151
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Kungulovski G, Mauser R, Reinhardt R, Jeltsch A. Application of recombinant TAF3 PHD domain instead of anti-H3K4me3 antibody. Epigenetics Chromatin 2016; 9:11. [PMID: 27006701 PMCID: PMC4802638 DOI: 10.1186/s13072-016-0061-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/11/2016] [Indexed: 12/16/2022] Open
Abstract
Background Histone posttranslational modifications (PTMs) represent a focal point of chromatin regulation. The genome-wide and locus-specific distribution and the presence of distinct histone PTMs is most commonly examined with the application of histone PTM-specific antibodies. In spite of their central role in chromatin research, polyclonal antibodies suffer from disadvantages like batch-to-batch variability and insufficient documentation of their quality and specificity. Results To mitigate some of the pitfalls of using polyclonal antibodies against H3K4me3, we successfully validated the application of a recombinant TAF3 PHD domain as anti-H3K4me3 affinity reagent in peptide array, western blot and ChIP-like experiments coupled with qPCR and deep sequencing. Conclusions The successful addition of the TAF3 PHD domain to the growing catalog of recombinant affinity reagents for histone PTMs could help to improve the reproducibility, interpretation and cross-laboratory validation of chromatin data. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0061-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Goran Kungulovski
- Faculty of Chemistry, Institute of Biochemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Rebekka Mauser
- Faculty of Chemistry, Institute of Biochemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Albert Jeltsch
- Faculty of Chemistry, Institute of Biochemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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152
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Abstract
Histones are subject to frequent combinatorial post-translational modifications (PTMs), forming a complex chemical "language" that is interpreted by PTM-specific histone-interacting protein modules (reader domains). These specific interactions are thought to instruct gene expression and downstream biological functions. While the majority of studies have focused on individual modifications, our current understanding of the combinatorial PTM patterns on histones is starting to emerge, benefiting from the convergence of multiple technologies. Here, we review the key technical advances and progress on discovery and characterization of combinatorial histone PTM patterns. We focus on the interactions between reader domains and combinatorial PTMs, which is essential for understanding the mechanism and biological meaning of establishing and interpreting information embedded in histone PTM patterns.
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Affiliation(s)
- Zhangli Su
- Department
of Biomolecular
Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin—Madison, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Department
of Biomolecular
Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin—Madison, Madison, Wisconsin 53715, United States
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153
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Tsunaka Y, Fujiwara Y, Oyama T, Hirose S, Morikawa K. Integrated molecular mechanism directing nucleosome reorganization by human FACT. Genes Dev 2016; 30:673-86. [PMID: 26966247 PMCID: PMC4803053 DOI: 10.1101/gad.274183.115] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/05/2016] [Indexed: 11/24/2022]
Abstract
Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Tsunaka et al. studied human FACT–histone interactions that present precise views of nucleosome reorganization, conducted by the FACT-SPT16 Mid domain and its adjacent acidic AID segment. Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT–histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3–H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular β structure with H4. At the other site, the Mid–H2A steric collision on the H2A-docking surface of the H3–H4 tetramer within the nucleosome induces H2A–H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone.
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Affiliation(s)
- Yasuo Tsunaka
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Sakyo-ku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606-8501, Japan; International Institute for Advanced Studies, Kizugawa-shi, Kyoto 619-0225, Japan
| | - Yoshie Fujiwara
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuji Oyama
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Susumu Hirose
- Department of Developmental Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kosuke Morikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606-8501, Japan; International Institute for Advanced Studies, Kizugawa-shi, Kyoto 619-0225, Japan
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154
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Giebel NL, Shadley JD, McCarver DG, Dorko K, Gramignoli R, Strom SC, Yan K, Simpson PM, Hines RN. Role of Chromatin Structural Changes in Regulating Human CYP3A Ontogeny. ACTA ACUST UNITED AC 2016; 44:1027-37. [PMID: 26921389 DOI: 10.1124/dmd.116.069344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/25/2016] [Indexed: 11/22/2022]
Abstract
Variability in drug-metabolizing enzyme developmental trajectories contributes to interindividual differences in susceptibility to chemical toxicity and adverse drug reactions, particularly in the first years of life. Factors linked to these interindividual differences are largely unknown, but molecular mechanisms regulating ontogeny are likely involved. To evaluate chromatin structure dynamics as a likely contributing mechanism, age-dependent changes in modified and variant histone occupancy were evaluated within known CYP3A4 and 3A7 regulatory domains. Chromatin immunoprecipitation using fetal or postnatal human hepatocyte chromatin pools followed by quantitative polymerase chain reaction DNA amplification was used to determine relative chromatin occupancy by modified and variant histones. Chromatin structure representing a poised transcriptional state (bivalent chromatin), indicated by the occupancy by modified histones associated with both active and repressed transcription, was observed for CYP3A4 and most 3A7 regulatory regions in both postnatal and fetal livers. However, the CYP3A4 regulatory regions had significantly greater occupancy by modified histones associated with repressed transcription in the fetal liver. Conversely, some modified histones associated with active transcription exhibited greater occupancy in the postnatal liver. CYP3A7 regulatory regions also had significantly greater occupancy by modified histones associated with repressed transcription in the fetus. The observed occupancy by modified histones is consistent with chromatin structural dynamics contributing to CYP3A4 ontogeny, although the data are less conclusive regarding CYP3A7. Interpretation of the latter data may be confounded by cell-type heterogeneity in the fetal liver.
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Affiliation(s)
- Nicholas L Giebel
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
| | - Jeffrey D Shadley
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
| | - D Gail McCarver
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
| | - Kenneth Dorko
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
| | - Roberto Gramignoli
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
| | - Stephen C Strom
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
| | - Ke Yan
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
| | - Pippa M Simpson
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
| | - Ronald N Hines
- Departments of Pediatrics and Pharmacology and Toxicology, Medical College of Wisconsin, and Children's Research Institute, Children's Hospital and Health Systems, Milwaukee, Wisconsin (N.L.G., J.D.S., D.G.M., K.Y., P.M.S., R.N.H.); and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (K.D., R.G., S.C.S.)
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155
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Ganesan A. Multitarget Drugs: an Epigenetic Epiphany. ChemMedChem 2016; 11:1227-41. [PMID: 26891251 DOI: 10.1002/cmdc.201500394] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/28/2016] [Indexed: 12/22/2022]
Abstract
Epigenetics refers to changes in a biological phenotype that are not due to an underlying change in genotype. In eukaryotes, epigenetics involves a set of chemical modifications of the DNA and the histone proteins in nucleosomes. These dynamic changes are carried out by enzymes and modulate protein-protein and protein-nucleic acid interactions to determine whether specific genes are expressed or silenced. Both the epigenetic enzymes and recognition domains are currently important drug discovery targets, particularly for the treatment of cancer. This review summarizes the progress of epigenetic targets that have reached a clinical stage: DNA methyltransferases, histone deacetylases, lysine methyltransferases, lysine demethylases, and bromodomains; this is followed by a comprehensive survey of multitarget drugs that have included an epigenetic target as one of their mechanisms of action.
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Affiliation(s)
- A Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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156
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Chang LC, Yu YL. Dietary components as epigenetic-regulating agents against cancer. Biomedicine (Taipei) 2016; 6:2. [PMID: 26872811 PMCID: PMC4752550 DOI: 10.7603/s40681-016-0002-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/08/2016] [Indexed: 12/12/2022] Open
Abstract
Carcinogenesis is a complicated process that involves the deregulation of epigenetics resulting in cellular transformational events, such proliferation, differentiation, and metastasis. Epigenetic machinery changes the accessibility of chromatin to transcriptional regulation through DNA modification. The collaboration of epigenetics and gene transcriptional regulation creates a suitable microenvironment for cancer development, which is proved by the alternation in cell proliferation, differentiation, division, metabolism, DNA repair and movement. Therefore, the reverse of epigenetic dysfunction may provide a possible strategy and new therapeutic targets for cancer treatment. Many dietary components such as sulforaphane and epigallocatechin- 3-gallate have been demonstrated to exert chemopreventive influences, such as reducing tumor growth and enhancing cancer cell death. Anticancer mechanistic studies also indicated that dietary components could display the ability to reverse epigenetic deregulation in assorted tumors via reverting the adverse epigenetic regulation, including alternation of DNA methylation and histone modification, and modulation of microRNA expression. Therefore, dietary components as therapeutic agents on epigenetics becomes an attractive approach for cancer prevention and intervention at the moment. In this review, we summarize the recent discoveries and underlying mechanisms of the most common dietary components for cancer prevention via epigenetic regulation.
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Affiliation(s)
- Ling-Chu Chang
- Chinese Medicinal Research and Development Center, China Medical University Hospital, 404, Taichung, Taiwan
| | - Yung-Luen Yu
- Graduate Institute of Cancer Biology, China Medical University, 404, Taichung, Taiwan. .,Center for Molecular Medicine, China Medical University Hospital, 404, Taichung, Taiwan. .,Department of Biotechnology, Asia University, 413, Taichung, Taiwan.
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157
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Taormina G, Mirisola MG. Longevity: epigenetic and biomolecular aspects. Biomol Concepts 2016; 6:105-17. [PMID: 25883209 DOI: 10.1515/bmc-2014-0038] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/04/2015] [Indexed: 12/28/2022] Open
Abstract
Many aging theories and their related molecular mechanisms have been proposed. Simple model organisms such as yeasts, worms, fruit flies and others have massively contributed to their clarification, and many genes and pathways have been associated with longevity regulation. Among them, insulin/IGF-1 plays a key and evolutionary conserved role. Interestingly, dietary interventions can modulate this pathway. Calorie restriction (CR), intermittent fasting, and protein and amino acid restriction prolong the lifespan of mammals by IGF-1 regulation. However, some recent findings support the hypothesis that the long-term effects of diet also involve epigenetic mechanisms. In this review, we describe the best characterized aging pathways and highlight the role of epigenetics in diet-mediated longevity.
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158
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Veith N, Ziehr H, MacLeod RAF, Reamon-Buettner SM. Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines. BMC Biotechnol 2016; 16:6. [PMID: 26800878 PMCID: PMC4722726 DOI: 10.1186/s12896-016-0238-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/15/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Recombinant cell lines developed for therapeutic antibody production often suffer instability or lose recombinant protein expression during long-term culture. Heterogeneous gene expression among cell line subclones may result from epigenetic modifications of DNA or histones, the protein component of chromatin. We thus investigated in such cell lines, DNA methylation and the chromatin environment along the human eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) promoter in an antibody protein-expression vector which was integrated into the Chinese hamster ovary (CHO) cell line genome. RESULTS We analyzed four PT1-CHO cell lines which exhibited losses of protein expression at advanced passage number (>P35) growing in adherent conditions and in culture medium with 10 % FCS. These cell lines exhibited different integration sites and transgene copy numbers as determined by fluorescence in situ hybridization (FISH) and quantitative PCR (qPCR), respectively. By qRT-PCR, we analyzed the recombinant mRNA expression and correlated it with DNA methylation and with results from various approaches interrogating the chromatin landscape along the EEF1A1 promoter region. Each PT1-CHO cell line displayed specific epigenetic signatures or chromatin marks correlating with recombinant mRNA expression. The cell line with the lowest recombinant mRNA expression (PT1-1) was characterized by the highest nucleosome occupancy and displayed the lowest enrichment for histone marks associated with active transcription. In contrast, the cell line with the highest recombinant mRNA expression (PT1-55) exhibited the highest numbers of formaldehyde-assisted isolation of regulatory elements (FAIRE)-enriched regions, and was marked by enrichment for histone modifications H3K9ac and H3K9me3. Another cell line with the second highest recombinant mRNA transcription and the most stable protein expression (PT1-7) had the highest enrichments of the histone variants H3.3 and H2A.Z, and the histone modification H3K9ac. A further cell line (PT1-30) scored the highest enrichments for the bivalent marks H3K4me3 and H3K27me3. Finally, DNA methylation made a contribution, but only in the culture medium with reduced FCS or in a different expression vector. CONCLUSIONS Our results suggest that the chromatin state along the EEF1A1 promoter region can help predict recombinant mRNA expression, and thus may assist in selecting desirable clones during cell line development for protein production.
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Affiliation(s)
- Nathalie Veith
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Holger Ziehr
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Roderick A F MacLeod
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany.
| | - Stella Marie Reamon-Buettner
- Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs Strasse 1, 30625, Hannover, Germany.
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159
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Valero ML, Sendra R, Pamblanco M. Tandem affinity purification of histones, coupled to mass spectrometry, identifies associated proteins and new sites of post-translational modification in Saccharomyces cerevisiae. J Proteomics 2016; 136:183-92. [PMID: 26778144 DOI: 10.1016/j.jprot.2016.01.004] [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] [Received: 07/29/2015] [Revised: 12/17/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023]
Abstract
Histones and their post-translational modifications contribute to regulating fundamental biological processes in all eukaryotic cells. We have applied a conventional tandem affinity purification strategy to histones H3 and H4 of the yeast Saccharomyces cerevisiae. Mass spectrometry analysis of the co-purified proteins revealed multiple associated proteins, including core histones, which indicates that tagged histones may be incorporated to the nucleosome particle. Among the many other co-isolated proteins there are histone chaperones, elements of chromatin remodeling, of nucleosome assembly/disassembly, and of histone modification complexes. The histone chaperone Rtt106p, two members of chromatin assembly FACT complex and Psh1p, an ubiquitin ligase, were the most abundant proteins obtained with both H3-TAP and H4-TAP, regardless of the cell extraction medium stringency. Our mass spectrometry analyses have also revealed numerous novel post-translational modifications, including 30 new chemical modifications in histones, mainly by ubiquitination. We have discovered not only new sites of ubiquitination but that, besides lysine, also serine and threonine residues are targets of ubiquitination on yeast histones. Our results show the standard tandem affinity purification procedure is suitable for application to yeast histones, in order to isolate and characterize histone-binding proteins and post-translational modifications, avoiding the bias caused by histone purification from a chromatin-enriched fraction.
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Affiliation(s)
- M Luz Valero
- Secció de Proteòmica, Servei Central de Suport a la Investigació Experimental (SCSIE), Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
| | - Ramon Sendra
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
| | - Mercè Pamblanco
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
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160
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Blasi T, Feller C, Feigelman J, Hasenauer J, Imhof A, Theis F, Becker P, Marr C. Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions. Cell Syst 2016; 2:49-58. [DOI: 10.1016/j.cels.2016.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 11/18/2015] [Accepted: 01/05/2016] [Indexed: 11/25/2022]
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161
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Yan K, You L, Degerny C, Ghorbani M, Liu X, Chen L, Li L, Miao D, Yang XJ. The Chromatin Regulator BRPF3 Preferentially Activates the HBO1 Acetyltransferase but Is Dispensable for Mouse Development and Survival. J Biol Chem 2015; 291:2647-63. [PMID: 26677226 DOI: 10.1074/jbc.m115.703041] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 12/12/2022] Open
Abstract
To interpret epigenetic information, chromatin readers utilize various protein domains for recognition of DNA and histone modifications. Some readers possess multidomains for modification recognition and are thus multivalent. Bromodomain- and plant homeodomain-linked finger-containing protein 3 (BRPF3) is such a chromatin reader, containing two plant homeodomain-linked fingers, one bromodomain and a PWWP domain. However, its molecular and biological functions remain to be investigated. Here, we report that endogenous BRPF3 preferentially forms a tetrameric complex with HBO1 (also known as KAT7) and two other subunits but not with related acetyltransferases such as MOZ, MORF, TIP60, and MOF (also known as KAT6A, KAT6B, KAT5, and KAT8, respectively). We have also characterized a mutant mouse strain with a lacZ reporter inserted at the Brpf3 locus. Systematic analysis of β-galactosidase activity revealed dynamic spatiotemporal expression of Brpf3 during mouse embryogenesis and high expression in the adult brain and testis. Brpf3 disruption, however, resulted in no obvious gross phenotypes. This is in stark contrast to Brpf1 and Brpf2, whose loss causes lethality at E9.5 and E15.5, respectively. In Brpf3-null mice and embryonic fibroblasts, RT-quantitative PCR uncovered no changes in levels of Brpf1 and Brpf2 transcripts, confirming no compensation from them. These results indicate that BRPF3 forms a functional tetrameric complex with HBO1 but is not required for mouse development and survival, thereby distinguishing BRPF3 from its paralogs, BRPF1 and BRPF2.
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Affiliation(s)
- Kezhi Yan
- From the Rosalind and Morris Goodman Cancer Research Center, Departments of Biochemistry and Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Linya You
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Cindy Degerny
- From the Rosalind and Morris Goodman Cancer Research Center
| | - Mohammad Ghorbani
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Xin Liu
- From the Rosalind and Morris Goodman Cancer Research Center
| | - Lulu Chen
- the State Key Laboratory of Reproductive Medicine, Research Center for Bone and Stem Cells, Department of Human Anatomy, Nanjing Medical University, Nanjing 210029, China, and
| | - Lin Li
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Dengshun Miao
- the State Key Laboratory of Reproductive Medicine, Research Center for Bone and Stem Cells, Department of Human Anatomy, Nanjing Medical University, Nanjing 210029, China, and
| | - Xiang-Jiao Yang
- From the Rosalind and Morris Goodman Cancer Research Center, Departments of Biochemistry and Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada, the McGill University Health Center, Montreal, Quebec H3A 1A3, Canada
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162
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Zan H, Casali P. Epigenetics of Peripheral B-Cell Differentiation and the Antibody Response. Front Immunol 2015; 6:631. [PMID: 26697022 PMCID: PMC4677338 DOI: 10.3389/fimmu.2015.00631] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, such as histone post-translational modifications, DNA methylation, and alteration of gene expression by non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are heritable changes that are independent from the genomic DNA sequence. These regulate gene activities and, therefore, cellular functions. Epigenetic modifications act in concert with transcription factors and play critical roles in B cell development and differentiation, thereby modulating antibody responses to foreign- and self-antigens. Upon antigen encounter by mature B cells in the periphery, alterations of these lymphocytes epigenetic landscape are induced by the same stimuli that drive the antibody response. Such alterations instruct B cells to undergo immunoglobulin (Ig) class switch DNA recombination (CSR) and somatic hypermutation (SHM), as well as differentiation to memory B cells or long-lived plasma cells for the immune memory. Inducible histone modifications, together with DNA methylation and miRNAs modulate the transcriptome, particularly the expression of activation-induced cytidine deaminase, which is essential for CSR and SHM, and factors central to plasma cell differentiation, such as B lymphocyte-induced maturation protein-1. These inducible B cell-intrinsic epigenetic marks guide the maturation of antibody responses. Combinatorial histone modifications also function as histone codes to target CSR and, possibly, SHM machinery to the Ig loci by recruiting specific adaptors that can stabilize CSR/SHM factors. In addition, lncRNAs, such as recently reported lncRNA-CSR and an lncRNA generated through transcription of the S region that form G-quadruplex structures, are also important for CSR targeting. Epigenetic dysregulation in B cells, including the aberrant expression of non-coding RNAs and alterations of histone modifications and DNA methylation, can result in aberrant antibody responses to foreign antigens, such as those on microbial pathogens, and generation of pathogenic autoantibodies, IgE in allergic reactions, as well as B cell neoplasia. Epigenetic marks would be attractive targets for new therapeutics for autoimmune and allergic diseases, and B cell malignancies.
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Affiliation(s)
- Hong Zan
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
| | - Paolo Casali
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
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163
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Matharu N, Ahituv N. Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease. PLoS Genet 2015; 11:e1005640. [PMID: 26632825 PMCID: PMC4669122 DOI: 10.1371/journal.pgen.1005640] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The organization and folding of chromatin within the nucleus can determine the outcome of gene expression. Recent technological advancements have enabled us to study chromatin interactions in a genome-wide manner at high resolution. These studies have increased our understanding of the hierarchy and dynamics of chromatin domains that facilitate cognate enhancer–promoter looping, defining the transcriptional program of different cell types. In this review, we focus on vertebrate chromatin long-range interactions as they relate to transcriptional regulation. In addition, we describe how the alteration of boundaries that mark discrete regions in the genome with high interaction frequencies within them, called topological associated domains (TADs), could lead to various phenotypes, including human diseases, which we term as “TADopathies.”
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Affiliation(s)
- Navneet Matharu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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164
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van Nuland R, Gozani O. Histone H4 Lysine 20 (H4K20) Methylation, Expanding the Signaling Potential of the Proteome One Methyl Moiety at a Time. Mol Cell Proteomics 2015; 15:755-64. [PMID: 26598646 DOI: 10.1074/mcp.r115.054742] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Indexed: 12/13/2022] Open
Abstract
Covalent post-translational modifications (PTMs) of proteins can regulate the structural and functional state of a protein in the absence of primary changes in the underlying sequence. Common PTMs include phosphorylation, acetylation, and methylation. Histone proteins are critical regulators of the genome and are subject to a highly abundant and diverse array of PTMs. To highlight the functional complexity added to the proteome by lysine methylation signaling, here we will focus on lysine methylation of histone proteins, an important modification in the regulation of chromatin and epigenetic processes. We review the signaling pathways and functions associated with a single residue, H4K20, as a model chromatin and clinically important mark that regulates biological processes ranging from the DNA damage response and DNA replication to gene expression and silencing.
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Affiliation(s)
- Rick van Nuland
- From the Department of Biology, Stanford University, Stanford, California 94305
| | - Or Gozani
- From the Department of Biology, Stanford University, Stanford, California 94305
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165
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Schick S, Fournier D, Thakurela S, Sahu SK, Garding A, Tiwari VK. Dynamics of chromatin accessibility and epigenetic state in response to UV damage. J Cell Sci 2015; 128:4380-94. [PMID: 26446258 DOI: 10.1242/jcs.173633] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/29/2015] [Indexed: 12/27/2022] Open
Abstract
Epigenetic mechanisms determine the access of regulatory factors to DNA during events such as transcription and the DNA damage response. However, the global response of histone modifications and chromatin accessibility to UV exposure remains poorly understood. Here, we report that UV exposure results in a genome-wide reduction in chromatin accessibility, while the distribution of the active regulatory mark H3K27ac undergoes massive reorganization. Genomic loci subjected to epigenetic reprogramming upon UV exposure represent target sites for sequence-specific transcription factors. Most of these are distal regulatory regions, highlighting their importance in the cellular response to UV exposure. Furthermore, UV exposure results in an extensive reorganization of super-enhancers, accompanied by expression changes of associated genes, which may in part contribute to the stress response. Taken together, our study provides the first comprehensive resource for genome-wide chromatin changes upon UV irradiation in relation to gene expression and elucidates new aspects of this relationship.
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Affiliation(s)
- Sandra Schick
- Institute of Molecular Biology (IMB), Mainz, Germany
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166
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Kungulovski G, Mauser R, Jeltsch A. Affinity reagents for studying histone modifications & guidelines for their quality control. Epigenomics 2015; 7:1185-96. [DOI: 10.2217/epi.15.59] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Histone post-translational modifications (PTMs) have pivotal functions in many chromatin processes, which makes their detection and characterization an imperative in chromatin biology. The established approaches for histone PTM characterization are generally based on affinity reagents specific for modified histone tails such as antibodies and, most recently, recombinant reading domains. Hence, the proper performance of these reagents is a critical precondition for the validity of the generated experimental data. In this review, we evaluate and update the quality criteria for assessment of the binding specificity of histone PTM affinity reagents. In addition, we discuss in detail the advantages and pitfalls of using antibodies and recombinant reading domains in chromatin biology research. Reading domains provide key advantages, such as consistent quality and recombinant production, but the future will tell if this emerging technology keeps its promises.
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Affiliation(s)
- Goran Kungulovski
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Rebekka Mauser
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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167
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Abstract
DNA damage is caused by either endogenous cellular metabolic processes such as hydrolysis, oxidation, alkylation, and DNA base mismatches, or exogenous sources including ultraviolet (UV) light, ionizing radiation, and chemical agents. Damaged DNA that is not properly repaired can lead to genomic instability, driving tumorigenesis. To protect genomic stability, mammalian cells have evolved highly conserved DNA repair mechanisms to remove and repair DNA lesions. Telomeres are composed of long tandem TTAGGG repeats located at the ends of chromosomes. Maintenance of functional telomeres is critical for preventing genome instability. The telomeric sequence possesses unique features that predispose telomeres to a variety of DNA damage induced by environmental genotoxins. This review briefly describes the relevance of excision repair pathways in telomere maintenance, with the focus on base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). By summarizing current knowledge on excision repair of telomere damage and outlining many unanswered questions, it is our hope to stimulate further interest in a better understanding of excision repair processes at telomeres and in how these processes contribute to telomere maintenance.
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Affiliation(s)
- Pingping Jia
- Elson S. Floyd College of Medicine, United States
| | - Chengtao Her
- School of Molecular Biosciences, Washington State University, United States
| | - Weihang Chai
- Elson S. Floyd College of Medicine, United States; School of Molecular Biosciences, Washington State University, United States.
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168
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Abstract
DNA in human cells is constantly assaulted by endogenous and exogenous DNA damaging agents. It is vital for the cell to respond rapidly and precisely to DNA damage to maintain genome integrity and reduce the risk of mutagenesis. Sophisticated reactions occur in chromatin surrounding the damaged site leading to the activation of DNA damage response (DDR), including transcription reprogramming, cell cycle checkpoint, and DNA repair. Histone proteins around the DNA damage play essential roles in DDR, through extensive post-translational modifications (PTMs) by a variety of modifying enzymes. One PTM on histones, mono-ubiquitylation, has emerged as a key player in cellular response to DNA damage. In this review, we will (1) briefly summarize the history of histone H2A and H2B ubiquitylation (H2Aub and H2Bub, respectively), (2) discuss their roles in transcription, and (3) their functions in DDR.
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169
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Ernst UR, Van Hiel MB, Depuydt G, Boerjan B, De Loof A, Schoofs L. Epigenetics and locust life phase transitions. ACTA ACUST UNITED AC 2015; 218:88-99. [PMID: 25568455 DOI: 10.1242/jeb.107078] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Insects are one of the most successful classes on Earth, reflected in an enormous species richness and diversity. Arguably, this success is partly due to the high degree to which polyphenism, where one genotype gives rise to more than one phenotype, is exploited by many of its species. In social insects, for instance, larval diet influences the development into distinct castes; and locust polyphenism has tricked researchers for years into believing that the drastically different solitarious and gregarious phases might be different species. Solitarious locusts behave much as common grasshoppers. However, they are notorious for forming vast, devastating swarms upon crowding. These gregarious animals are shorter lived, less fecund and transmit their phase characteristics to their offspring. The behavioural gregarisation occurs within hours, yet the full display of gregarious characters takes several generations, as does the reversal to the solitarious phase. Hormones, neuropeptides and neurotransmitters influence some of the phase traits; however, none of the suggested mechanisms can account for all the observed differences, notably imprinting effects on longevity and fecundity. This is why, more recently, epigenetics has caught the interest of the polyphenism field. Accumulating evidence points towards a role for epigenetic regulation in locust phase polyphenism. This is corroborated in the economically important locust species Locusta migratoria and Schistocerca gregaria. Here, we review the key elements involved in phase transition in locusts and possible epigenetic regulation. We discuss the relative role of DNA methylation, histone modification and small RNA molecules, and suggest future research directions.
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Affiliation(s)
- Ulrich R Ernst
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Matthias B Van Hiel
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Geert Depuydt
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Bart Boerjan
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Arnold De Loof
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
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170
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Jiang XX, Chou Y, Jones L, Wang T, Sanchez S, Huang XF, Zhang L, Wang C, Chen SY. Epigenetic Regulation of Antibody Responses by the Histone H2A Deubiquitinase MYSM1. Sci Rep 2015; 5:13755. [PMID: 26348977 PMCID: PMC4562257 DOI: 10.1038/srep13755] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/04/2015] [Indexed: 01/25/2023] Open
Abstract
B cell-mediated antibody response plays critical roles in protective immunity, as well as in the pathogenesis of allergic and autoimmune diseases. Epigenetic histone and DNA modifications regulate gene transcription and immunity; however, so far, little is known about the role of epigenetic regulation in antibody responses. In this study, we found that mice deficient in the histone H2A deubiquitinase MYSM1, despite their severe defect in B cell development, exhibit an enhanced antibody response against both T cell-dependent and independent antigens. We revealed that MYSM1 intrinsically represses plasma cell differentiation and antibody production. Mechanistic studies demonstrated that MYSM1 is a transcriptional activator of Pax5, the repressors of plasma cell differentiation, by facilitating key transcriptional factor recruitment and coordinating histone modifications at the Pax5 loci. Hence, this study uncovers a critical role for MYSM1 in epigenetically repressing plasma cell differentiation and antibody production, in addition to its opposing, active role in B cell development. Importantly, this study further provides a new target and strategy to modulate antibody production and responses with profound therapeutic implications.
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Affiliation(s)
- Xiao-Xia Jiang
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA.,Department of Advanced Interdisciplinary Studies, Institute of Basic Medical Sciences, Beijing, 100850, China
| | - YuChia Chou
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
| | - Lindsey Jones
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
| | - Tao Wang
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
| | - Suzi Sanchez
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
| | - Xue F Huang
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
| | - Lei Zhang
- Department of Advanced Interdisciplinary Studies, Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Changyong Wang
- Department of Advanced Interdisciplinary Studies, Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Si-Yi Chen
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
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171
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Page A, Mann DA. Epigenetic regulation of liver fibrosis. Clin Res Hepatol Gastroenterol 2015; 39 Suppl 1:S64-8. [PMID: 26189981 DOI: 10.1016/j.clinre.2015.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/10/2015] [Indexed: 02/04/2023]
Abstract
Fibrosis is a common and important pathology associated with progressive chronic liver diseases and underlies the development of cirrhosis and hepatocellular carcinoma. Research into the molecular regulation of fibrosis has discovered that it is under the control of a number of epigenetic mechanisms including DNA methylation, histone modifications and the activities of non-coding RNAs. A deeper understanding of how epigenetic regulators such as DNA methyltranserases, methyl-DNA binding proteins, histone modifying enzymes and regulatory RNA molecules impact on the fibrogenic process is expected to result in new biomarkers for disease progression as well as novel therapeutic targets. The aim of this mini-review is to briefly introduce the reader to the major epigenetic regulators so far identified as being implicated in fibrosis.
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Affiliation(s)
- Agata Page
- Fibrosis Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Derek A Mann
- Fibrosis Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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172
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Yao X, Tang Z, Fu X, Yin J, Liang Y, Li C, Li H, Tian Q, Roeder RG, Wang G. The Mediator subunit MED23 couples H2B mono-ubiquitination to transcriptional control and cell fate determination. EMBO J 2015; 34:2885-902. [PMID: 26330467 DOI: 10.15252/embj.201591279] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/10/2015] [Indexed: 01/18/2023] Open
Abstract
The Mediator complex orchestrates multiple transcription factors with the Pol II apparatus for precise transcriptional control. However, its interplay with the surrounding chromatin remains poorly understood. Here, we analyze differential histone modifications between WT and MED23(-/-) (KO) cells and identify H2B mono-ubiquitination at lysine 120 (H2Bub) as a MED23-dependent histone modification. Using tandem affinity purification and mass spectrometry, we find that MED23 associates with the RNF20/40 complex, the enzyme for H2Bub, and show that this association is critical for the recruitment of RNF20/40 to chromatin. In a cell-free system, Mediator directly and substantially increases H2Bub on recombinant chromatin through its cooperation with RNF20/40 and the PAF complex. Integrative genome-wide analyses show that MED23 depletion specifically reduces H2Bub on a subset of MED23-controlled genes. Importantly, MED23-coupled H2Bub levels are oppositely regulated during myogenesis and lung carcinogenesis. In sum, these results establish a mechanistic link between the Mediator complex and a critical chromatin modification in coordinating transcription with cell growth and differentiation.
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Affiliation(s)
- Xiao Yao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Jingwen Yin
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Yan Liang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Chonghui Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Huayun Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Qing Tian
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Gang Wang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
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173
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Deb M, Sengupta D, Rath SK, Kar S, Parbin S, Shilpi A, Pradhan N, Bhutia SK, Roy S, Patra SK. Clusterin gene is predominantly regulated by histone modifications in human colon cancer and ectopic expression of the nuclear isoform induces cell death. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1630-45. [DOI: 10.1016/j.bbadis.2015.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 04/15/2015] [Accepted: 04/20/2015] [Indexed: 12/14/2022]
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174
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Meeting report: The biology of genomes and proteomes. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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175
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Wang Z, Zhu L, Guo T, Wang Y, Yang J. Decreased H2B monoubiquitination and overexpression of ubiquitin-specific protease enzyme 22 in malignant colon carcinoma. Hum Pathol 2015; 46:1006-14. [DOI: 10.1016/j.humpath.2015.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 02/07/2023]
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176
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Point mutations in an epigenetic factor lead to multiple types of bone tumors: role of H3.3 histone variant in bone development and disease. BONEKEY REPORTS 2015; 4:715. [PMID: 26157578 DOI: 10.1038/bonekey.2015.84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/24/2015] [Indexed: 12/27/2022]
Abstract
Coordinated post-translational modifications (PTMs) of nucleosomal histones emerge as a key mechanism of gene regulation by defining chromatin configuration. Patterns of histone modifications vary in different cells and constitute core elements of cell-specific epigenomes. Recently, in addition to canonical histone proteins produced during the S phase of cell cycle, several non-canonical histone variants have been identified and shown to express in a DNA replication-independent manner. These histone variants generate diversity in nucleosomal structures and add further complexity to mechanisms of epigenetic regulation. Cell-specific functions of histone variants remain to be determined. Several recent studies reported an association between some point mutations in the non-canonical histone H3.3 and particular types of brain and bone tumors. This suggests a possibility of differential physiological effects of histone variants in different cells and tissues, including bone. In this review, we outline the roles of histone variants and their PTMs in the epigenetic regulation of chromatin structure and discuss possible mechanisms of biological effects of the non-canonical histone mutations found in bone tumors on tumorigenesis in differentiating bone stem cells.
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177
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Casati L, Sendra R, Sibilia V, Celotti F. Endocrine disrupters: the new players able to affect the epigenome. Front Cell Dev Biol 2015; 3:37. [PMID: 26151052 PMCID: PMC4471431 DOI: 10.3389/fcell.2015.00037] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/17/2015] [Indexed: 01/27/2023] Open
Abstract
Epigenetics represents the way by which the environment is able to program the genome; there are three main levels of epigenetic control on genome: DNA methylation, post-translational histone modification and microRNA expression. The term Epigenetics has been widened by NIH to include “both heritable changes in gene activity and expression but also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable.” These changes might be produced mostly by the early life environment and might affect health influencing the susceptibility to develop diseases, from cancer to mental disorder, during the entire life span. The most studied environmental influences acting on epigenome are diet, infections, wasting, child care, smoking and environmental pollutants, in particular endocrine disrupters (EDs). These are environmental xenobiotics able to interfere with the normal development of the male and female reproductive systems of wildlife, of experimental animals and possibly of humans, disrupting the normal reproductive functions. Data from literature indicate that EDs can act at different levels of epigenetic control, in some cases transgenerationally, in particular when the exposure to these compounds occurs during the prenatal and earliest period of life. Some of the best characterized EDs will be considered in this review. Among the EDs, vinclozolin (VZ), and methoxychlor (MXC) promote epigenetic transgenerational effects. Polychlorinated biphenils (PCBs), the most widespread environmental EDs, affect histone post-translational modifications in a dimorphic way, possibly as the result of an alteration of gene expression of the enzymes involved in histone modification, as the demethylase Jarid1b, an enzyme also involved in regulating the interaction of androgens with their receptor.
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Affiliation(s)
- Lavinia Casati
- Department of Medical Biotechnology and Translational Medicine, University of Milan Milan, Italy
| | - Ramon Sendra
- Departament de Bioquímica i Biologia Molecular, Universitat de València Valencia, Spain
| | - Valeria Sibilia
- Department of Medical Biotechnology and Translational Medicine, University of Milan Milan, Italy
| | - Fabio Celotti
- Department of Pharmacological and Biomolecular Sciences, University of Milan Milan, Italy
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178
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Sharma R, Zhou MM. Partners in crime: The role of tandem modules in gene transcription. Protein Sci 2015; 24:1347-59. [PMID: 26059070 DOI: 10.1002/pro.2711] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/16/2022]
Abstract
Histones and their modifications play an important role in the regulation of gene transcription. Numerous modifications, such as acetylation, phosphorylation, methylation, ubiquitination, and SUMOylation, have been described. These modifications almost always co-occur and thereby increase the combinatorial complexity of post-translational modification detection. The domains that recognize these histone modifications often occur in tandem in the context of larger proteins and complexes. The presence of multiple modifications can positively or negatively regulate the binding of these tandem domains, influencing downstream cellular function. Alternatively, these tandem domains can have novel functions from their independent parts. Here we summarize structural and functional information known about major tandem domains and their histone binding properties. An understanding of these interactions is key for the development of epigenetic therapy.
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Affiliation(s)
- Rajal Sharma
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
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179
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Gómez AV, Córdova G, Munita R, Parada GE, Barrios ÁP, Cancino GI, Álvarez AR, Andrés ME. Characterizing HSF1 Binding and Post-Translational Modifications of hsp70 Promoter in Cultured Cortical Neurons: Implications in the Heat-Shock Response. PLoS One 2015; 10:e0129329. [PMID: 26053851 PMCID: PMC4459960 DOI: 10.1371/journal.pone.0129329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 05/08/2015] [Indexed: 11/21/2022] Open
Abstract
Causes of lower induction of Hsp70 in neurons during heat shock are still a matter of debate. To further inquire into the mechanisms regulating Hsp70 expression in neurons, we studied the activity of Heat Shock Factor 1 (HSF1) and histone posttranslational modifications (PTMs) at the hsp70 promoter in rat cortical neurons. Heat shock induced a transient and efficient translocation of HSF1 to neuronal nuclei. However, no binding of HSF1 at the hsp70 promoter was detected while it bound to the hsp25 promoter in cortical neurons during heat shock. Histone PTMs analysis showed that the hsp70 promoter harbors lower levels of histone H3 and H4 acetylation in cortical neurons compared to PC12 cells under basal conditions. Transcriptomic profiling data analysis showed a predominant usage of cryptic transcriptional start sites at hsp70 gene in the rat cerebral cortex, compared with the whole brain. These data support a weaker activation of hsp70 canonical promoter. Heat shock increased H3Ac at the hsp70 promoter in PC12 cells, which correlated with increased Hsp70 expression while no modifications occurred at the hsp70 promoter in cortical neurons. Increased histone H3 acetylation by Trichostatin A led to hsp70 mRNA and protein induction in cortical neurons. In conclusion, we found that two independent mechanisms maintain a lower induction of Hsp70 in cortical neurons. First, HSF1 fails to bind specifically to the hsp70 promoter in cortical neurons during heat shock and, second, the hsp70 promoter is less accessible in neurons compared to non-neuronal cells due to histone deacetylases repression.
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Affiliation(s)
- Andrea V. Gómez
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
- * E-mail: (AVG); (MEA)
| | - Gonzalo Córdova
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Roberto Munita
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Guillermo E. Parada
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Álvaro P. Barrios
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Gonzalo I. Cancino
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Alejandra R. Álvarez
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - María E. Andrés
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
- * E-mail: (AVG); (MEA)
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180
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Salminen A, Haapasalo A, Kauppinen A, Kaarniranta K, Soininen H, Hiltunen M. Impaired mitochondrial energy metabolism in Alzheimer's disease: Impact on pathogenesis via disturbed epigenetic regulation of chromatin landscape. Prog Neurobiol 2015; 131:1-20. [PMID: 26001589 DOI: 10.1016/j.pneurobio.2015.05.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 05/05/2015] [Accepted: 05/11/2015] [Indexed: 12/14/2022]
Abstract
The amyloid cascade hypothesis for the pathogenesis of Alzheimer's disease (AD) was proposed over twenty years ago. However, the mechanisms of neurodegeneration and synaptic loss have remained elusive delaying the effective drug discovery. Recent studies have revealed that amyloid-β peptides as well as phosphorylated and fragmented tau proteins accumulate within mitochondria. This process triggers mitochondrial fission (fragmentation) and disturbs Krebs cycle function e.g. by inhibiting the activity of 2-oxoglutarate dehydrogenase. Oxidative stress, hypoxia and calcium imbalance also disrupt the function of Krebs cycle in AD brains. Recent studies on epigenetic regulation have revealed that Krebs cycle intermediates control DNA and histone methylation as well as histone acetylation and thus they have fundamental roles in gene expression. DNA demethylases (TET1-3) and histone lysine demethylases (KDM2-7) are included in the family of 2-oxoglutarate-dependent oxygenases (2-OGDO). Interestingly, 2-oxoglutarate is the obligatory substrate of 2-OGDO enzymes, whereas succinate and fumarate are the inhibitors of these enzymes. Moreover, citrate can stimulate histone acetylation via acetyl-CoA production. Epigenetic studies have revealed that AD is associated with changes in DNA methylation and histone acetylation patterns. However, the epigenetic results of different studies are inconsistent but one possibility is that they represent both coordinated adaptive responses and uncontrolled stochastic changes, which provoke pathogenesis in affected neurons. Here, we will review the changes observed in mitochondrial dynamics and Krebs cycle function associated with AD, and then clarify the mechanisms through which mitochondrial metabolites can control the epigenetic landscape of chromatin and induce pathological changes in AD.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland.
| | - Annakaisa Haapasalo
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 100, FI-70029 KYS, Finland
| | - Anu Kauppinen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, P.O. Box 100, FI-70029 KYS, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, P.O. Box 100, FI-70029 KYS, Finland
| | - Hilkka Soininen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 100, FI-70029 KYS, Finland
| | - Mikko Hiltunen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 100, FI-70029 KYS, Finland; Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
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181
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Winogradoff D, Echeverria I, Potoyan DA, Papoian GA. The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects. J Am Chem Soc 2015; 137:6245-53. [DOI: 10.1021/jacs.5b00235] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- David Winogradoff
- Chemical
Physics Program and ‡Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | - Ignacia Echeverria
- Chemical
Physics Program and ‡Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | - Davit A. Potoyan
- Chemical
Physics Program and ‡Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | - Garegin A. Papoian
- Chemical
Physics Program and ‡Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
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182
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The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations. Mol Cell 2015; 58:1113-23. [PMID: 25959393 DOI: 10.1016/j.molcel.2015.03.030] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/25/2015] [Accepted: 03/25/2015] [Indexed: 12/14/2022]
Abstract
H2A.Z is a highly conserved histone variant involved in several key nuclear processes. It is incorporated into promoters by SWR-C-related chromatin remodeling complexes, but whether it is also actively excluded from non-promoter regions is not clear. Here we provide genomic and biochemical evidence that the RNA polymerase II (RNA Pol II) elongation-associated histone chaperones FACT and Spt6 both contribute to restricting H2A.Z from intragenic regions. In the absence of FACT or Spt6, the lack of efficient nucleosome reassembly coupled to pervasive incorporation of H2A.Z by mislocalized SWR-C alters chromatin composition and contributes to cryptic initiation. Therefore, chaperone-mediated H2A.Z confinement is crucial for restricting the chromatin signature of gene promoters that otherwise may license or promote cryptic transcription.
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183
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Yang XJ. MOZ and MORF acetyltransferases: Molecular interaction, animal development and human disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1818-26. [PMID: 25920810 DOI: 10.1016/j.bbamcr.2015.04.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/17/2015] [Accepted: 04/22/2015] [Indexed: 01/16/2023]
Abstract
Lysine residues are subject to many forms of covalent modification and one such modification is acetylation of the ε-amino group. Initially identified on histone proteins in the 1960s, lysine acetylation is now considered as an important form of post-translational modification that rivals phosphorylation. However, only about a dozen of human lysine acetyltransferases have been identified. Among them are MOZ (monocytic leukemia zinc finger protein; a.k.a. MYST3 and KAT6A) and its paralog MORF (a.k.a. MYST4 and KAT6B). Although there is a distantly related protein in Drosophila and sea urchin, these two enzymes are vertebrate-specific. They form tetrameric complexes with BRPF1 (bromodomain- and PHD finger-containing protein 1) and two small non-catalytic subunits. These two acetyltransferases and BRPF1 play key roles in various developmental processes; for example, they are important for development of hematopoietic and neural stem cells. The human KAT6A and KAT6B genes are recurrently mutated in leukemia, non-hematologic malignancies, and multiple developmental disorders displaying intellectual disability and various other abnormalities. In addition, the BRPF1 gene is mutated in childhood leukemia and adult medulloblastoma. Therefore, these two acetyltransferases and their partner BRPF1 are important in animal development and human disease.
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Affiliation(s)
- Xiang-Jiao Yang
- The Rosalind & Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada; Department of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada; McGill University Health Center, Montreal, Quebec H3A 1A3, Canada.
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184
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Ryu HW, Lee DH, Won HR, Kim KH, Seong YJ, Kwon SH. Influence of toxicologically relevant metals on human epigenetic regulation. Toxicol Res 2015; 31:1-9. [PMID: 25874027 PMCID: PMC4395649 DOI: 10.5487/tr.2015.31.1.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/11/2015] [Accepted: 03/13/2015] [Indexed: 12/11/2022] Open
Abstract
Environmental toxicants such as toxic metals can alter epigenetic regulatory features such as DNA methylation, histone modification, and non-coding RNA expression. Heavy metals influence gene expression by epigenetic mechanisms and by directly binding to various metal response elements in the target gene promoters. Given the role of epigenetic alterations in regulating genes, there is potential for the integration of toxic metal-induced epigenetic alterations as informative factors in the risk assessment process. Here, we focus on recent advances in understanding epigenetic changes, gene expression, and biological effects induced by toxic metals.
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Affiliation(s)
- Hyun-Wook Ryu
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - Hye-Rim Won
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - Kyeong Hwan Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - Yun Jeong Seong
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
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185
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Atwell LL, Beaver LM, Shannon J, Williams DE, Dashwood RH, Ho E. Epigenetic Regulation by Sulforaphane: Opportunities for Breast and Prostate Cancer Chemoprevention. ACTA ACUST UNITED AC 2015; 1:102-111. [PMID: 26042194 DOI: 10.1007/s40495-014-0002-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sulforaphane (SFN) is a phytochemical derived from cruciferous vegetables that has multiple molecular targets and anti-cancer properties. Researchers have demonstrated several chemopreventive benefits of SFN consumption, such as reductions in tumor growth, increases in cancer cell apoptosis, and disruption of signaling within tumor microenvironments both in vitro and in vivo. Emerging evidence indicates that SFN exerts several of its chemopreventive effects by altering epigenetic mechanisms. This review summarizes evidence of the impact of SFN on epigenetic events and how they relate to the chemopreventive effects of SFN observed in preclinical and clinical studies of breast and prostate cancers. Specific areas of focus include the role of SFN in the regulation of cell cycle, apoptosis, inflammation, antioxidant defense, and cancer cell signaling and their relationships to epigenetic mechanisms. Finally, remaining challenges and research needs for translating mechanistic work with SFN into human studies and clinical intervention trials are discussed.
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Affiliation(s)
- Lauren L Atwell
- 103 Milam Hall, School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Laura M Beaver
- 103 Milam Hall, School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA ; 307 Linus Pauling Science Center, Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
| | - Jackilen Shannon
- 3181 SW Sam Jackson Park Road, Mail Code CB L606, Department of Public Health and Preventive Medicine, Oregon Health and Science University, Portland, OR 97239, USA
| | - David E Williams
- 307 Linus Pauling Science Center, Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA ; 1007 Agriculture & Life Sciences Building, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Roderick H Dashwood
- 2121 West Holcombe Boulevard, Center for Epigenetics & Disease Prevention, Houston, TX 77030
| | - Emily Ho
- 103 Milam Hall, School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR 97331, USA ; 307 Linus Pauling Science Center, Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA ; 212 Milam Hall, Moore Family Center for Whole Grain Foods, Nutrition and Preventive Health, Oregon State University, Corvallis, OR 97331, USA
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186
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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187
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Okada H, Schittenhelm RB, Straessle A, Hafen E. Multi-functional regulation of 4E-BP gene expression by the Ccr4-Not complex. PLoS One 2015; 10:e0113902. [PMID: 25793896 PMCID: PMC4368434 DOI: 10.1371/journal.pone.0113902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 11/01/2014] [Indexed: 12/24/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) signaling pathway is highly conserved from yeast to humans. It senses various environmental cues to regulate cellular growth and homeostasis. Deregulation of the pathway has been implicated in many pathological conditions including cancer. Phosphorylation cascades through the pathway have been extensively studied but not much is known about the regulation of gene expression of the pathway components. Here, we report that the mRNA level of eukaryotic translation initiation factor (eIF) subunit 4E-binding protein (4E-BP) gene, one of the key mTOR signaling components, is regulated by the highly conserved Ccr4-Not complex. RNAi knockdown of Not1, a putative scaffold protein of this protein complex, increases the mRNA level of 4E-BP in Drosophila Kc cells. Examination of the gene expression mechanism using reporter swap constructs reveals that Not1 depletion increases reporter mRNAs with the 3'UTR of 4E-BP gene, but decreases the ones with the 4E-BP promoter region, suggesting that Ccr4-Not complex regulates both degradation and transcription of 4E-BP mRNA. These results indicate that the Ccr4-Not complex controls expression of a single gene at multiple levels and adjusts the magnitude of the total effect. Thus, our study reveals a novel regulatory mechanism of a key component of the mTOR signaling pathway at the level of gene expression.
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Affiliation(s)
- Hirokazu Okada
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Wolfgang Pauli Str. 16, 8093, Zürich, Switzerland
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton Campus, Wellington Road, Clayton, Victoria, 3800, Australia
| | - Anna Straessle
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Wolfgang Pauli Str. 16, 8093, Zürich, Switzerland
| | - Ernst Hafen
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Wolfgang Pauli Str. 16, 8093, Zürich, Switzerland
- * E-mail:
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188
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You L, Yan K, Zou J, Zhao H, Bertos NR, Park M, Wang E, Yang XJ. The chromatin regulator Brpf1 regulates embryo development and cell proliferation. J Biol Chem 2015; 290:11349-64. [PMID: 25773539 DOI: 10.1074/jbc.m115.643189] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 12/22/2022] Open
Abstract
With hundreds of chromatin regulators identified in mammals, an emerging issue is how they modulate biological and pathological processes. BRPF1 (bromodomain- and PHD finger-containing protein 1) is a unique chromatin regulator possessing two PHD fingers, one bromodomain and a PWWP domain for recognizing multiple histone modifications. In addition, it binds to the acetyltransferases MOZ, MORF, and HBO1 (also known as KAT6A, KAT6B, and KAT7, respectively) to promote complex formation, restrict substrate specificity, and enhance enzymatic activity. We have recently showed that ablation of the mouse Brpf1 gene causes embryonic lethality at E9.5. Here we present systematic analyses of the mutant animals and demonstrate that the ablation leads to vascular defects in the placenta, yolk sac, and embryo proper, as well as abnormal neural tube closure. At the cellular level, Brpf1 loss inhibits proliferation of embryonic fibroblasts and hematopoietic progenitors. Molecularly, the loss reduces transcription of a ribosomal protein L10 (Rpl10)-like gene and the cell cycle inhibitor p27, and increases expression of the cell-cycle inhibitor p16 and a novel protein homologous to Scp3, a synaptonemal complex protein critical for chromosome association and embryo survival. These results uncover a crucial role of Brpf1 in controlling mouse embryo development and regulating cellular and gene expression programs.
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Affiliation(s)
- Linya You
- From the The Rosalind and Morris Goodman Cancer Research Center, Department of Medicine, and
| | - Kezhi Yan
- From the The Rosalind and Morris Goodman Cancer Research Center, Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3
| | - Jinfeng Zou
- National Research Council Canada, Montreal, Quebec H4P 2R2, and
| | - Hong Zhao
- From the The Rosalind and Morris Goodman Cancer Research Center
| | | | - Morag Park
- From the The Rosalind and Morris Goodman Cancer Research Center, Department of Medicine, and Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, McGill University Health Center, Montreal, Quebec H3A 1A3, Canada
| | - Edwin Wang
- National Research Council Canada, Montreal, Quebec H4P 2R2, and
| | - Xiang-Jiao Yang
- From the The Rosalind and Morris Goodman Cancer Research Center, Department of Medicine, and Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, McGill University Health Center, Montreal, Quebec H3A 1A3, Canada
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189
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Pazin MJ. Using the ENCODE Resource for Functional Annotation of Genetic Variants. Cold Spring Harb Protoc 2015; 2015:522-36. [PMID: 25762420 DOI: 10.1101/pdb.top084988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article illustrates the use of the Encyclopedia of DNA Elements (ENCODE) resource to generate or refine hypotheses from genomic data on disease and other phenotypic traits. First, the goals and history of ENCODE and related epigenomics projects are reviewed. Second, the rationale for ENCODE and the major data types used by ENCODE are briefly described, as are some standard heuristics for their interpretation. Third, the use of the ENCODE resource is examined. Standard use cases for ENCODE, accessing the ENCODE resource, and accessing data from related projects are discussed. Although the focus of this article is the use of ENCODE data, some of the same approaches can be used with data from other projects.
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Affiliation(s)
- Michael J Pazin
- Division of Genome Sciences, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
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190
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Hayashi G, Sakamoto R, Okamoto A. 2-Oxazoline formation for selective chemical labeling of 5-hydroxylysine. Chem Asian J 2015; 10:1138-41. [PMID: 25757225 DOI: 10.1002/asia.201500172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 11/07/2022]
Abstract
Hydroxylation of lysine, one of posttranslational modifications of proteins, generates 5-hydroxylysine (Koh) and plays a crucial role in regulating protein functions in cellular activity. We have developed a chemical labeling method of Koh. The 1,2-aminoalcohol moiety of Koh in synthetic peptide sequences was trapped by an alkyne-containing benzimidate to form a 2-oxazoline ring. An additional ammonia treatment process removed the undesirable amidine residue formed between benzimidate and lysine. During the ammonia treatment, the oxazoline residue formed at Koh mainly remained intact, and the ring opening to the amide form was observed for only part of oxazoline, indicating that the chemical labeling is amino acid selective. Azide-substituted biotin or fluorescent dye was attached to the peptide through Huisgen cycloaddition at Koh and converted into an alkyne-labeled oxazoline form. The Koh-labeling assay could provide a platform to enhance proteomic research of lysine hydroxylation.
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Affiliation(s)
- Gosuke Hayashi
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)
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191
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Huffman SR, Pak Y, Rivera RM. Superovulation induces alterations in the epigenome of zygotes, and results in differences in gene expression at the blastocyst stage in mice. Mol Reprod Dev 2015; 82:207-17. [DOI: 10.1002/mrd.22463] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/14/2015] [Indexed: 12/17/2022]
Affiliation(s)
| | - Youngju Pak
- UCLA Clinical and Translational Science Institute-Biostatistics; Torrance California
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192
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Sainathan S, Paul S, Ramalingam S, Baranda J, Anant S, Dhar A. Histone Demethylases in Cancer. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40495-015-0025-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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193
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Mao P, Smerdon MJ. Rescue of DNA damage-stalled RNA Pol II: histone H2B in action. RNA & DISEASE (HOUSTON, TEX.) 2015; 1. [PMID: 25705722 DOI: 10.14800/rd.422;] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
RNA Pol II elongation in eukaryotes is coupled with a series of histone modifications. Elongating RNA Pol II can be strongly stalled by lesions on the DNA template. However, it is unclear whether RNA Pol II stalling affects elongation-associated histone modifications. We have explored this important question by investigating the function of histone H2B mono-ubiquitylation (H2Bub), a well-characterized epigenetic mark associated with RNA Pol II elongation, in the cellular response to DNA lesions induced by ultraviolet (UV) radiation. We found that, in contrast to transcription elongation, RNA Pol II stalling induced by UV lesions triggers rapid and significant H2B deubiquitylation that removes ubiquitin from H2B. Interestingly, in yeast mutant cells that lack H2B deubiquitylation enzymes, rescue of the stalled RNA Pol II by transcription-coupled repair (TCR) is significantly impaired. Thus, our study has established a direct connection between RNA Pol II stalling and a histone modification response.
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Affiliation(s)
- Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
| | - Michael J Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
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194
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Weng L, Zhou C, Greenberg MM. Probing interactions between lysine residues in histone tails and nucleosomal DNA via product and kinetic analysis. ACS Chem Biol 2015; 10:622-30. [PMID: 25475712 PMCID: PMC4336632 DOI: 10.1021/cb500737y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The
histone proteins in nucleosome core particles are known to
catalyze DNA cleavage at abasic and oxidized abasic sites, which are
produced by antitumor antibiotics and as a consequence of other modalities
of DNA damage. The lysine rich histone tails whose post-translational
modifications regulate genetic expression in cells are mainly responsible
for this chemistry. Cleavage at a C4′-oxidized abasic site
(C4-AP) concomitantly results in modification of lysine residues in
histone tails. Using LC-MS/MS, we demonstrate here that that Lys8,
-12, -16, and -20 of histone H4 were modified when C4-AP was incorporated
at a hot spot (superhelical location 1.5) for DNA damage within a
nucleosome core particle. A new DNA–protein cross-linking method
that provides a more quantitative analysis of individual amino acid
reactivity is also described. DNA–protein cross-links were
produced by an irreversible reaction between a nucleic acid electrophile
that was produced following oxidatively induced rearrangement of a
phenyl selenide derivative of thymidine (3) and nucleophilic
residues within proteins. In addition to providing high yields of
DNA–protein cross-links, kinetic analysis of the cross-linking
reaction yielded rate constants that enabled ranking the contributions
by individual or groups of amino acids. Cross-linking from 3 at superhelical location 1.5 revealed the following order of reactivity
for the nucleophilic amino acids in the histone H4 tail: His18 >
Lys16
> Lys20 ≈ Lys8, Lys12 > Lys5. Cross-linking via 3 will be generally useful for investigating DNA–protein
interactions.
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Affiliation(s)
- Liwei Weng
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Chuanzheng Zhou
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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195
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Lysine deacetylases regulate the heat shock response including the age-associated impairment of HSF1. J Mol Biol 2015; 427:1644-54. [PMID: 25688804 DOI: 10.1016/j.jmb.2015.02.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 11/22/2022]
Abstract
Heat shock factor 1 (HSF1) is critical for defending cells from both acute and chronic stresses. In aging cells, the DNA binding activity of HSF1 deteriorates correlating with the onset of pathological events including neurodegeneration and heart disease. We find that DNA binding by HSF1 is controlled by lysine deacetylases with HDAC7, HDAC9, and SIRT1 distinctly increasing the magnitude and length of a heat shock response (HSR). In contrast, HDAC1 inhibits HSF1 in a deacetylase-independent manner. In aging cells, the levels of HDAC1 are elevated and the HSR is impaired, yet reduction of HDAC1 in aged cells restores the HSR. Our results provide a mechanistic basis for the age-associated regulation of the HSR. Besides HSF1, the deacetylases differentially modulate the activities of unrelated DNA binding proteins. Taken together, our data further support the model that lysine deacetylases are selective regulators of DNA binding proteins.
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196
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Chemical proteomics approaches to examine novel histone posttranslational modifications. Curr Opin Chem Biol 2015; 24:80-90. [DOI: 10.1016/j.cbpa.2014.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023]
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197
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You L, Zou J, Zhao H, Bertos NR, Park M, Wang E, Yang XJ. Deficiency of the chromatin regulator BRPF1 causes abnormal brain development. J Biol Chem 2015; 290:7114-29. [PMID: 25568313 DOI: 10.1074/jbc.m114.635250] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Epigenetic mechanisms are important in different neurological disorders, and one such mechanism is histone acetylation. The multivalent chromatin regulator BRPF1 (bromodomain- and plant homeodomain-linked (PHD) zinc finger-containing protein 1) recognizes different epigenetic marks and activates three histone acetyltransferases, so it is both a reader and a co-writer of the epigenetic language. The three histone acetyltransferases are MOZ, MORF, and HBO1, which are also known as lysine acetyltransferase 6A (KAT6A), KAT6B, and KAT7, respectively. The MORF gene is mutated in four neurodevelopmental disorders sharing the characteristic of intellectual disability and frequently displaying callosal agenesis. Here, we report that forebrain-specific inactivation of the mouse Brpf1 gene caused early postnatal lethality, neocortical abnormalities, and partial callosal agenesis. With respect to the control, the mutant forebrain contained fewer Tbr2-positive intermediate neuronal progenitors and displayed aberrant neurogenesis. Molecularly, Brpf1 loss led to decreased transcription of multiple genes, such as Robo3 and Otx1, important for neocortical development. Surprisingly, elevated expression of different Hox genes and various other transcription factors, such as Lhx4, Foxa1, Tbx5, and Twist1, was also observed. These results thus identify an important role of Brpf1 in regulating forebrain development and suggest that it acts as both an activator and a silencer of gene expression in vivo.
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Affiliation(s)
- Linya You
- From the Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Quebec H3A 1A3
| | - Jinfeng Zou
- the National Research Council Canada, Montreal, Quebec H4P 2R2, and
| | - Hong Zhao
- From the Rosalind & Morris Goodman Cancer Research Center
| | | | - Morag Park
- From the Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Quebec H3A 1A3, the Department of Biochemistry, McGill University and McGill University Health Center, Montreal, Quebec H3A 1A3, Canada
| | - Edwin Wang
- the National Research Council Canada, Montreal, Quebec H4P 2R2, and
| | - Xiang-Jiao Yang
- From the Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Quebec H3A 1A3, the Department of Biochemistry, McGill University and McGill University Health Center, Montreal, Quebec H3A 1A3, Canada
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198
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Abstract
Pluripotent cells in embryos are situated near the apex of the hierarchy of developmental potential. They are capable of generating all cell types of the mammalian body proper. Therefore, they are the exemplar of stem cells. In vivo, pluripotent cells exist transiently and become expended within a few days of their establishment. Yet, when explanted into artificial culture conditions, they can be indefinitely propagated in vitro as pluripotent stem cell lines. A host of transcription factors and regulatory genes are now known to underpin the pluripotent state. Nonetheless, how pluripotent cells are equipped with their vast multilineage differentiation potential remains elusive. Consensus holds that pluripotency transcription factors prevent differentiation by inhibiting the expression of differentiation genes. However, this does not explain the developmental potential of pluripotent cells. We have presented another emergent perspective, namely, that pluripotency factors function as lineage specifiers that enable pluripotent cells to differentiate into specific lineages, therefore endowing pluripotent cells with their multilineage potential. Here we provide a comprehensive overview of the developmental biology, transcription factors, and extrinsic signaling associated with pluripotent cells, and their accompanying subtypes, in vitro heterogeneity and chromatin states. Although much has been learned since the appreciation of mammalian pluripotency in the 1950s and the derivation of embryonic stem cell lines in 1981, we will specifically emphasize what currently remains unclear. However, the view that pluripotency factors capacitate differentiation, recently corroborated by experimental evidence, might perhaps address the long-standing question of how pluripotent cells are endowed with their multilineage differentiation potential.
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Affiliation(s)
- Kyle M. Loh
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
| | - Bing Lim
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
| | - Lay Teng Ang
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
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199
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Mouriz A, López-González L, Jarillo JA, Piñeiro M. PHDs govern plant development. PLANT SIGNALING & BEHAVIOR 2015; 10:e993253. [PMID: 26156103 PMCID: PMC4622442 DOI: 10.4161/15592324.2014.993253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/18/2014] [Indexed: 05/22/2023]
Abstract
Posttranslational modifications present in the amino-terminal tails of histones play a pivotal role in the chromatin-mediated regulation of gene expression patterns that control plant developmental transitions. Therefore, the function of protein domains that specifically recognize these histone covalent modifications and recruit chromatin remodeling complexes and the transcriptional machinery to modulate gene expression is essential for a proper control of plant development. Plant HomeoDomain (PHD) motifs act as effectors that can specifically bind a number of histone modifications and mediate the activation or repression of underlying genes. In this review we summarize recent findings that emphasize the crucial role of this versatile family of chromatin "reader" domains in the transcriptional regulation of plant developmental processes such as meiosis and postmeiotic events during pollen maturation, embryo meristem initiation and root development, germination as well as flowering time.
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Affiliation(s)
- Alfonso Mouriz
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
| | - Leticia López-González
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
| | - Jose A Jarillo
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
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200
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Thinnes CC, England KS, Kawamura A, Chowdhury R, Schofield CJ, Hopkinson RJ. Targeting histone lysine demethylases - progress, challenges, and the future. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:1416-32. [PMID: 24859458 PMCID: PMC4316176 DOI: 10.1016/j.bbagrm.2014.05.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 05/06/2014] [Accepted: 05/13/2014] [Indexed: 12/20/2022]
Abstract
N-Methylation of lysine and arginine residues has emerged as a major mechanism of transcriptional regulation in eukaryotes. In humans, N(ε)-methyllysine residue demethylation is catalysed by two distinct subfamilies of demethylases (KDMs), the flavin-dependent KDM1 subfamily and the 2-oxoglutarate- (2OG) dependent JmjC subfamily, which both employ oxidative mechanisms. Modulation of histone methylation status is proposed to be important in epigenetic regulation and has substantial medicinal potential for the treatment of diseases including cancer and genetic disorders. This article provides an introduction to the enzymology of the KDMs and the therapeutic possibilities and challenges associated with targeting them, followed by a review of reported KDM inhibitors and their mechanisms of action from kinetic and structural perspectives.
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Affiliation(s)
- Cyrille C Thinnes
- The Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Akane Kawamura
- The Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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