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Challis D, Lippis T, Wilson R, Wilkinson E, Dickinson J, Black A, Azimi I, Holloway A, Taberlay P, Brettingham-Moore K. Multiomics analysis of adaptation to repeated DNA damage in prostate cancer cells. Epigenetics 2023; 18:2214047. [PMID: 37196186 DOI: 10.1080/15592294.2023.2214047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023] Open
Abstract
DNA damage is frequently utilized as the basis for cancer therapies; however, resistance to DNA damage remains one of the biggest challenges for successful treatment outcomes. Critically, the molecular drivers behind resistance are poorly understood. To address this question, we created an isogenic model of prostate cancer exhibiting more aggressive characteristics to better understand the molecular signatures associated with resistance and metastasis. 22Rv1 cells were repeatedly exposed to DNA damage daily for 6 weeks, similar to patient treatment regimes. Using Illumina Methylation EPIC arrays and RNA-seq, we compared DNA methylation and transcriptional profiles between the parental 22Rv1 cell line and the lineage exposed to prolonged DNA damage. Here we show that repeated DNA damage drives the molecular evolution of cancer cells to a more aggressive phenotype and identify molecular candidates behind this process. Total DNA methylation was increased while RNA-seq demonstrated these cells had dysregulated expression of genes involved in metabolism and the unfolded protein response (UPR) with Asparagine synthetase (ASNS) identified as central to this process. Despite the limited overlap between RNA-seq and DNA methylation, oxoglutarate dehydrogenase-like (OGDHL) was identified as altered in both data sets. Utilising a second approach we profiled the proteome in 22Rv1 cells following a single dose of radiotherapy. This analysis also highlighted the UPR in response to DNA damage. Together, these analyses identified dysregulation of metabolism and the UPR and identified ASNS and OGDHL as candidates for resistance to DNA damage. This work provides critical insight into molecular changes which underpin treatment resistance and metastasis.
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Affiliation(s)
- D Challis
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - T Lippis
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - R Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia
| | - E Wilkinson
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - J Dickinson
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - A Black
- Medical Oncology, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - I Azimi
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, Tasmania, Australia
| | - A Holloway
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - P Taberlay
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - K Brettingham-Moore
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
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Abstract
Genomic DNA is organized three-dimensionally in the nucleus as chromatin. Recent accumulating evidence has demonstrated that chromatin organizes into numerous dynamic domains in higher eukaryotic cells, which act as functional units of the genome. These compacted domains facilitate DNA replication and gene regulation. Undamaged chromatin is critical for healthy cells to function and divide. However, the cellular genome is constantly threatened by many sources of DNA damage (e.g., radiation). How do cells maintain their genome integrity when subjected to DNA damage? This chapter describes how the compact state of chromatin safeguards the genome from radiation damage and chemical attacks. Together with recent genomics data, our finding suggests that DNA compaction, such as chromatin domain formation, plays a critical role in maintaining genome integrity. But does the formation of such domains limit DNA accessibility inside the domain and hinder the recruitment of repair machinery to the damaged site(s) during DNA repair? To approach this issue, we first describe a sensitive imaging method to detect changes in chromatin states in living cells (single-nucleosome imaging/tracking). We then use this method to explain how cells can overcome potential recruiting difficulties; cells can decompact chromatin domains following DNA damage and temporarily increase chromatin motion (∼DNA accessibility) to perform efficient DNA repair. We also speculate on how chromatin compaction affects DNA damage-resistance in the clinical setting.
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Affiliation(s)
- Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan.
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3
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Elevated HDAC activity and altered histone phospho-acetylation confer acquired radio-resistant phenotype to breast cancer cells. Clin Epigenetics 2020; 12:4. [PMID: 31900196 PMCID: PMC6942324 DOI: 10.1186/s13148-019-0800-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022] Open
Abstract
Background Poor-responsiveness of tumors to radiotherapy is a major clinical problem. Owing to the dynamic nature of the epigenome, the identification and targeting of potential epigenetic modifiers may be helpful to curb radio-resistance. This requires a detailed exploration of the epigenetic changes that occur during the acquirement of radio-resistance. Such an understanding can be applied for effective utilization of treatment adjuncts to enhance the efficacy of radiotherapy and reduce the incidence of tumor recurrence. Results This study explored the epigenetic alterations that occur during the acquirement of radio-resistance. Sequential irradiation of MCF7 breast cancer cell line up to 20 Gy generated a radio-resistant model. Micrococcal nuclease digestion demonstrated the presence of compact chromatin architecture coupled with decreased levels of histone PTMs H3K9ac, H3K27 ac, and H3S10pK14ac in the G0/G1 and mitotic cell cycle phases of the radio-resistant cells. Further investigation revealed that the radio-resistant population possessed high HDAC and low HAT activity, thus making them suitable candidates for HDAC inhibitor–based radio-sensitization. Treatment of radio-resistant cells with HDAC inhibitor valproic acid led to the retention of γH2AX and decreased H3S10p after irradiation. Additionally, an analysis of 38 human patient samples obtained from 8 different tumor types showed variable tumor HDAC activity, thus demonstrating inter-tumoral epigenetic heterogeneity in a patient population. Conclusion The study revealed that an imbalance of HAT and HDAC activities led to the loss of site-specific histone acetylation and chromatin compaction as breast cancer cells acquired radio-resistance. Due to variation in the tumor HDAC activity among patients, our report suggests performing a prior assessment of the tumor epigenome to maximize the benefit of HDAC inhibitor–based radio-sensitization. Graphical abstract ![]()
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Avgousti DC, Della Fera AN, Otter CJ, Herrmann C, Pancholi NJ, Weitzman MD. Adenovirus Core Protein VII Downregulates the DNA Damage Response on the Host Genome. J Virol 2017; 91:e01089-17. [PMID: 28794020 PMCID: PMC5625504 DOI: 10.1128/jvi.01089-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
Viral manipulation of cellular proteins allows viruses to suppress host defenses and generate infectious progeny. Due to the linear double-stranded DNA nature of the adenovirus genome, the cellular DNA damage response (DDR) is considered a barrier to successful infection. The adenovirus genome is packaged with protein VII, a virally encoded histone-like core protein that is suggested to protect incoming viral genomes from detection by the cellular DNA damage machinery. We showed that protein VII localizes to host chromatin during infection, leading us to hypothesize that protein VII may affect DNA damage responses on the cellular genome. Here we show that protein VII at cellular chromatin results in a significant decrease in accumulation of phosphorylated H2AX (γH2AX) following irradiation, indicating that protein VII inhibits DDR signaling. The oncoprotein SET was recently suggested to modulate the DDR by affecting access of repair proteins to chromatin. Since protein VII binds SET, we investigated a role for SET in DDR inhibition by protein VII. We show that knockdown of SET partially rescues the protein VII-induced decrease in γH2AX accumulation on the host genome, suggesting that SET is required for inhibition. Finally, we show that knockdown of SET also allows ATM to localize to incoming viral genomes bound by protein VII during infection with a mutant lacking early region E4. Together, our data suggest that the protein VII-SET interaction contributes to DDR evasion by adenovirus. Our results provide an additional example of a strategy used by adenovirus to abrogate the host DDR and show how viruses can modify cellular processes through manipulation of host chromatin.IMPORTANCE The DNA damage response (DDR) is a cellular network that is crucial for maintaining genome integrity. DNA viruses replicating in the nucleus challenge the resident genome and must overcome cellular responses, including the DDR. Adenoviruses are prevalent human pathogens that can cause a multitude of diseases, such as respiratory infections and conjunctivitis. Here we describe how a small adenovirus core protein that localizes to host chromatin during infection can globally downregulate the DDR. Our study focuses on key players in the damage signaling pathway and highlights how viral manipulation of chromatin may influence access of DDR proteins to the host genome.
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Affiliation(s)
- Daphne C Avgousti
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ashley N Della Fera
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Clayton J Otter
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christin Herrmann
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Neha J Pancholi
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Jdey W, Thierry S, Popova T, Stern MH, Dutreix M. Micronuclei Frequency in Tumors Is a Predictive Biomarker for Genetic Instability and Sensitivity to the DNA Repair Inhibitor AsiDNA. Cancer Res 2017; 77:4207-4216. [PMID: 28588010 DOI: 10.1158/0008-5472.can-16-2693] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 03/08/2017] [Accepted: 05/24/2017] [Indexed: 11/16/2022]
Abstract
Therapeutic strategies targeting DNA repair pathway defects have been widely explored, but often only benefit small numbers of patients. Here we characterized potential predictive biomarkers for treatment with AsiDNA, a novel first-in-class DNA repair inhibitor. We evaluated genetic instability and DNA repair defects by direct and indirect assays in 12 breast cancer cell lines to estimate the spontaneous occurrence of single-strand and double-strand breaks (DSB). For each cell line, we monitored constitutive PARP activation, spontaneous DNA damage by alkaline comet assay, basal micronuclei levels, the number of large-scale chromosomal rearrangements (LST), and the status of several DNA repair pathways by transcriptome and genome analysis. Sensitivity to AsiDNA was associated with a high spontaneous frequency of cells with micronuclei and LST and specific alterations in DNA repair pathways that essentially monitor DSB repair defects. A high basal level of micronuclei as a predictive biomarker for AsiDNA treatment was validated in 43 tumor cell lines from various tissues and 15 models of cell- and patient-derived xenografts. Micronuclei quantification was also possible in patient biopsies. Overall, this study identified genetic instability as a predictive biomarker for sensitivity to AsiDNA treatment. That micronuclei frequency can be measured in biopsies and does not reveal the same genetic instability as conventional genome assays opens new perspectives for refining the classification of tumors with genetic instability. Cancer Res; 77(16); 4207-16. ©2017 AACR.
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Affiliation(s)
- Wael Jdey
- Institut Curie, CNRS, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Orsay, France.,DNA Therapeutics/Onxeo, Paris, France
| | - Sylvain Thierry
- Institut Curie, CNRS, INSERM, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Tatiana Popova
- Institut Curie, PSL Research University, INSERM, Paris, France
| | | | - Marie Dutreix
- Institut Curie, CNRS, INSERM, Orsay, France. .,Université Paris Sud, Université Paris-Saclay, Orsay, France
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6
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Mondal S, Go YS, Lee SS, Chung BY, Kim JH. Characterization of histone modifications associated with DNA damage repair genes upon exposure to gamma rays in Arabidopsis seedlings. JOURNAL OF RADIATION RESEARCH 2016; 57:646-654. [PMID: 27534791 PMCID: PMC5137295 DOI: 10.1093/jrr/rrw077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/03/2016] [Accepted: 06/12/2016] [Indexed: 05/02/2023]
Abstract
Dynamic histone modifications play an important role in controlling gene expression in response to various environmental cues. This mechanism of regulation of gene expression is important for sessile organisms, like land plants. We have previously reported consistent upregulation of various marker genes in response to gamma rays at various post-irradiation times. In the present study, we performed various chromatin modification analyses at selected loci using the standard chromatin immunoprecipitation procedure, and demonstrate that upregulation of these genes is associated with histone H3 lysine 4 tri-methylation (H3K4me3) at the gene body or transcription start sites of these loci. Further, at specific AtAgo2 loci, both H3K4me3 and histone H3 lysine 9 acetylation (H3K9ac) are important in controlling gene expression in response to gamma irradiation. There was no change in DNA methylation in these selected loci. We conclude that specific histone modification such as H3K4me3 and H3K9ac may be more important in activating gene expression in these selected loci in response to gamma irradiation than a change in DNA methylation.
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Affiliation(s)
- Suvendu Mondal
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Young Sam Go
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Byung Yeoup Chung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
- Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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7
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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: 1.8] [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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8
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Friedman DA, Tait L, Vaughan ATM. Influence of nuclear structure on the formation of radiation-induced lethal lesions. Int J Radiat Biol 2016; 92:229-40. [DOI: 10.3109/09553002.2016.1144941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination.
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Affiliation(s)
- Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
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10
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Cell transcriptional state alters genomic patterns of DNA double-strand break repair in human astrocytes. Nat Commun 2014; 5:5799. [PMID: 25517576 DOI: 10.1038/ncomms6799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/07/2014] [Indexed: 01/11/2023] Open
Abstract
The misrepair of DNA double-strand breaks in close spatial proximity within the nucleus can result in chromosomal rearrangements that are important in the pathogenesis of haematopoietic and solid malignancies. It is unknown why certain epigenetic states, such as those found in stem or progenitor cells, appear to facilitate neoplastic transformation. Here we show that altering the transcriptional state of human astrocytes alters patterns of DNA damage repair from ionizing radiation at a gene locus-specific and genome-wide level. Astrocytes induced into a reactive state exhibit increased DNA repair, compared with non-reactive cells, in actively transcribed chromatin after irradiation. In mapping these repair sites, we identify misrepair events and repair hotspots that are unique to each state. The precise characterization of genomic regions susceptible to mutation in specific transcriptional states provides new opportunities for addressing clonal evolution in solid cancers, in particular those where double-strand break induction is a cornerstone of clinical intervention.
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11
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Liddle P, Lafon-Hughes L, Di Tomaso MV, Reyes-Ábalos AL, Jara J, Cerda M, Härtel S, Folle GA. Bleomycin-induced γH2AX foci map preferentially to replicating domains in CHO9 interphase nuclei. Chromosome Res 2014; 22:463-81. [DOI: 10.1007/s10577-014-9433-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 12/28/2022]
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Takata H, Hanafusa T, Mori T, Shimura M, Iida Y, Ishikawa K, Yoshikawa K, Yoshikawa Y, Maeshima K. Chromatin compaction protects genomic DNA from radiation damage. PLoS One 2013; 8:e75622. [PMID: 24130727 PMCID: PMC3794047 DOI: 10.1371/journal.pone.0075622] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 08/20/2013] [Indexed: 12/02/2022] Open
Abstract
Genomic DNA is organized three-dimensionally in the nucleus, and is thought to form compact chromatin domains. Although chromatin compaction is known to be essential for mitosis, whether it confers other advantages, particularly in interphase cells, remains unknown. Here, we report that chromatin compaction protects genomic DNA from radiation damage. Using a newly developed solid-phase system, we found that the frequency of double-strand breaks (DSBs) in compact chromatin after ionizing irradiation was 5–50-fold lower than in decondensed chromatin. Since radical scavengers inhibited DSB induction in decondensed chromatin, condensed chromatin had a lower level of reactive radical generation after ionizing irradiation. We also found that chromatin compaction protects DNA from attack by chemical agents. Our findings suggest that genomic DNA compaction plays an important role in maintaining genomic integrity.
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Affiliation(s)
- Hideaki Takata
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Frontier Research Base for Global Young Researchers, Graduate School of Engineering Osaka University, Suita, Osaka, Japan
- * E-mail: (HT); (KM)
| | - Tomo Hanafusa
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Toshiaki Mori
- Radiation Research Center, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Mari Shimura
- Department of Intractable Diseases, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Yutaka Iida
- Inorganic Analysis Laboratories, Toray Research Center, Inc., Otsu, Shiga, Japan
| | - Kenichi Ishikawa
- Advanced Radiation Biology Research Program, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Inage, Chiba, Japan
| | - Kenichi Yoshikawa
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yuko Yoshikawa
- Research Organization of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Kazuhiro Maeshima
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka, Japan
- * E-mail: (HT); (KM)
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13
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DNA double-strand breaks: linking gene expression to chromosome morphology and mobility. Chromosoma 2013; 123:103-15. [DOI: 10.1007/s00412-013-0432-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 08/06/2013] [Accepted: 08/08/2013] [Indexed: 11/27/2022]
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14
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Soldi M, Bonaldi T. The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components. Mol Cell Proteomics 2013; 12:764-80. [PMID: 23319141 PMCID: PMC3591667 DOI: 10.1074/mcp.m112.024307] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent mass spectrometry analysis. Here we describe a modified protocol for chromatin immunoprecipitation combined with quantitative proteomics based on stable isotope labeling by amino acids in cell culture to identify known and novel histone modifications, variants, and complexes that specifically associate with silent and active chromatin domains. Our chromatin proteomics strategy revealed unique functional interactions among various chromatin modifiers, suggesting new regulatory pathways, such as a heterochromatin-specific modulation of DNA damage response involving H2A.X and WICH, both enriched in silent domains. Chromatin proteomics expands the arsenal of tools for deciphering how all the distinct protein components act together to enforce a given region-specific chromatin status.
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Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, Milan, Italy
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15
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Terry SYA, Vallis KA. Relationship between chromatin structure and sensitivity to molecularly targeted auger electron radiation therapy. Int J Radiat Oncol Biol Phys 2012; 83:1298-305. [PMID: 22336201 PMCID: PMC6175060 DOI: 10.1016/j.ijrobp.2011.09.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/13/2011] [Accepted: 09/20/2011] [Indexed: 12/17/2022]
Abstract
PURPOSE The open structure of euchromatin renders it susceptible to DNA damage by ionizing radiation (IR) compared with compact heterochromatin. The effect of chromatin configuration on the efficacy of Auger electron radiotherapy was investigated. METHODS AND MATERIALS Chromatin structure was altered in MDA-MB-468 and 231-H2N human breast cancer cells by suberoylanilide hydroxamic acid (SAHA), 5-aza-2-deoxycytidine, or hypertonic treatment. The extent and duration of chromatin structural changes were evaluated using the micrococcal nuclease assay. DNA damage (γH2AX assay) and clonogenic survival were evaluated after exposure to (111)In-DTPA-hEGF, an Auger electron-emitting radiopharmaceutical, or IR. The intracellular distribution of (111)In-DTPA-hEGF after chromatin modification was investigated in cell fractionation experiments. RESULTS Chromatin remained condensed for up to 20 minutes after NaCl and in a relaxed state 24 hours after SAHA treatment. The number of γH2AX foci per cell was greater in MDA-MB-468 and 231-H2N cells after IR (0.5 Gy) plus SAHA (1 μM) compared with IR alone (16 ± 0.6 and 14 ± 0.3 vs. 12 ± 0.4 and 11 ± 0.2, respectively). More γH2AX foci were observed in MDA-MB-468 and 231-H2N cells exposed to (111)In-DTPA-hEGF (6 MBq/μg) plus SAHA vs. (111)In-DTPA-hEGF alone (11 ± 0.3 and 12 ± 0.7 vs. 9 ± 0.4 and 7 ± 0.3, respectively). 5-aza-2-deoxycytidine enhanced the DNA damage caused by IR and (111)In-DTPA-hEGF. Clonogenic survival was reduced in MDA-MB-468 and 231-H2N cells after IR (6 Gy) plus SAHA (1 μM) vs. IR alone (0.6% ± 0.01 and 0.3% ± 0.2 vs. 5.8% ± 0.2 and 2% ± 0.1, respectively) and after (111)In-DTPA-hEGF plus SAHA compared to (111)In-DTPA-hEGF alone (21% ± 0.4% and 19% ± 4.6 vs. 33% ± 2.3 and 32% ± 3.7). SAHA did not affect (111)In-DTPA-hEGF nuclear localization. Hypertonic treatment resulted in fewer γH2AX foci per cell after IR and (111)In-DTPA-hEGF compared to controls but did not significantly alter clonogenic survival. CONCLUSIONS Chromatin structure affects DNA damage and cell survival after exposure to Auger electron radiation.
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Affiliation(s)
- Samantha Y A Terry
- CR-UK/MRC Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Oxford, UK
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Ho B, Baker PM, Singh S, Shih SJ, Vaughan AT. Localized DNA cleavage secondary to genotoxic exposure adjacent to an Alu inverted repeat. Genes Chromosomes Cancer 2012; 51:501-9. [PMID: 22334386 DOI: 10.1002/gcc.21938] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 01/05/2012] [Indexed: 01/12/2023] Open
Abstract
Radiation is a potent inducer of DNA damage leading to both random DNA loss and mutation. As part of a study focused on the mechanism whereby cells undergo loss of heterozygosity (LOH), a region of common LOH telomeric termination at 11q24 was observed in clones of H292 mucoepidermoid cells established after irradiation (IR). A 10-kbp region including the telomeric extent of LOH termination was analyzed after IR using six sets of ligation-mediated polymerase chain reaction (PCR) primers to detect the presence of DNA breaks. A cluster of DNA breaks was detected that closely mapped to the telomeric extent of LOH and which were observed up to 8 hr after IR. Repeating the experiment in the presence of the inhibitor of apoptosis, zVAD.fmk, did not change the location or amount of cleavage. A similar distribution of breaks was also seen in the MCF-10A breast cancer cell line after IR. Further inspection of the involved region showed that 22/32 and 7/7 DNA breaks found in H292 and MCF-10A cells, respectively, were located either in or immediately adjacent to an AluSx1 sequence, itself ≈ 1 kbp 5' to an AluSq2 that was in an inverted orientation to the AluSx1. The region between the inverted Alu repeats was notable for both DNAse hypersensitivity and an open chromatin conformation inferred from histone modification data. These factors may contribute to genomic instability at this location.
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Affiliation(s)
- Bay Ho
- Department of Radiation Oncology, University of California at Davis, Sacramento, CA 95817, USA
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17
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Jakob B, Splinter J, Conrad S, Voss KO, Zink D, Durante M, Löbrich M, Taucher-Scholz G. DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin. Nucleic Acids Res 2011; 39:6489-99. [PMID: 21511815 PMCID: PMC3159438 DOI: 10.1093/nar/gkr230] [Citation(s) in RCA: 229] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
DNA double-strand breaks (DSBs) can induce chromosomal aberrations and carcinogenesis and their correct repair is crucial for genetic stability. The cellular response to DSBs depends on damage signaling including the phosphorylation of the histone H2AX (γH2AX). However, a lack of γH2AX formation in heterochromatin (HC) is generally observed after DNA damage induction. Here, we examine γH2AX and repair protein foci along linear ion tracks traversing heterochromatic regions in human or murine cells and find the DSBs and damage signal streaks bending around highly compacted DNA. Given the linear particle path, such bending indicates a relocation of damage from the initial induction site to the periphery of HC. Real-time imaging of the repair protein GFP-XRCC1 confirms fast recruitment to heterochromatic lesions inside murine chromocenters. Using single-ion microirradiation to induce localized DSBs directly within chromocenters, we demonstrate that H2AX is early phosphorylated within HC, but the damage site is subsequently expelled from the center to the periphery of chromocenters within ∼20 min. While this process can occur in the absence of ATM kinase, the repair of DSBs bordering HC requires the protein. Finally, we describe a local decondensation of HC at the sites of ion hits, potentially allowing for DSB movement via physical forces.
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Affiliation(s)
- Burkhard Jakob
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Planckstrasse 1, 64291 Darmstadt, Germany
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18
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Cann KL, Dellaire G. Heterochromatin and the DNA damage response: the need to relaxThis paper is one of a selection of papers in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2011; 89:45-60. [DOI: 10.1139/o10-113] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Higher order chromatin structure has an impact on all nuclear functions, including the DNA damage response. Over the past several years, it has become increasingly clear that heterochromatin and euchromatin represent separate entities with respect to both damage sensitivity and repair. The chromatin compaction present in heterochromatin helps to protect this DNA from damage; however, when lesions do occur, the compaction restricts the ability of DNA damage response proteins to access the site, as evidenced by its ability to block the expansion of H2AX phosphorylation. As such, DNA damage in heterochromatin is refractory to repair, which requires the surrounding chromatin structure to be decondensed. In the case of DNA double-strand breaks, this relaxation is at least partially mediated by the ATM kinase phosphorylating and inhibiting the function of the transcriptional repressor KAP1. This review will focus on the functions of KAP1 and other proteins involved in the maintenance or restriction of heterochromatin, including HP1 and TIP60, in the DNA damage response. As heterochromatin is important for maintaining genomic stability, cells must maintain a delicate balance between allowing repair factors access to these regions and ensuring that these regions retain their organization to prevent increased DNA damage and chromosomal mutations.
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Affiliation(s)
- Kendra L. Cann
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Graham Dellaire
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
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19
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Mah LJ, Orlowski C, Ververis K, Vasireddy RS, El-Osta A, Karagiannis TC. Evaluation of the efficacy of radiation-modifying compounds using γH2AX as a molecular marker of DNA double-strand breaks. Genome Integr 2011; 2:3. [PMID: 21261999 PMCID: PMC3037297 DOI: 10.1186/2041-9414-2-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 01/25/2011] [Indexed: 12/23/2022] Open
Abstract
Radiation therapy is a widely used therapeutic approach for cancer. To improve the efficacy of radiotherapy there is an intense interest in combining this modality with two broad classes of compounds, radiosensitizers and radioprotectors. These either enhance tumour-killing efficacy or mitigate damage to surrounding non-malignant tissue, respectively. Radiation exposure often results in the formation of DNA double-strand breaks, which are marked by the induction of H2AX phosphorylation to generate γH2AX. In addition to its essential role in DDR signalling and coordination of double-strand break repair, the ability to visualize and quantitate γH2AX foci using immunofluorescence microscopy techniques enables it to be exploited as an indicator of therapeutic efficacy in a range of cell types and tissues. This review will explore the emerging applicability of γH2AX as a marker for monitoring the effectiveness of radiation-modifying compounds.
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Affiliation(s)
- Li-Jeen Mah
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Christian Orlowski
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Katherine Ververis
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Anatomy and Cell Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Raja S Vasireddy
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Medicine, Monash University, Melbourne, Victoria, Australia.,Epigenomic Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
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20
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Aypar U, Morgan WF, Baulch JE. Radiation-induced genomic instability: Are epigenetic mechanisms the missing link? Int J Radiat Biol 2010; 87:179-91. [DOI: 10.3109/09553002.2010.522686] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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21
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Vasireddy RS, Tang MM, Mah LJ, Georgiadis GT, El-Osta A, Karagiannis TC. Evaluation of the spatial distribution of gammaH2AX following ionizing radiation. J Vis Exp 2010:2203. [PMID: 20736911 DOI: 10.3791/2203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
An early molecular response to DNA double-strand breaks (DSBs) is phosphorylation of the Ser-139 residue within the terminal SQEY motif of the histone H2AX. This phosphorylation of H2AX is mediated by the phosphatidyl-inosito 3-kinase (PI3K) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR). The phosphorylated form of H2AX, referred to as gammaH2AX, spreads to adjacent regions of chromatin from the site of the DSB, forming discrete foci, which are easily visualized by immunofluorescence microscopy. Analysis and quantitation of gammaH2AX foci has been widely used to evaluate DSB formation and repair, particularly in response to ionizing radiation and for evaluating the efficacy of various radiation modifying compounds and cytotoxic compounds. Given the exquisite specificity and sensitivity of this de novo marker of DSBs, it has provided new insights into the processes of DNA damage and repair in the context of chromatin. For example, in radiation biology the central paradigm is that the nuclear DNA is the critical target with respect to radiation sensitivity. Indeed, the general consensus in the field has largely been to view chromatin as a homogeneous template for DNA damage and repair. However, with the use of gammaH2AX as molecular marker of DSBs, a disparity in gamma-irradiation-induced gammaH2AX foci formation in euchromatin and heterochromatin has been observed. Recently, we used a panel of antibodies to either mono-, di- or tri- methylated histone H3 at lysine 9 (H3K9me1, H3K9me2, H3K9me3) which are epigenetic imprints of constitutive heterochromatin and transcriptional silencing and lysine 4 (H3K4me1, H3K4me2, H3K4me3), which are tightly correlated actively transcribing euchromatic regions, to investigate the spatial distribution of gammaH2AX following ionizing radiation. In accordance with the prevailing ideas regarding chromatin biology, our findings indicated a close correlation between gammaH2AX formation and active transcription. Here we demonstrate our immunofluorescence method for detection and quantitation of gammaH2AX foci in non-adherent cells, with a particular focus on co-localization with other epigenetic markers, image analysis and 3D-modeling.
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Affiliation(s)
- Raja S Vasireddy
- Epigenetics in Human Health and Disease, BakerIDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct
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22
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Li A, Yu Y, Lee SC, Ishibashi T, Lees-Miller SP, Ausió J. Phosphorylation of histone H2A.X by DNA-dependent protein kinase is not affected by core histone acetylation, but it alters nucleosome stability and histone H1 binding. J Biol Chem 2010; 285:17778-88. [PMID: 20356835 DOI: 10.1074/jbc.m110.116426] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphorylation of the C-terminal end of histone H2A.X is the most characterized histone post-translational modification in DNA double-stranded breaks (DSB). DNA-dependent protein kinase (DNA-PK) is one of the three phosphatidylinositol 3 kinase-like family of kinase members that is known to phosphorylate histone H2A.X during DNA DSB repair. There is a growing body of evidence supporting a role for histone acetylation in DNA DSB repair, but the mechanism or the causative relation remains largely unknown. Using bacterially expressed recombinant mutants and stably and transiently transfected cell lines, we find that DNA-PK can phosphorylate Thr-136 in addition to Ser-139 both in vitro and in vivo. Furthermore, the phosphorylation reaction is not inhibited by the presence of H1, which in itself is a substrate of the reaction. We also show that, in contrast to previous reports, the ability of the enzyme to phosphorylate these residues is not affected by the extent of acetylation of the core histones. In vitro assembled nucleosomes and HeLa S3 native oligonucleosomes consisting of non-acetylated and acetylated histones are equally phosphorylated by DNA-PK. We demonstrate that the apparent differences in the extent of phosphorylation previously observed can be accounted for by the differential chromatin solubility under the MgCl(2) concentrations required for the phosphorylation reaction in vitro. Finally, we show that although H2A.X does not affect nucleosome conformation, it has a de-stabilizing effect that is enhanced by the DNA-PK-mediated phosphorylation and results in an impaired histone H1 binding.
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Affiliation(s)
- Andra Li
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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