151
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Tiwari M, Parvez S, Agrawala PK. Role of some epigenetic factors in DNA damage response pathway. AIMS GENETICS 2017; 4:69-83. [PMID: 31435504 PMCID: PMC6690236 DOI: 10.3934/genet.2017.1.69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/17/2017] [Indexed: 01/01/2023]
Abstract
The current review gives a brief account of the DNA damage response pathway and involvement of various epigenetic mechanisms in DNA damage response pathway. The main focus is on histone modifications leading to structural alterations in chromatin since the compact chromatin structure poses a major limitation in the DNA repair process. Based on this hypothesis, our laboratory has also evaluated certain histone deacetylase inhibitors as potential radiomitigators and the same has been discussed in brief at the end of the review.
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Affiliation(s)
- Mrinalini Tiwari
- Department of Radiation Genetics and Epigenetics, Institute of Nuclear Medicine and Allied Sciences, Brig SK Mazumdar Road, Timarpur, Delhi 110054 India
| | - Suhel Parvez
- Department of Toxicology, Jamia Hamdard University, Hamdard Nagar, Delhi 110062 India
| | - Paban K Agrawala
- Department of Radiation Genetics and Epigenetics, Institute of Nuclear Medicine and Allied Sciences, Brig SK Mazumdar Road, Timarpur, Delhi 110054 India
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152
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Weaver ICG, Korgan AC, Lee K, Wheeler RV, Hundert AS, Goguen D. Stress and the Emerging Roles of Chromatin Remodeling in Signal Integration and Stable Transmission of Reversible Phenotypes. Front Behav Neurosci 2017; 11:41. [PMID: 28360846 PMCID: PMC5350110 DOI: 10.3389/fnbeh.2017.00041] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/24/2017] [Indexed: 01/02/2023] Open
Abstract
The influence of early life experience and degree of parental-infant attachment on emotional development in children and adolescents has been comprehensively studied. Structural and mechanistic insight into the biological foundation and maintenance of mammalian defensive systems (metabolic, immune, nervous and behavioral) is slowly advancing through the emerging field of developmental molecular (epi)genetics. Initial evidence revealed that differential nurture early in life generates stable differences in offspring hypothalamic-pituitary-adrenal (HPA) regulation, in part, through chromatin remodeling and changes in DNA methylation of specific genes expressed in the brain, revealing physical, biochemical and molecular paths for the epidemiological concept of gene-environment interactions. Herein, a primary molecular mechanism underpinning the early developmental programming and lifelong maintenance of defensive (emotional) responses in the offspring is the alteration of chromatin domains of specific genomic regions from a condensed state (heterochromatin) to a transcriptionally accessible state (euchromatin). Conversely, DNA methylation promotes the formation of heterochromatin, which is essential for gene silencing, genomic integrity and chromosome segregation. Therefore, inter-individual differences in chromatin modifications and DNA methylation marks hold great potential for assessing the impact of both early life experience and effectiveness of intervention programs—from guided psychosocial strategies focused on changing behavior to pharmacological treatments that target chromatin remodeling and DNA methylation enzymes to dietary approaches that alter cellular pools of metabolic intermediates and methyl donors to affect nutrient bioavailability and metabolism. In this review article, we discuss the potential molecular mechanism(s) of gene regulation associated with chromatin modeling and programming of endocrine (e.g., HPA and metabolic or cardiovascular) and behavioral (e.g., fearfulness, vigilance) responses to stress, including alterations in DNA methylation and the role of DNA repair machinery. From parental history (e.g., drugs, housing, illness, nutrition, socialization) to maternal-offspring exchanges of nutrition, microbiota, antibodies and stimulation, the nature of nurture provides not only mechanistic insight into how experiences propagate from external to internal variables, but also identifies a composite therapeutic target, chromatin modeling, for gestational/prenatal stress, adolescent anxiety/depression and adult-onset neuropsychiatric disease.
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Affiliation(s)
- Ian C G Weaver
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Austin C Korgan
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Kristen Lee
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Ryan V Wheeler
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Amos S Hundert
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Donna Goguen
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
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153
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Densham RM, Morris JR. The BRCA1 Ubiquitin ligase function sets a new trend for remodelling in DNA repair. Nucleus 2017; 8:116-125. [PMID: 28032817 PMCID: PMC5403137 DOI: 10.1080/19491034.2016.1267092] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 11/24/2016] [Indexed: 02/05/2023] Open
Abstract
The protein product of the breast and ovarian cancer gene, BRCA1, is part of an obligate heterodimer with BARD1. Together these RING bearing proteins act as an E3 ubiquitin ligase. Several functions have been attributed to BRCA1 that contribute to genome integrity but which of these, if any, require this enzymatic function was unclear. Here we review recent studies clarifying the role of BRCA1 E3 ubiquitin ligase in DNA repair. Perhaps the most surprising finding is the narrow range of BRCA1 functions this activity relates to. Remarkably ligase activity promotes chromatin remodelling and 53BP1 positioning through the remodeller SMARCAD1, but the activity is dispensable for the cellular survival in response to cisplatin or replication stressing agents. Implications for therapy response and tumor susceptibility are discussed.
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Affiliation(s)
- Ruth M. Densham
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Joanna R. Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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154
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Leung JWC, Makharashvili N, Agarwal P, Chiu LY, Pourpre R, Cammarata MB, Cannon JR, Sherker A, Durocher D, Brodbelt JS, Paull TT, Miller KM. ZMYM3 regulates BRCA1 localization at damaged chromatin to promote DNA repair. Genes Dev 2017; 31:260-274. [PMID: 28242625 PMCID: PMC5358723 DOI: 10.1101/gad.292516.116] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/30/2017] [Indexed: 12/02/2022]
Abstract
In this study, Leung et al. identified ZMYM3 (zinc finger, myeloproliferative, and mental retardation-type 3) as a chromatin-interacting protein that promotes DNA repair by homologous recombination. This work identifies a critical chromatin-binding DNA damage response factor, ZMYM3, which modulates BRCA1 functions within chromatin to ensure the maintenance of genome integrity. Chromatin connects DNA damage response factors to sites of damaged DNA to promote the signaling and repair of DNA lesions. The histone H2A variants H2AX, H2AZ, and macroH2A represent key chromatin constituents that facilitate DNA repair. Through proteomic screening of these variants, we identified ZMYM3 (zinc finger, myeloproliferative, and mental retardation-type 3) as a chromatin-interacting protein that promotes DNA repair by homologous recombination (HR). ZMYM3 is recruited to DNA double-strand breaks through bivalent interactions with both histone and DNA components of the nucleosome. We show that ZMYM3 links the HR factor BRCA1 to damaged chromatin through specific interactions with components of the BRCA1-A subcomplex, including ABRA1 and RAP80. By regulating ABRA1 recruitment to damaged chromatin, ZMYM3 facilitates the fine-tuning of BRCA1 interactions with DNA damage sites and chromatin. Consistent with a role in regulating BRCA1 function, ZMYM3 deficiency results in impaired HR repair and genome instability. Thus, our work identifies a critical chromatin-binding DNA damage response factor, ZMYM3, which modulates BRCA1 functions within chromatin to ensure the maintenance of genome integrity.
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Affiliation(s)
- Justin W C Leung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Nodar Makharashvili
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,The Howard Hughes Medical Institute, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Poonam Agarwal
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Li-Ya Chiu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Renaud Pourpre
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Michael B Cammarata
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joe R Cannon
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alana Sherker
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G1X5, Canada
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G1X5, Canada
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,The Howard Hughes Medical Institute, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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155
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Buschbeck M, Hake SB. Variants of core histones and their roles in cell fate decisions, development and cancer. Nat Rev Mol Cell Biol 2017; 18:299-314. [DOI: 10.1038/nrm.2016.166] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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156
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Picchi GFA, Zulkievicz V, Krieger MA, Zanchin NT, Goldenberg S, de Godoy LMF. Post-translational Modifications of Trypanosoma cruzi Canonical and Variant Histones. J Proteome Res 2017; 16:1167-1179. [DOI: 10.1021/acs.jproteome.6b00655] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Vanessa Zulkievicz
- Instituto Carlos Chagas, Fiocruz Parana, Curitiba, Paraná 81350-010, Brazil
| | - Marco A. Krieger
- Instituto Carlos Chagas, Fiocruz Parana, Curitiba, Paraná 81350-010, Brazil
| | - Nilson T. Zanchin
- Instituto Carlos Chagas, Fiocruz Parana, Curitiba, Paraná 81350-010, Brazil
| | - Samuel Goldenberg
- Instituto Carlos Chagas, Fiocruz Parana, Curitiba, Paraná 81350-010, Brazil
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157
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Circulating Nucleosomes and Nucleosome Modifications as Biomarkers in Cancer. Cancers (Basel) 2017; 9:cancers9010005. [PMID: 28075351 PMCID: PMC5295776 DOI: 10.3390/cancers9010005] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/31/2016] [Accepted: 01/01/2017] [Indexed: 12/17/2022] Open
Abstract
Traditionally the stratification of many cancers involves combining tumour and clinicopathological features (e.g., patient age; tumour size, grade, receptor status and location) to inform treatment options and predict recurrence risk and survival. However, current biomarkers often require invasive excision of the tumour for profiling, do not allow monitoring of the response to treatment and stratify patients into broad heterogeneous groups leading to inconsistent treatment responses. Here we explore and describe the benefits of using circulating biomarkers (nucleosomes and/or modifications to nucleosomes) as a non-invasive method for detecting cancer and monitoring response to treatment. Nucleosomes (DNA wound around eight core histone proteins) are responsible for compacting our genome and their composition and post-translational modifications are responsible for regulating gene expression. Here, we focus on breast and colorectal cancer as examples where utilizing circulating nucleosomes as biomarkers hold real potential as liquid biopsies. Utilizing circulating nucleosomes as biomarkers is an exciting new area of research that promises to allow both the early detection of cancer and monitoring of treatment response. Nucleosome-based biomarkers combine with current biomarkers, increasing both specificity and sensitivity of current tests and have the potential to provide individualised precision-medicine based treatments for patients.
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158
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Sultanov DC, Gerasimova NS, Kudryashova KS, Maluchenko NV, Kotova EY, Langelier MF, Pascal JM, Kirpichnikov MP, Feofanov AV, Studitsky VM. Unfolding of core nucleosomes by PARP-1 revealed by spFRET microscopy. AIMS GENETICS 2017; 4:21-31. [PMID: 28804761 PMCID: PMC5552189 DOI: 10.3934/genet.2017.1.21] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA accessibility to various protein complexes is essential for various processes in the cell and is affected by nucleosome structure and dynamics. Protein factor PARP-1 (poly(ADP-ribose) polymerase 1) increases the accessibility of DNA in chromatin to repair proteins and transcriptional machinery, but the mechanism and extent of this chromatin reorganization are unknown. Here we report on the effects of PARP-1 on single nucleosomes revealed by spFRET (single-particle Förster Resonance Energy Transfer) microscopy. PARP-1 binding to a double-strand break in the vicinity of a nucleosome results in a significant increase of the distance between the adjacent gyres of nucleosomal DNA. This partial uncoiling of the entire nucleosomal DNA occurs without apparent loss of histones and is reversed after poly(ADP)-ribosylation of PARP-1. Thus PARP-1-nucleosome interactions result in reversible, partial uncoiling of the entire nucleosomal DNA.
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Affiliation(s)
- Daniel C Sultanov
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.,Fox Chase Cancer Center, Philadelphia, PA, 19111-2497, USA
| | | | - Kseniya S Kudryashova
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Elena Y Kotova
- Fox Chase Cancer Center, Philadelphia, PA, 19111-2497, USA
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | | | - Alexey V Feofanov
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vasily M Studitsky
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.,Fox Chase Cancer Center, Philadelphia, PA, 19111-2497, USA
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159
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The Role of Epigenetic Regulation in Transcriptional Memory in the Immune System. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:43-69. [DOI: 10.1016/bs.apcsb.2016.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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160
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Abramowicz I, Carpenter G, Alfieri M, Colnaghi R, Outwin E, Parent P, Thauvin-Robinet C, Iaconis D, Franco B, O'Driscoll M. Oral-facial-digital syndrome type I cells exhibit impaired DNA repair; unanticipated consequences of defective OFD1 outside of the cilia network. Hum Mol Genet 2017; 26:19-32. [PMID: 27798113 DOI: 10.1093/hmg/ddw364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/18/2016] [Indexed: 02/11/2024] Open
Abstract
Defects in OFD1 underlie the clinically complex ciliopathy, Oral-Facial-Digital syndrome Type I (OFD Type I). Our understanding of the molecular, cellular and clinical consequences of impaired OFD1 originates from its characterised roles at the centrosome/basal body/cilia network. Nonetheless, the first described OFD1 interactors were components of the TIP60 histone acetyltransferase complex. We find that OFD1 can also localise to chromatin and its reduced expression is associated with mis-localization of TIP60 in patient-derived cell lines. TIP60 plays important roles in controlling DNA repair. OFD Type I cells exhibit reduced histone acetylation and altered chromatin dynamics in response to DNA double strand breaks (DSBs). Furthermore, reduced OFD1 impaired DSB repair via homologous recombination repair (HRR). OFD1 loss also adversely impacted upon the DSB-induced G2-M checkpoint, inducing a hypersensitive and prolonged arrest. Our findings show that OFD Type I patient cells have pronounced defects in the DSB-induced histone modification, chromatin remodelling and DSB-repair via HRR; effectively phenocopying loss of TIP60. These data extend our knowledge of the molecular and cellular consequences of impaired OFD1, demonstrating that loss of OFD1 can negatively impact upon important nuclear events; chromatin plasticity and DNA repair.
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Affiliation(s)
- Iga Abramowicz
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Gillian Carpenter
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | | | - Rita Colnaghi
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Emily Outwin
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Philippe Parent
- Service de Génétique, Centre Hospitalier Universitaire de Brest, France
| | | | | | - Brunella Franco
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Department of Medical Translational Sciences, Federico II University, Naples, Italy
| | - Mark O'Driscoll
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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161
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Feng YL, Xiang JF, Kong N, Cai XJ, Xie AY. Buried territories: heterochromatic response to DNA double-strand breaks. Acta Biochim Biophys Sin (Shanghai) 2016; 48:594-602. [PMID: 27151295 DOI: 10.1093/abbs/gmw033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/28/2016] [Indexed: 12/22/2022] Open
Abstract
Cellular response to DNA double-strand breaks (DSBs), the most deleterious type of DNA damage, is highly influenced by higher-order chromatin structure in eukaryotic cells. Compared with euchromatin, the compacted structure of heterochromatin not only protects heterochromatic DNA from damage, but also adds an extra layer of control over the response to DSBs occurring in heterochromatin. One key step in this response is the decondensation of heterochromatin structure. This decondensation process facilitates the DNA damage signaling and promotes proper heterochromatic DSB repair, thus helping to prevent instability of heterochromatic regions of genomes. This review will focus on the functions of the ataxia telangiectasia mutated (ATM) signaling cascade involving ATM, heterochromatin protein 1 (HP1), Krüppel-associated box (KRAB)-associated protein-1 (KAP-1), tat-interacting protein 60 (Tip60), and many other protein factors in DSB-induced decondensation of heterochromatin and subsequent repair of heterochromatic DSBs. As some subsets of DSBs may be repaired in heterochromatin independently of the ATM signaling, a possible repair model is also proposed for ATM-independent repair of these heterochromatic DSBs.
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Affiliation(s)
- Yi-Li Feng
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Ji-Feng Xiang
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Na Kong
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Xiu-Jun Cai
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China
| | - An-Yong Xie
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
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162
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Önder Ö, Sidoli S, Carroll M, Garcia BA. Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Expert Rev Proteomics 2016; 12:499-517. [PMID: 26400466 DOI: 10.1586/14789450.2015.1084231] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin biology and epigenetics are scientific fields that are rapid expanding due to their fundamental role in understanding cell development, heritable characters and progression of diseases. Histone post-translational modifications (PTMs) are major regulators of the epigenetic machinery due to their ability to modulate gene expression, DNA repair and chromosome condensation. Large-scale strategies based on mass spectrometry have been impressively improved in the last decade, so that global changes of histone PTM abundances are quantifiable with nearly routine proteomics analyses and it is now possible to determine combinatorial patterns of modifications. Presented here is an overview of the most utilized and newly developed proteomics strategies for histone PTM characterization and a number of case studies where epigenetic mechanisms have been comprehensively characterized. Moreover, a number of current epigenetic therapies are illustrated, with an emphasis on cancer.
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Affiliation(s)
- Özlem Önder
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA.,b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Martin Carroll
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA
| | - Benjamin A Garcia
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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163
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Abstract
Organism viability relies on the stable maintenance of specific chromatin landscapes, established during development, that shape cell functions and identities by driving distinct gene expression programs. Yet epigenome maintenance is challenged during transcription, replication, and repair of DNA damage, all of which elicit dynamic changes in chromatin organization. Here, we review recent advances that have shed light on the specialized mechanisms contributing to the restoration of epigenome structure and function after DNA damage in the mammalian cell nucleus. By drawing a parallel with epigenome maintenance during replication, we explore emerging concepts and highlight open issues in this rapidly growing field. In particular, we present our current knowledge of molecular players that support the coordinated maintenance of genome and epigenome integrity in response to DNA damage, and we highlight how nuclear organization impacts genome stability. Finally, we discuss possible functional implications of epigenome plasticity in response to genotoxic stress.
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Affiliation(s)
- Juliette Dabin
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France
| | - Anna Fortuny
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France
| | - Sophie E Polo
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France.
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164
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Fenoy IM, Bogado SS, Contreras SM, Gottifredi V, Angel SO. The Knowns Unknowns: Exploring the Homologous Recombination Repair Pathway in Toxoplasma gondii. Front Microbiol 2016; 7:627. [PMID: 27199954 PMCID: PMC4853372 DOI: 10.3389/fmicb.2016.00627] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 04/18/2016] [Indexed: 12/17/2022] Open
Abstract
Toxoplasma gondii is an apicomplexan parasite of medical and veterinary importance which causes toxoplasmosis in humans. Great effort is currently being devoted toward the identification of novel drugs capable of targeting such illness. In this context, we believe that the thorough understanding of the life cycle of this model parasite will facilitate the identification of new druggable targets in T. gondii. It is important to exploit the available knowledge of pathways which could modulate the sensitivity of the parasite to DNA damaging agents. The homologous recombination repair (HRR) pathway may be of particular interest in this regard as its inactivation sensitizes other cellular models such as human cancer to targeted therapy. Herein we discuss the information available on T. gondii's HRR pathway from the perspective of its conservation with respect to yeast and humans. Special attention was devoted to BRCT domain-containing and end-resection associated proteins in T. gondii as in other experimental models such proteins have crucial roles in early/late steps or HRR and in the pathway choice for double strand break resolution. We conclude that T. gondii HRR pathway is a source of several lines of investigation that allow to to comprehend the extent of diversification of HRR in T. gondii. Such an effort will serve to determine if HRR could represent a potential targer for the treatment of toxoplasmosis.
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Affiliation(s)
- Ignacio M Fenoy
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM Chascomús, Argentina
| | - Silvina S Bogado
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM Chascomús, Argentina
| | - Susana M Contreras
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM Chascomús, Argentina
| | - Vanesa Gottifredi
- Cell Cycle Genomic Instability Laboratory, Fundación Instituto Leloir, IIBBA-CONICET Chascomús, Argentina
| | - Sergio O Angel
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM Chascomús, Argentina
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165
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Gursoy-Yuzugullu O, House N, Price BD. Patching Broken DNA: Nucleosome Dynamics and the Repair of DNA Breaks. J Mol Biol 2016; 428:1846-60. [PMID: 26625977 PMCID: PMC4860187 DOI: 10.1016/j.jmb.2015.11.021] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/12/2015] [Accepted: 11/21/2015] [Indexed: 01/07/2023]
Abstract
The ability of cells to detect and repair DNA double-strand breaks (DSBs) is dependent on reorganization of the surrounding chromatin structure by chromatin remodeling complexes. These complexes promote access to the site of DNA damage, facilitate processing of the damaged DNA and, importantly, are essential to repackage the repaired DNA. Here, we will review the chromatin remodeling steps that occur immediately after DSB production and that prepare the damaged chromatin template for processing by the DSB repair machinery. DSBs promote rapid accumulation of repressive complexes, including HP1, the NuRD complex, H2A.Z and histone methyltransferases at the DSB. This shift to a repressive chromatin organization may be important to inhibit local transcription and limit mobility of the break and to maintain the DNA ends in close contact. Subsequently, the repressive chromatin is rapidly dismantled through a mechanism involving dynamic exchange of the histone variant H2A.Z. H2A.Z removal at DSBs alters the acidic patch on the nucleosome surface, promoting acetylation of the H4 tail (by the NuA4-Tip60 complex) and shifting the chromatin to a more open structure. Further, H2A.Z removal promotes chromatin ubiquitination and recruitment of additional DSB repair proteins to the break. Modulation of the nucleosome surface and nucleosome function during DSB repair therefore plays a vital role in processing of DNA breaks. Further, the nucleosome surface may function as a central hub during DSB repair, directing specific patterns of histone modification, recruiting DNA repair proteins and modulating chromatin packing during processing of the damaged DNA template.
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Affiliation(s)
- Ozge Gursoy-Yuzugullu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02132, USA, T: 617 632-4946,
| | - Nealia House
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02132, USA, T: 617 632-4946,
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02132, USA, T: 617 632-4946,
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166
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Abstract
A new study suggests that fumarase, a metabolic enzyme normally associated with ATP production in mitochondria, is recruited to sites of DNA damage where it produces fumarate to inhibit histone demethylation and promote repair of DNA double strand breaks.
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Affiliation(s)
- Susan P Lees-Miller
- Departments of Biochemistry &Molecular Biology and Oncology, Robson DNA Science Centre, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
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167
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Agarwal P, Miller KM. The nucleosome: orchestrating DNA damage signaling and repair within chromatin. Biochem Cell Biol 2016; 94:381-395. [PMID: 27240007 DOI: 10.1139/bcb-2016-0017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.
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Affiliation(s)
- Poonam Agarwal
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA.,Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA.,Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA
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168
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Wang Q, Goldstein M. Small RNAs Recruit Chromatin-Modifying Enzymes MMSET and Tip60 to Reconfigure Damaged DNA upon Double-Strand Break and Facilitate Repair. Cancer Res 2016; 76:1904-15. [DOI: 10.1158/0008-5472.can-15-2334] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 01/03/2016] [Indexed: 11/16/2022]
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169
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Albulym OM, Kennerson ML, Harms MB, Drew AP, Siddell AH, Auer-Grumbach M, Pestronk A, Connolly A, Baloh RH, Zuchner S, Reddel SW, Nicholson GA. MORC2 mutations cause axonal Charcot-Marie-Tooth disease with pyramidal signs. Ann Neurol 2016; 79:419-27. [PMID: 26659848 DOI: 10.1002/ana.24575] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/02/2015] [Accepted: 12/04/2015] [Indexed: 01/14/2023]
Abstract
OBJECTIVE To use linkage analysis and whole exome sequencing to identify the genetic mutation in a multigenerational Australian family with Charcot-Marie-Tooth disease type 2 (CMT2) and pyramidal signs. METHODS Genome-wide linkage analysis was performed to map the locus. Whole exome sequencing was undertaken on selected individuals (3 affected, 1 normal), and segregation analysis and mutation screening were carried out using high-resolution melt analysis. The GEM.app database was queried to identify additional families with mutations. RESULTS Significant linkage (2-point LOD score ≥ +3) and haplotype analysis mapped a new locus for CMT2 and pyramidal signs to a 6.6Mb interval on chromosome 22q12.1-q12.3. Whole exome sequencing identified a novel mutation (p.R252W) in the microrchidia CW-type zinc finger 2 (MORC2) gene mapping within the linkage region. The mutation fully segregated with the disease phenotype in the family. Screening additional families and querying unsolved CMT2 exomes, we identified the p.R252W mutation in 2 unrelated early onset CMT2 families and a second mutation p.E236G in 2 unrelated CMT2 families. Both the mutations occurred at highly conserved amino acid residues and were absent in the normal population. INTERPRETATION We have identified a new locus in which MORC2 mutations are the likely pathogenic cause of CMT2 and pyramidal signs in these families. MORC2 encodes the human CW-type zinc finger 2 protein, which is a chromatin modifier involved in the regulation of DNA repair as well as gene transcription.
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Affiliation(s)
- Obaid M Albulym
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Matthew B Harms
- Department of Neurology, Washington University School of Medicine, St Louis, MO
| | - Alexander P Drew
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Anna H Siddell
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | - Alan Pestronk
- Department of Neurology, Washington University School of Medicine, St Louis, MO
| | - Anne Connolly
- Department of Neurology, Washington University School of Medicine, St Louis, MO
| | - Robert H Baloh
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, CA
| | - Stephan Zuchner
- Dr John T. MacDonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL
| | - Stephen W Reddel
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Garth A Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
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170
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Pradhan SK, Su T, Yen L, Jacquet K, Huang C, Côté J, Kurdistani SK, Carey MF. EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation. Mol Cell 2015; 61:27-38. [PMID: 26669263 DOI: 10.1016/j.molcel.2015.10.039] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/28/2015] [Accepted: 10/26/2015] [Indexed: 11/15/2022]
Abstract
Gene activation in metazoans is accompanied by the presence of histone variants H2AZ and H3.3 within promoters and enhancers. It is not known, however, what protein deposits H3.3 into chromatin or whether variant chromatin plays a direct role in gene activation. Here we show that chromatin containing acetylated H2AZ and H3.3 stimulates transcription in vitro. Analysis of the Pol II pre-initiation complex on immobilized chromatin templates revealed that the E1A binding protein p400 (EP400) was bound preferentially to and required for transcription stimulation by acetylated double-variant chromatin. EP400 also stimulated H2AZ/H3.3 deposition into promoters and enhancers and influenced transcription in vivo at a step downstream of the Mediator complex. EP400 efficiently exchanged recombinant histones H2A and H3.1 with H2AZ and H3.3, respectively, in a chromatin- and ATP-stimulated manner in vitro. Our data reveal that EP400 deposits H3.3 into chromatin alongside H2AZ and contributes to gene regulation after PIC assembly.
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Affiliation(s)
- Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA
| | - Linda Yen
- The Molecular Biology Institute, UCLA, Paul D. Boyer Hall, 611 Charles E. Young Drive South, Los Angeles, CA 90095-1570, USA
| | - Karine Jacquet
- Laval University Cancer Research Center, CHU de Québec Research Center-Oncology, Hôtel-Dieu de Québec, 9 McMahon Street, Quebec City, QC G1R 2J6, Canada
| | - Chengyang Huang
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec Research Center-Oncology, Hôtel-Dieu de Québec, 9 McMahon Street, Quebec City, QC G1R 2J6, Canada
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA; The Molecular Biology Institute, UCLA, Paul D. Boyer Hall, 611 Charles E. Young Drive South, Los Angeles, CA 90095-1570, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, 351A Biomedical Sciences Research Building, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737, USA; The Molecular Biology Institute, UCLA, Paul D. Boyer Hall, 611 Charles E. Young Drive South, Los Angeles, CA 90095-1570, USA.
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171
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ATM and SIRT6/SNF2H Mediate Transient H2AX Stabilization When DSBs Form by Blocking HUWE1 to Allow Efficient γH2AX Foci Formation. Cell Rep 2015; 13:2728-40. [DOI: 10.1016/j.celrep.2015.11.054] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 11/03/2015] [Accepted: 11/17/2015] [Indexed: 01/07/2023] Open
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172
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Taty-Taty GC, Chailleux C, Quaranta M, So A, Guirouilh-Barbat J, Lopez BS, Bertrand P, Trouche D, Canitrot Y. Control of alternative end joining by the chromatin remodeler p400 ATPase. Nucleic Acids Res 2015; 44:1657-68. [PMID: 26578561 PMCID: PMC4770216 DOI: 10.1093/nar/gkv1202] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022] Open
Abstract
Repair of DNA double-strand breaks occurs in a chromatin context that needs to be modified and remodeled to allow suitable access to the different DNA repair machineries. Of particular importance for the maintenance of genetic stability is the tight control of error-prone pathways, such as the alternative End Joining pathway. Here, we show that the chromatin remodeler p400 ATPase is a brake to the use of alternative End Joining. Using specific intracellular reporter susbstrates we observed that p400 depletion increases the frequency of alternative End Joining events, and generates large deletions following repair of double-strand breaks. This increase of alternative End Joining events is largely dependent on CtIP-mediated resection, indicating that it is probably related to the role of p400 in late steps of homologous recombination. Moreover, p400 depletion leads to the recruitment of poly(ADP) ribose polymerase (PARP) and DNA ligase 3 at DNA double-strand breaks, driving to selective killing by PARP inhibitors. All together these results show that p400 acts as a brake to prevent alternative End Joining-dependent genetic instability and underline its potential value as a clinical marker.
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Affiliation(s)
- Gemael-Cedrick Taty-Taty
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
| | - Catherine Chailleux
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
| | - Muriel Quaranta
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
| | - Ayeong So
- Université Paris Sud, CNRS UMR8200, IGR, Villejuif, France
| | | | | | - Pascale Bertrand
- CEA DSV, UMR 967 CEA-INSERM-Université Paris Diderot-Université Paris Sud, Fontenay aux roses, France
| | - Didier Trouche
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
| | - Yvan Canitrot
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
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173
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Yu ZC, Huang YF, Shieh SY. Requirement for human Mps1/TTK in oxidative DNA damage repair and cell survival through MDM2 phosphorylation. Nucleic Acids Res 2015; 44:1133-50. [PMID: 26531827 PMCID: PMC4756815 DOI: 10.1093/nar/gkv1173] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/21/2015] [Indexed: 01/25/2023] Open
Abstract
Human Mps1 (hMps1) is a protein kinase essential for mitotic checkpoints and the DNA damage response. Here, we present new evidence that hMps1 also participates in the repair of oxidative DNA lesions and cell survival through the MDM2-H2B axis. In response to oxidative stress, hMps1 phosphorylates MDM2, which in turn promotes histone H2B ubiquitination and chromatin decompaction. These events facilitate oxidative DNA damage repair and ATR-CHK1, but not ATM-CHK2 signaling. Depletion of hMps1 or MDM2 compromised H2B ubiquitination, DNA repair and cell survival. The impairment could be rescued by re-expression of WT but not the phospho-deficient MDM2 mutant, supporting the involvement of hMps1-dependent MDM2 phosphorylation in the oxidative stress response. In line with these findings, localization of RPA and base excision repair proteins to damage foci also requires MDM2 and hMps1. Significantly, like MDM2, hMps1 is upregulated in human sarcoma, suggesting high hMps1 and MDM2 expression may be beneficial for tumors constantly challenged by an oxidative micro-environment. Our study therefore identified an hMps1-MDM2-H2B signaling axis that likely plays a relevant role in tumor progression.
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Affiliation(s)
- Zheng-Cheng Yu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, No 1, Sec. 1, Jen-Ai Road, Taipei 100, Taiwan Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Road, Taipei 115, Taiwan
| | - Yi-Fu Huang
- Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Road, Taipei 115, Taiwan
| | - Sheau-Yann Shieh
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, No 1, Sec. 1, Jen-Ai Road, Taipei 100, Taiwan Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Road, Taipei 115, Taiwan
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174
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O'Connor HF, Lyon N, Leung JW, Agarwal P, Swaim CD, Miller KM, Huibregtse JM. Ubiquitin-Activated Interaction Traps (UBAITs) identify E3 ligase binding partners. EMBO Rep 2015; 16:1699-712. [PMID: 26508657 DOI: 10.15252/embr.201540620] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/28/2015] [Indexed: 12/27/2022] Open
Abstract
We describe a new class of reagents for identifying substrates, adaptors, and regulators of HECT and RING E3s. UBAITs (Ubiquitin-Activated Interaction Traps) are E3-ubiquitin fusion proteins and, in an E1- and E2-dependent manner, the C-terminal ubiquitin moiety forms an amide linkage to proteins that interact with the E3, enabling covalent co-purification of the E3 with partner proteins. We designed UBAITs for both HECT (Rsp5, Itch) and RING (Psh1, RNF126, RNF168) E3s. For HECT E3s, trapping of interacting proteins occurred in vitro either through an E3 thioester-linked lariat intermediate or through an E2 thioester intermediate, and both WT and active-site mutant UBAITs trapped known interacting proteins in yeast and human cells. Yeast Psh1 and human RNF126 and RNF168 UBAITs also trapped known interacting proteins when expressed in cells. Human RNF168 is a key mediator of ubiquitin signaling that promotes DNA double-strand break repair. Using the RNF168 UBAIT, we identify H2AZ--a histone protein involved in DNA repair--as a new target of this E3 ligase. These results demonstrate that UBAITs represent powerful tools for profiling a wide range of ubiquitin ligases.
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Affiliation(s)
- Hazel F O'Connor
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Nancy Lyon
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin W Leung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Poonam Agarwal
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Caleb D Swaim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Kyle M Miller
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jon M Huibregtse
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
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175
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Melters DP, Nye J, Zhao H, Dalal Y. Chromatin Dynamics in Vivo: A Game of Musical Chairs. Genes (Basel) 2015; 6:751-76. [PMID: 26262644 PMCID: PMC4584328 DOI: 10.3390/genes6030751] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/17/2015] [Accepted: 07/28/2015] [Indexed: 01/30/2023] Open
Abstract
Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.
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Affiliation(s)
- Daniël P Melters
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Jonathan Nye
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Haiqing Zhao
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA.
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
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176
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Bhatt S, Gupta MK, Khamaisi M, Martinez R, Gritsenko MA, Wagner BK, Guye P, Busskamp V, Shirakawa J, Wu G, Liew CW, Clauss TR, Valdez I, El Ouaamari A, Dirice E, Takatani T, Keenan HA, Smith RD, Church G, Weiss R, Wagers AJ, Qian WJ, King GL, Kulkarni RN. Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes. Cell Metab 2015; 22:239-52. [PMID: 26244933 PMCID: PMC4589213 DOI: 10.1016/j.cmet.2015.07.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/18/2015] [Accepted: 07/20/2015] [Indexed: 01/03/2023]
Abstract
The mechanisms underlying the development of complications in type 1 diabetes (T1D) are poorly understood. Disease modeling of induced pluripotent stem cells (iPSCs) from patients with longstanding T1D (disease duration ≥ 50 years) with severe (Medalist +C) or absent to mild complications (Medalist -C) revealed impaired growth, reprogramming, and differentiation in Medalist +C. Genomics and proteomics analyses suggested differential regulation of DNA damage checkpoint proteins favoring protection from cellular apoptosis in Medalist -C. In silico analyses showed altered expression patterns of DNA damage checkpoint factors among the Medalist groups to be targets of miR200, whose expression was significantly elevated in Medalist +C serum. Notably, neurons differentiated from Medalist +C iPSCs exhibited enhanced susceptibility to genotoxic stress that worsened upon miR200 overexpression. Furthermore, knockdown of miR200 in Medalist +C fibroblasts and iPSCs rescued checkpoint protein expression and reduced DNA damage. We propose miR200-regulated DNA damage checkpoint pathway as a potential therapeutic target for treating complications of diabetes.
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Affiliation(s)
- Shweta Bhatt
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Manoj K Gupta
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Mogher Khamaisi
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Section of Vascular Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Rachael Martinez
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Bridget K Wagner
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Patrick Guye
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Volker Busskamp
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Shirakawa
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Gongxiong Wu
- Section of Vascular Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Chong Wee Liew
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Therese R Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ivan Valdez
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Abdelfattah El Ouaamari
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Ercument Dirice
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Tomozumi Takatani
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Hillary A Keenan
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Section of Vascular Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amy J Wagers
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - George L King
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Section of Vascular Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.
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177
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Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation. Nat Cell Biol 2015; 17:1158-68. [PMID: 26237645 PMCID: PMC4800990 DOI: 10.1038/ncb3209] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 06/19/2015] [Indexed: 02/05/2023]
Abstract
Histone methylation regulates DNA repair. However, the mechanisms that underlie the regulation of histone methylation during this repair remain to be further defined. Here, we show that exposure to ionizing radiation induces DNA-PK-dependent phosphorylation of nuclear fumarase at Thr 236, which leads to an interaction between fumarase and the histone variant H2A.Z at DNA double-strand break (DSB) regions. Locally generated fumarate inhibits KDM2B histone demethylase activity, resulting in enhanced dimethylation of histone H3 Lys 36; in turn, this increases the accumulation of the Ku70-containing DNA-PK at DSB regions for non-homologous end-joining DNA repair and cell survival. These findings reveal a feedback mechanism that underlies DNA-PK regulation by chromatin-associated fumarase and an instrumental function of fumarase in regulating histone H3 methylation and DNA repair.
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178
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Alatwi HE, Downs JA. Removal of H2A.Z by INO80 promotes homologous recombination. EMBO Rep 2015; 16:986-94. [PMID: 26142279 PMCID: PMC4552491 DOI: 10.15252/embr.201540330] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 11/09/2022] Open
Abstract
The mammalian INO80 remodelling complex facilitates homologous recombination (HR), but the mechanism by which it does this is unclear. Budding yeast INO80 can remove H2A.Z/H2B dimers from chromatin and replace them with H2A/H2B dimers. H2A.Z is actively incorporated at sites of damage in mammalian cells, raising the possibility that H2A.Z may need to be subsequently removed for resolution of repair. Here, we show that H2A.Z in human cells is indeed rapidly removed from chromatin flanking DNA damage by INO80. We also report that the histone chaperone ANP32E, which is implicated in removing H2AZ from chromatin, similarly promotes HR and appears to work on the same pathway as INO80 in these assays. Importantly, we demonstrate that the HR defect in cells depleted of INO80 or ANP32E can be rescued by H2A.Z co-depletion, suggesting that H2A.Z removal from chromatin is the primary function of INO80 and ANP32E in promoting homologous recombination.
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Affiliation(s)
- Hanan E Alatwi
- MRC Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, UK
| | - Jessica A Downs
- MRC Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, UK
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179
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Donà M, Mittelsten Scheid O. DNA Damage Repair in the Context of Plant Chromatin. PLANT PHYSIOLOGY 2015; 168:1206-18. [PMID: 26089404 PMCID: PMC4528755 DOI: 10.1104/pp.15.00538] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/17/2015] [Indexed: 05/03/2023]
Abstract
The integrity of DNA molecules is constantly challenged. All organisms have developed mechanisms to detect and repair multiple types of DNA lesions. The basic principles of DNA damage repair (DDR) in prokaryotes and unicellular and multicellular eukaryotes are similar, but the association of DNA with nucleosomes in eukaryotic chromatin requires mechanisms that allow access of repair enzymes to the lesions. This is achieved by chromatin-remodeling factors, and their necessity for efficient DDR has recently been demonstrated for several organisms and repair pathways. Plants share many features of chromatin organization and DNA repair with fungi and animals, but they differ in other, important details, which are both interesting and relevant for our understanding of genome stability and genetic diversity. In this Update, we compare the knowledge of the role of chromatin and chromatin-modifying factors during DDR in plants with equivalent systems in yeast and humans. We emphasize plant-specific elements and discuss possible implications.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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180
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Structural basis for inhibition of the histone chaperone activity of SET/TAF-Iβ by cytochrome c. Proc Natl Acad Sci U S A 2015. [PMID: 26216969 DOI: 10.1073/pnas.1508040112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chromatin is pivotal for regulation of the DNA damage process insofar as it influences access to DNA and serves as a DNA repair docking site. Recent works identify histone chaperones as key regulators of damaged chromatin's transcriptional activity. However, understanding how chaperones are modulated during DNA damage response is still challenging. This study reveals that the histone chaperone SET/TAF-Iβ interacts with cytochrome c following DNA damage. Specifically, cytochrome c is shown to be translocated into cell nuclei upon induction of DNA damage, but not upon stimulation of the death receptor or stress-induced pathways. Cytochrome c was found to competitively hinder binding of SET/TAF-Iβ to core histones, thereby locking its histone-binding domains and inhibiting its nucleosome assembly activity. In addition, we have used NMR spectroscopy, calorimetry, mutagenesis, and molecular docking to provide an insight into the structural features of the formation of the complex between cytochrome c and SET/TAF-Iβ. Overall, these findings establish a framework for understanding the molecular basis of cytochrome c-mediated blocking of SET/TAF-Iβ, which subsequently may facilitate the development of new drugs to silence the oncogenic effect of SET/TAF-Iβ's histone chaperone activity.
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181
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Jarillo JA, Piñeiro M. H2A.Z mediates different aspects of chromatin function and modulates flowering responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:96-109. [PMID: 25943140 DOI: 10.1111/tpj.12873] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/17/2015] [Accepted: 04/22/2015] [Indexed: 05/23/2023]
Abstract
Eukaryotic organisms have canonical histones and a number of histone variants that perform specialized functions and confer particular structural properties to the nucleosomes that contain them. The histone H2A family comprises several variants, with H2A.Z being the most evolutionarily conserved. This variant is essential in eukaryotes and has emerged as a key player in chromatin function, performing an essential role in gene transcription and genome stability. During recent years, biochemical, genetic and genomic studies have begun to uncover the role of several ATP-dependent chromatin-remodeling complexes in H2A.Z deposition and removal. These ATPase complexes are widely conserved from yeast to mammals. In Arabidopsis there are homologs for most of the subunits of these complexes, and their functions are just beginning to be unveiled. In this review, we discuss the major contributions made in relation to the biology of the H2A.Z in plants, and more specifically concerning the function of this histone variant in the transition from vegetative to reproductive development. Recent advances in the understanding of the molecular mechanisms underlying the H2A.Z-mediated modulation of the floral transition, and thermosensory flowering responses in particular, are discussed. The emerging picture shows that plants contain chromatin-remodeling complexes related to those involved in modulating the dynamics of H2A.Z in other eukaryotes, but their precise biochemical nature remains elusive.
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Affiliation(s)
- José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223, Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223, Madrid, Spain
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182
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Histone chaperone Anp32e removes H2A.Z from DNA double-strand breaks and promotes nucleosome reorganization and DNA repair. Proc Natl Acad Sci U S A 2015; 112:7507-12. [PMID: 26034280 DOI: 10.1073/pnas.1504868112] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) requires open, flexible chromatin domains. The NuA4-Tip60 complex creates these flexible chromatin structures by exchanging histone H2A.Z onto nucleosomes and promoting acetylation of histone H4. Here, we demonstrate that the accumulation of H2A.Z on nucleosomes at DSBs is transient, and that rapid eviction of H2A.Z is required for DSB repair. Anp32e, an H2A.Z chaperone that interacts with the C-terminal docking domain of H2A.Z, is rapidly recruited to DSBs. Anp32e functions to remove H2A.Z from nucleosomes, so that H2A.Z levels return to basal within 10 min of DNA damage. Further, H2A.Z removal by Anp32e disrupts inhibitory interactions between the histone H4 tail and the nucleosome surface, facilitating increased acetylation of histone H4 following DNA damage. When H2A.Z removal by Anp32e is blocked, nucleosomes at DSBs retain elevated levels of H2A.Z, and assume a more stable, hypoacetylated conformation. Further, loss of Anp32e leads to increased CtIP-dependent end resection, accumulation of single-stranded DNA, and an increase in repair by the alternative nonhomologous end joining pathway. Exchange of H2A.Z onto the chromatin and subsequent rapid removal by Anp32e are therefore critical for creating open, acetylated nucleosome structures and for controlling end resection by CtIP. Dynamic modulation of H2A.Z exchange and removal by Anp32e reveals the importance of the nucleosome surface and nucleosome dynamics in processing the damaged chromatin template during DSB repair.
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183
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Ai X, Jia ZM, Wang J, DI GP, Zhang XU, Sun F, Zang T, Liao X. Bioinformatics analysis of the target gene of fibroblast growth factor receptor 3 in bladder cancer and associated molecular mechanisms. Oncol Lett 2015; 10:543-549. [PMID: 26171066 DOI: 10.3892/ol.2015.3231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 04/24/2015] [Indexed: 12/20/2022] Open
Abstract
The aim of the present study was to elucidate the molecular mechanisms of fibroblast growth factor receptor 3 (FGFR3) activation via overexpression or mutation of the FGFR3 target gene in bladder cancer (BC). The transcription profile data GSE41035, which included 18 BC samples, containing 3 independent FGFR3 short hairpin (sh)RNA, and 6 control samples, containing enhanced green fluorescent protein (EGFP) shRNA, were obtained from the National Center of Biotechnology Information Gene Expression Omnibus database. The Limma package with multiple testing correction was used to identify differentially expressed genes (DEGs) between FGFR3 knockdown and control samples. Gene ontology (GO) and pathway enrichment analysis were conducted in order to investigate the DEGs at the functional level. In addition, differential co-expression analysis was employed to construct a gene co-expression network. A total of 196 DEGs were acquired, of which 101 were downregulated and 95 were upregulated. In addition, a gene signature was identified linking FGFR3 signaling with de novo sterol biosynthesis and metabolism using GO and pathway enrichment analysis. Furthermore, the present study demonstrated that the genes NME2, CCNB1 and H2AFZ were significantly associated with BC, as determined by the protein-protein interaction network of DEGs and co-expressed genes. In conclusion, the present study revealed the involvement of FGFR3 in the regulation of sterol biosynthesis and metabolism in the maintenance of BC; in addition, the present study provided a novel insight into the molecular mechanisms of FGFR3 in BC. These results may therefore contribute to the theoretical guidance into the detection and therapy of BC.
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Affiliation(s)
- Xing Ai
- Department of Urology, Military General Hospital of Beijing PLA, Beijing 100700, P.R. China
| | - Zhuo-Min Jia
- Department of Urology, Military General Hospital of Beijing PLA, Beijing 100700, P.R. China ; Department of Urology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Juan Wang
- Department of Medicine, Military General Hospital of Beijing PLA, Beijing 100700, P.R. China
| | - Gui-Ping DI
- Department of Urology, Military General Hospital of Beijing PLA, Beijing 100700, P.R. China
| | - X U Zhang
- Department of Urology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Fengling Sun
- Department of Urology, Military General Hospital of Beijing PLA, Beijing 100700, P.R. China
| | - Tong Zang
- Department of Urology, Military General Hospital of Beijing PLA, Beijing 100700, P.R. China
| | - Xiumei Liao
- Department of Urology, Military General Hospital of Beijing PLA, Beijing 100700, P.R. China
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184
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Abstract
DNA damage poses a major threat to cell function and viability by compromising both genome and epigenome integrity. The DNA damage response indeed operates in the context of chromatin and relies on dynamic changes in chromatin organization. Here, we review the molecular bases of chromatin alterations in response to DNA damage, focusing on core histone mobilization in mammalian cells. Building on our current view of nucleosome dynamics in response to DNA damage, we highlight open challenges and avenues for future development. In particular, we discuss the different levels of regulation of chromatin plasticity during the DNA damage response and their potential impact on cell function and epigenome maintenance.
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185
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Monteiro FL, Baptista T, Amado F, Vitorino R, Jerónimo C, Helguero LA. Expression and functionality of histone H2A variants in cancer. Oncotarget 2015; 5:3428-43. [PMID: 25003966 PMCID: PMC4116493 DOI: 10.18632/oncotarget.2007] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Regulation of gene expression includes the replacement of canonical histones for non-allelic histone variants, as well as their multiple targeting by postranslational modifications. H2A variants are highly conserved between species suggesting they execute important functions that cannot be accomplished by canonical histones. Altered expression of many H2A variants is associated to cancer. MacroH2A variants are enriched in heterocromatic foci and are necessary for chromatin condensation. MacroH2A1.1 and macroH2A1.2 are two mutually exclusive isoforms. MacroH2A1.1 and macroH2A2 inhibit proliferation and are associated with better cancer prognosis; while macroH2A1.2 is associated to cancer progression. H2AX variant functions as a sensor of DNA damage and defines the cellular response towards DNA repair or apoptosis; therefore, screening approaches and therapeutic options targeting H2AX have been proposed. H2A.Z is enriched in euchromatin, acting as a proto-oncogene with established roles in hormone responsive cancers and overexpressed in endocrine-resistant disease. Other H2A family members have also been found altered in cancer, but their function remains unknown. Substantial progress has been made to understand histone H2A variants, their contribution to normal cellular function and to cancer development and progression. Yet, implementation of high resolution mass spectrometry is needed to further our knowledge on highly homologous H2A variants expression and function.
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Affiliation(s)
- Fátima Liliana Monteiro
- Mass Specrometry Center, Organic Chemistry and Natural Products Unit (QOPNA), Department of Chemistry, Universidade de Aveiro., Aveiro, Portugal
| | | | | | | | | | - Luisa A Helguero
- Mass Specrometry Center, Organic Chemistry and Natural Products Unit (QOPNA), Dep. of Chemistry, Universidade de Aveiro., Aveiro, Portugal
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186
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Overlapping Functions between SWR1 Deletion and H3K56 Acetylation in Candida albicans. EUKARYOTIC CELL 2015; 14:578-87. [PMID: 25862154 DOI: 10.1128/ec.00002-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/03/2015] [Indexed: 11/20/2022]
Abstract
Nucleosome destabilization by histone variants and modifications has been implicated in the epigenetic regulation of gene expression, with the histone variant H2A.Z and acetylation of H3K56 (H3K56ac) being two examples. Here we find that deletion of SWR1, the major subunit of the SWR1 complex depositing H2A.Z into chromatin in exchange for H2A, promotes epigenetic white-opaque switching in Candida albicans. We demonstrate through nucleosome mapping that SWR1 is required for proper nucleosome positioning on the promoter of WOR1, the master regulator of switching, and that its effects differ in white and opaque cells. Furthermore, we find that H2A.Z is enriched adjacent to nucleosome-free regions at the WOR1 promoter in white cells, suggesting a role in the stabilization of a repressive chromatin state. Deletion of YNG2, a subunit of the NuA4 H4 histone acetyltransferase (HAT) that targets SWR1 activity through histone acetylation, produces a switching phenotype similar to that of swr1, and both may act downstream of the GlcNAc signaling pathway. We further uncovered a genetic interaction between swr1 and elevated H3K56ac with the discovery that the swr1 deletion mutant is highly sensitive to nicotinamide. Our results suggest that the interaction of H2A.Z and H3K56ac regulates epigenetic switching at the nucleosome level, as well as having global effects.
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187
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Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40610-015-0005-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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188
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Histone variants: the artists of eukaryotic chromatin. SCIENCE CHINA-LIFE SCIENCES 2015; 58:232-9. [DOI: 10.1007/s11427-015-4817-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/23/2015] [Indexed: 10/24/2022]
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189
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Wang LH, Chi YH, Guo FG, Li-Byarlay H, Balfe S, Fang JC, Pittendrigh BR, Zhu-Salzman K. Transcriptomic response of cowpea bruchids to N-acetylglucosamine-specific lectins. INSECT SCIENCE 2015; 22:83-94. [PMID: 24446316 DOI: 10.1111/1744-7917.12108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/12/2014] [Indexed: 06/03/2023]
Abstract
Griffonia simplicifolia lectin II (GSII) and wheat germ agglutinin (WGA) are N-acetylglucosamine-binding lectins. Previous studies demonstrated that they have anti-insect activity, a property potentially useful in pest control. To gain some insight into the insect response to dietary lectins, we performed transcriptomic analysis using the cowpea bruchid (Callosobruchus maculatus) midgut microarray platform we built. Compared to the nonnutritional cellulose treatment, dietary lectins induced more profound changes in gene expression. Ingestion of relatively high doses of lectins for 24 h resulted in alteration of gene expression involved in sugar and lipid metabolism, transport, development, defense, and stress tolerance. Metabolic genes were largely downregulated. Moreover, we observed disorganized microvilli resulting from ingestion of WGA. This morphological change is consistent with the lectin-induced changes in genes related to midgut epithelial cell repair. In addition, suboptimal nutrient conditions may serve as a stress signal to trigger senescence processes, leading to growth arrest and developmental delay.
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Affiliation(s)
- Li-Hua Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China; Department of Entomology, Texas A&M University, College Station, TX, USA
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190
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Sak A, Kübler D, Bannik K, Groneberg M, Stuschke M. Dependence of radiation-induced H2AX phosphorylation on histone methylation: Evidence from the chromatin immunoprecipitation assay. Int J Radiat Biol 2015; 91:346-53. [DOI: 10.3109/09553002.2015.997895] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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191
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Abstract
Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes. Investigations into the evolution, structure, and metabolism of histone variants provide a foundation for understanding the participation of chromatin in important cellular processes and in epigenetic memory.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024
| | - M Mitchell Smith
- Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908
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192
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Subramanian* V, Fields* PA, Boyer LA. H2A.Z: a molecular rheostat for transcriptional control. F1000PRIME REPORTS 2015; 7:01. [PMID: 25705384 PMCID: PMC4311278 DOI: 10.12703/p7-01] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The replacement of nucleosomal H2A with the histone variant H2A.Z is critical for regulating DNA-mediated processes across eukaryotes and for early development of multicellular organisms. How this variant performs these seemingly diverse roles has remained largely enigmatic. Here, we discuss recent mechanistic insights that have begun to reveal how H2A.Z functions as a molecular rheostat for gene control. We focus on specific examples in metazoans as a model for understanding how H2A.Z integrates information from histone post-translational modifications, other histone variants, and transcription factors (TFs) to regulate proper induction of gene expression programs in response to cellular cues. Finally, we propose a general model of how H2A.Z incorporation regulates chromatin states in diverse processes.
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193
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Ferreira LL, Couto R, Oliveira PJ. Bisphenol A as epigenetic modulator: setting the stage for carcinogenesis? Eur J Clin Invest 2015; 45 Suppl 1:32-6. [PMID: 25524584 DOI: 10.1111/eci.12362] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Bisphenol A (BPA) is one of the most widely produced chemicals worldwide and is often used in the production of food and beverage containers. As a result of BPA contact with food, drink and toiletries, its ingestion and absorption by humans has been growing. The industrialization and modern lifestyles brought a constant exposure to several health-disturbing compounds and ushered a new era of chronic diseases. The endocrine disruptor potential of BPA is well known, but the research around its epigenotoxic effects raised further concerns whether chronic exposure to BPA can contribute to chronic human illness, including cancer in hormone-sensitive organs. MATERIALS AND METHODS Focusing on computerized databases, we reviewed original and review articles which elucidate and link some of the information already available about BPA and related epigenetic alterations. RESULTS A number of studies indicate that short-term administration of low or high-doses of BPA may be associated with an increased risk of epigenetic modifications, increasing the risk for carcinogenesis. However, it is clear that more studies considering real daily exposures are essential to define a real tolerable daily intake and to tighten up manufactory regulations. CONCLUSION In this review, we highlight some evidences suggesting a relationship between BPA exposure, genotoxic activity and epigenetic modifications, which may prime for carcinogenesis.
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Affiliation(s)
- Luciana L Ferreira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Doctoral Programme in Medical Biochemistry and Biophysics, University of Coimbra, Coimbra, Portugal
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194
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Li Z, Mon H, Mitsunobu H, Zhu L, Xu J, Lee JM, Kusakabe T. Dynamics of polycomb proteins-mediated histone modifications during UV irradiation-induced DNA damage. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 55:9-18. [PMID: 25308962 DOI: 10.1016/j.ibmb.2014.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/28/2014] [Accepted: 10/02/2014] [Indexed: 06/04/2023]
Abstract
Polycomb group (PcG) complexes are known to be chromatin modifiers and transcriptional repressors. In this work, we reported that the histone-modifying PcG complexes are able to participate in the repair process of ultraviolet (UV)-induced DNA lesions in the silkworm, Bombyx mori. The silkworm cells with depletion of PcG genes showed hypersensitive to UV-C irradiation and increased inhibition of cell proliferation. Interestingly, an SQ site in the silkworm-human chimeric H2A protein synthesized here was phosphorylated rapidly upon UV-C exposure, which could be used as a marker for monitoring the response to DNA damage in silkworm cells. Under these UV-C irradiated conditions, we found that PRC1-mediated ubiquitylation of H2AX, but not of H2AZ, were decreased and this deubiquitylation was independent of its phosphorylation event. In contrast, UV-C irradiation induced the increase of trimethylation of lysine 27 on histone H3 (H3K27me3), a mark of transcriptionally silent chromatin catalyzed by another PcG subcomplex, PRC2. Collectively, we provided the first evidence on chromatin remodeling in response to UV-C lesion in silkworm and revealed another layer role for PcG complexes-mediated histone modifications in contributing to creating an open chromatin structure for the efficient repair of DNA damages.
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Affiliation(s)
- Zhiqing Li
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Hiroaki Mon
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Hitoshi Mitsunobu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Li Zhu
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Jian Xu
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Jae Man Lee
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Takahiro Kusakabe
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.
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195
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De Jesus DF, Kulkarni RN. Epigenetic modifiers of islet function and mass. Trends Endocrinol Metab 2014; 25:628-36. [PMID: 25246382 DOI: 10.1016/j.tem.2014.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 08/22/2014] [Accepted: 08/25/2014] [Indexed: 01/28/2023]
Abstract
Type 2 diabetes (T2D) is associated with insulin resistance in target tissues including the β-cell, leading to significant β-cell loss and secretory dysfunction. T2D is also associated with aging, and the underlying mechanisms that increase susceptibility of an individual to develop the disease implicate epigenetics: interactions between susceptible loci and the environment. In this review, we discuss the effects of aging on β-cell function and adaptation, besides the significance of mitochondria in islet bioenergetics and epigenome. We highlight three important modulators of the islet epigenome, namely: metabolites, hormones, and the nutritional state. Unraveling the signaling pathways that regulate the islet epigenome during aging will help to better understand the development of disease progression and to design novel therapies for diabetes prevention.
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Affiliation(s)
- Dario F De Jesus
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Graduate Program in Areas of Basic and Applied Biology (GABBA), Abdel Salazar Biomedical Sciences Institute, University of Porto, 5000 Porto, Portugal
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.
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196
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Jeggo PA, Downs JA. Roles of chromatin remodellers in DNA double strand break repair. Exp Cell Res 2014; 329:69-77. [PMID: 25278484 DOI: 10.1016/j.yexcr.2014.09.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 10/24/2022]
Abstract
Now that we have a good understanding of the DNA double strand break (DSB) repair mechanisms and DSB-induced damage signalling, attention is focusing on the changes to the chromatin environment needed for efficient DSB repair. Mutations in chromatin remodelling complexes have been identified in cancers, making it important to evaluate how they impact upon genomic stability. Our current understanding of the DSB repair pathways suggests that each one has distinct requirements for chromatin remodelling. Moreover, restricting the extent of chromatin modifications could be a significant factor regulating the decision of pathway usage. In this review, we evaluate the distinct DSB repair pathways for their potential need for chromatin remodelling and review the roles of ATP-driven chromatin remodellers in the pathways.
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Affiliation(s)
- Penny A Jeggo
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton BN19RQ, UK.
| | - Jessica A Downs
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton BN19RQ, UK.
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197
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Dahlin JL, Chen X, Walters MA, Zhang Z. Histone-modifying enzymes, histone modifications and histone chaperones in nucleosome assembly: Lessons learned from Rtt109 histone acetyltransferases. Crit Rev Biochem Mol Biol 2014; 50:31-53. [PMID: 25365782 DOI: 10.3109/10409238.2014.978975] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During DNA replication, nucleosomes ahead of replication forks are disassembled to accommodate replication machinery. Following DNA replication, nucleosomes are then reassembled onto replicated DNA using both parental and newly synthesized histones. This process, termed DNA replication-coupled nucleosome assembly (RCNA), is critical for maintaining genome integrity and for the propagation of epigenetic information, dysfunctions of which have been implicated in cancers and aging. In recent years, it has been shown that RCNA is carefully orchestrated by a series of histone modifications, histone chaperones and histone-modifying enzymes. Interestingly, many features of RCNA are also found in processes involving DNA replication-independent nucleosome assembly like histone exchange and gene transcription. In yeast, histone H3 lysine K56 acetylation (H3K56ac) is found in newly synthesized histone H3 and is critical for proper nucleosome assembly and for maintaining genomic stability. The histone acetyltransferase (HAT) regulator of Ty1 transposition 109 (Rtt109) is the sole enzyme responsible for H3K56ac in yeast. Much research has centered on this particular histone modification and histone-modifying enzyme. This Critical Review summarizes much of our current understanding of nucleosome assembly and highlights many important insights learned from studying Rtt109 HATs in fungi. We highlight some seminal features in nucleosome assembly conserved in mammalian systems and describe some of the lingering questions in the field. Further studying fungal and mammalian chromatin assembly may have important public health implications, including deeper understandings of human cancers and aging as well as the pursuit of novel anti-fungal therapies.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine , Rochester, MN , USA
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198
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Petriz BA, Almeida JA, Gomes CPC, Pereira RW, Murad AM, Franco OL. NanoUPLC/MS(E) proteomic analysis reveals modulation on left ventricle proteome from hypertensive rats after exercise training. J Proteomics 2014; 113:351-65. [PMID: 25451014 DOI: 10.1016/j.jprot.2014.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/03/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED NanoUPLC/MS(E) was used to verify the effects of 8weeks of low (SHR-LIT=4) and high (SHR-HIT=4) intensity training over the left ventricle proteome of hypertensive rats (SHR-C=4). Training enhanced the aerobic capacity and reduced the systolic blood pressure in all exercised rats. NanoUPLC/MS(E) identified 250 proteins, with 233 in common to all groups and 16 exclusive to SHR-C, 2 to SHR-LIT, and 2 to the SHR-HIT. Cardiac hypertrophy related proteins appeared only in SHR-C. The SHR-LIT enhanced the abundance of 30 proteins and diminished 6, while SHR-HIT enhanced the abundance of 39 proteins and reduced other 7. The levels of metabolic (β and γ-enolase, adenine phosphoribosultransferase, and cytochrome b-c1), myofibril (myosin light chain 4, tropomyosin α and β-chain), and transporter proteins (hemoglobin, serum albumin, and hemopexin) were increased by both intensities. Transcription regulator and histone variants were enhanced by SHR-LIT and SHR-HIT respectively. SHR-LIT reduced the concentration of myosin binding protein C, while desmin and membrane voltage dependent anion selective channel protein-3 were reduced only by SHR-HIT. In addition, polyubiquitin B and C, and transcription regulators decreased in both intensities. Exercise also increased the concentration of anti-oxidant proteins, peroxiredozin-6 and glutathione peroxidase-1. BIOLOGICAL SIGNIFICANCE Pathologic left ventricle hypertrophy if one of the major outcomes of hypertension being a strong predictor of heart failure. Among the various risk factors for cardiovascular disorders, arterial hypertension is responsible for the highest rates of mortality worldwide. In this way, this present study contribute to the understanding of the molecular mechanisms involved in the attenuation of hypertension and the regression of pathological cardiac hypertrophy induced by exercise training.
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Affiliation(s)
- Bernardo A Petriz
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; UDF - Centro Universitário, Brasília, DF, Brazil
| | - Jeeser A Almeida
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; UDF - Centro Universitário, Brasília, DF, Brazil; Programa de Pós Graduação em Ciências e Tecnologias em Saúde, Universidade de Brasília - UnB, Ceilândia-DF, Brazil
| | - Clarissa P C Gomes
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Rinaldo W Pereira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Programa de Pós-Graduação em Educação Física, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - André M Murad
- Embrapa Recursos Genéticos e Biotecnologia - Laboratório de Biologia Sintética, Brasília-DF, Brazil
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; S-Inova, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande MS, Brazil; Programa de Pós-Graduação em Educação Física, Universidade Católica de Brasília, Brasília-DF, Brazil.
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199
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House NCM, Koch MR, Freudenreich CH. Chromatin modifications and DNA repair: beyond double-strand breaks. Front Genet 2014; 5:296. [PMID: 25250043 PMCID: PMC4155812 DOI: 10.3389/fgene.2014.00296] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 08/08/2014] [Indexed: 12/28/2022] Open
Abstract
DNA repair must take place in the context of chromatin, and chromatin modifications and DNA repair are intimately linked. The study of double-strand break repair has revealed numerous histone modifications that occur after induction of a DSB, and modification of the repair factors themselves can also occur. In some cases the function of the modification is at least partially understood, but in many cases it is not yet clear. Although DSB repair is a crucial activity for cell survival, DSBs account for only a small percentage of the DNA lesions that occur over the lifetime of a cell. Repair of single-strand gaps, nicks, stalled forks, alternative DNA structures, and base lesions must also occur in a chromatin context. There is increasing evidence that these repair pathways are also regulated by histone modifications and chromatin remodeling. In this review, we will summarize the current state of knowledge of chromatin modifications that occur during non-DSB repair, highlighting similarities and differences to DSB repair as well as remaining questions.
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Affiliation(s)
| | - Melissa R Koch
- Department of Biology, Tufts University Medford, MA, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University Medford, MA, USA ; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University Boston, MA, USA
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Basal activity of a PARP1-NuA4 complex varies dramatically across cancer cell lines. Cell Rep 2014; 8:1808-1818. [PMID: 25199834 DOI: 10.1016/j.celrep.2014.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/30/2014] [Accepted: 08/05/2014] [Indexed: 01/14/2023] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) catalyze poly(ADP-ribose) addition onto proteins, an important posttranslational modification involved in transcription, DNA damage repair, and stem cell identity. Previous studies established the activation of PARP1 in response to DNA damage, but little is known about PARP1 regulation outside of DNA repair. We developed an assay for measuring PARP activity in cell lysates and found that the basal activity of PARP1 was highly variable across breast cancer cell lines, independent of DNA damage. Sucrose gradient fractionation demonstrated that PARP1 existed in at least three biochemically distinct states in both high- and low-activity lines. A discovered complex containing the NuA4 chromatin-remodeling complex and PARP1 was responsible for high basal PARP1 activity, and NuA4 subunits were required for this activity. These findings present a pathway for PARP1 activation and a direct link between PARP1 and chromatin remodeling outside of the DNA damage response.
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