve the clinical prognosis of patients with cancer.
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Affiliation(s)
- Xiaoyuan Yu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Menglu Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Chunyan Guo
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuesheng Wu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Li Zhao
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Qinying Shi
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianbo Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Bin Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
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4
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Martinez-Useros J, Martin-Galan M, Florez-Cespedes M, Garcia-Foncillas J. Epigenetics of Most Aggressive Solid Tumors: Pathways, Targets and Treatments. Cancers (Basel) 2021; 13:3209. [PMID: 34198989 PMCID: PMC8267921 DOI: 10.3390/cancers13133209] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
Highly aggressive tumors are characterized by a highly invasive phenotype, and they display chemoresistance. Furthermore, some of the tumors lack expression of biomarkers for target therapies. This is the case of small-cell lung cancer, triple-negative breast cancer, pancreatic ductal adenocarcinoma, glioblastoma, metastatic melanoma, and advanced ovarian cancer. Unfortunately, these patients show a low survival rate and most of the available drugs are ineffective. In this context, epigenetic modifications have emerged to provide the causes and potential treatments for such types of tumors. Methylation and hydroxymethylation of DNA, and histone modifications, are the most common targets of epigenetic therapy, to influence gene expression without altering the DNA sequence. These modifications could impact both oncogenes and tumor suppressor factors, which influence several molecular pathways such as epithelial-to-mesenchymal transition, WNT/β-catenin, PI3K-mTOR, MAPK, or mismatch repair machinery. However, epigenetic changes are inducible and reversible events that could be influenced by some environmental conditions, such as UV exposure, smoking habit, or diet. Changes in DNA methylation status and/or histone modification, such as acetylation, methylation or phosphorylation, among others, are the most important targets for epigenetic cancer therapy. Therefore, the present review aims to compile the basic information of epigenetic modifications, pathways and factors, and provide a rationale for the research and treatment of highly aggressive tumors with epigenetic drugs.
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Affiliation(s)
- Javier Martinez-Useros
- Translational Oncology Division, OncoHealth Institute, Fundacion Jimenez Diaz University Hospital, Avenida Reyes Catolicos 2, 28040 Madrid, Spain;
| | - Mario Martin-Galan
- Translational Oncology Division, OncoHealth Institute, Fundacion Jimenez Diaz University Hospital, Avenida Reyes Catolicos 2, 28040 Madrid, Spain;
| | | | - Jesus Garcia-Foncillas
- Translational Oncology Division, OncoHealth Institute, Fundacion Jimenez Diaz University Hospital, Avenida Reyes Catolicos 2, 28040 Madrid, Spain;
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5
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Carpentier P, Leprêtre C, Basset C, Douki T, Torelli S, Duarte V, Hamdane D, Fontecave M, Atta M. Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. Nucleic Acids Res 2020; 48:9918-9930. [PMID: 32785618 PMCID: PMC7515727 DOI: 10.1093/nar/gkaa667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022] Open
Abstract
MiaE (2-methylthio-N6-isopentenyl-adenosine37-tRNA monooxygenase) is a unique non-heme diiron enzyme that catalyzes the O2-dependent post-transcriptional allylic hydroxylation of a hypermodified nucleotide 2-methylthio-N6-isopentenyl-adenosine (ms2i6A37) at position 37 of selected tRNA molecules to produce 2-methylthio-N6–4-hydroxyisopentenyl-adenosine (ms2io6A37). Here, we report the in vivo activity, biochemical, spectroscopic characterization and X-ray crystal structure of MiaE from Pseudomonas putida. The investigation demonstrates that the putative pp-2188 gene encodes a MiaE enzyme. The structure shows that Pp-MiaE consists of a catalytic diiron(III) domain with a four alpha-helix bundle fold. A docking model of Pp-MiaE in complex with tRNA, combined with site directed mutagenesis and in vivo activity shed light on the importance of an additional linker region for substrate tRNA recognition. Finally, krypton-pressurized Pp-MiaE experiments, revealed the presence of defined O2 site along a conserved hydrophobic tunnel leading to the diiron active center.
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Affiliation(s)
- Philippe Carpentier
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France.,European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Chloé Leprêtre
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Christian Basset
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, SyMMES, F-38000, 17 avenue des martyrs Grenoble, France
| | - Stéphane Torelli
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Victor Duarte
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, UMR CNRS 8229, Collège de France-CNRS-Sorbonne Université, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR CNRS 8229, Collège de France-CNRS-Sorbonne Université, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Mohamed Atta
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
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6
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Dobrovolska O, Brilkov M, Madeleine N, Ødegård-Fougner Ø, Strømland Ø, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, Halskau Ø. The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection. FEBS J 2020; 287:4458-4480. [PMID: 32083791 DOI: 10.1111/febs.15256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/17/2019] [Accepted: 02/20/2020] [Indexed: 12/27/2022]
Abstract
Chromatin post-translational modifications are thought to be important for epigenetic effects on gene expression. Methylation of histone N-terminal tail lysine residues constitutes one of many such modifications, executed by families of histone lysine methyltransferase (HKMTase). One such protein is ASHH2 from the flowering plant Arabidopsis thaliana, equipped with the interaction domain, CW, and the HKMTase domain, SET. The CW domain of ASHH2 is a selective binder of monomethylation at lysine 4 on histone H3 (H3K4me1) and likely helps the enzyme dock correctly onto chromatin sites. The study of CW and related interaction domains has so far been emphasizing lock-key models, missing important aspects of histone-tail CW interactions. We here present an analysis of the ASHH2 CW-H3K4me1 complex using NMR and molecular dynamics, as well as mutation and affinity studies of flexible coils. β-augmentation and rearrangement of coils coincide with changes in the flexibility of the complex, in particular the η1, η3 and C-terminal coils, but also in the β1 and β2 strands and the C-terminal part of the ligand. Furthermore, we show that mutating residues with outlier dynamic behaviour affect the complex binding affinity despite these not being in direct contact with the ligand. Overall, the binding process is consistent with conformational selection. We propose that this binding mechanism presents an advantage when searching for the correct post-translational modification state among the highly modified and flexible histone tails, and also that the binding shifts the catalytic SET domain towards the nucleosome. DATABASES: Structural data are available in the PDB database under the accession code 6QXZ. Resonance assignments for CW42 in its apo- and holo-forms are available in the BMRB database under the accession code 27251.
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Affiliation(s)
- Olena Dobrovolska
- Department of Biological Sciences, University of Bergen, Norway, Bergen
| | - Maxim Brilkov
- Department of Biological Sciences, University of Bergen, Norway, Bergen
| | - Noelly Madeleine
- Department of Biological Sciences, University of Bergen, Norway, Bergen.,Department of Biomedicine, University of Bergen, Norway, Bergen
| | - Øyvind Ødegård-Fougner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Stephen R Martin
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | | | | | - Knut Teigen
- Department of Biomedicine, University of Bergen, Norway, Bergen
| | - Johan Isaksson
- Department of Chemistry, The Arctic University of Tromsø, Norway
| | - Jarl Underhaug
- Department of Chemistry, University of Bergen, Norway, Bergen
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Norway, Bergen
| | | | - Rein Aasland
- Department of Biosciences, University of Oslo, Norway, Oslo
| | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Norway, Bergen
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7
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Benzo[ b]tellurophenes as a Potential Histone H3 Lysine 9 Demethylase (KDM4) Inhibitor. Int J Mol Sci 2019; 20:ijms20235908. [PMID: 31775247 PMCID: PMC6928947 DOI: 10.3390/ijms20235908] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 12/19/2022] Open
Abstract
Gene expression and tumor growth can be regulated by methylation levels of lysine residues on histones, which are controlled by histone lysine demethylases (KDMs). Series of benzo[b]tellurophene and benzo[b]selenophene compounds were designed and synthesized and they were evaluated for histone H3 lysine 9 demethylase (KDM4) inhibitory activity. Among the carbamates, alcohol and aromatic derivatives, tert-butyl benzo[b]tellurophen-2-ylmethylcarbamate (compound 1c) revealed KDM4 specific inhibitory activity in cervical cancer HeLa cells, whereas the corresponding selenium or oxygen substitute compounds did not display any inhibitory activity toward KDM4. Compound 1c also induced cell death in cervical and colon cancer but not in normal cells. Thus, compound 1c, a novel inhibitor of KDM4, constitutes a potential therapeutic and research tool against cancer.
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8
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Zhang Q, Thakur C, Shi J, Sun J, Fu Y, Stemmer P, Chen F. New discoveries of mdig in the epigenetic regulation of cancers. Semin Cancer Biol 2019; 57:27-35. [PMID: 31276784 PMCID: PMC6844078 DOI: 10.1016/j.semcancer.2019.06.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 06/17/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022]
Abstract
Mineral dust-induced gene (mdig) encodes a member of the evolutionarily conserved JmjC family proteins that play fundamental roles in regulating chromatin-based processes as well as transcription of the genes in eukaryotic cells. This gene is also named as myc-induced nuclear antigen 53 (MINA), nucleolar protein 52 (NO52) and ribosomal oxygenase 2 (RIOX2). Increased expression of mdig had been noted in a number of human cancers, esp. lung cancer. Emerging evidence suggests that the oncogenic activity of mdig is most likely achieved through its regulation on the demethylation of histone proteins, despite it lacks the structural identities of the demethylases. Here, we discuss the latest discoveries on the characteristics of the mdig protein and its roles in a wide variety of normal and carcinogenic processes. We will also provide perspectives on how mdig is involved in the maintenance and differentiation of the embryonic stem cells, somatic stem cells and cancer stem cells.
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Affiliation(s)
- Qian Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201, USA
| | - Chitra Thakur
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201, USA
| | - Junwei Shi
- Nantong Pulmonary Hospital, 500 Yonghe Road, Gangzha Qu, Nantong, 226011, Jiangsu Province, China
| | - Jiaying Sun
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201, USA
| | - Yao Fu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201, USA
| | - Paul Stemmer
- Institute of Environmental Health Sciences, School of Medicine, Wayne State University, 6135 Woodward Avenue, Detroit, MI, 48202, USA
| | - Fei Chen
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201, USA.
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9
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Leon KE, Aird KM. Jumonji C Demethylases in Cellular Senescence. Genes (Basel) 2019; 10:genes10010033. [PMID: 30634491 PMCID: PMC6356615 DOI: 10.3390/genes10010033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022] Open
Abstract
Senescence is a stable cell cycle arrest that is either tumor suppressive or tumor promoting depending on context. Epigenetic changes such as histone methylation are known to affect both the induction and suppression of senescence by altering expression of genes that regulate the cell cycle and the senescence-associated secretory phenotype. A conserved group of proteins containing a Jumonji C (JmjC) domain alter chromatin state, and therefore gene expression, by demethylating histones. Here, we will discuss what is currently known about JmjC demethylases in the induction of senescence, and how these enzymes suppress senescence to contribute to tumorigenesis.
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Affiliation(s)
- Kelly E Leon
- Department of Cellular & Molecular Physiology, Penn Stage College of Medicine, Hershey, PA 17033, USA.
| | - Katherine M Aird
- Department of Cellular & Molecular Physiology, Penn Stage College of Medicine, Hershey, PA 17033, USA.
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10
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Neumann P, Jaé N, Knau A, Glaser SF, Fouani Y, Rossbach O, Krüger M, John D, Bindereif A, Grote P, Boon RA, Dimmeler S. The lncRNA GATA6-AS epigenetically regulates endothelial gene expression via interaction with LOXL2. Nat Commun 2018; 9:237. [PMID: 29339785 PMCID: PMC5770451 DOI: 10.1038/s41467-017-02431-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/30/2017] [Indexed: 12/21/2022] Open
Abstract
Impaired or excessive growth of endothelial cells contributes to several diseases. However, the functional involvement of regulatory long non-coding RNAs in these processes is not well defined. Here, we show that the long non-coding antisense transcript of GATA6 (GATA6-AS) interacts with the epigenetic regulator LOXL2 to regulate endothelial gene expression via changes in histone methylation. Using RNA deep sequencing, we find that GATA6-AS is upregulated in endothelial cells during hypoxia. Silencing of GATA6-AS diminishes TGF-β2-induced endothelial-mesenchymal transition in vitro and promotes formation of blood vessels in mice. We identify LOXL2, known to remove activating H3K4me3 chromatin marks, as a GATA6-AS-associated protein, and reveal a set of angiogenesis-related genes that are inversely regulated by LOXL2 and GATA6-AS silencing. As GATA6-AS silencing reduces H3K4me3 methylation of two of these genes, periostin and cyclooxygenase-2, we conclude that GATA6-AS acts as negative regulator of nuclear LOXL2 function.
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Affiliation(s)
- Philipp Neumann
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Nicolas Jaé
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Andrea Knau
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Simone F Glaser
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Youssef Fouani
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 17, Giessen, 35392, Germany
| | - Marcus Krüger
- Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, Bad Nauheim, 61231, Germany
| | - David John
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 17, Giessen, 35392, Germany
| | - Phillip Grote
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Reinier A Boon
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany.,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany. .,German Center of Cardiovascular Research (DZHK), Frankfurt am Main, 60590, Germany.
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11
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Dobrynin G, McAllister TE, Leszczynska KB, Ramachandran S, Krieg AJ, Kawamura A, Hammond EM. KDM4A regulates HIF-1 levels through H3K9me3. Sci Rep 2017; 7:11094. [PMID: 28894274 PMCID: PMC5593970 DOI: 10.1038/s41598-017-11658-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/25/2017] [Indexed: 01/11/2023] Open
Abstract
Regions of hypoxia (low oxygen) occur in most solid tumours and cells in these areas are the most aggressive and therapy resistant. In response to decreased oxygen, extensive changes in gene expression mediated by Hypoxia-Inducible Factors (HIFs) contribute significantly to the aggressive hypoxic tumour phenotype. In addition to HIFs, multiple histone demethylases are altered in their expression and activity, providing a secondary mechanism to extend the hypoxic signalling response. In this study, we demonstrate that the levels of HIF-1α are directly controlled by the repressive chromatin mark, H3K9me3. In conditions where the histone demethylase KDM4A is depleted or inactive, H3K9me3 accumulates at the HIF-1α locus, leading to a decrease in HIF-1α mRNA and a reduction in HIF-1α stabilisation. Loss of KDM4A in hypoxic conditions leads to a decreased HIF-1α mediated transcriptional response and correlates with a reduction in the characteristics associated with tumour aggressiveness, including invasion, migration, and oxygen consumption. The contribution of KDM4A to the regulation of HIF-1α is most robust in conditions of mild hypoxia. This suggests that KDM4A can enhance the function of HIF-1α by increasing the total available protein to counteract any residual activity of prolyl hydroxylases.
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Affiliation(s)
- Grzegorz Dobrynin
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Tom E McAllister
- Department of Chemistry, Chemistry Research Laboratory, The University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Katarzyna B Leszczynska
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Shaliny Ramachandran
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - Akane Kawamura
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre of Human Genetics, Roosevelt Drive, The University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Chemistry Research Laboratory, The University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ester M Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK.
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12
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Herranz N, Dave N, Millanes-Romero A, Pascual-Reguant L, Morey L, Díaz VM, Lórenz-Fonfría V, Gutierrez-Gallego R, Jerónimo C, Iturbide A, Di Croce L, García de Herreros A, Peiró S. Lysyl oxidase-like 2 (LOXL2) oxidizes trimethylated lysine 4 in histone H3. FEBS J 2016; 283:4263-4273. [PMID: 27735137 DOI: 10.1111/febs.13922] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022]
Abstract
Methylation of histone H3 lysine 4 is linked to active transcription and can be removed by LSD1 or the JmjC domain-containing proteins by amino-oxidation or hydroxylation, respectively. Here we describe that its deamination can be catalyzed by lysyl oxidase-like 2 protein (LOXL2), presenting an unconventional chemical mechanism for H3K4 modification. Infrared spectroscopy and mass spectrometry analyses demonstrated that recombinant LOXL2 specifically deaminates trimethylated H3K4. Moreover, by regulating H3K4me3 deamination, LOXL2 activity is linked with the transcriptional control of the CDH1 gene. These results reveal the existence of further H3 modification as well as a novel mechanism for H3K4me3 demethylation. DATABASE The GEO accession number for the data referred to this paper is GSE35600.
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Affiliation(s)
- Nicolás Herranz
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Natàlia Dave
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Alba Millanes-Romero
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Laura Pascual-Reguant
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Lluis Morey
- Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Víctor M Díaz
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Víctor Lórenz-Fonfría
- Unitat de Biofísica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | | | - Ane Iturbide
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Luciano Di Croce
- Centre de Regulació Genòmica (CRG), Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sandra Peiró
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
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13
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de Lera AR, Ganesan A. Epigenetic polypharmacology: from combination therapy to multitargeted drugs. Clin Epigenetics 2016; 8:105. [PMID: 27752293 PMCID: PMC5062873 DOI: 10.1186/s13148-016-0271-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/21/2016] [Indexed: 12/20/2022] Open
Abstract
The modern drug discovery process has largely focused its attention in the so-called magic bullets, single chemical entities that exhibit high selectivity and potency for a particular target. This approach was based on the assumption that the deregulation of a protein was causally linked to a disease state, and the pharmacological intervention through inhibition of the deregulated target was able to restore normal cell function. However, the use of cocktails or multicomponent drugs to address several targets simultaneously is also popular to treat multifactorial diseases such as cancer and neurological disorders. We review the state of the art with such combinations that have an epigenetic target as one of their mechanisms of action. Epigenetic drug discovery is a rapidly advancing field, and drugs targeting epigenetic enzymes are in the clinic for the treatment of hematological cancers. Approved and experimental epigenetic drugs are undergoing clinical trials in combination with other therapeutic agents via fused or linked pharmacophores in order to benefit from synergistic effects of polypharmacology. In addition, ligands are being discovered which, as single chemical entities, are able to modulate multiple epigenetic targets simultaneously (multitarget epigenetic drugs). These multiple ligands should in principle have a lower risk of drug-drug interactions and drug resistance compared to cocktails or multicomponent drugs. This new generation may rival the so-called magic bullets in the treatment of diseases that arise as a consequence of the deregulation of multiple signaling pathways provided the challenge of optimization of the activities shown by the pharmacophores with the different targets is addressed.
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Affiliation(s)
- Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, CINBIO and IIS Galicia Sur, 36310 Vigo, Spain
| | - A Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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14
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Song Y, Wu F, Wu J. Targeting histone methylation for cancer therapy: enzymes, inhibitors, biological activity and perspectives. J Hematol Oncol 2016; 9:49. [PMID: 27316347 PMCID: PMC4912745 DOI: 10.1186/s13045-016-0279-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/07/2016] [Indexed: 12/31/2022] Open
Abstract
Post-translational methylation of histone lysine or arginine residues plays important roles in gene regulation and other physiological processes. Aberrant histone methylation caused by a gene mutation, translocation, or overexpression can often lead to initiation of a disease such as cancer. Small molecule inhibitors of such histone modifying enzymes that correct the abnormal methylation could be used as novel therapeutics for these diseases, or as chemical probes for investigation of epigenetics. Discovery and development of histone methylation modulators are in an early stage and undergo a rapid expansion in the past few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Several compounds have been in clinical trials for safety, pharmacokinetics, and efficacy, targeting several types of cancer. This review summarizes the biochemistry, structures, and biology of cancer-relevant histone methylation modifying enzymes, small molecule inhibitors and their preclinical and clinical antitumor activities. Perspectives for targeting histone methylation for cancer therapy are also discussed.
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Affiliation(s)
- Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Fangrui Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Jingyu Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
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15
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Abstract
Growing evidence demonstrates that metabolism and chromatin dynamics are not separate processes but that they functionally intersect in many ways. For example, the lysine biosynthetic enzyme homocitrate synthase was recently shown to have unexpected functions in DNA damage repair, raising the question of whether other amino acid metabolic enzymes participate in chromatin regulation. Using an in silico screen combined with reporter assays, we discovered that a diverse range of metabolic enzymes function in heterochromatin regulation. Extended analysis of the glutamate dehydrogenase 1 (Gdh1) revealed that it regulates silent information regulator complex recruitment to telomeres and ribosomal DNA. Enhanced N-terminal histone H3 proteolysis is observed in GDH1 mutants, consistent with telomeric silencing defects. A conserved catalytic Asp residue is required for Gdh1's functions in telomeric silencing and H3 clipping. Genetic modulation of α-ketoglutarate levels demonstrates a key regulatory role for this metabolite in telomeric silencing. The metabolic activity of glutamate dehydrogenase thus has important and previously unsuspected roles in regulating chromatin-related processes.
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16
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Krishnan S, Trievel RC. Purification, Biochemical Analysis, and Structure Determination of JmjC Lysine Demethylases. Methods Enzymol 2016; 573:279-301. [PMID: 27372758 DOI: 10.1016/bs.mie.2016.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Jumonji C (JmjC) lysine demethylases (KDMs) catalyze the site- and state-specific demethylation of lysine residues in histone and nonhistone protein substrates. These enzymes have been implicated in diverse genomic processes, including epigenetic gene regulation, DNA damage response, DNA replication, and regulation of heterochromatin structure. In addition, a number of JmjC KDMs contribute to the incidence of numerous cancers, rendering them targets for the development of novel chemotherapeutic drugs. Using the JMJD2 KDM subfamily as representative examples, this chapter outlines strategies for purifying highly active, recombinant JmjC KDMs lacking inhibitory transition metal ions, characterizing kinetic parameters of these enzymes using a coupled fluorescent assay, and determining crystal structures of the enzymes in complex with methylated histone peptides. Together, these approaches provide a foundation for structural and biochemical characterization of the JmjC KDMs and facilitate efforts to identify small molecule inhibitors through high-throughput screening and structure-guided design.
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Affiliation(s)
- S Krishnan
- University of Michigan, Ann Arbor, MI, United States
| | - R C Trievel
- University of Michigan, Ann Arbor, MI, United States.
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17
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Liu LJ, Lu L, Zhong HJ, He B, Kwong DWJ, Ma DL, Leung CH. An Iridium(III) Complex Inhibits JMJD2 Activities and Acts as a Potential Epigenetic Modulator. J Med Chem 2015. [DOI: 10.1021/acs.jmedchem.5b00375] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Li-Juan Liu
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
| | - Lihua Lu
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Hai-Jing Zhong
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
| | - Bingyong He
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Daniel W. J. Kwong
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Dik-Lung Ma
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Chung-Hang Leung
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
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18
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Accari SL, Fisher PR. Emerging Roles of JmjC Domain-Containing Proteins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 319:165-220. [DOI: 10.1016/bs.ircmb.2015.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Guerra-Calderas L, González-Barrios R, Herrera LA, Cantú de León D, Soto-Reyes E. The role of the histone demethylase KDM4A in cancer. Cancer Genet 2014; 208:215-24. [PMID: 25633974 DOI: 10.1016/j.cancergen.2014.11.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 10/20/2014] [Accepted: 11/05/2014] [Indexed: 12/31/2022]
Abstract
Histone posttranslational modifications are important components of epigenetic regulation. One extensively studied modification is the methylation of lysine residues. These modifications were thought to be irreversible. However, several proteins with histone lysine demethylase functions have been discovered and characterized. Among these proteins, KDM4A is the first histone lysine demethylase shown to demethylate trimethylated residues. This enzyme plays an important role in gene expression, cellular differentiation, and animal development. Recently, it has also been shown to be involved in cancer. In this review, we focus on describing the structure, mechanisms, and function of KDM4A. We primarily discuss the role of KDM4A in cancer development and the importance of KDM4A as a potential therapeutic target.
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Affiliation(s)
- Lissania Guerra-Calderas
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - David Cantú de León
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ernesto Soto-Reyes
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.
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20
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Shi M, Shahsafaei A, Liu C, Yu H, Dorfman DM. Enhancer of zeste homolog 2 is widely expressed in T-cell neoplasms, is associated with high proliferation rate and correlates with MYC and pSTAT3 expression in a subset of cases. Leuk Lymphoma 2014; 56:2087-91. [PMID: 25263318 DOI: 10.3109/10428194.2014.968780] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhancer of zeste homolog 2 (EZH2), an epigenetic regulator and H3k27-specific histone methyltransferase, is important for transcriptional regulation. EZH2 has been found to be overexpressed in B-cell lymphomas, as well as some T-cell lymphomas. Here we investigated the expression of EZH2 by immunohistochemical staining in a wide range of T-cell neoplasms. We found that EZH2 is highly expressed in all categories of T-cell neoplasia studied, and its expression strongly correlates with a high proliferation rate. Although up-regulation of EZH2 has been reported to be modulated by the pSTAT3-MYC pathway, our data indicate that EZH2 expression is correlated with MYC and/or pSTAT3 expression in only a subset of T-cell lymphomas, and that other mechanisms may control the overexpression of EZH2 in many T-cell lymphomas. The high level of EZH2 expression in T cell lymphomas suggest that these neoplasms may benefit from targeted treatment with a small molecule inhibitor of EZH2 currently in use in clinical trials.
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Affiliation(s)
- Min Shi
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School , Boston, MA , USA
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21
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el Bahhaj F, Dekker FJ, Martinet N, Bertrand P. Delivery of epidrugs. Drug Discov Today 2014; 19:1337-52. [DOI: 10.1016/j.drudis.2014.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/28/2014] [Accepted: 03/19/2014] [Indexed: 12/22/2022]
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22
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Lawrence P, Conderino JS, Rieder E. Redistribution of demethylated RNA helicase A during foot-and-mouth disease virus infection: role of Jumonji C-domain containing protein 6 in RHA demethylation. Virology 2014; 452-453:1-11. [PMID: 24606677 DOI: 10.1016/j.virol.2013.12.040] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/20/2013] [Accepted: 12/28/2013] [Indexed: 11/20/2022]
Abstract
Previously, RNA helicase A (RHA) re-localization from the nucleus to the cytoplasm in foot-and-mouth disease virus (FMDV) infected cells was shown to coincide with loss of RHA methylated arginine residues at its C-terminus. The potential interaction between RHA and Jumonji C-domain (JmjC) protein 6 (JMJD6) arginine demethylase in infected cells was investigated. Treatment with N-oxalylglycine (NOG) inhibitor of JmjC demethylases prevented FMDV-induced RHA demethylation and re-localization, and also decreased viral protein synthesis and virus titers. Physical interaction between JMJD6 and RHA was demonstrated via reciprocal co-immunoprecipitation, where RHA preferentially bound JMJD6 monomers. Nuclear efflux of demethylated RHA (DM-RHA) coincided with nuclear influx of JMJD6, which was not observed using another picornavirus. A modified biochemical assay demonstrated JMJD6 induced dose-dependent demethylation of RHA and two RHA-derived isoforms, which could be inhibited by NOG. We propose a role for JMJD6 in RHA demethylation stimulated by FMDV, that appears to facilitate virus replication.
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Affiliation(s)
- Paul Lawrence
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, NAA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY 11944-0848, USA
| | - Joseph S Conderino
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, NAA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY 11944-0848, USA
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, NAA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY 11944-0848, USA.
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23
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Zou C, Mallampalli RK. Regulation of histone modifying enzymes by the ubiquitin-proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:694-702. [PMID: 24389248 DOI: 10.1016/j.bbamcr.2013.12.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/17/2013] [Accepted: 12/24/2013] [Indexed: 11/30/2022]
Abstract
Histone post-translational modification is a key step that may result in an epigenetic mark that regulates chromatin structure and gene transcriptional activity thereby impacting many fundamental aspects of human biology. Subtypes of post-translational modification such as acetylation and methylation are executed by a variety of distinct modification enzymes. The cytoplasmic and nuclear concentrations of these enzymes are dynamically and tightly controlled at the protein level to precisely fine-tune transcriptional activity in response to environmental clues and during pathophysiological states. Recent data have emerged demonstrating that the life span of these critical nuclear enzymes involved in histone modification that impact chromatin structure and gene expression are controlled at the level of protein turnover by ubiquitin-proteasomal processing. This review focuses on the recent progress on mechanisms for ubiquitin-proteasomal degradation of histone modification enzymes and the potential pathophysiological significance of this process.
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Affiliation(s)
- Chunbin Zou
- Department of Medicine, The Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Rama K Mallampalli
- Department of Medicine, The Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Cell Biology and Physiology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA 15240, USA.
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24
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Kogure M, Takawa M, Cho HS, Toyokawa G, Hayashi K, Tsunoda T, Kobayashi T, Daigo Y, Sugiyama M, Atomi Y, Nakamura Y, Hamamoto R. Deregulation of the histone demethylase JMJD2A is involved in human carcinogenesis through regulation of the G(1)/S transition. Cancer Lett 2013; 336:76-84. [PMID: 23603248 DOI: 10.1016/j.canlet.2013.04.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/08/2013] [Accepted: 04/10/2013] [Indexed: 01/11/2023]
Abstract
Although a number of JmjC-containing histone demethylases have been identified and biochemically characterized, pathological roles of their dysfunction in human disease such as cancer have not been well elucidated. Here, we report the Jumonji domain containing 2A (JMJD2A) is integral to proliferation of cancer cells. Quantitative real-time PCR analysis revealed higher expression of JMJD2A in clinical bladder cancer tissues than in corresponding non-neoplastic tissues (P<0.0001). Immunohistochemical analysis also showed positive staining for JMJD2A in 288 out of 403 lung cancer cases, whereas no staining was observed in lung normal tissues. Suppression of JMJD2A expression in lung and bladder cancer cells overexpressing this gene, using specific siRNAs, inhibited incorporation of BrdU and resulted in significant suppression of cell growth. Furthermore, JMJD2A appears to directly transactivate the expression of some tumor associated proteins including ADAM12 through the regulation of histone H3K9 methylation. As expression levels of JMJD2A are low in normal tissues, it may be feasible to develop specific inhibitors targeting the enzyme as anti-tumor agents which should have a minimal risk of adverse reaction.
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Affiliation(s)
- Masaharu Kogure
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Tokyo 108-8639, Japan
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25
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Hoffmann I, Roatsch M, Schmitt ML, Carlino L, Pippel M, Sippl W, Jung M. The role of histone demethylases in cancer therapy. Mol Oncol 2012; 6:683-703. [PMID: 22902149 DOI: 10.1016/j.molonc.2012.07.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 07/30/2012] [Indexed: 10/28/2022] Open
Abstract
Reversible histone methylation has emerged in the last few years as an important mechanism of epigenetic regulation. Histone methyltransferases and demethylases have been identified as contributing factors in the development of several diseases, especially cancer. Therefore, they have been postulated to be new drug targets with high therapeutic potential. Here, we review histone demethylases with a special focus on their potential role in oncology drug discovery. We present an overview over the different classes of enzymes, their biochemistry, selected data on their role in physiology and already available inhibitors.
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Affiliation(s)
- Inga Hoffmann
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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26
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Herranz N, Dave N, Millanes-Romero A, Morey L, Díaz VM, Lórenz-Fonfría V, Gutierrez-Gallego R, Jerónimo C, Di Croce L, García de Herreros A, Peiró S. Lysyl oxidase-like 2 deaminates lysine 4 in histone H3. Mol Cell 2012; 46:369-76. [PMID: 22483618 DOI: 10.1016/j.molcel.2012.03.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 12/12/2011] [Accepted: 02/28/2012] [Indexed: 10/28/2022]
Abstract
Methylation of lysine 4 (K4) within histone H3 has been linked to active transcription and is removed by LSD1 and the JmjC domain-containing proteins by amino-oxidation or hydroxylation, respectively. Here, we describe the deamination catalyzed by Lysyl oxidase-like 2 protein (LOXL2) as an unconventional chemical mechanism for H3K4 modification. Infrared spectroscopy and mass spectrometry analyses demonstrated that recombinant LOXL2 specifically deaminates trimethylated H3K4. Moreover, LOXL2 activity is linked with the transcriptional control of CDH1 gene by regulating H3K4me3 deamination. These results reveal another H3 modification and provide a different mechanism for H3K4 modification.
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Affiliation(s)
- Nicolás Herranz
- Programa de Recerca en Càncer, IMIM-Hospital del Mar, Barcelona, Spain
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27
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Krishnan S, Collazo E, Ortiz-Tello PA, Trievel RC. Purification and assay protocols for obtaining highly active Jumonji C demethylases. Anal Biochem 2012; 420:48-53. [DOI: 10.1016/j.ab.2011.08.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 08/15/2011] [Accepted: 08/19/2011] [Indexed: 11/27/2022]
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28
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Brunschweiger A, Hall J. A decade of the human genome sequence--how does the medicinal chemist benefit? ChemMedChem 2011; 7:194-203. [PMID: 22170741 DOI: 10.1002/cmdc.201100498] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Indexed: 12/11/2022]
Abstract
Many have claimed that the sequencing of the human genome has failed to deliver the promised new era of drug discovery and development. Here, we argue that in fact, the availability of the human genome sequence and the genomics technologies that resulted from those research efforts have had a major impact on drug discovery. Medicinal chemists are actively using the data gleaned from structural genomics projects over the past decade to design more selective and more effective drug candidates. For example, large superfamilies of related enzymes, such as the kinome, proteome, proteasome, transportome, identified because of the sequencing of the human genome represent a huge number of potential drug targets. Ten years on, we're able to design multitarget drugs where the selectivity for a certain subgroup of receptors can lead to increased efficacy rather than the side effects traditionally associated with "off-targets". New trends and discoveries in biomedical research are notoriously slow to show their value, and this is also true for genomics technologies. However, the examples we've selected show that these are firmly set in the drug-discovery process, and without the human genome sequence, a number of current clinical candidates and promising drug leads would not have been possible.
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Affiliation(s)
- Andreas Brunschweiger
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
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29
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Abstract
Nuclear receptors (NRs) represent a vital class of ligand-activated transcription factors responsible for coordinately regulating the expression of genes involved in numerous biological processes. Transcriptional regulation by NRs is conducted through interactions with multiple coactivator or corepressor complexes that modify the chromatin environment to facilitate or inhibit RNA polymerase II binding and transcription initiation. In recent years, studies have identified specific biological roles for cofactors mediating NR signaling through epigenetic modifications such as acetylation and methylation of histones. Intriguingly, genome-wide analysis of NR and cofactor localization has both confirmed findings from single-gene studies and revealed new insights into the relationships between NRs, cofactors and target genes in determining gene expression. Here, we review recent developments in the understanding of epigenetic regulation by NRs across the genome within the context of the well-established background of cofactor complexes and their roles in histone modification.
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Affiliation(s)
- Christopher D Green
- Chinese Academy of Sciences Key Laboratory of Molecular Developmental Biology, Center for Molecular Systems Biology, Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing, 100101, China
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences–MaxPlanck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
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Inflammation, HIF-1, and the epigenetics that follows. Mediators Inflamm 2010; 2010:263914. [PMID: 21197398 PMCID: PMC3010677 DOI: 10.1155/2010/263914] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 11/07/2010] [Accepted: 11/15/2010] [Indexed: 02/07/2023] Open
Abstract
We summarize recent findings linking inflammatory hypoxia to chromatin modifications, in particular to repressive histone signatures. We focus on the role of Hypoxia-Induced Factor-1 in promoting the activity of specific histone demethylases thus deeply modifying chromatin configuration. The consequences of these changes are depicted in terms of gene expression and cellular phenotypes. We finally integrate available data to introduce novel speculations on the relationship between inflammation, histones, and DNA function and integrity.
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The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation. Cell Res 2010; 20:908-18. [PMID: 20548336 DOI: 10.1038/cr.2010.81] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent studies have identified mutations in PHF8, an X-linked gene encoding a JmjC domain-containing protein, as a causal factor for X-linked mental retardation (XLMR) and cleft lip/cleft palate. However, the underlying mechanism is unknown. Here we show that PHF8 is a histone demethylase and coactivator for retinoic acid receptor (RAR). Although activities for both H3K4me3/2/1 and H3K9me2/1 demethylation were detected in cellular-based assays, recombinant PHF8 exhibited only H3K9me2/1 demethylase activity in vitro, suggesting that PHF8 is an H3K9me2/1 demethylase whose specificity may be modulated in vivo. Importantly, a mutant PHF8 (phenylalanine at position 279 to serine) identified in the XLMR patients is defective in enzymatic activity, indicating that the loss of histone demethylase activity is causally linked with the onset of disease. In addition, we show that PHF8 binds specifically to H3K4me3/2 peptides via an N-terminal PHD finger domain. Consistent with a role for PHF8 in neuronal differentiation, knockdown of PHF8 in mouse embryonic carcinoma P19 cells impairs RA-induced neuronal differentiation, whereas overexpression of the wild-type but not the F279S mutant PHF8 drives P19 cells toward neuronal differentiation. Furthermore, we show that PHF8 interacts with RARalpha and functions as a coactivator for RARalpha. Taken together, our results suggest that histone methylation modulated by PHF8 plays a critical role in neuronal differentiation.
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Malik S, Bhaumik SR. Mixed lineage leukemia: histone H3 lysine 4 methyltransferases from yeast to human. FEBS J 2010; 277:1805-21. [PMID: 20236312 DOI: 10.1111/j.1742-4658.2010.07607.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fourth lysine of histone H3 is post-translationally modified by a methyl group via the action of histone methyltransferase, and such a covalent modification is associated with transcriptionally active and/or repressed chromatin states. Thus, histone H3 lysine 4 methylation has a crucial role in maintaining normal cellular functions. In fact, misregulation of this covalent modification has been implicated in various types of cancer and other diseases. Therefore, a large number of studies over recent years have been directed towards histone H3 lysine 4 methylation and the enzymes involved in this covalent modification in eukaryotes ranging from yeast to human. These studies revealed a set of histone H3 lysine 4 methyltransferases with important cellular functions in different eukaryotes, as discussed here.
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Affiliation(s)
- Shivani Malik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
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Spannhoff A, Hauser AT, Heinke R, Sippl W, Jung M. The emerging therapeutic potential of histone methyltransferase and demethylase inhibitors. ChemMedChem 2009; 4:1568-82. [PMID: 19739196 DOI: 10.1002/cmdc.200900301] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Epigenetics is defined as heritable changes to the transcriptome that are independent of changes in the genome. The biochemical modifications that govern epigenetics are DNA methylation and posttranslational histone modifications. Among the histone modifications, acetylation and deacetylation are well characterized, whereas the fields of histone methylation and especially demethylation are still in their infancy. This is particularly true with regard to drug discovery. There is strong evidence that these modifications play an important role in the maintenance of transcription as well as in the development of certain diseases. This article gives an overview of the mechanisms of action of histone methyltransferases and demethylases, their role in the formation of certain diseases, and available inhibitors. Special emphasis is placed on the strategies that led to the first inhibitors which are currently available and the screening approaches that were used in that process.
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Affiliation(s)
- Astrid Spannhoff
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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Beshara CS, Jones CE, Daze KD, Lilgert BJ, Hof F. A Simple Calixarene Recognizes Post-translationally Methylated Lysine. Chembiochem 2009; 11:63-6. [DOI: 10.1002/cbic.200900633] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Nottke A, Colaiácovo MP, Shi Y. Developmental roles of the histone lysine demethylases. Development 2009; 136:879-89. [PMID: 19234061 DOI: 10.1242/dev.020966] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the discovery of the first histone lysine demethylase in 2004, two protein families with numerous members have been identified that demethylate various histone lysine residues. Initial studies of the histone lysine demethylases focused on their in vitro enzymatic activity but, more recently, model organisms have been used to examine the roles of these enzymes in vivo. Here, we review recent insights into the roles of the histone lysine demethylases in multiple aspects of development across various species, including in germline maintenance and meiosis, in early embryonic development and differentiation, and in hormone receptor-mediated transcriptional regulation.
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Affiliation(s)
- Amanda Nottke
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Sun H, Zhou X, Chen H, Li Q, Costa M. Modulation of histone methylation and MLH1 gene silencing by hexavalent chromium. Toxicol Appl Pharmacol 2009; 237:258-66. [PMID: 19376149 DOI: 10.1016/j.taap.2009.04.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 04/02/2009] [Accepted: 04/06/2009] [Indexed: 01/08/2023]
Abstract
Hexavalent chromium [Cr(VI)] is a mutagen and carcinogen, and occupational exposure can lead to lung cancers and other adverse health effects. Genetic changes resulting from DNA damage have been proposed as an important mechanism that mediates chromate's carcinogenicity. Here we show that chromate exposure of human lung A549 cells increased global levels of di- and tri-methylated histone H3 lysine 9 (H3K9) and lysine 4 (H3K4) but decreased the levels of tri-methylated histone H3 lysine 27 (H3K27) and di-methylated histone H3 arginine 2 (H3R2). Most interestingly, H3K9 dimethylation was enriched in the human MLH1 gene promoter following chromate exposure and this was correlated with decreased MLH1 mRNA expression. Chromate exposure increased the protein as well as mRNA levels of G9a a histone methyltransferase that specifically methylates H3K9. This Cr(VI)-induced increase in G9a may account for the global elevation of H3K9 dimethylation. Furthermore, supplementation with ascorbate, the primary reductant of Cr(VI) and also an essential cofactor for the histone demethylase activity, partially reversed the H3K9 dimethylation induced by chromate. Thus our studies suggest that Cr(VI) may target histone methyltransferases and demethylases, which in turn affect both global and gene promoter specific histone methylation, leading to the silencing of specific tumor suppressor genes such as MLH1.
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Affiliation(s)
- Hong Sun
- Nelson Institute of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, New York 10987, USA
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Insights into the Post-Translational Methylation of Arginine from Studies of Guanidinium-Water Nanodroplets. Chemistry 2008; 14:6483-9. [DOI: 10.1002/chem.200800101] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Cell cycle association of the retinoblastoma protein Rb and the histone demethylase LSD1 with the Epstein-Barr virus latency promoter Cp. J Virol 2008; 82:3428-37. [PMID: 18216119 DOI: 10.1128/jvi.01412-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Epstein-Barr virus C promoter (Cp) regulates the major multicistronic transcript encoding the EBNA-LP, 1, 2, and 3 genes required for B-cell proliferation during latency. The growth-transforming potential of these viral genes suggests that they must be tightly regulated with the host cell cycle and differentiation process. To better understand Cp regulation, we used DNA affinity purification to identify cellular and viral proteins that bind to Cp in latently infected cells. Several previously unknown factors were identified, including the cell cycle regulatory proteins E2F1 and Rb. E2F1 bound to a specific site in Cp located in the core Cp region 3' of the known EBNA2-responsive RBP-Jk (CSL, CBF1) binding site. The histone H3 K4 demethylase LSD1 (BCC110) was also identified by DNA affinity and was shown to form a stable complex with Rb. Coimmunoprecipitation assays demonstrated that E2F1, Rb, and LSD1 bind to Cp in a cell cycle-dependent manner. Rb and LSD1 binding to Cp increased after the S phase, corresponding to a decrease in histone H3 K4 methylation and Cp transcription. Coimmunoprecipitation and immunofluorescence assays reveal that LSD1 interacts with Rb. Surprisingly, LSD1 did not coimmunoprecipitate with E2F1, suggesting that it associates with Rb independently of E2F1. Depletion of LSD1 by small interfering RNAs inhibited Cp basal transcription levels, and overexpression of LSD1 altered the cell cycle profile in p53-positive (p53(+)), but not p53-negative (p53(-)), HCT cells. These findings indicate that Cp is a cell cycle-regulated promoter that is under the control of Rb and the histone demethylase LSD1 in multiple latency types.
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Drosophila UTX is a histone H3 Lys27 demethylase that colocalizes with the elongating form of RNA polymerase II. Mol Cell Biol 2007; 28:1041-6. [PMID: 18039863 DOI: 10.1128/mcb.01504-07] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Histone H3 methylation at Lys27 (H3K27 methylation) is a hallmark of silent chromatin, while H3K4 methylation is associated with active chromatin regions. Here we report that a Drosophila JmjC family member, dUTX, specifically demethylates di- and trimethylated but not monomethylated H3K27. dUTX localization on chromatin correlates with the elongating form of RNA polymerase II (Pol II), and dUTX can associate with Pol II. Furthermore, heat shock induction results in the recruitment of dUTX to the hsp70 gene, like that of several other Pol II elongation factors. Our data indicate that dUTX is intimately associated with actively transcribed genes and may provide a paradigm for how H3K27 demethylation is required for the activation of preinitiated Pol II on transcriptionally poised genes.
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40
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Roy TW, Bhagwat AS. Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation. Nucleic Acids Res 2007; 35:e147. [PMID: 18003660 PMCID: PMC2175350 DOI: 10.1093/nar/gkm1031] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli AlkB protein catalyzes the direct reversal of alkylation damage to DNA; primarily 1-methyladenine (1mA) and 3-methylcytosine (3mC) lesions created by endogenous or environmental alkylating agents. AlkB is a member of the non-heme iron (II) α-ketoglutarate-dependent dioxygenase superfamily, which removes the alkyl group through oxidation eliminating a methyl group as formaldehyde. We have developed a fluorescence-based assay for the dealkylation activity of this family of enzymes. It uses formaldehyde dehydrogenase to convert formaldehyde to formic acid and monitors the creation of an NADH analog using fluorescence. This assay is a great improvement over the existing assays for DNA demethylation in that it is continuous, rapid and does not require radioactively labeled material. It may also be used to study other demethylation reactions including demethylation of histones. We used it to determine the kinetic constants for AlkB and found them to be somewhat different than previously reported values. The results show that AlkB demethylates 1mA and 3mC with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart.
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Affiliation(s)
- Todd W Roy
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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41
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Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol 2007; 14:1008-16. [PMID: 17984963 DOI: 10.1038/nsmb1337] [Citation(s) in RCA: 478] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Covalent modifications of histones are central to the regulation of chromatin dynamics, and, therefore, many biological processes involving chromatin, such as replication, repair, transcription and genome stability, are regulated by chromatin and its modifications. In this review, we discuss the biochemical, molecular and genetic properties of the enzymatic machinery involved in four different types of histone modification: acetylation, ubiquitination, phosphorylation and methylation. We also discuss how perturbation of the activity of this enzymatic machinery can cause developmental defects and disease.
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Mathevon C, Pierrel F, Oddou JL, Garcia-Serres R, Blondin G, Latour JM, Ménage S, Gambarelli S, Fontecave M, Atta M. tRNA-modifying MiaE protein from Salmonella typhimurium is a nonheme diiron monooxygenase. Proc Natl Acad Sci U S A 2007; 104:13295-300. [PMID: 17679698 PMCID: PMC1948905 DOI: 10.1073/pnas.0704338104] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Indexed: 11/18/2022] Open
Abstract
MiaE catalyzes the posttranscriptional allylic hydroxylation of 2-methylthio-N-6-isopentenyl adenosine in tRNAs. The Salmonella typhimurium enzyme was heterologously expressed in Escherichia coli. The purified enzyme is a monomer with two iron atoms and displays activity in in vitro assays. The type and properties of the iron center were investigated by using a combination of UV-visible absorption, EPR, HYSCORE, and Mössbauer spectroscopies which demonstrated that the MiaE enzyme contains a nonheme dinuclear iron cluster, similar to that found in the hydroxylase component of methane monooxygenase. This is the first example of an enzyme from this important class of diiron monooxygenases to be involved in the hydroxylation of a biological macromolecule and the second example of a redox metalloenzyme participating in tRNA modification.
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Affiliation(s)
- Carole Mathevon
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
| | - Fabien Pierrel
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
| | - Jean-Louis Oddou
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
| | - Ricardo Garcia-Serres
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
| | - Geneviève Blondin
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
| | - Jean-Marc Latour
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
| | - Stéphane Ménage
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
| | - Serge Gambarelli
- Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, Service de Chimie Inorganique et Biologique (SCIB)-Département de Recherche Fondamentale sur la Matière Condensée, Unité Mixte de la Recherche-E 3, Commissariat à l'Energie Atomique/Université Joseph Fourier, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France
| | - Marc Fontecave
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
| | - Mohamed Atta
- *Laboratoire de Chimie et Biologie des Métaux, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV-LCBM), Unité Mixte de la Recherche 5249, Commissariat à l'Energie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, Commissariat à l'Energie Atomique/Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France; and
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Couture JF, Collazo E, Ortiz-Tello PA, Brunzelle JS, Trievel RC. Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol 2007; 14:689-95. [PMID: 17589523 DOI: 10.1038/nsmb1273] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 06/15/2007] [Indexed: 12/25/2022]
Abstract
JMJD2A is a JmjC histone demethylase (HDM) that catalyzes the demethylation of di- and trimethylated Lys9 and Lys36 in histone H3 (H3K9me2/3 and H3K36me2/3). Here we present the crystal structures of the JMJD2A catalytic domain in complex with H3K9me3, H3K36me2 and H3K36me3 peptides. The structures reveal that histone substrates are recognized through a network of backbone hydrogen bonds and hydrophobic interactions that deposit the trimethyllysine into the active site. The trimethylated epsilon-ammonium cation is coordinated within a methylammonium-binding pocket through carbon-oxygen (CH...O) hydrogen bonds that position one of the zeta-methyl groups adjacent to the Fe(II) center for hydroxylation and demethylation. Mutations of the residues comprising this pocket abrogate demethylation by JMJD2A, with the exception of an S288A substitution, which augments activity, particularly toward H3K9me2. We propose that this residue modulates the methylation-state specificities of JMJD2 enzymes and other trimethyllysine-specific JmjC HDMs.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-0606, USA
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Pérez-Balado C, Nebbioso A, Rodríguez-Graña P, Minichiello A, Miceli M, Altucci L, de Lera AR. Bispyridinium Dienes: Histone Deacetylase Inhibitors with Selective Activities. J Med Chem 2007; 50:2497-505. [PMID: 17447750 DOI: 10.1021/jm070028m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel synthetic route to the cyclostellettamines 1 using as the key step a microwave-mediated macrocyclic ring-closing metathesis of precursors bispyridinium dienes 10 followed by catalytic hydrogenation has been developed. The open-chain bispyridinium dienes 10 showed uniformly higher histone deacetylase (HDAC) inhibitory potency than the natural products. Diene 10b inhibited HDAC1 and was inactive on HDAC4, whereas 10a showed a weak inhibition of HDAC1 and a higher activity on HDAC4. Neither 10b nor 10a inhibited isoforms HDAC2 and HDAC3. Cell cycle analysis, cell differentiation, and apoptosis as well as evaluation of the acetylation status of H3 lysine tails, up-regulation of p21WAF1/CIP1, and alpha-tubulin acetylation induced by the dienes 10 and cyclostellettamines 1 were also carried out on the human leukemia U937 cell line. These enzymatic and functional assays suggest that 10b is a HDAC1-selective inhibitor and 10a is a HDAC subclass IIa-selective inhibitor.
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Affiliation(s)
- Carlos Pérez-Balado
- Departamento de Química Orgánica, Universidade de Vigo, Lagoas-Marcosende, 36310 Vigo, Spain
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45
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Eissenberg JC, Lee MG, Schneider J, Ilvarsonn A, Shiekhattar R, Shilatifard A. The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase. Nat Struct Mol Biol 2007; 14:344-6. [PMID: 17351630 DOI: 10.1038/nsmb1217] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 02/20/2007] [Indexed: 01/09/2023]
Abstract
Histone H3 Lys4 (H3K4) is methylated by yeast Set1-COMPASS and its mammalian homolog, the MLL complex. Human JARID1d can demethylate trimethyl-H3K4 (H3K4me3). We identified Drosophila melanogaster little imaginal discs (Lid) as the JARID1d homolog. We report that Lid knockdown using RNA interference results in a specific genome-wide increase in H3K4me3 levels without affecting other patterns of H3 methylation, and results in an altered distribution of the chromo-helicase protein Chd1.
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Affiliation(s)
- Joel C Eissenberg
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, Missouri 63104, USA
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46
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Freberg CT, Dahl JA, Timoskainen S, Collas P. Epigenetic reprogramming of OCT4 and NANOG regulatory regions by embryonal carcinoma cell extract. Mol Biol Cell 2007; 18:1543-53. [PMID: 17314394 PMCID: PMC1855029 DOI: 10.1091/mbc.e07-01-0029] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Analyses of molecular events associated with reprogramming somatic nuclei to pluripotency are scarce. We previously reported the reprogramming of epithelial cells by extract of undifferentiated embryonal carcinoma (EC) cells. We now demonstrate reprogramming of DNA methylation and histone modifications on regulatory regions of the developmentally regulated OCT4 and NANOG genes by exposure of 293T cells to EC cell extract. OCT4 and NANOG are transcriptionally up-regulated and undergo mosaic cytosine-phosphate-guanosine demethylation. OCT4 demethylation occurs as early as week 1, is enhanced by week 2, and is most prominent in the proximal promoter and distal enhancer. Targeted OCT4 and NANOG demethylation does not occur in 293T extract-treated cells. Retinoic acid-mediated differentiation of reprogrammed cells elicits OCT4 promoter remethylation and transcriptional repression. Chromatin immunoprecipitation analyses of lysines K4, K9, and K27 of histone H3 on OCT4 and NANOG indicate that primary chromatin remodeling determinants are acetylation of H3K9 and demethylation of dimethylated H3K9. H3K4 remains di- and trimethylated. Demethylation of trimethylated H3K9 and H3K27 also occurs; however, trimethylation seems more stable than dimethylation. We conclude that a central epigenetic reprogramming event is relaxation of chromatin at loci associated with pluripotency to create a conformation compatible with transcriptional activation.
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Affiliation(s)
- Christel T. Freberg
- Department of Biochemistry, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - John Arne Dahl
- Department of Biochemistry, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Sanna Timoskainen
- Department of Biochemistry, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Philippe Collas
- Department of Biochemistry, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
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Abstract
Posttranslational modifications of histones, both in the tails and in the globular cores, alter the functional landscape of chromatin by modulating DNA accessibility and chromatin stability, and by providing an enormous variety of alternative interaction surfaces for trans-acting factors. Complex patterns of acetylation, methylation, phosphorylation, ubiquitylation (and others) result in spatial domains of meaningful chromatin modifications, often referred to as the histone code. Whole genome studies have uncovered striking genome-wide patterns of specific modifications, and individual modifications have been linked to a variety of functional consequences for transcription, replication and repair. A key aspect of the role of histone modifications, however, is their dynamic nature-the precise timing of the addition and removal of specific marks is an essential part of the histone code. This review will highlight examples from budding yeast that illustrate the importance of these dynamic modifications in controlling transcription and repair.
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Affiliation(s)
- Jocelyn E Krebs
- University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.
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Hoffart LM, Barr EW, Guyer RB, Bollinger JM, Krebs C. Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase. Proc Natl Acad Sci U S A 2006; 103:14738-43. [PMID: 17003127 PMCID: PMC1578498 DOI: 10.1073/pnas.0604005103] [Citation(s) in RCA: 255] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The Fe(II)- and alpha-ketoglutarate (alphaKG)-dependent dioxygenases use mononuclear nonheme iron centers to effect hydroxylation of their substrates and decarboxylation of their cosubstrate, alphaKG, to CO(2) and succinate. Our recent dissection of the mechanism of taurine:alphaKG dioxygenase (TauD), a member of this enzyme family, revealed that two transient complexes accumulate during catalysis in the presence of saturating substrates. The first complex contains the long-postulated C-H-cleaving Fe(IV)-oxo intermediate, J, and the second is an enzyme.product(s) complex. Here, we demonstrate the accumulation of two transient complexes in the reaction of a prolyl-4-hydroxylase (P4H), a functional homologue of human alphaKG-dependent dioxygenases with essential roles in collagen biosynthesis and oxygen sensing. The kinetic and spectroscopic properties of these two P4H complexes suggest that they are homologues of the TauD intermediates. Most notably, the first exhibits optical absorption and Mössbauer spectra similar to those of J and, like J, a large substrate deuterium kinetic isotope on its decay. The close correspondence of the accumulating states in the P4H and TauD reactions supports the hypothesis of a conserved mechanism for substrate hydroxylation by enzymes in this family.
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Affiliation(s)
| | - Eric W. Barr
- Departments of *Biochemistry and Molecular Biology and
| | | | - J. Martin Bollinger
- Departments of *Biochemistry and Molecular Biology and
- Chemistry, Pennsylvania State University, University Park, PA 16802
- To whom correspondence may be addressed. E-mail:
or
| | - Carsten Krebs
- Departments of *Biochemistry and Molecular Biology and
- Chemistry, Pennsylvania State University, University Park, PA 16802
- To whom correspondence may be addressed. E-mail:
or
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Tegen SB. Enhancing the Web Experience. ACS Chem Biol 2006. [DOI: 10.1021/cb600105g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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