1
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Sjodin BMF, Schmidt DA, Galbreath KE, Russello MA. Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients. Sci Rep 2024; 14:8568. [PMID: 38609461 PMCID: PMC11014952 DOI: 10.1038/s41598-024-59157-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.
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Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Danielle A Schmidt
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, 1401 Presque Isle Ave, Marquette, MI, 49855, USA
| | - Michael A Russello
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada.
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2
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Kim HM, Zheng X, Lee E. Experimental Insights into the Interplay between Histone Modifiers and p53 in Regulating Gene Expression. Int J Mol Sci 2023; 24:11032. [PMID: 37446210 PMCID: PMC10342072 DOI: 10.3390/ijms241311032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Chromatin structure plays a fundamental role in regulating gene expression, with histone modifiers shaping the structure of chromatin by adding or removing chemical changes to histone proteins. The p53 transcription factor controls gene expression, binds target genes, and regulates their activity. While p53 has been extensively studied in cancer research, specifically in relation to fundamental cellular processes, including gene transcription, apoptosis, and cell cycle progression, its association with histone modifiers has received limited attention. This review explores the interplay between histone modifiers and p53 in regulating gene expression. We discuss how histone modifications can influence how p53 binds to target genes and how this interplay can be disrupted in cancer cells. This review provides insights into the complex mechanisms underlying gene regulation and their implications for potential cancer therapy.
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Affiliation(s)
- Hyun-Min Kim
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan 215316, China
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3
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Kreienbaum C, Paasche LW, Hake SB. H2A.Z's 'social' network: functional partners of an enigmatic histone variant. Trends Biochem Sci 2022; 47:909-920. [PMID: 35606214 DOI: 10.1016/j.tibs.2022.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
Abstract
The histone variant H2A.Z has been extensively studied to understand its manifold DNA-based functions. In the past years, researchers identified its specific binding partners, the 'H2A.Z interactome', that convey H2A.Z-dependent chromatin changes. Here, we summarize the latest findings regarding vertebrate H2A.Z-associated factors and focus on their roles in gene activation and repression, cell cycle regulation, (neuro)development, and tumorigenesis. Additionally, we demonstrate how protein-protein interactions and post-translational histone modifications can fine-tune the complex interplay of H2A.Z-regulated gene expression. Last, we review the most recent results on interactors of the two isoforms H2A.Z.1 and H2A.Z.2.1, which differ in only three amino acids, and focus on cancer-associated mutations of H2A and H2A.Z, which reveal fascinating insights into the functional importance of such minuscule changes.
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Affiliation(s)
| | - Lena W Paasche
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany.
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4
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Lashgari A, Kougnassoukou Tchara PE, Lambert JP, Côté J. New insights into the DNA repair pathway choice with NuA4/TIP60. DNA Repair (Amst) 2022; 113:103315. [PMID: 35278769 DOI: 10.1016/j.dnarep.2022.103315] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 11/03/2022]
Abstract
In eukaryotic cells, DNA double-strand breaks (DSBs) can be repaired through two main pathways, non-homologous end-joining (NHEJ) or homologous recombination (HR). The selection of the repair pathway choice is governed by an antagonistic relationship between repair factors specific to each pathway, in a cell cycle-dependent manner. The molecular mechanisms of this decision implicate post-translational modifications of chromatin surrounding the break. Here, we discuss the recent advances regarding the function of the NuA4/TIP60 histone acetyltransferase/chromatin remodeling complex during DSBs repair. In particular, we emphasise the contribution of NuA4/TIP60 in repair pathway choice, in collaboration with the SAGA acetyltransferase complex, and how they regulate chromatin dynamics, modify non-histone substrates to allow DNA end resection and recombination.
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Affiliation(s)
- Anahita Lashgari
- St-Patrick Research Group in Basic Oncology, Canada; Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada
| | - Pata-Eting Kougnassoukou Tchara
- Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada
| | - Jean-Philippe Lambert
- Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada.
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Canada; Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada.
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5
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Herchenröther A, Wunderlich TM, Lan J, Hake SB. Spotlight on histone H2A variants: From B to X to Z. Semin Cell Dev Biol 2022; 135:3-12. [PMID: 35365397 DOI: 10.1016/j.semcdb.2022.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 12/30/2022]
Abstract
Chromatin, the functional organization of DNA with histone proteins in eukaryotic nuclei, is the tightly-regulated template for several biological processes, such as transcription, replication, DNA damage repair, chromosome stability and sister chromatid segregation. In order to achieve a reversible control of local chromatin structure and DNA accessibility, various interconnected mechanisms have evolved. One of such processes includes the deposition of functionally-diverse variants of histone proteins into nucleosomes, the building blocks of chromatin. Among core histones, the family of H2A histone variants exhibits the largest number of members and highest sequence-divergence. In this short review, we report and discuss recent discoveries concerning the biological functions of the animal histone variants H2A.B, H2A.X and H2A.Z and how dysregulation or mutation of the latter impacts the development of disease.
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Affiliation(s)
| | - Tim M Wunderlich
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany
| | - Jie Lan
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany.
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6
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Tessier TM, Dodge MJ, MacNeil KM, Evans AM, Prusinkiewicz MA, Mymryk JS. Almost famous: Human adenoviruses (and what they have taught us about cancer). Tumour Virus Res 2021; 12:200225. [PMID: 34500123 PMCID: PMC8449131 DOI: 10.1016/j.tvr.2021.200225] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 12/11/2022] Open
Abstract
Papillomaviruses, polyomaviruses and adenoviruses are collectively categorized as the small DNA tumour viruses. Notably, human adenoviruses were the first human viruses demonstrated to be able to cause cancer, albeit in non-human animal models. Despite their long history, no human adenovirus is a known causative agent of human cancers, unlike a subset of their more famous cousins, including human papillomaviruses and human Merkel cell polyomavirus. Nevertheless, seminal research using human adenoviruses has been highly informative in understanding the basics of cell cycle control, gene expression, apoptosis and cell differentiation. This review highlights the contributions of human adenovirus research in advancing our knowledge of the molecular basis of cancer.
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Affiliation(s)
- Tanner M Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Mackenzie J Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Andris M Evans
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Martin A Prusinkiewicz
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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7
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Swift ML, Beishline K, Azizkhan-Clifford J. Sp1-dependent recruitment of the histone acetylase p300 to DSBs facilitates chromatin remodeling and recruitment of the NHEJ repair factor Ku70. DNA Repair (Amst) 2021; 105:103171. [PMID: 34252870 DOI: 10.1016/j.dnarep.2021.103171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/18/2021] [Accepted: 07/04/2021] [Indexed: 11/18/2022]
Abstract
In response to DNA damage, most factors involved in damage recognition and repair are tightly regulated to ensure proper repair pathway choice. Histone acetylation at DNA double strand breaks (DSBs) by p300 histone acetyltransferase (HAT) is critical for the recruitment of DSB repair proteins to chromatin. Here, we show that phosphorylation of Sp1 by ATM increases its interaction with p300 and that Sp1-dependent recruitment of p300 to DSBs is necessary to modify the histones associated with p300 activity and NHEJ repair factor recruitment and repair. p300 is known to acetylate multiple residues on histones H3 and H4 necessary for NHEJ. Acetylation of H3K18 by p300 is associated with the recruitment of the SWI/SNF chromatin remodeling complex and Ku70 to DSBs for NHEJ repair. Depletion of Sp1 results in decreased acetylation of lysines on histones H3 and H4. Specifically, cells depleted of Sp1 display defects in the acetylation of H3K18, resulting in defective SWI/SNF and Ku70 recruitment to DSBs. These results shed light on mechanisms by which chromatin remodelers are regulated to ensure activation of the appropriate DSB repair pathway.
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Affiliation(s)
- Michelle L Swift
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kate Beishline
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jane Azizkhan-Clifford
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA.
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8
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Chronic exposure of humans to high level natural background radiation leads to robust expression of protective stress response proteins. Sci Rep 2021; 11:1777. [PMID: 33469066 PMCID: PMC7815775 DOI: 10.1038/s41598-020-80405-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding exposures to low doses of ionizing radiation are relevant since most environmental, diagnostic radiology and occupational exposures lie in this region. However, the molecular mechanisms that drive cellular responses at these doses, and the subsequent health outcomes, remain unclear. A local monazite-rich high level natural radiation area (HLNRA) in the state of Kerala on the south-west coast of Indian subcontinent show radiation doses extending from ≤ 1 to ≥ 45 mGy/y and thus, serve as a model resource to understand low dose mechanisms directly on healthy humans. We performed quantitative discovery proteomics based on multiplexed isobaric tags (iTRAQ) coupled with LC–MS/MS on human peripheral blood mononuclear cells from HLNRA individuals. Several proteins involved in diverse biological processes such as DNA repair, RNA processing, chromatin modifications and cytoskeletal organization showed distinct expression in HLNRA individuals, suggestive of both recovery and adaptation to low dose radiation. In protein–protein interaction (PPI) networks, YWHAZ (14-3-3ζ) emerged as the top-most hub protein that may direct phosphorylation driven pro-survival cellular processes against radiation stress. PPI networks also identified an integral role for the cytoskeletal protein ACTB, signaling protein PRKACA; and the molecular chaperone HSPA8. The data will allow better integration of radiation biology and epidemiology for risk assessment [Data are available via ProteomeXchange with identifier PXD022380].
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9
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Giaimo BD, Ferrante F, Vallejo DM, Hein K, Gutierrez-Perez I, Nist A, Stiewe T, Mittler G, Herold S, Zimmermann T, Bartkuhn M, Schwarz P, Oswald F, Dominguez M, Borggrefe T. Histone variant H2A.Z deposition and acetylation directs the canonical Notch signaling response. Nucleic Acids Res 2019; 46:8197-8215. [PMID: 29986055 PMCID: PMC6144792 DOI: 10.1093/nar/gky551] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 06/28/2018] [Indexed: 02/04/2023] Open
Abstract
A fundamental as yet incompletely understood feature of Notch signal transduction is a transcriptional shift from repression to activation that depends on chromatin regulation mediated by transcription factor RBP-J and associated cofactors. Incorporation of histone variants alter the functional properties of chromatin and are implicated in the regulation of gene expression. Here, we show that depletion of histone variant H2A.Z leads to upregulation of canonical Notch target genes and that the H2A.Z-chaperone TRRAP/p400/Tip60 complex physically associates with RBP-J at Notch-dependent enhancers. When targeted to RBP-J-bound enhancers, the acetyltransferase Tip60 acetylates H2A.Z and upregulates Notch target gene expression. Importantly, the Drosophila homologs of Tip60, p400 and H2A.Z modulate Notch signaling response and growth in vivo. Together, our data reveal that loading and acetylation of H2A.Z are required to assure tight control of canonical Notch activation.
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Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), Albertstrasse 19A, 79104 Freiburg, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Diana M Vallejo
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Kerstin Hein
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Irene Gutierrez-Perez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Gerhard Mittler
- Max-Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Susanne Herold
- Department of Internal Medicine II, Universities Giessen & Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Peggy Schwarz
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Maria Dominguez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
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10
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Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
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Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
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11
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Cheung ACM, Díaz-Santín LM. Share and share alike: the role of Tra1 from the SAGA and NuA4 coactivator complexes. Transcription 2019; 10:37-43. [PMID: 30375921 PMCID: PMC6351133 DOI: 10.1080/21541264.2018.1530936] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 01/12/2023] Open
Abstract
SAGA and NuA4 are coactivator complexes required for transcription on chromatin. Although they contain different enzymatic and biochemical activities, both contain the large Tra1 subunit. Recent electron microscopy studies have resolved the complete structure of Tra1 and its integration in SAGA/NuA4, providing important insight into Tra1 function.
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Affiliation(s)
- Alan C. M. Cheung
- Department of Structural and Molecular Biology, University College London, Institute of Structural and Molecular Biology, London, UK
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, UK
| | - Luis Miguel Díaz-Santín
- Department of Structural and Molecular Biology, University College London, Institute of Structural and Molecular Biology, London, UK
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, UK
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12
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Drissi R, Chauvin A, McKenna A, Lévesque D, Blais-Brochu S, Jean D, Boisvert FM. Destabilization of the MiniChromosome Maintenance (MCM) complex modulates the cellular response to DNA double strand breaks. Cell Cycle 2018; 17:2593-2609. [PMID: 30516086 PMCID: PMC6300108 DOI: 10.1080/15384101.2018.1553336] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA replication during S phase involves thousands of replication forks that must be coordinated to ensure that every DNA section is replicated only once. The minichromosome maintenance proteins, MCM2 to MCM7, form a heteromeric DNA helicase required for both the initiation and elongation of DNA replication. Although only two DNA helicase activities are necessary to establish a bidirectional replication fork from each replication origin, a large excess of MCM complexes is amassed and distributed along the chromatin. The function of the additional MCM complexes is not well understood, as most are displaced from the DNA during the S-phase, apparently without playing an active role in DNA replication. DNA damage response (DDR) kinases activated by stalled forks prevent the replication machinery from being activated, indicating a tight relationship between DDR and DNA replication. To investigate the role of MCM proteins in the cellular response to DNA damage, we used shRNA targeting MCM2 or MCM3 to determine the impact of a reduction in MCM complex. The alteration of MCM proteins induced a change in the activation of key factors of the DDR in response to Etoposide treatment. Etoposide-induced DNA damage affected the phosphorylation of γ-H2AX, CHK1 and CHK2 without affecting cell viability. Using assays measuring homologous recombination (HR) and non-homologous end-joining (NHEJ), we identified a decrease in both HR and NHEJ associated with a decrease in MCM complex.
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Affiliation(s)
- Romain Drissi
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Anaïs Chauvin
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Alyson McKenna
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Dominique Lévesque
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Simon Blais-Brochu
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Dominique Jean
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - François-Michel Boisvert
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
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13
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Lynham J, Houry WA. The Multiple Functions of the PAQosome: An R2TP- and URI1 Prefoldin-Based Chaperone Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:37-72. [DOI: 10.1007/978-3-030-00737-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Lashgari A, Fauteux M, Maréchal A, Gaudreau L. Cellular Depletion of BRD8 Causes p53-Dependent Apoptosis and Induces a DNA Damage Response in Non-Stressed Cells. Sci Rep 2018; 8:14089. [PMID: 30237520 PMCID: PMC6147888 DOI: 10.1038/s41598-018-32323-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 09/06/2018] [Indexed: 12/30/2022] Open
Abstract
Regulation of the chromatin state is crucial for biological processes such as the regulation of transcription, DNA replication, and DNA damage repair. Here we show that knockdown of the BRD8 bromodomain protein – a subunit of the p400/Tip60 complex - leads to p21 induction, and concomitant cell cycle arrest in G1/S. We further demonstrate that the p53 transcriptional pathway is activated in BRD8-depleted cells, and this accounts for upregulation of not only p21 but also of pro-apoptotic genes, leading to subsequent apoptosis. Importantly, the DNA damage response (DDR) is induced upon BRD8 depletion, and DNA damage foci are detectable in BRD8-depleted cells under normal growth conditions. Consistently with an activated DDR, we find that in BRD8-depleted cells, the ATM-CHK2 DDR pathway is turned on but, CHK1 proteins levels are severely reduced and replication stress is detectable as enhanced replication protein A (RPA32) phosphorylation levels. Notably, acetylation of histone H4 at K16 (H4K16ac) is reduced in BRD8-depleted cells, suggesting that BRD8 may have a role in the recruitment and/or stabilization of the p400/Tip60 complex within chromatin, thereby facilitating DNA repair. Taken together, our results suggest that BRD8 is involved not only in p53-dependent gene suppression, but also in the maintenance of genome stability.
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Affiliation(s)
- Anahita Lashgari
- Département de biologie, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, QC, J1K 2R1, Canada
| | - Myriam Fauteux
- Département de biologie, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, QC, J1K 2R1, Canada
| | - Alexandre Maréchal
- Département de biologie, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, QC, J1K 2R1, Canada
| | - Luc Gaudreau
- Département de biologie, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, QC, J1K 2R1, Canada.
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15
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Torrecilla I, Oehler J, Ramadan K. The role of ubiquitin-dependent segregase p97 (VCP or Cdc48) in chromatin dynamics after DNA double strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0282. [PMID: 28847819 PMCID: PMC5577460 DOI: 10.1098/rstb.2016.0282] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/27/2022] Open
Abstract
DNA double strand breaks (DSBs) are the most cytotoxic DNA lesions and, if not repaired, lead to chromosomal rearrangement, genomic instability and cell death. Cells have evolved a complex network of DNA repair and signalling molecules which promptly detect and repair DSBs, commonly known as the DNA damage response (DDR). The DDR is orchestrated by various post-translational modifications such as phosphorylation, methylation, ubiquitination or SUMOylation. As DSBs are located in complex chromatin structures, the repair of DSBs is engineered at two levels: (i) at sites of broken DNA and (ii) at chromatin structures that surround DNA lesions. Thus, DNA repair and chromatin remodelling machineries must work together to efficiently repair DSBs. Here, we summarize the current knowledge of the ubiquitin-dependent molecular unfoldase/segregase p97 (VCP in vertebrates and Cdc48 in worms and lower eukaryotes) in DSB repair. We identify p97 as an essential factor that regulates DSB repair. p97-dependent extraction of ubiquitinated substrates mediates spatio-temporal protein turnover at and around the sites of DSBs, thus orchestrating chromatin remodelling and DSB repair. As p97 is a druggable target, p97 inhibition in the context of DDR has great potential for cancer therapy, as shown for other DDR components such as PARP, ATR and CHK1.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Judith Oehler
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
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16
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Feng YL, Xiang JF, Liu SC, Guo T, Yan GF, Feng Y, Kong N, Li HD, Huang Y, Lin H, Cai XJ, Xie AY. H2AX facilitates classical non-homologous end joining at the expense of limited nucleotide loss at repair junctions. Nucleic Acids Res 2017; 45:10614-10633. [PMID: 28977657 PMCID: PMC5737864 DOI: 10.1093/nar/gkx715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/04/2017] [Indexed: 12/20/2022] Open
Abstract
Phosphorylated histone H2AX, termed 'γH2AX', mediates the chromatin response to DNA double strand breaks (DSBs) in mammalian cells. H2AX deficiency increases the numbers of unrepaired DSBs and translocations, which are partly associated with defects in non-homologous end joining (NHEJ) and contributing to genomic instability in cancer. However, the role of γH2AX in NHEJ of general DSBs has yet to be clearly defined. Here, we showed that despite little effect on overall NHEJ efficiency, H2AX deficiency causes a surprising bias towards accurate NHEJ and shorter deletions in NHEJ products. By analyzing CRISPR/Cas9-induced NHEJ and by using a new reporter for mutagenic NHEJ, we found that γH2AX, along with its interacting protein MDC1, is required for efficient classical NHEJ (C-NHEJ) but with short deletions and insertions. Epistasis analysis revealed that ataxia telangiectasia mutated (ATM) and the chromatin remodeling complex Tip60/TRRAP/P400 are essential for this H2AX function. Taken together, these data suggest that a subset of DSBs may require γH2AX-mediated short-range nucleosome repositioning around the breaks to facilitate C-NHEJ with loss of a few extra nucleotides at NHEJ junctions. This may prevent outcomes such as non-repair and translocations, which are generally more destabilizing to genomes than short deletions and insertions from local NHEJ.
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Affiliation(s)
- Yi-Li Feng
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China.,Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Ji-Feng Xiang
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China.,Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Si-Cheng Liu
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China.,Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Tao Guo
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China.,Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Guo-Fang Yan
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China.,Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China.,Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Na Kong
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China.,Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Hao-Dan Li
- Shurui Tech Ltd, Hangzhou, Zhejiang 310005, China
| | - Yang Huang
- Shurui Tech Ltd, Hangzhou, Zhejiang 310005, China
| | - Hui Lin
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China
| | - Xiu-Jun Cai
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China
| | - An-Yong Xie
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310019, China.,Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China
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17
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Díaz-Santín LM, Lukoyanova N, Aciyan E, Cheung AC. Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution. eLife 2017; 6:28384. [PMID: 28767037 PMCID: PMC5576489 DOI: 10.7554/elife.28384] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 01/30/2023] Open
Abstract
Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the Phosphoinositide 3-Kinase-related kinase (PIKK) family and a direct target for multiple sequence-specific activators. We present the Cryo-EM structure of Saccharomyces cerevsisae Tra1 to 3.7 Å resolution, revealing an extensive network of alpha-helical solenoids organized into a diamond ring conformation and is strikingly reminiscent of DNA-PKcs, suggesting a direct role for Tra1 in DNA repair. The structure was fitted into an existing SAGA EM reconstruction and reveals limited contact surfaces to Tra1, hence it does not act as a molecular scaffold within SAGA. Mutations that affect activator targeting are distributed across the Tra1 structure, but also cluster within the N-terminal Finger region, indicating the presence of an activator interaction site. The structure of Tra1 is a key milestone in deciphering the mechanism of multiple coactivator complexes. Inside our cells, histone proteins package and condense DNA so that it can fit into the cell nucleus. However, this also switches off the genes, since the machines that read and interpret them can no longer access the underlying DNA. Turning genes on requires specific enzymes that chemically modify the histone proteins to regain access to the DNA. This must be carefully controlled, otherwise the ‘wrong’ genes can be activated, causing undesired effects and endangering the cell. Histone modifying enzymes often reside in large protein complexes. Two well-known examples are the SAGA and NuA4 complexes. Both have different roles during gene activation, but share a protein called Tra1. This protein enables SAGA and NuA4 to act on specific genes by binding to ‘activator proteins’ that are found on the DNA. Tra1 is one of the biggest proteins in the cell, but its size makes it difficult to study and until now, its structure was unknown. To determine the structure of Tra1, Díaz-Santín et al. extracted the protein from baker’s yeast, and examined it using electron microscopy. The structure of Tra1 resembled a diamond ring with multiple protein domains that correspond to a band, setting and a centre stone. The structure was detailed enough so that Díaz-Santín et al. could locate various mutations that affect the role of Tra1. These locations are likely to be direct interfaces to the ‘activator proteins’. Moreover, the study showed that Tra1 was similar to another protein that repairs damaged DNA. These results suggest that Tra1 not only works as an activator target, but may also have a role in repairing damaged DNA, and might even connect these two processes. Yeast Tra1 is also very similar to its human counterpart, which has been shown to stimulate cells to become cancerous. Further studies based on these results may help us understand how cancer begins.
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Affiliation(s)
- Luis Miguel Díaz-Santín
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Natasha Lukoyanova
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, United Kingdom
| | - Emir Aciyan
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, United Kingdom
| | - Alan Cm Cheung
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London, United Kingdom.,Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, United Kingdom
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18
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Vosnakis N, Koch M, Scheer E, Kessler P, Mély Y, Didier P, Tora L. Coactivators and general transcription factors have two distinct dynamic populations dependent on transcription. EMBO J 2017; 36:2710-2725. [PMID: 28724529 PMCID: PMC5599802 DOI: 10.15252/embj.201696035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 06/08/2017] [Accepted: 06/15/2017] [Indexed: 12/29/2022] Open
Abstract
SAGA and ATAC are two distinct chromatin modifying co‐activator complexes with distinct enzymatic activities involved in RNA polymerase II (Pol II) transcription regulation. To investigate the mobility of co‐activator complexes and general transcription factors in live‐cell nuclei, we performed imaging experiments based on photobleaching. SAGA and ATAC, but also two general transcription factors (TFIID and TFIIB), were highly dynamic, exhibiting mainly transient associations with chromatin, contrary to Pol II, which formed more stable chromatin interactions. Fluorescence correlation spectroscopy analyses revealed that the mobile pool of the two co‐activators, as well as that of TFIID and TFIIB, can be subdivided into “fast” (free) and “slow” (chromatin‐interacting) populations. Inhibiting transcription elongation decreased H3K4 trimethylation and reduced the “slow” population of SAGA, ATAC, TFIIB and TFIID. In addition, inhibiting histone H3K4 trimethylation also reduced the “slow” populations of SAGA and ATAC. Thus, our results demonstrate that in the nuclei of live cells the equilibrium between fast and slow population of SAGA or ATAC complexes is regulated by active transcription via changes in the abundance of H3K4me3 on chromatin.
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Affiliation(s)
- Nikolaos Vosnakis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Marc Koch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pascal Kessler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Yves Mély
- Université de Strasbourg, Illkirch, France.,Laboratoire de Biophotonique et Pharmacologie, Illkirch, France
| | - Pascal Didier
- Université de Strasbourg, Illkirch, France.,Laboratoire de Biophotonique et Pharmacologie, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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19
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Smith RJ, Savoian MS, Weber LE, Park JH. Ataxia telangiectasia mutated (ATM) interacts with p400 ATPase for an efficient DNA damage response. BMC Mol Biol 2016; 17:22. [PMID: 27814680 PMCID: PMC5097431 DOI: 10.1186/s12867-016-0075-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 10/29/2016] [Indexed: 11/13/2022] Open
Abstract
Background Ataxia telangiectasia mutated (ATM) and TRRAP proteins belong to the phosphatidylinositol 3-kinase-related kinase family and are involved in DNA damage repair and chromatin remodeling. ATM is a checkpoint kinase that is recruited to sites of DNA double-strand breaks where it phosphorylates a diverse range of proteins that are part of the chromatin and DNA repair machinery. As an integral subunit of the TRRAP-TIP60 complexes, p400 ATPase is a chromatin remodeler that is also targeted to DNA double-strand break sites. While it is understood that DNA binding transcriptional activators recruit p400 ATPase into a regulatory region of the promoter, how p400 recognises and moves to DNA double-strand break sites is far less clear. Here we investigate a possibility whether ATM serves as a shuttle to deliver p400 to break sites. Results Our data indicate that p400 co-immunoprecipitates with ATM independently of DNA damage state and that the N-terminal domain of p400 is vital for this interaction. Heterologous expression studies using Sf9 cells revealed that the ATM-p400 complex can be reconstituted without other mammalian bridging proteins. Overexpression of ATM-interacting p400 regions in U2OS cells induced dominant negative effects including the inhibition of both DNA damage repair and cell proliferation. Consistent with the dominant negative effect, the stable expression of an N-terminal p400 fragment showed a decrease in the association of p400 with ATM, but did not alter the association of p400 with TRRAP. Conclusion Taken together, our findings suggest that a protein–protein interaction between ATM and p400 ATPase occurs independently of DNA damage and contributes to efficient DNA damage response and repair. Electronic supplementary material The online version of this article (doi:10.1186/s12867-016-0075-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebecca J Smith
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Matthew S Savoian
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Lauren E Weber
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Jeong Hyeon Park
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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20
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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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21
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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: 86] [Impact Index Per Article: 9.6] [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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22
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Ravens S, Yu C, Ye T, Stierle M, Tora L. Tip60 complex binds to active Pol II promoters and a subset of enhancers and co-regulates the c-Myc network in mouse embryonic stem cells. Epigenetics Chromatin 2015; 8:45. [PMID: 26550034 PMCID: PMC4636812 DOI: 10.1186/s13072-015-0039-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/29/2015] [Indexed: 01/24/2023] Open
Abstract
Background Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood. Results Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of “free” Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50–60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions. Conclusions Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0039-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarina Ravens
- Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, 67404 Illkirch Cedex, France
| | - Changwei Yu
- Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, 67404 Illkirch Cedex, France
| | - Tao Ye
- Microarrays and Deep Sequencing Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, UdS, BP 10142, CU de Strasbourg, 67404 Illkirch Cedex, France
| | - Matthieu Stierle
- Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, 67404 Illkirch Cedex, France
| | - Laszlo Tora
- Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, 67404 Illkirch Cedex, France
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23
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Acetylation of Histone H2AX at Lys 5 by the TIP60 Histone Acetyltransferase Complex Is Essential for the Dynamic Binding of NBS1 to Damaged Chromatin. Mol Cell Biol 2015; 35:4147-57. [PMID: 26438602 DOI: 10.1128/mcb.00757-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/02/2015] [Indexed: 11/20/2022] Open
Abstract
The association and dissociation of DNA damage response (DDR) factors with damaged chromatin occurs dynamically, which is crucial for the activation of DDR signaling in a spatiotemporal manner. We previously showed that the TIP60 histone acetyltransferase complex acetylates histone H2AX, to facilitate H2AX exchange at sites of DNA damage. However, it remained unclear how the acetylation of histone H2AX by TIP60 is related to the DDR signaling. We found that the acetylation but not the phosphorylation of H2AX is essential for the turnover of NBS1 on damaged chromatin. The loss of H2AX acetylation at Lys 5 by TIP60 in cells disturbed the accumulation of NBS1 at sites of DNA damage. Although the phosphorylation of H2AX is also reportedly required for the retention of NBS1 at damage sites, our data indicated that the acetylation-dependent NBS1 turnover by TIP60 on damaged chromatin restricts the dispersal of NBS1 foci from the sites of DNA damage. These findings indicate the importance of the acetylation-dependent dynamic binding of NBS1 to damaged chromatin, created by histone H2AX exchange, for the proper accumulation of NBS1 at DNA damage sites.
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24
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De Cicco M, Rahim MSA, Dames SA. Regulation of the Target of Rapamycin and Other Phosphatidylinositol 3-Kinase-Related Kinases by Membrane Targeting. MEMBRANES 2015; 5:553-75. [PMID: 26426064 PMCID: PMC4703999 DOI: 10.3390/membranes5040553] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/24/2015] [Indexed: 01/05/2023]
Abstract
Phosphatidylinositol 3-kinase-related kinases (PIKKs) play vital roles in the regulation of cell growth, proliferation, survival, and consequently metabolism, as well as in the cellular response to stresses such as ionizing radiation or redox changes. In humans six family members are known to date, namely mammalian/mechanistic target of rapamycin (mTOR), ataxia-telangiectasia mutated (ATM), ataxia- and Rad3-related (ATR), DNA-dependent protein kinase catalytic subunit (DNA-PKcs), suppressor of morphogenesis in genitalia-1 (SMG-1), and transformation/transcription domain-associated protein (TRRAP). All fulfill rather diverse functions and most of them have been detected in different cellular compartments including various cellular membranes. It has been suggested that the regulation of the localization of signaling proteins allows for generating a locally specific output. Moreover, spatial partitioning is expected to improve the reliability of biochemical signaling. Since these assumptions may also be true for the regulation of PIKK function, the current knowledge about the regulation of the localization of PIKKs at different cellular (membrane) compartments by a network of interactions is reviewed. Membrane targeting can involve direct lipid-/membrane interactions as well as interactions with membrane-anchored regulatory proteins, such as, for example, small GTPases, or a combination of both.
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Affiliation(s)
- Maristella De Cicco
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, Garching 85747, Germany.
| | - Munirah S Abd Rahim
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, Garching 85747, Germany.
| | - Sonja A Dames
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, Garching 85747, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.
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O’Hagan HM. Chromatin modifications during repair of environmental exposure-induced DNA damage: a potential mechanism for stable epigenetic alterations. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:278-91. [PMID: 24259318 PMCID: PMC4020002 DOI: 10.1002/em.21830] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/31/2013] [Accepted: 10/31/2013] [Indexed: 05/22/2023]
Abstract
Exposures to environmental toxicants and toxins cause epigenetic changes that likely play a role in the development of diseases associated with exposure. The mechanism behind these exposure-induced epigenetic changes is currently unknown. One commonality between most environmental exposures is that they cause DNA damage either directly or through causing an increase in reactive oxygen species, which can damage DNA. Like transcription, DNA damage repair must occur in the context of chromatin requiring both histone modifications and ATP-dependent chromatin remodeling. These chromatin changes aid in DNA damage accessibility and signaling. Several proteins and complexes involved in epigenetic silencing during both development and cancer have been found to be localized to sites of DNA damage. The chromatin-based response to DNA damage is considered a transient event, with chromatin being restored to normal as DNA damage repair is completed. However, in individuals chronically exposed to environmental toxicants or with chronic inflammatory disease, repeated DNA damage-induced chromatin rearrangement may ultimately lead to permanent epigenetic alterations. Understanding the mechanism behind exposure-induced epigenetic changes will allow us to develop strategies to prevent or reverse these changes. This review focuses on epigenetic changes and DNA damage induced by environmental exposures, the chromatin changes that occur around sites of DNA damage, and how these transient chromatin changes may lead to heritable epigenetic alterations at sites of chronic exposure.
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Affiliation(s)
- Heather M. O’Hagan
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN
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Stanley FKT, Moore S, Goodarzi AA. CHD chromatin remodelling enzymes and the DNA damage response. Mutat Res 2013; 750:31-44. [PMID: 23954449 DOI: 10.1016/j.mrfmmm.2013.07.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/22/2013] [Accepted: 07/26/2013] [Indexed: 01/08/2023]
Abstract
The protein and DNA complex known as chromatin is a dynamic structure, adapting to alter the spatial arrangement of genetic information within the nucleus to meet the ever changing demands of life. Following decades of research, a dizzying array of regulatory factors is now known to control the architecture of chromatin at nearly every level. Amongst these, ATP-dependent chromatin remodelling enzymes play a key role, required for the establishment, maintenance and re-organization of chromatin through their ability to adjust the contact points between DNA and histones, the spacing between individual nucleosomes and the over-arching chromatin superstructure. Utilizing energy from ATP hydrolysis, these enzymes serve as the gatekeepers of genomic access and are essential for transcriptional regulation, DNA replication and cell division. In recent years, a vital role in DNA Double Strand Break (DSB) repair has emerged, particularly within complex chromatin environments such as heterochromatin, or regions undergoing energetic transactions such as transcription or DNA replication. Here, we will provide an overview of what is understood about ATP-dependent chromatin remodelling enzymes in the context of the DNA damage response. We will first touch upon all four major chromatin remodelling enzyme families and then focus chiefly on the nine members of the Chromodomain, Helicase, DNA-binding (CHD) family, particularly CHD3, CHD4, CHD5 and CHD6. These four proteins have established and emerging roles in DNA repair, the oxidative stress response, the maintenance of genomic stability and/or cancer prevention.
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Affiliation(s)
- Fintan K T Stanley
- Southern Alberta Cancer Research Institute, Department of Biochemistry and Molecular Biology and Department of Oncology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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Sommer LAM, Schaad M, Dames SA. NMR- and circular dichroism-monitored lipid binding studies suggest a general role for the FATC domain as membrane anchor of phosphatidylinositol 3-kinase-related kinases (PIKK). J Biol Chem 2013; 288:20046-63. [PMID: 23671275 DOI: 10.1074/jbc.m113.467233] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The FATC domain is shared by all members of the family of phosphatidylinositol-3 kinase-related kinases (PIKKs). It has been shown that the FATC domain plays an important role for the regulation of each PIKK. However, other than an involvement in protein-protein interactions, a common principle for the action of the FATC domain has not been detected. A detailed characterization of the structure and lipid binding properties of the FATC domain of the Ser/Thr kinase target of rapamycin (TOR) revealed that it contains a redox-sensitive membrane anchor in its C terminus. Because the C-terminal regions of the FATC domains of all known PIKKs are rather hydrophobic and especially rich in aromatic residues, we examined whether the ability to interact with lipids and membranes might be a general property. Here, we present the characterization of the interactions with lipids and different membrane mimetics for the FATC domains of human DNA-PKcs, human ATM, human ATR, human SMG-1, and human TRRAP by NMR and CD spectroscopy. The data indicate that all of these can interact with different membrane mimetics and may have different preferences only for membrane properties such as surface charge, curvature, and lipid packing. The oxidized form of the TOR FATC domain is well structured overall and forms an α-helix that is followed by a disulfide-bonded loop. In contrast, the FATC domains of the other PIKKs are rather unstructured in the isolated form and only significantly populate α-helical secondary structure upon interaction with membrane mimetics.
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Affiliation(s)
- Lisa A M Sommer
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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28
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Pavan S, Olivero M, Corà D, Di Renzo MF. IRF-1 expression is induced by cisplatin in ovarian cancer cells and limits drug effectiveness. Eur J Cancer 2013; 49:964-73. [DOI: 10.1016/j.ejca.2012.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 09/11/2012] [Accepted: 09/15/2012] [Indexed: 10/27/2022]
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Ichim G, Mola M, Finkbeiner MG, Cros MP, Herceg Z, Hernandez-Vargas H. The histone acetyltransferase component TRRAP is targeted for destruction during the cell cycle. Oncogene 2013; 33:181-92. [PMID: 23318449 DOI: 10.1038/onc.2012.570] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 09/18/2012] [Accepted: 10/26/2012] [Indexed: 11/09/2022]
Abstract
Chromosomes are dynamic structures that must be reversibly condensed and unfolded to accommodate mitotic division and chromosome segregation. Histone modifications are involved in the striking chromatin reconfiguration taking place during mitosis. However, the mechanisms that regulate activity and function of histone-modifying factors as cells enter and exit mitosis are poorly understood. Here, we show that the anaphase-promoting complex or cyclosome (APC/C) is involved in the mitotic turnover of TRRAP (TRansformation/tRanscription domain-Associated Protein), a common component of histone acetyltransferase (HAT) complexes, and that the pre-mitotic degradation of TRRAP is mediated by the APC/C ubiquitin ligase activators Cdc20 and Cdh1. Ectopic expression of both Cdh1 and Cdc20 reduced the levels of coexpressed TRRAP protein and induced its ubiquitination. TRRAP overexpression or stabilization induces multiple mitotic defects, including lagging chromosomes, chromosome bridges and multipolar spindles. In addition, lack of sister chromatid cohesion and impaired chromosome condensation were found after TRRAP overexpression or stabilization. By using a truncated form of TRRAP, we show that mitotic delay is associated with a global histone H4 hyperacetylation induced by TRRAP overexpression. These results demonstrate that the chromatin modifier TRRAP is targeted for destruction in a cell cycle-dependent fashion. They also suggest that degradation of TRRAP by the APC/C is necessary for a proper condensation of chromatin and proper chromosome segregation. Chromatin compaction mediated by histone modifiers may represent a fundamental arm for APC/C orchestration of the mitotic machinery.
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Affiliation(s)
- G Ichim
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - M Mola
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - M G Finkbeiner
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - M-P Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Z Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - H Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
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Izumi N, Yamashita A, Ohno S. Integrated regulation of PIKK-mediated stress responses by AAA+ proteins RUVBL1 and RUVBL2. Nucleus 2012; 3:29-43. [PMID: 22540023 PMCID: PMC3337166 DOI: 10.4161/nucl.18926] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Proteins of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family are activated by various cellular stresses, including DNA damage, premature termination codon and nutritional status, and induce appropriate cellular responses. The importance of PIKK functions in the maintenance of genome integrity, accurate gene expression and the proper control of cell growth/proliferation is established. Recently, ATPase associated diverse cellular activities (AAA+) proteins RUVBL1 and RUVBL2 (RUVBL1/2) have been shown to be common regulators of PIKKs. The RUVBL1/2 complex regulates PIKK-mediated stress responses through physical interactions with PIKKs and by controlling PIKK mRNA levels. In this review, the functions of PIKKs in stress responses are outlined and the physiological significance of the integrated regulation of PIKKs by the RUVBL1/2 complex is presented. We also discuss a putative "PIKK regulatory chaperone complex" including other PIKK regulators, Hsp90 and the Tel2 complex.
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Affiliation(s)
- Natsuko Izumi
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
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31
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Helmlinger D. New insights into the SAGA complex from studies of the Tra1 subunit in budding and fission yeast. Transcription 2012; 3:13-8. [PMID: 22456315 DOI: 10.4161/trns.3.1.19271] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The SAGA complex is a conserved, multifunctional co-activator that controls the transcription of many inducible genes in response to environmental changes. Recent studies have provided new insights into the functions of one of its subunits, Tra1/TRRAP, and suggest that it controls SAGA activity in response to external stimuli.
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Affiliation(s)
- Dominique Helmlinger
- Macromolecular Biochemistry Research Center, CNRS UMR 5237, University of Montpellier 1 & 2, Montpellier, France.
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32
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Thompson LH. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography. Mutat Res 2012; 751:158-246. [PMID: 22743550 DOI: 10.1016/j.mrrev.2012.06.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 06/09/2012] [Accepted: 06/16/2012] [Indexed: 12/15/2022]
Abstract
The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.
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Affiliation(s)
- Larry H Thompson
- Biology & Biotechnology Division, L452, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-0808, United States.
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33
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Zhang H, Photiou A, Grothey A, Stebbing J, Giamas G. The role of pseudokinases in cancer. Cell Signal 2012; 24:1173-84. [PMID: 22330072 DOI: 10.1016/j.cellsig.2012.01.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/27/2012] [Indexed: 01/12/2023]
Abstract
Kinases play a critical role in regulating many cellular functions including development, differentiation and proliferation. To date, over 518 proteins with kinase activity, comprising ~2-3% of total cellular proteins, have been identified from within the human kinome. Interestingly, approximately 10% of kinases are categorised as pseudokinases since they lack one or more conserved catalytic residues within their kinase domain and were originally thought to have no enzymatic activity. Recently, there has been strong evidence to suggest that some pseudokinsases can not only function as scaffold proteins, but may also possess kinase activity leading to modulation of cell signalling pathways. Altered activity of these pseudokinases can result in impaired cellular function, particularly in malignancies. In this review we are discussing recent evidence that apart from a scaffolding role, pseudokinases also orchestrate cellular processes as active kinases per se in signalling pathways of malignant cells.
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Affiliation(s)
- Hua Zhang
- Department of Cancer and Surgery, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
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34
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Izumi N, Yamashita A, Hirano H, Ohno S. Heat shock protein 90 regulates phosphatidylinositol 3-kinase-related protein kinase family proteins together with the RUVBL1/2 and Tel2-containing co-factor complex. Cancer Sci 2012; 103:50-7. [PMID: 21951644 PMCID: PMC11164146 DOI: 10.1111/j.1349-7006.2011.02112.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Heat shock protein 90 (Hsp90), a conserved molecular chaperone for a specific set of proteins critical for signal transduction including several oncogenic proteins, has been recognized as a promising target for anticancer therapy. Hsp90 inhibition also sensitizes cancer cells to DNA damage. However, the underlying mechanisms are not fully understood. Here, we provide evidence that Hsp90 is a general regulator of phosphatidylinositol 3-kinase-related protein kinase (PIKK) family proteins, central regulators of stress responses including DNA damage. Inhibition of Hsp90 causes a reduction of all PIKK and suppresses PIKK-mediated signaling. In addition, Hsp90 forms complexes with RUVBL1/2 complex and Tel2 complex, both of which have been shown to interact with all PIKK and control their abundance and functions. These results suggest that Hsp90 can form multiple complexes with the RUVBL1/2 complex and Tel2 complex and function in the regulation of PIKK, providing additional rationale for the effectiveness of Hsp90 inhibition for anticancer therapy, including sensitization to DNA damage.
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Affiliation(s)
- Natsuko Izumi
- Department of Molecular Biology, School of Medicine, Yokohama City University, Yokohama, Japan
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35
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Xu Y, Xu C, Price BD. Mechanistic links between ATM and histone methylation codes during DNA repair. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:263-88. [PMID: 22749149 DOI: 10.1016/b978-0-12-387665-2.00010-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ataxia telangiectasia-mutated (ATM) protein kinase is the master regulator of the DNA double-strand break (DSB) repair pathway. The activation of ATM involves its recruitment to the DSB through interaction with the mre11-rad50-nbs1 complex, followed by the acetylation of ATM by the Tip60 acetyltransferase. This acetylation of ATM within its regulatory domain is essential for activating ATM's kinase activity. Further work has now revealed that Tip60 is activated through direct interaction between Tip60's chromodomain and histone H3 trimethylated on lysine 9 (H3K9me3). The loading of Tip60 onto the chromatin at DSBs therefore represents the primary mechanism for activation of Tip60's acetyltransferase activity in response to DNA damage. The ability of H3K9me3 at DSBs to regulate the activity of Tip60 and the subsequent activation of ATM emphasizes the crucial role played by chromatin architecture in regulating DSB repair. Further, histone methylation and chromatin structure are disrupted in human cancers, implying that altered chromatin structure in tumor cells may impact DSB repair, increasing genomic instability and contributing to the progression of cancer.
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Affiliation(s)
- Ye Xu
- Division of Genome Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
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36
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Bhatti S, Kozlov S, Farooqi AA, Naqi A, Lavin M, Khanna KK. ATM protein kinase: the linchpin of cellular defenses to stress. Cell Mol Life Sci 2011; 68:2977-3006. [PMID: 21533982 PMCID: PMC11115042 DOI: 10.1007/s00018-011-0683-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/24/2011] [Accepted: 03/29/2011] [Indexed: 01/23/2023]
Abstract
ATM is the most significant molecule involved in monitoring the genomic integrity of the cell. Any damage done to DNA relentlessly challenges the cellular machinery involved in recognition, processing and repair of these insults. ATM kinase is activated early to detect and signal lesions in DNA, arrest the cell cycle, establish DNA repair signaling and faithfully restore the damaged chromatin. ATM activation plays an important role as a barrier to tumorigenesis, metabolic syndrome and neurodegeneration. Therefore, studies of ATM-dependent DNA damage signaling pathways hold promise for treatment of a variety of debilitating diseases through the development of new therapeutics capable of modulating cellular responses to stress. In this review, we have tried to untangle the complex web of ATM signaling pathways with the purpose of pinpointing multiple roles of ATM underlying the complex phenotypes observed in AT patients.
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Affiliation(s)
- Shahzad Bhatti
- Institute of Molecular Biology and Biotechnology, The University of Lahore, 1 Km Raiwind Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Sergei Kozlov
- Queensland Institute of Medical Research, QIMR, 300 Herston Rd, Herston, Brisbane, 4029 Australia
| | - Ammad Ahmad Farooqi
- Institute of Molecular Biology and Biotechnology, The University of Lahore, 1 Km Raiwind Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Ali Naqi
- Institute of Molecular Biology and Biotechnology, The University of Lahore, 1 Km Raiwind Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Martin Lavin
- Queensland Institute of Medical Research, QIMR, 300 Herston Rd, Herston, Brisbane, 4029 Australia
| | - Kum Kum Khanna
- Queensland Institute of Medical Research, QIMR, 300 Herston Rd, Herston, Brisbane, 4029 Australia
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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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Ogiwara H, Ui A, Otsuka A, Satoh H, Yokomi I, Nakajima S, Yasui A, Yokota J, Kohno T. Histone acetylation by CBP and p300 at double-strand break sites facilitates SWI/SNF chromatin remodeling and the recruitment of non-homologous end joining factors. Oncogene 2011; 30:2135-46. [PMID: 21217779 DOI: 10.1038/onc.2010.592] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Non-homologous end joining (NHEJ) is a major repair pathway for DNA double-strand breaks (DSBs) generated by ionizing radiation (IR) and anti-cancer drugs. Therefore, inhibiting the activity of proteins involved in this pathway is a promising way of sensitizing cancer cells to both radiotherapy and chemotherapy. In this study, we developed an assay for evaluating NHEJ activity against DSBs in chromosomal DNA in human cells to identify the chromatin modification/remodeling proteins involved in NHEJ. We showed that ablating the activity of the homologous histone acetyltransferases, CBP and p300, using inhibitors or small interfering RNAs-suppressed NHEJ. Ablation of CBP or p300 impaired IR-induced DSB repair and sensitized lung cancer cells to IR and the anti-cancer drug, etoposide, which induces DSBs that are repaired by NHEJ. The CBP/p300 proteins were recruited to sites of DSBs and their ablation suppressed acetylation of lysine 18 within histone H3, and lysines 5, 8, 12, and 16 within histone H4, at the DSB sites. This then suppressed the recruitment of KU70 and KU80, both key proteins for NHEJ, to the DSB sites. Ablation of CBP/p300 also impaired the recruitment of BRM, a catalytic subunit of the SWI/SNF complex involved in chromatin remodeling at DSB sites. These results indicate that CBP and p300 function as histone H3 and H4 acetyltransferases at DSB sites in NHEJ and facilitate chromatin relaxation. Therefore, inhibition CBP and p300 activity may sensitize cancer cells to radiotherapy and chemotherapy.
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Affiliation(s)
- H Ogiwara
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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Xu Y, Sun Y, Jiang X, Ayrapetov MK, Moskwa P, Yang S, Weinstock DM, Price BD. The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair. ACTA ACUST UNITED AC 2010; 191:31-43. [PMID: 20876283 PMCID: PMC2953432 DOI: 10.1083/jcb.201001160] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
p400 unwinds chromatin from nucleosomes flanking double-strand breaks to facilitate recruitment of the DNA repair components brca1 and 53BP1. The complexity of chromatin architecture presents a significant barrier to the ability of the DNA repair machinery to access and repair DNA double-strand breaks (DSBs). Consequently, remodeling of the chromatin landscape adjacent to DSBs is vital for efficient DNA repair. Here, we demonstrate that DNA damage destabilizes nucleosomes within chromatin regions that correspond to the γ-H2AX domains surrounding DSBs. This nucleosome destabilization is an active process requiring the ATPase activity of the p400 SWI/SNF ATPase and histone acetylation by the Tip60 acetyltransferase. p400 is recruited to DSBs by a mechanism that is independent of ATM but requires mdc1. Further, the destabilization of nucleosomes by p400 is required for the RNF8-dependent ubiquitination of chromatin, and for the subsequent recruitment of brca1 and 53BP1 to DSBs. These results identify p400 as a novel DNA damage response protein and demonstrate that p400-mediated alterations in nucleosome and chromatin structure promote both chromatin ubiquitination and the accumulation of brca1 and 53BP1 at sites of DNA damage.
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Affiliation(s)
- Ye Xu
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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40
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Vaissière T, Herceg Z. Histone code in the cross-talk during DNA damage signaling. Cell Res 2010; 20:113-5. [PMID: 20118964 DOI: 10.1038/cr.2010.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Thomas Vaissière
- Epigenetics Group, International Agency for Research on Cancer, 150 cours Albert Thomas, 69008 Lyon, France
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41
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Transformation/transcription domain-associated protein (TRRAP)-mediated regulation of Wee1. Genetics 2010; 185:81-93. [PMID: 20194963 DOI: 10.1534/genetics.110.114769] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The G2 DNA damage checkpoint inhibits Cdc2 and mitotic entry through the dual regulation of Wee1 and Cdc25 by the Chk1 effector kinase. Upregulation of Chk1 by mutation or overexpression bypasses the requirement for upstream regulators or DNA damage to promote a G2 cell cycle arrest. We screened in fission yeast for mutations that rendered cells resistant to overexpressed chk1(+). We identified a mutation in tra1, which encodes one of two homologs of transformation/transcription domain-associated protein (TRRAP), an ATM/R-related pseudokinase that scaffolds several histone acetyltransferase (HAT) complexes. Inhibition of histone deacetylases reverts the resistance to overexpressed chk1(+), suggesting this phenotype is due to a HAT activity, although expression of checkpoint and cell cycle genes is not greatly affected. Cells with mutant or deleted tra1 activate Chk1 normally and are checkpoint proficient. However, these cells are semi-wee even when overexpressing chk1(+) and accumulate inactive Wee1 protein. The changed division response (Cdr) kinases Cdr1 and Cdr2 are negative regulators of Wee1, and we show that they are required for the Tra1-dependent alterations to Wee1 function. This identifies Tra1 as another component controlling the timing of entry into mitosis via Cdc2 activation.
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Chailleux C, Tyteca S, Papin C, Boudsocq F, Puget N, Courilleau C, Grigoriev M, Canitrot Y, Trouche D. Physical interaction between the histone acetyl transferase Tip60 and the DNA double-strand breaks sensor MRN complex. Biochem J 2010; 426:365-71. [PMID: 20070254 DOI: 10.1042/bj20091329] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chromatin modifications and chromatin-modifying enzymes are believed to play a major role in the process of DNA repair. The histone acetyl transferase Tip60 is physically recruited to DNA DSBs (double-strand breaks) where it mediates histone acetylation. In the present study, we show, using a reporter system in mammalian cells, that Tip60 expression is required for homology-driven repair, strongly suggesting that Tip60 participates in DNA DSB repair through homologous recombination. Moreover, Tip60 depletion inhibits the formation of Rad50 foci following ionizing radiation, indicating that Tip60 expression is necessary for the recruitment of the DNA damage sensor MRN (Mre11-Rad50-Nbs1) complex to DNA DSBs. Moreover, we found that endogenous Tip60 physically interacts with endogenous MRN proteins in a complex which is distinct from the classical Tip60 complex. Taken together, our results describe a physical link between a DNA damage sensor and a histone-modifying enzyme, and provide important new insights into the role and mechanism of action of Tip60 in the process of DNA DSB repair.
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Affiliation(s)
- Catherine Chailleux
- LBCMCP, CNRS and University of Toulouse, 118 route de Narbonne, 31062 Toulouse, France
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43
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Wurdak H, Zhu S, Romero A, Lorger M, Watson J, Chiang CY, Zhang J, Natu VS, Lairson LL, Walker JR, Trussell CM, Harsh GR, Vogel H, Felding-Habermann B, Orth AP, Miraglia LJ, Rines DR, Skirboll SL, Schultz PG. An RNAi Screen Identifies TRRAP as a Regulator of Brain Tumor-Initiating Cell Differentiation. Cell Stem Cell 2010; 6:37-47. [DOI: 10.1016/j.stem.2009.11.002] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 09/30/2009] [Accepted: 11/06/2009] [Indexed: 01/05/2023]
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Reinhardt HC, Yaffe MB. Kinases that control the cell cycle in response to DNA damage: Chk1, Chk2, and MK2. Curr Opin Cell Biol 2009; 21:245-55. [PMID: 19230643 DOI: 10.1016/j.ceb.2009.01.018] [Citation(s) in RCA: 393] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Accepted: 01/15/2009] [Indexed: 01/08/2023]
Abstract
In response to DNA damage eukaryotic cells activate cell cycle checkpoints -- complex kinase signaling networks that prevent further progression through the cell cycle. Parallel to implementing a cell cycle arrest, checkpoint signaling also mediates the recruitment of DNA repair pathways. If the extent of damage exceeds repair capacity, additional signaling cascades are activated to ensure elimination of these damaged cells. The DNA damage response has traditionally been divided into two major kinase branches. The ATM/Chk2 module is activated after DNA double strand breaks and the ATR/Chk1 pathway responds primarily to DNA single strand breaks or bulky lesions. Both pathways converge on Cdc25, a positive regulator of cell cycle progression, which is inhibited by Chk1-mediated or Chk2-mediated phosphorylation. Recently a third effector kinase complex consisting of p38MAPK and MK2 has emerged. This pathway is activated downstream of ATM and ATR in response to DNA damage. MK2 has been shown to share substrate homology with both Chk1 and Chk2. Here we will discuss recent advances in our understanding of the eukaryotic DNA damage response with emphasis on the Chk1, Chk2, and the newly emerged effector kinases p38MAPK and MK2.
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Affiliation(s)
- H Christian Reinhardt
- David H Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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45
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Song S, McCann KE, Brown JM. Radiosensitization of yeast cells by inhibition of histone h4 acetylation. Radiat Res 2008; 170:618-627. [PMID: 18959465 DOI: 10.1667/rr1420.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 07/22/2008] [Indexed: 01/25/2023]
Abstract
Deletion of genes for proteins involved in histone H4 acetylation produces sensitivity to DNA-damaging agents in both Saccharomyces cerevisiae and mammalian cells. In the present studies, we show that treating wild-type yeast cells with histone acetyl transferase (HAT) inhibitors, which are chemicals that cause a global decrease in histone H4 acetylation, sensitizes the cells to ionizing radiation. Using HAT inhibitors, we have placed histone H4 acetylation into the RAD51-mediated homologous recombination repair pathway. We further show that yeast cells with functionally defective HAT proteins have normal phospho-H2A (gamma-H2A) induction after irradiation but a reduced rate of loss of gamma-H2A. This argues that HAT-defective cells are able to detect DNA double-strand breaks normally but have a defect in the repair of these lesions. We also show that cells treated with HAT inhibitors have intact G1 and G2 checkpoints after exposure to ionizing radiation, suggesting that G1 and G2 checkpoint activation is independent of histone H4 acetylation.
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Affiliation(s)
- Suisui Song
- Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University of School of Medicine, Stanford, California
| | - Kelly E McCann
- Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University of School of Medicine, Stanford, California
| | - J Martin Brown
- Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University of School of Medicine, Stanford, California
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46
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Iijima K, Ohara M, Seki R, Tauchi H. Dancing on damaged chromatin: functions of ATM and the RAD50/MRE11/NBS1 complex in cellular responses to DNA damage. JOURNAL OF RADIATION RESEARCH 2008; 49:451-64. [PMID: 18772547 DOI: 10.1269/jrr.08065] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In order to preserve and protect genetic information, eukaryotic cells have developed a signaling or communications network to help the cell respond to DNA damage, and ATM and NBS1 are key players in this network. ATM is a protein kinase which is activated immediately after a DNA double strand break (DSB) is formed, and the resulting signal cascade generated in response to cellular DSBs is regulated by post-translational protein modifications such as phosphorylation and acetylation. In addition, to ensure the efficient functioning of DNA repair and cell cycle checkpoints, the highly ordered structure of eukaryotic chromatin must be appropriately altered to permit access of repair-related factors to DNA. These alterations are termed chromatin remodeling, and are executed by a specific remodeling complex in conjunction with histone modifications. Current advances in the molecular analysis of DNA damage responses have shown that the auto-phosphorylation of ATM and the interaction between ATM and NBS1 are key steps for ATM activation, and that the association of ATM and NBS1 is involved in chromatin remodeling. Identification of novel factors which function in ubiquitination (RNF8, Ubc13, Rap80, etc.) has also enabled us to understand more details of the early stages in DNA repair pathways which respond to DSBs. In this review, the focus is on the role of ATM and the RAD50/MRE11/NBS1 complex in DSB response pathways, and their role in DSB repair and in the regulation of chromatin remodeling.
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Affiliation(s)
- Kenta Iijima
- Department of Environmental Sciences, Faculty of Science, Ibaraki University, Bunkyo 2-1-1, Mito, Ibaraki, Japan
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Iijima K, Muranaka C, Kobayashi J, Sakamoto S, Komatsu K, Matsuura S, Kubota N, Tauchi H. NBS1 regulates a novel apoptotic pathway through Bax activation. DNA Repair (Amst) 2008; 7:1705-16. [PMID: 18644472 DOI: 10.1016/j.dnarep.2008.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 06/24/2008] [Accepted: 06/25/2008] [Indexed: 11/26/2022]
Abstract
DNA damage induced apoptosis, along with precise DNA damage repair, is a critical cellular function, and both of these functions are necessary for cancer prevention. The NBS1 protein is known to be a key regulator of DNA damage repair. It acts by forming a complex with Rad50/Mre11 and by activating ATM. We show here that NBS1 regulates a novel p53 independent apoptotic pathway in response to DNA damage. DNA damage induced apoptosis was significantly reduced in NBS1 deficient cells regardless of their p53 status. Experiments using a series of cell lines expressing mutant NBS1 proteins revealed that NBS1 is able to regulate the activation of Bax and Caspase-3 without the FHA, Mre11-binding, or the ATM-interacting domains, whereas the phosphorylation sites of NBS1 were essential for Bax activation. Expression of apoptosis-related transcription factors such as E2F1 and their downstream pro-apoptotic factors were not related to this apoptosis induction. Interestingly, NBS1 regulates a novel Bax activation pathway by disrupting the Ku70-Bax complex which is required for activation of the mitochondrial apoptotic pathway. This dissociation of the Ku70-Bax complex can be mediated by acetylation of Ku70, and NBS1 can function in this process through a protein-protein interaction with Ku70. Thus, NBS1 is a key protein involved in the prevention of carcinogenesis, not only through the precise repair of damaged DNA by homologous recombination (HR) but also by its role in the elimination of inappropriately repaired cells.
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Affiliation(s)
- Kenta Iijima
- Department of Environmental Sciences, Faculty of Science, Ibaraki University, Bunkyo 2-1-1, Mito, Ibaraki, Japan
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48
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Schizosaccharomyces pombe histone acetyltransferase Mst1 (KAT5) is an essential protein required for damage response and chromosome segregation. Genetics 2008; 179:757-71. [PMID: 18505873 DOI: 10.1534/genetics.107.085779] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Schizosaccharomyces pombe Mst1 is a member of the MYST family of histone acetyltransferases and is the likely ortholog of Saccharomyces cerevisiae Esa1 and human Tip60 (KAT5). We have isolated a temperature-sensitive allele of this essential gene. mst1 cells show a pleiotropic phenotype at the restrictive temperature. They are sensitive to a variety of DNA-damaging agents and to the spindle poison thiabendazole. mst1 has an increased frequency of Rad22 repair foci, suggesting endogenous damage. Two-hybrid results show that Mst1 interacts with a number of proteins involved in chromosome integrity and centromere function, including the methyltransferase Skb1, the recombination mediator Rad22 (Sc Rad52), the chromatin assembly factor Hip1 (Sc Hir1), and the Msc1 protein related to a family of histone demethylases. mst1 mutant sensitivity to hydroxyurea suggests a defect in recovery following HU arrest. We conclude that Mst1 plays essential roles in maintenance of genome stability and recovery from DNA damage.
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49
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Meyer KD, Donner AJ, Knuesel MT, York AG, Espinosa JM, Taatjes DJ. Cooperative activity of cdk8 and GCN5L within Mediator directs tandem phosphoacetylation of histone H3. EMBO J 2008; 27:1447-57. [PMID: 18418385 DOI: 10.1038/emboj.2008.78] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2007] [Accepted: 03/27/2008] [Indexed: 11/09/2022] Open
Abstract
The human Mediator complex is generally required for expression of protein-coding genes. Here, we show that the GCN5L acetyltransferase stably associates with Mediator together with the TRRAP polypeptide. Yet, contrary to expectations, TRRAP/GCN5L does not associate with the transcriptionally active core Mediator but rather with Mediator that contains the cdk8 subcomplex. Consequently, this derivative 'T/G-Mediator' complex does not directly activate transcription in a reconstituted human transcription system. However, within T/G-Mediator, cdk8 phosphorylates serine-10 on histone H3, which in turn stimulates H3K14 acetylation by GCN5L within the complex. Tandem phosphoacetylation of H3 correlates with transcriptional activation, and ChIP assays demonstrate co-occupancy of T/G-Mediator components at several activated genes in vivo. Moreover, cdk8 knockdown causes substantial reduction of global H3 phosphoacetylation, suggesting that T/G-Mediator is a major regulator of this H3 mark. Cooperative H3 modification provides a mechanistic basis for GCN5L association with cdk8-Mediator and also identifies a biochemical means by which cdk8 can indirectly activate gene expression. Indeed our results suggest that T/G-Mediator directs early events-such as modification of chromatin templates-in transcriptional activation.
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Affiliation(s)
- Krista D Meyer
- Department of Chemistry and Biochemistry, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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50
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Epigenetic drivers and genetic passengers on the road to cancer. Mutat Res 2008; 642:1-13. [PMID: 18471836 DOI: 10.1016/j.mrfmmm.2008.03.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 02/29/2008] [Accepted: 03/19/2008] [Indexed: 12/31/2022]
Abstract
Cancer is traditionally viewed as a primarily genetic disorder, however it is now becoming accepted that cancer is also a consequence of abnormal epigenetic events. Genetic changes and aneuploidy are associated with alterations in DNA sequence, and they are a hallmark of the malignant process. Epigenetic alterations are universally present in human cancer and result in heritable changes in gene expression and chromatin structure over many cell generations without changes in DNA sequence, leading to functional consequences equivalent to those induced by genetic alterations. Importantly, intriguing evidence emerged suggesting that epigenetic changes may precede and provoke genetic changes. In this scenario, epigenetic events are primary events while genetic changes (such as mutations) may simply be a consequence of disrupted epigenetic states. This fact may explain why many genetic screens proved to be limited with regard to cancer causality and pathogenesis. Aberrant epigenetic events affect multiple genes and cellular pathways in a non-random fashion and this can predispose to induction and accumulation of genetic changes in the course of tumour initiation and progression. These considerations are critical for a better understanding of tumourigenesis and molecular events underlying the acquisition of drug resistance, as well as development of novel strategies for cancer therapy and prevention.
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