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Zhang Y, Xu M, Yuan J, Hu Z, Jiang J, Huang J, Wang B, Shen J, Long M, Fan Y, Montone KT, Tanyi JL, Tavana O, Chan HM, Hu X, Zhang L. Repression of PRMT activities sensitize homologous recombination-proficient ovarian and breast cancer cells to PARP inhibitor treatment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595159. [PMID: 38826355 PMCID: PMC11142138 DOI: 10.1101/2024.05.21.595159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
An "induced PARP inhibitor (PARPi) sensitivity by epigenetic modulation" strategy is being evaluated in the clinic to sensitize homologous recombination (HR)-proficient tumors to PARPi treatments. To expand its clinical applications and identify more efficient combinations, we performed a drug screen by combining PARPi with 74 well-characterized epigenetic modulators that target five major classes of epigenetic enzymes. Both type I PRMT inhibitor and PRMT5 inhibitor exhibit high combination and clinical priority scores in our screen. PRMT inhibition significantly enhances PARPi treatment-induced DNA damage in HR-proficient ovarian and breast cancer cells. Mechanistically, PRMTs maintain the expression of genes associated with DNA damage repair and BRCAness and regulate intrinsic innate immune pathways in cancer cells. Analyzing large-scale genomic and functional profiles from TCGA and DepMap further confirms that PRMT1, PRMT4, and PRMT5 are potential therapeutic targets in oncology. Finally, PRMT1 and PRMT5 inhibition act synergistically to enhance PARPi sensitivity. Our studies provide a strong rationale for the clinical application of a combination of PRMT and PARP inhibitors in patients with HR-proficient ovarian or breast cancer.
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Affiliation(s)
- Youyou Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Mu Xu
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Jiao Yuan
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Zhongyi Hu
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Junjie Jiang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Jie Huang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Bingwei Wang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Jianfeng Shen
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Meixiao Long
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, Ohio, 43210, USA
| | - Yi Fan
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Janos L Tanyi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Center for Gynecologic Cancer Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Omid Tavana
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts, 02451, USA
| | - Ho Man Chan
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts, 02451, USA
| | - Xiaowen Hu
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Lin Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Center for Gynecologic Cancer Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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de Luna Vitorino FN, Levy MJ, Mansano Wailemann RA, Lopes M, Silva ML, Sardiu ME, Garcia BA, Machado Motta MC, Oliveira CC, Armelin HA, Florens LA, Washburn MP, Pinheiro Chagas da Cunha J. The antiproliferative effect of FGF2 in K-Ras-driven tumor cells involves modulation of rRNA and the nucleolus. J Cell Sci 2023; 136:jcs260989. [PMID: 37921359 PMCID: PMC11166202 DOI: 10.1242/jcs.260989] [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: 01/18/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023] Open
Abstract
The nucleolus is sensitive to stress and can orchestrate a chain of cellular events in response to stress signals. Despite being a growth factor, FGF2 has antiproliferative and tumor-suppressive functions in some cellular contexts. In this work, we investigated how the antiproliferative effect of FGF2 modulates chromatin-, nucleolus- and rDNA-associated proteins. The chromatin and nucleolar proteome indicated that FGF2 stimulation modulates proteins related to transcription, rRNA expression and chromatin-remodeling proteins. The global transcriptional rate and nucleolus area increased along with nucleolar disorganization upon 24 h of FGF2 stimulation. FGF2 stimulation induced immature rRNA accumulation by increasing rRNA transcription. The rDNA-associated protein analysis reinforced that FGF2 stimulus interferes with transcription and rRNA processing. RNA Pol I inhibition partially reversed the growth arrest induced by FGF2, indicating that changes in rRNA expression might be crucial for triggering the antiproliferative effect. Taken together, we demonstrate that the antiproliferative FGF2 stimulus triggers significant transcriptional changes and modulates the main cell transcription site, the nucleolus.
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Affiliation(s)
- Francisca N. de Luna Vitorino
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | | | - Rosangela A. Mansano Wailemann
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
| | - Mariana Lopes
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
| | - Mariana Loterio Silva
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
| | | | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Maria Cristina Machado Motta
- Laboratório de Ultraestrutura Celular Hertha Meyer, Centro de Pesquisa em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ 21491-590, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ 21941-902, Brazil
| | - Carla Columbano Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Hugo Aguirre Armelin
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
| | | | | | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
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Li W, Jones K, Burke TJ, Hossain MA, Lariscy L. Epigenetic Regulation of Nucleotide Excision Repair. Front Cell Dev Biol 2022; 10:847051. [PMID: 35465333 PMCID: PMC9023881 DOI: 10.3389/fcell.2022.847051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Genomic DNA is constantly attacked by a plethora of DNA damaging agents both from endogenous and exogenous sources. Nucleotide excision repair (NER) is the most versatile repair pathway that recognizes and removes a wide range of bulky and/or helix-distorting DNA lesions. Even though the molecular mechanism of NER is well studied through in vitro system, the NER process inside the cell is more complicated because the genomic DNA in eukaryotes is tightly packaged into chromosomes and compacted into a nucleus. Epigenetic modifications regulate gene activity and expression without changing the DNA sequence. The dynamics of epigenetic regulation play a crucial role during the in vivo NER process. In this review, we summarize recent advances in our understanding of the epigenetic regulation of NER.
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Rapid recruitment of p53 to DNA damage sites directs DNA repair choice and integrity. Proc Natl Acad Sci U S A 2022; 119:e2113233119. [PMID: 35235448 PMCID: PMC8915893 DOI: 10.1073/pnas.2113233119] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our work focuses on the critical longstanding question of the nontranscriptional role of p53 in tumor suppression. We demonstrate here that poly(ADP-ribose) polymerase (PARP)–dependent modification of p53 enables rapid recruitment of p53 to damage sites, where it in turn directs early repair pathway selection. Specifically, p53-mediated recruitment of 53BP1 at early time points promotes nonhomologous end joining over the more error-prone microhomology end-joining. Similarly, p53 directs nucleotide excision repair by mediating DDB1 recruitment. This property of p53 also correlates with tumor suppression in vivo. Our study provides mechanistic insight into how certain transcriptionally deficient p53 mutants may retain tumor-suppressive functions through regulating the DNA damage response. p53 is primarily known as a downstream transcriptional effector in the DNA damage-response cascade. We report that endogenous p53 rapidly accumulates at DNA damage sites within 2 s of UVA microirradiation. The kinetics of p53 recruitment mimics those of known DNA damage-response proteins, such as Ku70 and poly(ADP-ribose) polymerase (PARP), and precedes recruitment of Nbs1, 53BP1, and DDB1. Mutations in the DNA-binding and C-terminal domains significantly suppress this rapid recruitment. The C-terminal domain of p53 contains key residues for PARP interaction that are required for rapid recruitment of p53 to DNA damage sites, as is PARP-dependent modification. The presence of p53 at damage sites influences the recruitment kinetics of 53BP1 and DDB1 and directs the choice of nonhomologous end joining repair (NHEJ) and nucleotide excision repair. Mutations that suppressed rapid recruitment of p53 promoted error-prone alternative end-joining (alt-NHEJ) and inhibited nucleotide excision repair. Our finding that p53 is a critical early responder to DNA damage stands in contrast with its extensively studied role as a downstream transcriptional regulator in DNA damage repair. We highlight an unrecognized role of p53 in directing DNA repair dynamics and integrity and suggest a parallel mode of p53 tumor suppression apart from its function as a transcription factor.
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Zebian A, El-Dor M, Shaito A, Mazurier F, Rezvani HR, Zibara K. XPC multifaceted roles beyond DNA damage repair: p53-dependent and p53-independent functions of XPC in cell fate decisions. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108400. [PMID: 35690409 DOI: 10.1016/j.mrrev.2021.108400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 06/15/2023]
Abstract
Xeroderma pigmentosum group C protein (XPC) acts as a DNA damage recognition factor for bulky adducts and as an initiator of global genome nucleotide excision repair (GG-NER). Novel insights have shown that the role of XPC is not limited to NER, but is also implicated in DNA damage response (DDR), as well as in cell fate decisions upon stress. Moreover, XPC has a proteolytic role through its interaction with p53 and casp-2S. XPC is also able to determine cellular outcomes through its interaction with downstream proteins, such as p21, ARF, and p16. XPC interactions with effector proteins may drive cells to various fates such as apoptosis, senescence, or tumorigenesis. In this review, we explore XPC's involvement in different molecular pathways in the cell and suggest that XPC can be considered not only as a genomic caretaker and gatekeeper but also as a tumor suppressor and cellular-fate decision maker. These findings envisage that resistance to cell death, induced by DNA-damaging therapeutics, in highly prevalent P53-deficent tumors might be overcome through new therapeutic approaches that aim to activate XPC in these tumors. Moreover, this review encourages care providers to consider XPC status in cancer patients before chemotherapy in order to improve the chances of successful treatment and enhance patients' survival.
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Affiliation(s)
- Abir Zebian
- University of Bordeaux, INSERM U1035, BMGIC, Bordeaux, France; PRASE, Lebanese University, Beirut, Lebanon
| | | | - Abdullah Shaito
- Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | | | | | - Kazem Zibara
- PRASE, Lebanese University, Beirut, Lebanon; Biology Department, Faculty of Sciences - I, Lebanese University, Beirut, Lebanon.
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6
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Control of the chromatin response to DNA damage: Histone proteins pull the strings. Semin Cell Dev Biol 2021; 113:75-87. [DOI: 10.1016/j.semcdb.2020.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022]
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7
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Yang CM, Kang MK, Jung WJ, Joo JS, Kim YJ, Choi Y, Kim HP. p53 expression confers sensitivity to 5-fluorouracil via distinct chromatin accessibility dynamics in human colorectal cancer. Oncol Lett 2021; 21:226. [PMID: 33613715 PMCID: PMC7856692 DOI: 10.3892/ol.2021.12487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
One of the most commonly used drugs in chemotherapy, 5-fluorouracil (5-FU) has been shown to be effective in only 10-15% of patients with colon cancer. Thus, studies of the mechanisms affecting 5-FU sensitivity in these patients are necessary. The tumor suppressor protein p53 is a transcription factor that serves important roles in cell apoptosis by regulating the cell cycle. It has also been characterized as a key factor influencing drug sensitivity. Furthermore, accessible chromatin is a hallmark of active DNA regulatory elements and functions as a crucial epigenetic factor regulating cancer mechanisms. The present study assessed the genetic regulatory landscape in colon cancer by performing RNA sequencing and Assay for Transposase-Accessible Chromatin sequencing, and investigated the effects of 5-FU on chromatin accessibility and gene expression. Notably, while treatment with 5-FU mediated global increases in chromatin accessibility, chromatin organization in several genomic regions differed depending on the expression status of p53. Since the occupancy of p53 does not overlap with accessible chromatin regions, the 5-FU-mediated changes in chromatin accessibility were not regulated by direct binding of p53. In the p53-expressing condition, the 5-FU-mediated accessible chromatin region was primarily associated with genes encoding cell death pathways. Additionally, 5-FU was revealed to induce open chromatin conformation at regions containing binding motifs for AP-1 family transcription factors, which may drive expression of apoptosis pathway genes. In conclusion, expression of p53 may confer 5-FU sensitivity by regulating chromatin accessibility of distinct genes associated with cell apoptosis in a transcription-independent manner.
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Affiliation(s)
- Chul Min Yang
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Moo-Koo Kang
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Woong-Jae Jung
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Jung-Sik Joo
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Yong-Jin Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Yeeun Choi
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Hyoung-Pyo Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea.,Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
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8
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Kciuk M, Marciniak B, Mojzych M, Kontek R. Focus on UV-Induced DNA Damage and Repair-Disease Relevance and Protective Strategies. Int J Mol Sci 2020; 21:ijms21197264. [PMID: 33019598 PMCID: PMC7582305 DOI: 10.3390/ijms21197264] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
The protective ozone layer is continually depleting due to the release of deteriorating environmental pollutants. The diminished ozone layer contributes to excessive exposure of cells to ultraviolet (UV) radiation. This leads to various cellular responses utilized to restore the homeostasis of exposed cells. DNA is the primary chromophore of the cells that absorbs sunlight energy. Exposure of genomic DNA to UV light leads to the formation of multitude of types of damage (depending on wavelength and exposure time) that are removed by effectively working repair pathways. The aim of this review is to summarize current knowledge considering cellular response to UV radiation with special focus on DNA damage and repair and to give a comprehensive insight for new researchers in this field. We also highlight most important future prospects considering application of the progressing knowledge of UV response for the clinical control of diverse pathologies.
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Affiliation(s)
- Mateusz Kciuk
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
- Correspondence:
| | - Beata Marciniak
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland;
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
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Manickavinayaham S, Velez-Cruz R, Biswas AK, Chen J, Guo R, Johnson DG. The E2F1 transcription factor and RB tumor suppressor moonlight as DNA repair factors. Cell Cycle 2020; 19:2260-2269. [PMID: 32787501 PMCID: PMC7513849 DOI: 10.1080/15384101.2020.1801190] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/19/2020] [Accepted: 07/06/2020] [Indexed: 02/08/2023] Open
Abstract
The E2F1 transcription factor and RB tumor suppressor are best known for their roles in regulating the expression of genes important for cell cycle progression but, they also have transcription-independent functions that facilitate DNA repair at sites of damage. Depending on the type of DNA damage, E2F1 can recruit either the GCN5 or p300/CBP histone acetyltransferases to deposit different histone acetylation marks in flanking chromatin. At DNA double-strand breaks, E2F1 also recruits RB and the BRG1 ATPase to remodel chromatin and promote loading of the MRE11-RAD50-NBS1 complex. Knock-in mouse models demonstrate important roles for E2F1 post-translational modifications in regulating DNA repair and physiological responses to DNA damage. This review highlights how E2F1 moonlights in DNA repair, thus revealing E2F1 as a versatile protein that recruits many of the same chromatin-modifying enzymes to sites of DNA damage to promote repair that it recruits to gene promoters to regulate transcription.
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Affiliation(s)
- Swarnalatha Manickavinayaham
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Renier Velez-Cruz
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies, Midwestern University, Downers Grove, IL, USA
| | - Anup K. Biswas
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Jie Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Ruifeng Guo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - David G. Johnson
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
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10
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Ho T, Tan BX, Lane D. How the Other Half Lives: What p53 Does When It Is Not Being a Transcription Factor. Int J Mol Sci 2019; 21:ijms21010013. [PMID: 31861395 PMCID: PMC6982169 DOI: 10.3390/ijms21010013] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/07/2019] [Accepted: 12/16/2019] [Indexed: 12/31/2022] Open
Abstract
It has been four decades since the discovery of p53, the designated ‘Guardian of the Genome’. P53 is primarily known as a master transcription factor and critical tumor suppressor, with countless studies detailing the mechanisms by which it regulates a host of gene targets and their consequent signaling pathways. However, transcription-independent functions of p53 also strongly define its tumor-suppressive capabilities and recent findings shed light on the molecular mechanisms hinted at by earlier efforts. This review highlights the transcription-independent mechanisms by which p53 influences the cellular response to genomic instability (in the form of replication stress, centrosome homeostasis, and transposition) and cell death. We also pinpoint areas for further investigation in order to better understand the context dependency of p53 transcription-independent functions and how these are perturbed when TP53 is mutated in human cancer.
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11
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Ticli G, Prosperi E. In Situ Analysis of DNA-Protein Complex Formation upon Radiation-Induced DNA Damage. Int J Mol Sci 2019; 20:ijms20225736. [PMID: 31731696 PMCID: PMC6888283 DOI: 10.3390/ijms20225736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/05/2023] Open
Abstract
The importance of determining at the cellular level the formation of DNA–protein complexes after radiation-induced lesions to DNA is outlined by the evidence that such interactions represent one of the first steps of the cellular response to DNA damage. These complexes are formed through recruitment at the sites of the lesion, of proteins deputed to signal the presence of DNA damage, and of DNA repair factors necessary to remove it. Investigating the formation of such complexes has provided, and will probably continue to, relevant information about molecular mechanisms and spatiotemporal dynamics of the processes that constitute the first barrier of cell defense against genome instability and related diseases. In this review, we will summarize and discuss the use of in situ procedures to detect the formation of DNA-protein complexes after radiation-induced DNA damage. This type of analysis provides important information on the spatial localization and temporal resolution of the formation of such complexes, at the single-cell level, allowing the study of heterogeneous cell populations.
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Affiliation(s)
- Giulio Ticli
- Istituto di Genetica Molecolare “Luca Cavalli Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy;
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare “Luca Cavalli Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy;
- Correspondence:
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12
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Chitale S, Richly H. H4K20me2: Orchestrating the recruitment of DNA repair factors in nucleotide excision repair. Nucleus 2019; 9:212-215. [PMID: 29482435 PMCID: PMC5973261 DOI: 10.1080/19491034.2018.1444327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The integrity of the genome is maintained by specific DNA repair pathways. The main pathway removing DNA lesions induced by exposure to UV light is nucleotide excision repair (NER). The DNA damage response at chromatin is accompanied by the recruitment of DNA repair factors to the lesion site and the deposition of specific histone marks. The function of these histone marks in NER stays for the most part elusive. We have recently reported that the methyltransferase MMSET catalyzes the dimethylation of histone H4 at lysine 20 (H4K20me2) at the lesion site. The deposition of H4K20me2 at DNA damage sites elicits the recruitment of the NER factor XPA providing evidence for an H4K20me2-dependent DNA repair factor recruitment mechanism during lesion recognition in the global-genomic branch of NER. Here we discuss how H4K20me2 might impact on the chromatin conformation and the DNA damage response.
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Affiliation(s)
- Shalaka Chitale
- a Laboratory of Molecular Epigenetics , Institute of Molecular Biology (IMB) , Mainz , Germany.,b Faculty of Biology , Johannes Gutenberg University , Mainz , Germany
| | - Holger Richly
- a Laboratory of Molecular Epigenetics , Institute of Molecular Biology (IMB) , Mainz , Germany
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13
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Martínez-López W, Moreno-Ortega D, Valencia-Payan J, Sammader P, Meschini R, Palitti F. Influence of chromatin remodeling in the removal of UVC-induced damage in TCR proficient and deficient Chinese hamster cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:124-131. [DOI: 10.1016/j.mrgentox.2018.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 01/12/2023]
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14
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Mirza-Aghazadeh-Attari M, Darband SG, Kaviani M, Mihanfar A, Aghazadeh Attari J, Yousefi B, Majidinia M. DNA damage response and repair in colorectal cancer: Defects, regulation and therapeutic implications. DNA Repair (Amst) 2018; 69:34-52. [PMID: 30055507 DOI: 10.1016/j.dnarep.2018.07.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/15/2018] [Accepted: 07/15/2018] [Indexed: 12/11/2022]
Abstract
DNA damage response, a key factor involved in maintaining genome integrity and stability, consists of several kinase-dependent signaling pathways, which sense and transduce DNA damage signal. The severity of damage appears to determine DNA damage responses, which can include cell cycle arrest, damage repair and apoptosis. A number of recent studies have demonstrated that defection in signaling through this network is thought to be an underlying mechanism behind the development and progression of various types of human malignancies, including colorectal cancer. In this review, colorectal cancer and its molecular pathology as well as DNA damage response is briefly introduced. Finally, the involvement of key components of this network in the initiation/progression, prognosis, response to treatment and development of drug resistance is comprehensively discussed.
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Affiliation(s)
- Mohammad Mirza-Aghazadeh-Attari
- Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saber Ghazizadeh Darband
- Danesh Pey Hadi Co., Health Technology Development Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Mojtaba Kaviani
- School of Nutrition and Dietetics, Acadia University, Wolfville, Nova Scotia, Canada
| | - Ainaz Mihanfar
- Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran.
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15
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Kim YJ, Lee YJ, Kim HJ, Kim HS, Kang MS, Lee SK, Park MK, Murata K, Kim HL, Seo YR. A molecular mechanism of nickel (II): reduction of nucleotide excision repair activity by structural and functional disruption of p53. Carcinogenesis 2018; 39:1157-1164. [DOI: 10.1093/carcin/bgy070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 05/29/2018] [Indexed: 01/23/2023] Open
Affiliation(s)
- Yeo Jin Kim
- Department of Life Science, Institute of Environmental Medicine, Dongguk University Biomedi Campus, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Young Ju Lee
- Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hyo Jeong Kim
- Department of Life Science, Institute of Environmental Medicine, Dongguk University Biomedi Campus, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Hyun Soo Kim
- Department of Life Science, Institute of Environmental Medicine, Dongguk University Biomedi Campus, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Mi-Sun Kang
- Department of Pharmacology, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Sung-Keun Lee
- Department of Pharmacology, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Moo Kyun Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kazuyoshi Murata
- Section of Electron Microscopy, Section of Brain Structure Information, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
| | - Hye Lim Kim
- Forensic DNA Division, Gwangju Institute of National Forensic Service, Jangseong-gun, Jeonnam, Republic of Korea
| | - Young Rok Seo
- Department of Life Science, Institute of Environmental Medicine, Dongguk University Biomedi Campus, Goyang-si, Gyeonggi-do, Republic of Korea
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16
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Alzoubi S, Brody L, Rahman S, Mahul-Mellier AL, Mercado N, Ito K, El-Bahrawy M, Silver A, Boobis A, Bell JD, Hajji N. Synergy between histone deacetylase inhibitors and DNA-damaging agents is mediated by histone deacetylase 2 in colorectal cancer. Oncotarget 2018; 7:44505-44521. [PMID: 27283986 PMCID: PMC5190114 DOI: 10.18632/oncotarget.9887] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 05/28/2016] [Indexed: 12/22/2022] Open
Abstract
Previous studies have associated the overexpression of histone deacetylase 2 (HDAC2) and the presence of TP53 mutations with the progression to advanced stage drug resistant colorectal cancer (CRC). However, the mechanistic link between HDAC2 expression and the TP53 mutational status has remained unexplored. Here, we investigated the function of HDAC2 in drug resistance by assessing the synergistic effects of DNA-targeted chemotherapeutic agents and HDAC inhibitors (HDACis) on two TP53-mutated colorectal adenocarcinoma CRC cell lines (SW480 and HT-29) and on the TP53-wild type carcinoma cell line (HCT116 p53+/+) and its TP53 deficient sub-line (HCT116 p53−/−). We showed that in the untreated SW480 and HT-29 cells the steady-state level of HDAC2 was low compared to a TP53-wild type carcinoma cell line (HCT116 p53+/+). Increased expression of HDAC2 correlated with drug resistance, and depletion by shRNA sensitised the multi-drug resistance cell line HT-29 to CRC chemotherapeutic drugs such as 5-fluorouracil (5-FU) and oxaliplatin (Oxa). Combined treatment with the HDACi suberoylanilide hydroxamic acid plus 5-FU or Oxa reduced the level of HDAC2 expression, modified chromatin structure and induced mitotic cell death in HT-29 cells. Non-invasive bioluminescence imaging revealed significant reductions in xenograft tumour growth with HDAC2 expression level reduced to <50% in treated animals. Elevated levels of histone acetylation on residues H3K9, H4K12 and H4K16 were also found to be associated with resistance to VPA/Dox or SAHA/Dox treatment. Our results suggest that HDAC2 expression rather than the p53 mutation status influences the outcome of combined treatment with a HDACi and DNA-damaging agents in CRC.
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Affiliation(s)
- Samer Alzoubi
- Department of Medicine, Division of Experimental Medicine, Centre for Pharmacology & Therapeutics, Toxicology Unit, Imperial College London, London, UK
| | - Leigh Brody
- Department of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, UK
| | - Sunniyat Rahman
- Department of Medicine, Division of Experimental Medicine, Centre for Pharmacology & Therapeutics, Toxicology Unit, Imperial College London, London, UK
| | - Anne-Laure Mahul-Mellier
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Mercado
- Airway Disease Section, National Heart and Lung Institute, Imperial College, London, UK
| | - Kazuhiro Ito
- Airway Disease Section, National Heart and Lung Institute, Imperial College, London, UK
| | - Mona El-Bahrawy
- Department of Histopathology, Imperial College London, London, UK
| | - Andrew Silver
- Colorectal Cancer Genetics, Centre for Genomics & Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, UK
| | - Alan Boobis
- Department of Medicine, Division of Experimental Medicine, Centre for Pharmacology & Therapeutics, Toxicology Unit, Imperial College London, London, UK
| | - Jimmy D Bell
- Department of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, UK
| | - Nabil Hajji
- Department of Medicine, Division of Experimental Medicine, Centre for Pharmacology & Therapeutics, Toxicology Unit, Imperial College London, London, UK
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17
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Rüthemann P, Balbo Pogliano C, Codilupi T, Garajovà Z, Naegeli H. Chromatin remodeler CHD1 promotes XPC-to-TFIIH handover of nucleosomal UV lesions in nucleotide excision repair. EMBO J 2017; 36:3372-3386. [PMID: 29018037 DOI: 10.15252/embj.201695742] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 08/10/2017] [Accepted: 09/08/2017] [Indexed: 12/27/2022] Open
Abstract
Ultraviolet (UV) light induces mutagenic cyclobutane pyrimidine dimers (CPDs) in nucleosomal DNA that is tightly wrapped around histone octamers. How global-genome nucleotide excision repair (GG-NER) processes CPDs despite that this chromatin arrangement is poorly understood. An increased chromatin association of CHD1 (chromodomain helicase DNA-binding 1) upon UV irradiation indicated possible roles of this chromatin remodeler in the UV damage response. Immunoprecipitation of chromatin fragments revealed that CHD1 co-localizes in part with GG-NER factors. Chromatin fractionation showed that the UV-dependent recruitment of CHD1 occurs to UV lesions in histone-assembled nucleosomal DNA and that this CHD1 relocation requires the lesion sensor XPC (xeroderma pigmentosum group C). In situ immunofluorescence analyses further demonstrate that CHD1 facilitates substrate handover from XPC to the downstream TFIIH (transcription factor IIH). Consequently, CHD1 depletion slows down CPD excision and sensitizes cells to UV-induced cytotoxicity. The finding of a CHD1-driven lesion handover between sequentially acting GG-NER factors on nucleosomal histone octamers suggests that chromatin provides a recognition scaffold enabling the detection of a subset of CPDs.
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Affiliation(s)
- Peter Rüthemann
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Chiara Balbo Pogliano
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Tamara Codilupi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Zuzana Garajovà
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
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18
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Chromatin Dynamics in Genome Stability: Roles in Suppressing Endogenous DNA Damage and Facilitating DNA Repair. Int J Mol Sci 2017; 18:ijms18071486. [PMID: 28698521 PMCID: PMC5535976 DOI: 10.3390/ijms18071486] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 02/06/2023] Open
Abstract
Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage.
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19
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Piekna-Przybylska D, Sharma G, Maggirwar SB, Bambara RA. Deficiency in DNA damage response, a new characteristic of cells infected with latent HIV-1. Cell Cycle 2017; 16:968-978. [PMID: 28388353 DOI: 10.1080/15384101.2017.1312225] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Viruses can interact with host cell molecules responsible for the recognition and repair of DNA lesions, resulting in dysfunctional DNA damage response (DDR). Cells with inefficient DDR are more vulnerable to therapeutic approaches that target DDR, thereby raising DNA damage to a threshold that triggers apoptosis. Here, we demonstrate that 2 Jurkat-derived cell lines with incorporated silent HIV-1 provirus show increases in DDR signaling that responds to formation of double strand DNA breaks (DSBs). We found that phosphorylation of histone H2AX on Ser139 (gamma-H2AX), a biomarker of DSBs, and phosphorylation of ATM at Ser1981, Chk2 at Thr68, and p53 at Ser15, part of signaling pathways associated with DSBs, are elevated in these cells. These results indicate a DDR defect even though the virus is latent. DDR-inducing agents, specifically high doses of nucleoside RT inhibitors (NRTIs), caused greater increases in gamma-H2AX levels in latently infected cells. Additionally, latently infected cells are more susceptible to long-term exposure to G-quadruplex stabilizing agents, and this effect is enhanced when the agent is combined with an inhibitor targeting DNA-PK, which is crucial for DSB repair and telomere maintenance. Moreover, exposing these cells to the cancer drug etoposide resulted in formation of DSBs at a higher rate than in un-infected cells. Similar effects of etoposide were also observed in population of primary memory T cells infected with latent HIV-1. Sensitivity to these agents highlights a unique vulnerability of latently infected cells, a new feature that could potentially be used in developing therapies to eliminate HIV-1 reservoirs.
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Affiliation(s)
- Dorota Piekna-Przybylska
- a Department of Microbiology and Immunology , School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Gaurav Sharma
- b Department of Electrical and Computer Engineering , University of Rochester , Rochester , NY , USA
| | - Sanjay B Maggirwar
- a Department of Microbiology and Immunology , School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Robert A Bambara
- a Department of Microbiology and Immunology , School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
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20
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Yusein-Myashkova S, Ugrinova I, Pasheva E. Non-histone protein HMGB1 inhibits the repair of damaged DNA by cisplatin in NIH-3T3 murine fibroblasts. BMB Rep 2016; 49:99-104. [PMID: 24325815 PMCID: PMC4915123 DOI: 10.5483/bmbrep.2016.49.2.238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Indexed: 11/20/2022] Open
Abstract
The nuclear non-histone protein high mobility group box (HMGB) 1 is known to having an inhibitory effect on the repair of DNA damaged by the antitumor drug cisplatin in vitro. To investigate the role of HMGB1 in living cells, we studied the DNA repair of cisplatin damages in mouse fibroblast cell line, NIH-3T3. We evaluated the effect of the post-synthetic acetylation and C-terminal domain of the protein by overexpression of the parental and mutant GFP fused forms of HMGB1. The results revealed that HMGB1 had also an inhibitory effect on the repair of cisplatin damaged DNA in vivo. The silencing of HMGB1 in NIH-3T3 cells increased the cellular DNA repair potential. The increased levels of repair synthesis could be "rescued" and returned to less than normal levels if the knockdown cells were transfected with plasmids encoding HMGB1 and HMGB1 K2A. In this case, the truncated form of HMGB1 also exhibited a slight inhibitory effect. [BMB Reports 2016; 49(2): 99-104].
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Affiliation(s)
- Shazie Yusein-Myashkova
- Institute of Molecular Biology, Roumen Tsanev, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Iva Ugrinova
- Institute of Molecular Biology, Roumen Tsanev, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Evdokia Pasheva
- Institute of Molecular Biology, Roumen Tsanev, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
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21
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Sharma V, Monti P, Fronza G, Inga A. Human transcription factors in yeast: the fruitful examples of P53 and NF-кB. FEMS Yeast Res 2016; 16:fow083. [PMID: 27683095 DOI: 10.1093/femsyr/fow083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2016] [Indexed: 12/31/2022] Open
Abstract
The observation that human transcription factors (TFs) can function when expressed in yeast cells has stimulated the development of various functional assays to investigate (i) the role of binding site sequences (herein referred to as response elements, REs) in transactivation specificity, (ii) the impact of polymorphic nucleotide variants on transactivation potential, (iii) the functional consequences of mutations in TFs and (iv) the impact of cofactors or small molecules. These approaches have found applications in basic as well as applied research, including the identification and the characterisation of mutant TF alleles from clinical samples. The ease of genome editing of yeast cells and the availability of regulated systems for ectopic protein expression enabled the development of quantitative reporter systems, integrated at a chosen chromosomal locus in isogenic yeast strains that differ only at the level of a specific RE targeted by a TF or for the expression of distinct TF alleles. In many cases, these assays were proven predictive of results in higher eukaryotes. The potential to work in small volume formats and the availability of yeast strains with modified chemical uptake have enhanced the scalability of these approaches. Next to well-established one-, two-, three-hybrid assays, the functional assays with non-chimeric human TFs enrich the palette of opportunities for functional characterisation. We review ∼25 years of research on human sequence-specific TFs expressed in yeast, with an emphasis on the P53 and NF-кB family of proteins, highlighting outcomes, advantages, challenges and limitations of these heterologous assays.
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Affiliation(s)
- Vasundhara Sharma
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
| | - Paola Monti
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Gilberto Fronza
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Alberto Inga
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
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22
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Gong F, Chiu LY, Miller KM. Acetylation Reader Proteins: Linking Acetylation Signaling to Genome Maintenance and Cancer. PLoS Genet 2016; 12:e1006272. [PMID: 27631103 PMCID: PMC5025232 DOI: 10.1371/journal.pgen.1006272] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromatin-based DNA damage response (DDR) pathways are fundamental for preventing genome and epigenome instability, which are prevalent in cancer. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) catalyze the addition and removal of acetyl groups on lysine residues, a post-translational modification important for the DDR. Acetylation can alter chromatin structure as well as function by providing binding signals for reader proteins containing acetyl-lysine recognition domains, including the bromodomain (BRD). Acetylation dynamics occur upon DNA damage in part to regulate chromatin and BRD protein interactions that mediate key DDR activities. In cancer, DDR and acetylation pathways are often mutated or abnormally expressed. DNA damaging agents and drugs targeting epigenetic regulators, including HATs, HDACs, and BRD proteins, are used or are being developed to treat cancer. Here, we discuss how histone acetylation pathways, with a focus on acetylation reader proteins, promote genome stability and the DDR. We analyze how acetylation signaling impacts the DDR in the context of cancer and its treatments. Understanding the relationship between epigenetic regulators, the DDR, and chromatin is integral for obtaining a mechanistic understanding of genome and epigenome maintenance pathways, information that can be leveraged for targeting acetylation signaling, and/or the DDR to treat diseases, including cancer.
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Affiliation(s)
- Fade Gong
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Li-Ya Chiu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Kyle M. Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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23
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Adam S, Dabin J, Chevallier O, Leroy O, Baldeyron C, Corpet A, Lomonte P, Renaud O, Almouzni G, Polo SE. Real-Time Tracking of Parental Histones Reveals Their Contribution to Chromatin Integrity Following DNA Damage. Mol Cell 2016; 64:65-78. [PMID: 27642047 PMCID: PMC5065526 DOI: 10.1016/j.molcel.2016.08.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/20/2016] [Accepted: 08/11/2016] [Indexed: 12/22/2022]
Abstract
Chromatin integrity is critical for cell function and identity but is challenged by DNA damage. To understand how chromatin architecture and the information that it conveys are preserved or altered following genotoxic stress, we established a system for real-time tracking of parental histones, which characterize the pre-damage chromatin state. Focusing on histone H3 dynamics after local UVC irradiation in human cells, we demonstrate that parental histones rapidly redistribute around damaged regions by a dual mechanism combining chromatin opening and histone mobilization on chromatin. Importantly, parental histones almost entirely recover and mix with new histones in repairing chromatin. Our data further define a close coordination of parental histone dynamics with DNA repair progression through the damage sensor DDB2 (DNA damage-binding protein 2). We speculate that this mechanism may contribute to maintaining a memory of the original chromatin landscape and may help preserve epigenome stability in response to DNA damage. Parental H3 histones redistribute to the periphery of UVC-damaged regions The redistribution involves histone mobilization on chromatin and chromatin opening Parental histones recover massively during repair progression Parental histone dynamics may help coordinate DNA repair with epigenome integrity
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Affiliation(s)
- Salomé Adam
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France; Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Juliette Dabin
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France
| | - Odile Chevallier
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France
| | - Olivier Leroy
- Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie, UMR3215 CNRS/U934 INSERM, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Céline Baldeyron
- Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Armelle Corpet
- Team Chromatin Assembly, Nuclear Domains, Virus, Institut NeuroMyoGène, LabEx DEVweCAN, Université Claude Bernard Lyon 1, UMR5310 CNRS/U1217 INSERM, F-69100 Lyon, France
| | - Patrick Lomonte
- Team Chromatin Assembly, Nuclear Domains, Virus, Institut NeuroMyoGène, LabEx DEVweCAN, Université Claude Bernard Lyon 1, UMR5310 CNRS/U1217 INSERM, F-69100 Lyon, France
| | - Olivier Renaud
- Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie, UMR3215 CNRS/U934 INSERM, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Geneviève Almouzni
- Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Sophie E Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France.
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24
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Abstract
Histone acetylation/deacetylation constitute the most relevant chromatin remodelling mechanism to control DNA access to nuclear machinery as well as to mutagenic agents. Thus, these epigenetics mechanisms could be involved in processing DNA lesions into chromosomal aberrations. Although radiation-induced DNA lesions are believed to occur randomly, in most cases chromosome breakpoints appear distributed in a non-random manner. In order to study the distribution of chromosome damage induced by clastogenic agents in relation to chromosome histone acetylation patterns, an experimental model based on treating Chinese hamster cells with endonucleases and ionizing radiations as well as immunolabelling metaphase chromosomes with antibodies to acetylated histone H4 was developed. The analysis of intra- and interchromosome breakpoint distribution has been carried out on G-banded chromosomes, and results obtained were correlated with chromosome acetylated histone H4 profiles. A co-localization of intrachromosomal breakpoints induced by AluI, BamHI and DNase I as well as by neutrons and g-rays was observed. Radiation- and endonuclease-induced breakpoints tend to cluster in less condensed chromosome regions (G-light bands) that show the highest levels of acetylated histone H4. The analysis of interchromosomal distribution of radiation-induced lesions showed a concentration of breakpoints in Chinese hamster chromosomes with particular histone acetylation patterns. The fact that chromosome breakpoints occur more frequently in transcriptionally competent chromosome regions suggests that chromatin conformation and nuclear architecture could play a role in the distribution of chromosome lesions.
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Affiliation(s)
- W Martínez-López
- Department of Genetic Toxicology and Chromosome Pathology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
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25
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Abstract
The cells in the human body are continuously challenged by a variety of genotoxic attacks. Erroneous repair of the DNA can lead to mutations and chromosomal aberrations that can alter the functions of tumor suppressor genes or oncogenes, thus causing cancer development. As a central tumor suppressor, p53 guards the genome by orchestrating a variety of DNA-damage-response (DDR) mechanisms. Already early in metazoan evolution, p53 started controlling the apoptotic demise of genomically compromised cells. p53 plays a prominent role as a facilitator of DNA repair by halting the cell cycle to allow time for the repair machineries to restore genome stability. In addition, p53 took on diverse roles to also directly impact the activity of various DNA-repair systems. It thus appears as if p53 is multitasking in providing protection from cancer development by maintaining genome stability.
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Affiliation(s)
- Ashley B Williams
- Medical Faculty, Institute for Genome Stability in Ageing and Disease, University of Cologne, 50931 Cologne, Germany Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne, University of Cologne, 50931 Cologne, Germany
| | - Björn Schumacher
- Medical Faculty, Institute for Genome Stability in Ageing and Disease, University of Cologne, 50931 Cologne, Germany Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne, University of Cologne, 50931 Cologne, Germany
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26
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The p53-like Protein CEP-1 Is Required for Meiotic Fidelity in C. elegans. Curr Biol 2016; 26:1148-58. [PMID: 27151662 DOI: 10.1016/j.cub.2016.03.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 02/05/2016] [Accepted: 03/14/2016] [Indexed: 11/21/2022]
Abstract
The passage of genetic information during meiosis requires exceptionally high fidelity to prevent birth defects and infertility. Accurate chromosome segregation during the first meiotic division relies on the formation of crossovers between homologous chromosomes and a series of precisely controlled steps to exchange genetic information. Many studies have hinted at a role for p53 in meiosis, but how it functions in this process is poorly understood. Here, we have identified a cooperative role for the p53-like protein CEP-1 and the meiotic protein HIM-5 in maintaining genome stability in the C. elegans germline. Loss of cep-1 and him-5 results in synthetic lethality that is dependent on the upstream DNA damage checkpoint but independent of the downstream core apoptotic pathway. We show that this synthetic lethality is the result of defective crossover formation due to reduced SPO-11-dependent double-strand breaks. Using cep-1 separation-of-function alleles, we show that cep-1 and him-5 also suppress inappropriate activation of the nonhomologous end joining (NHEJ) pathway. This work reveals an ancestral function for the p53 family in ensuring the fidelity of meiosis and establishes CEP-1 as a critical determinant of repair pathway choice.
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27
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Cui H, Li X, Han C, Wang QE, Wang H, Ding HF, Zhang J, Yan C. The Stress-responsive Gene ATF3 Mediates Dichotomous UV Responses by Regulating the Tip60 and p53 Proteins. J Biol Chem 2016; 291:10847-57. [PMID: 26994140 DOI: 10.1074/jbc.m115.713099] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 12/27/2022] Open
Abstract
The response to UV irradiation is important for a cell to maintain its genetic integrity when challenged by environmental genotoxins. An immediate early response to UV irradiation is the rapid induction of activating transcription factor 3 (ATF3) expression. Although emerging evidence has linked ATF3 to stress pathways regulated by the tumor suppressor p53 and the histone acetyltransferase Tip60, the role of ATF3 in the UV response remains largely unclear. Here, we report that ATF3 mediated dichotomous UV responses. Although UV irradiation enhanced the binding of ATF3 to Tip60, knockdown of ATF3 expression decreased Tip60 stability, thereby impairing Tip60 induction by UV irradiation. In line with the role of Tip60 in mediating UV-induced apoptosis, ATF3 promoted the death of p53-defective cells in response to UV irradiation. However, ATF3 could also activate p53 and promote p53-mediated DNA repair, mainly through altering histone modifications that could facilitate recruitment of DNA repair proteins (such as DDB2) to damaged DNA sites. As a result, ATF3 rather protected the p53 wild-type cells from UV-induced apoptosis. Our results thus indicate that ATF3 regulates cell fates upon UV irradiation in a p53-dependent manner.
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Affiliation(s)
| | | | - Chunhua Han
- the Department of Radiology, Ohio State University, Columbus, Ohio 43210
| | - Qi-En Wang
- the Department of Radiology, Ohio State University, Columbus, Ohio 43210
| | - Hongbo Wang
- the Key Laboratory of Molecular Pharmacology and Drug Evaluation, School of Pharmacy, Yantai University, Yantai 264005, China, and
| | - Han-Fei Ding
- From the Georgia Cancer Center and Departments of Pathology and
| | - Junran Zhang
- the Department of Radiation Oncology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Chunhong Yan
- From the Georgia Cancer Center and Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia 30912,
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Yusein-Myashkova S, Stoykov I, Gospodinov A, Ugrinova I, Pasheva E. The repair capacity of lung cancer cell lines A549 and H1299 depends on HMGB1 expression level and the p53 status. J Biochem 2016; 160:37-47. [PMID: 26896489 DOI: 10.1093/jb/mvw012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/16/2016] [Indexed: 11/14/2022] Open
Abstract
Elucidation of the cellular components responsive to chemotherapeutic agents as cisplatin rationalizes the strategy for anticancer chemotherapy. The removal of the cisplatin/DNA lesions gives the chance to the cancer cells to survive and compromises the chemotherapeutical treatment. Therefore, the cell repair efficiency is substantial for the clinical outcome. High mobility group box 1 (HMGB1) protein is considered to be involved in the removal of the lesions as it binds with high affinity to cisplatin/DNA adducts. We demonstrated that overexpression of HMGB1 protein inhibited cis-platinated DNA repair in vivo and the effect strongly depended on its C-terminus. We registered increased levels of DNA repair after HMGB1 silencing only in p53 defective H1299 lung cancer cells. Next, introduction of functional p53 resulted in DNA repair inhibition. H1299 cells overexpressing HMGB1 were significantly sensitized to treatment with cisplatin demonstrating the close relation between the role of HMGB1 in repair of cis-platinated DNA and the efficiency of the anticancer drug, the process being modulated by the C-terminus. In A549 cells with functional p53, the repair of cisplatin/DNA adducts is determined by а complex action of HMGB1 and p53 as an increase of DNA repair capacity was registered only after silencing of both proteins.
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Affiliation(s)
- Shazie Yusein-Myashkova
- Institute of Molecular Biology "Roumen Tsanev," Bulgarian Academy of Sciences, Akad. G.Bonchev Street, Bl. 21, 1113 Sofia, Bulgaria
| | - Ivan Stoykov
- Institute of Molecular Biology "Roumen Tsanev," Bulgarian Academy of Sciences, Akad. G.Bonchev Street, Bl. 21, 1113 Sofia, Bulgaria
| | - Anastas Gospodinov
- Institute of Molecular Biology "Roumen Tsanev," Bulgarian Academy of Sciences, Akad. G.Bonchev Street, Bl. 21, 1113 Sofia, Bulgaria
| | - Iva Ugrinova
- Institute of Molecular Biology "Roumen Tsanev," Bulgarian Academy of Sciences, Akad. G.Bonchev Street, Bl. 21, 1113 Sofia, Bulgaria
| | - Evdokia Pasheva
- Institute of Molecular Biology "Roumen Tsanev," Bulgarian Academy of Sciences, Akad. G.Bonchev Street, Bl. 21, 1113 Sofia, Bulgaria
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29
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Assessing Cell Cycle Independent Function of the CDK Inhibitor p21(CDKN¹A) in DNA Repair. Methods Mol Biol 2016; 1336:123-39. [PMID: 26231713 DOI: 10.1007/978-1-4939-2926-9_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The cyclin-dependent kinase (CDK) inhibitor p21(CDKN1A) is a small protein that is able to regulate many important cell functions, often independently of its activity of CDK inhibitor. In addition to cell cycle, this protein regulates cell transcription, apoptosis, cell motility, and DNA repair. In particular, p21 may participate in different DNA repair processes, like the nucleotide excision repair (NER), base excision repair (BER), and double-strand breaks (DSB) repair, because of its ability to interact with DNA repair proteins, such as proliferating cell nuclear antigen (PCNA), a master regulator of many DNA transactions. Although this role has been debated for a long time, the influence of p21 in DNA repair has been now established. However, it remain to be clarified how this role is coupled to proteasomal degradation that has been shown to occur after DNA damage. This chapter describes procedures to study p21 protein recruitment to localized DNA damage sites in the cell nucleus. In particular, we describe a technique based on local irrradiation with UV light through a polycarbonate filter with micropores; an in situ lysis procedure to detect chromatin-bound proteins by immunofluorescence; a cell fractionation procedure to study chromatin association of p21 by Western blot analysis, and p21 protein-protein interactions by an immunoprecipitation assay.
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30
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Schick S, Fournier D, Thakurela S, Sahu SK, Garding A, Tiwari VK. Dynamics of chromatin accessibility and epigenetic state in response to UV damage. J Cell Sci 2015; 128:4380-94. [PMID: 26446258 DOI: 10.1242/jcs.173633] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/29/2015] [Indexed: 12/27/2022] Open
Abstract
Epigenetic mechanisms determine the access of regulatory factors to DNA during events such as transcription and the DNA damage response. However, the global response of histone modifications and chromatin accessibility to UV exposure remains poorly understood. Here, we report that UV exposure results in a genome-wide reduction in chromatin accessibility, while the distribution of the active regulatory mark H3K27ac undergoes massive reorganization. Genomic loci subjected to epigenetic reprogramming upon UV exposure represent target sites for sequence-specific transcription factors. Most of these are distal regulatory regions, highlighting their importance in the cellular response to UV exposure. Furthermore, UV exposure results in an extensive reorganization of super-enhancers, accompanied by expression changes of associated genes, which may in part contribute to the stress response. Taken together, our study provides the first comprehensive resource for genome-wide chromatin changes upon UV irradiation in relation to gene expression and elucidates new aspects of this relationship.
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Affiliation(s)
- Sandra Schick
- Institute of Molecular Biology (IMB), Mainz, Germany
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31
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Abstract
Eukaryotic genomes are packaged into chromatin, which is the physiological substrate for all DNA transactions, including DNA damage and repair. Chromatin organization imposes major constraints on DNA damage repair and thus undergoes critical rearrangements during the repair process. These rearrangements have been integrated into the "access-repair-restore" (ARR) model, which provides a molecular framework for chromatin dynamics in response to DNA damage. Here, we take a historical perspective on the elaboration of this model and describe the molecular players involved in damaged chromatin reorganization in human cells. In particular, we present our current knowledge of chromatin assembly coupled to DNA damage repair, focusing on the role of histone variants and their dedicated chaperones. Finally, we discuss the impact of chromatin rearrangements after DNA damage on chromatin function and epigenome maintenance.
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32
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Abstract
Environmental agents are constantly challenging cells by damaging DNA, leading to the blockage of transcription elongation. How do cells deal with transcription-blockage and how is transcription restarted after the blocking lesions are removed? Here we review the processes responsible for the removal of transcription-blocking lesions, as well as mechanisms of transcription restart. We also discuss recent data suggesting that blocked RNA polymerases may not resume transcription from the site of the lesion following its removal but, rather, are forced to start over from the beginning of genes.
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33
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Bee L, Marini S, Pontarin G, Ferraro P, Costa R, Albrecht U, Celotti L. Nucleotide excision repair efficiency in quiescent human fibroblasts is modulated by circadian clock. Nucleic Acids Res 2015; 43:2126-37. [PMID: 25662220 PMCID: PMC4344517 DOI: 10.1093/nar/gkv081] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induced by UV-light is affected by the circadian phase at which irradiation occurred. NER activity has been analyzed in human quiescent fibroblasts (in the absence of the cell cycle effect), in which circadian rhythmicity has been synchronized with a pulse of dexamethasone. Our results demonstrate that both DNA damage induction and repair efficiency are strictly dependent on the phase of the circadian rhythm at which the cells are UV-exposed. Furthermore, the differences observed between fibroblasts irradiated at different circadian times (CTs) are abolished when the clock is obliterated. In addition, we observe that chromatin structure is regulated by circadian rhythmicity. Maximal chromatin relaxation occurred at the same CT when photoproduct formation and removal were highest. Our data suggest that the circadian clock regulates both the DNA sensitivity to UV damage and the efficiency of NER by controlling chromatin condensation mainly through histone acetylation.
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Affiliation(s)
- Leonardo Bee
- Department of Biology, University of Padova, Padova 35131, Italy
| | - Selena Marini
- Department of Biology, University of Padova, Padova 35131, Italy
| | | | - Paola Ferraro
- Department of Biology, University of Padova, Padova 35131, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova 35131, Italy
| | - Urs Albrecht
- Department of Biology, Unit for Biochemistry, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Lucia Celotti
- Department of Biology, University of Padova, Padova 35131, Italy
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34
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Shah P, He YY. Molecular regulation of UV-induced DNA repair. Photochem Photobiol 2015; 91:254-64. [PMID: 25534312 DOI: 10.1111/php.12406] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 12/09/2014] [Indexed: 12/21/2022]
Abstract
Ultraviolet (UV) radiation from sunlight is a major etiologic factor for skin cancer, the most prevalent cancer in the United States, as well as premature skin aging. In particular, UVB radiation causes formation of specific DNA damage photoproducts between pyrimidine bases. These DNA damage photoproducts are repaired by a process called nucleotide excision repair, also known as UV-induced DNA repair. When left unrepaired, UVB-induced DNA damage leads to accumulation of mutations, predisposing people to carcinogenesis as well as to premature aging. Genetic loss of nucleotide excision repair leads to severe disorders, namely, xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS), which are associated with predisposition to skin carcinogenesis at a young age as well as developmental and neurological conditions. Regulation of nucleotide excision repair is an attractive avenue to preventing or reversing these detrimental consequences of impaired nucleotide excision repair. Here, we review recent studies on molecular mechanisms regulating nucleotide excision repair by extracellular cues and intracellular signaling pathways, with a special focus on the molecular regulation of individual repair factors.
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Affiliation(s)
- Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL
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35
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Sonzogni SV, Ogara MF, Castillo DS, Sirkin PF, Radicella JP, Cánepa ET. Nuclear translocation of p19INK4d in response to oxidative DNA damage promotes chromatin relaxation. Mol Cell Biochem 2014; 398:63-72. [DOI: 10.1007/s11010-014-2205-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/30/2014] [Indexed: 12/23/2022]
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36
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House NCM, Koch MR, Freudenreich CH. Chromatin modifications and DNA repair: beyond double-strand breaks. Front Genet 2014; 5:296. [PMID: 25250043 PMCID: PMC4155812 DOI: 10.3389/fgene.2014.00296] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 08/08/2014] [Indexed: 12/28/2022] Open
Abstract
DNA repair must take place in the context of chromatin, and chromatin modifications and DNA repair are intimately linked. The study of double-strand break repair has revealed numerous histone modifications that occur after induction of a DSB, and modification of the repair factors themselves can also occur. In some cases the function of the modification is at least partially understood, but in many cases it is not yet clear. Although DSB repair is a crucial activity for cell survival, DSBs account for only a small percentage of the DNA lesions that occur over the lifetime of a cell. Repair of single-strand gaps, nicks, stalled forks, alternative DNA structures, and base lesions must also occur in a chromatin context. There is increasing evidence that these repair pathways are also regulated by histone modifications and chromatin remodeling. In this review, we will summarize the current state of knowledge of chromatin modifications that occur during non-DSB repair, highlighting similarities and differences to DSB repair as well as remaining questions.
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Affiliation(s)
| | - Melissa R Koch
- Department of Biology, Tufts University Medford, MA, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University Medford, MA, USA ; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University Boston, MA, USA
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37
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Understanding nucleotide excision repair and its roles in cancer and ageing. Nat Rev Mol Cell Biol 2014; 15:465-81. [PMID: 24954209 DOI: 10.1038/nrm3822] [Citation(s) in RCA: 788] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleotide excision repair (NER) eliminates various structurally unrelated DNA lesions by a multiwise 'cut and patch'-type reaction. The global genome NER (GG-NER) subpathway prevents mutagenesis by probing the genome for helix-distorting lesions, whereas transcription-coupled NER (TC-NER) removes transcription-blocking lesions to permit unperturbed gene expression, thereby preventing cell death. Consequently, defects in GG-NER result in cancer predisposition, whereas defects in TC-NER cause a variety of diseases ranging from ultraviolet radiation-sensitive syndrome to severe premature ageing conditions such as Cockayne syndrome. Recent studies have uncovered new aspects of DNA-damage detection by NER, how NER is regulated by extensive post-translational modifications, and the dynamic chromatin interactions that control its efficiency. Based on these findings, a mechanistic model is proposed that explains the complex genotype-phenotype correlations of transcription-coupled repair disorders.
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38
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Polo SE. Reshaping chromatin after DNA damage: the choreography of histone proteins. J Mol Biol 2014; 427:626-36. [PMID: 24887097 PMCID: PMC5111727 DOI: 10.1016/j.jmb.2014.05.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/19/2014] [Accepted: 05/21/2014] [Indexed: 01/03/2023]
Abstract
DNA damage signaling and repair machineries operate in a nuclear environment where DNA is wrapped around histone proteins and packaged into chromatin. Understanding how chromatin structure is restored together with the DNA sequence during DNA damage repair has been a topic of intense research. Indeed, chromatin integrity is central to cell functions and identity. However, chromatin shows remarkable plasticity in response to DNA damage. This review presents our current knowledge of chromatin dynamics in the mammalian cell nucleus in response to DNA double strand breaks and UV lesions. I provide an overview of the key players involved in regulating histone dynamics in damaged chromatin regions, focusing on histone chaperones and their concerted action with histone modifiers, chromatin remodelers and repair factors. I also discuss how these dynamics contribute to reshaping chromatin and, by altering the chromatin landscape, may affect the maintenance of epigenetic information.
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Affiliation(s)
- Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, 75205 Paris Cedex 13, France.
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39
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Dihydromyricetin promotes hepatocellular carcinoma regression via a p53 activation-dependent mechanism. Sci Rep 2014; 4:4628. [PMID: 24717393 PMCID: PMC3982169 DOI: 10.1038/srep04628] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/24/2014] [Indexed: 12/21/2022] Open
Abstract
The development of antitumor chemotherapy drugs remains a key goal for oncologists, and natural products provide a vast resource for anti-cancer drug discovery. In the current study, we found that the flavonoid dihydromyricetin (DHM) exhibited antitumor activity against liver cancer cells, including primary cells obtained from hepatocellular carcinoma (HCC) patients. In contrast, DHM was not cytotoxic to immortalized normal liver cells. Furthermore, DHM treatment resulted in the growth inhibition and remission of xenotransplanted tumors in nude mice. Our results further demonstrated that this antitumor activity was caused by the activation of the p53-dependent apoptosis pathway via p53 phosphorylation at serine (15Ser). Moreover, our results showed that DHM plays a dual role in the induction of cell death when administered in combination with cisplatin, a common clinical drug that kills primary hepatoma cells but not normal liver cells.
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40
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Frost B, Hemberg M, Lewis J, Feany MB. Tau promotes neurodegeneration through global chromatin relaxation. Nat Neurosci 2014; 17:357-66. [PMID: 24464041 PMCID: PMC4012297 DOI: 10.1038/nn.3639] [Citation(s) in RCA: 332] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/24/2013] [Indexed: 12/16/2022]
Abstract
The microtubule-associated protein tau is involved in a number of neurodegenerative disorders, including Alzheimer's disease. Previous studies have linked oxidative stress and subsequent DNA damage to neuronal death in Alzheimer's disease and related tauopathies. Given that DNA damage can substantially alter chromatin structure, we examined epigenetic changes in tau-induced neurodegeneration. We found widespread loss of heterochromatin in tau transgenic Drosophila and mice and in human Alzheimer's disease. Notably, genetic rescue of tau-induced heterochromatin loss substantially reduced neurodegeneration in Drosophila. We identified oxidative stress and subsequent DNA damage as a mechanistic link between transgenic tau expression and heterochromatin relaxation, and found that heterochromatin loss permitted aberrant gene expression in tauopathies. Furthermore, large-scale analyses from the brains of individuals with Alzheimer's disease revealed a widespread transcriptional increase in genes that were heterochromatically silenced in controls. Our results establish heterochromatin loss as a toxic effector of tau-induced neurodegeneration and identify chromatin structure as a potential therapeutic target in Alzheimer's disease.
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Affiliation(s)
- Bess Frost
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Martin Hemberg
- Department of Ophthalmology and Program in Neurobiology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Jada Lewis
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, 32610, USA
| | - Mel B. Feany
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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41
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Duan MR, Smerdon MJ. Histone H3 lysine 14 (H3K14) acetylation facilitates DNA repair in a positioned nucleosome by stabilizing the binding of the chromatin Remodeler RSC (Remodels Structure of Chromatin). J Biol Chem 2014; 289:8353-63. [PMID: 24515106 DOI: 10.1074/jbc.m113.540732] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Histone H3 acetylation is induced by UV damage in yeast and may play an important role in regulating the repair of UV photolesions in nucleosome-loaded genomic loci. However, it remains elusive how H3 acetylation facilitates repair. We generated a strongly positioned nucleosome containing homogeneously acetylated H3 at Lys-14 (H3K14ac) and investigated possible mechanisms by which H3K14 acetylation modulates repair. We show that H3K14ac does not alter nucleosome unfolding dynamics or enhance the repair of UV-induced cyclobutane pyrimidine dimers by UV photolyase. Importantly, however, nucleosomes with H3K14ac have a higher affinity for purified chromatin remodeling complex RSC (Remodels the Structure of Chromatin) and show greater cyclobutane pyrimidine dimer repair compared with unacetylated nucleosomes. Our study indicates that, by anchoring RSC, H3K14 acetylation plays an important role in the unfolding of strongly positioned nucleosomes during repair of UV damage.
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Affiliation(s)
- Ming-Rui Duan
- From Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520
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42
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Ibuki Y. Histone Modifications Induced by Chemicals and Photogenotoxicity. Genes Environ 2014. [DOI: 10.3123/jemsge.2014.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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43
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Alvarez-Gonzalez R, Mendoza-Alvarez H, Frey M, Zentgraf H. Up-regulation of two distinct p53-DNA binding functions by covalent poly(ADP-ribosyl)ation: transactivating and single strand break sensing. Cancer Invest 2013; 31:563-70. [PMID: 24164297 DOI: 10.3109/07357907.2013.845670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We used a [(32)P] p53 sequence-specific oligodeoxynucleotide and Electrophoretic-Mobility-Shift-Assays to monitor p53 DNA sequence-specific binding with p53-R267W, a nonbinding point mutant; and p53-Δ30, a deletion-mutant which lacks the carboxy-terminus that recognizes DNA-strand-breaks. Recombinant p53 and poly(ADP-ribose)polymerase-1 (PARP-1) were incubated with labeled βNAD(+) with/without DNA. The poly(ADP-ribosyl)ation of each protein increased with incubation-time and βNAD(+) and p53 concentration(s). Since p53-Δ30 was efficiently labeled, poly(ADP-ribosyl)ation target site(s) of wt-p53 must reside outside its carboxy-terminal-domain. The poly(ADP-ribosyl)ation of p53-Δ30 did not diminish its DNA binding; Instead, it enhanced DNA-sequence-specific-binding. Therefore, we conclude that DNA-sequence-specific-binding and DNA-nick-sensing of mutant-p53 are differentially regulated by poly(ADP-ribosyl)ation.
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44
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Zalmas LP, Coutts AS, Helleday T, La Thangue NB. E2F-7 couples DNA damage-dependent transcription with the DNA repair process. Cell Cycle 2013; 12:3037-51. [PMID: 23974101 PMCID: PMC3875678 DOI: 10.4161/cc.26078] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The cellular response to DNA damage, mediated by the DNA repair process, is essential in maintaining the integrity and stability of the genome. E2F-7 is an atypical member of the E2F family with a role in negatively regulating transcription and cell cycle progression under DNA damage. Surprisingly, we found that E2F-7 makes a transcription-independent contribution to the DNA repair process, which involves E2F-7 locating to and binding damaged DNA. Further, E2F-7 recruits CtBP and HDAC to the damaged DNA, altering the local chromatin environment of the DNA lesion. Importantly, the E2F-7 gene is a target for somatic mutation in human cancer and tumor-derived mutant alleles encode proteins with compromised transcription and DNA repair properties. Our results establish that E2F-7 participates in 2 closely linked processes, allowing it to directly couple the expression of genes involved in the DNA damage response with the DNA repair machinery, which has relevance in human malignancy.
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45
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Mammalian DNA repair: HATs and HDACs make their mark through histone acetylation. Mutat Res 2013; 750:23-30. [PMID: 23927873 DOI: 10.1016/j.mrfmmm.2013.07.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/03/2013] [Accepted: 07/09/2013] [Indexed: 12/20/2022]
Abstract
Genetic information is recorded in specific DNA sequences that must be protected to preserve normal cellular function. Genome maintenance pathways have evolved to sense and repair DNA damage. Importantly, deleterious mutations that occur from mis-repaired lesions can lead to diseases such as cancer. As eukaryotic DNA is bound by histone proteins and organized into chromatin, the true in vivo substrate of transcription, replication and DNA repair is chromatin. Almost 50 years ago, it was found that histones contained the post-translational modification (PTM), acetylation. With the cloning and identification of transcription associated histone acetyltransferase (HAT) and histone deacetylase (HDAC) enzymes that write and erase the histone acetylation mark respectively, it was realized that this histone modification could be dynamically regulated. Chromatin is subjected to numerous PTMs that regulate chromatin structure and function, including DNA repair. As different organisms contain different histone modifications, chromatin-associated proteins and chromatin states, it is likely that chromatin-templated processes such as DNA repair will exhibit organismal differences. This article focuses on the DNA damage response (DDR) in mammalian cells and how the concerted activities of HAT and HDAC enzymes, and their histone acetylation targets, specifically participate in DNA double-strand break (DSB) repair. Defects in DNA repair and chromatin pathways are observed in cancer, and these pathways represent cancer therapeutic targets. Therefore, understanding the relationship between DNA repair and histone acetylations is important for providing mechanistic details of DSB repair within chromatin that has the potential to be exploited in the clinic.
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46
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Keuser B, Khobta A, Gallé K, Anderhub S, Schulz I, Pauly K, Epe B. Influences of histone deacetylase inhibitors and resveratrol on DNA repair and chromatin compaction. Mutagenesis 2013; 28:569-76. [PMID: 23814181 DOI: 10.1093/mutage/get034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Accessibility of DNA is a prerequisite for both DNA damage and repair. Therefore, the chromatin structure is expected to have major impact on both processes, with opposite consequences for the stability of the genome. To analyse the influence of chromatin compaction on the generation and repair of various types of DNA modifications, we modulated the global chromatin structure of AS52 Chinese hamster ovary cells and HeLa cells by treatment with either histone deacetylase inhibitors or resveratrol and measured the repair kinetics of (i) pyrimidine dimers induced by ultraviolet B, (ii) oxidised purines generated by photosensitisation and (iii) single-strand breaks induced by H2O2, using an alkaline elution technique. The decrease of chromatin compaction (detected as reduced DNA accessibility to DNase I) after treatment with trichostatin A or butyrate slightly increased the damage generation but had no significant effect on the global repair rates. In contrast, incubation of AS52 cells with resveratrol at concentrations that caused significant chromatin compaction and that had only moderate influence on cell proliferation gave rise to a strong decrease of the repair rates of all three types of DNA modifications. Similar, but less pronounced effects were observed in HeLa cells. The effects of resveratrol on the repair rates were not antagonised by the sirtuin inhibitor EX-527 or by an increase of the intracellular thiol levels.
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Affiliation(s)
- Bettina Keuser
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, 55099 Mainz, Germany
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47
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Ogara MF, Sirkin PF, Carcagno AL, Marazita MC, Sonzogni SV, Ceruti JM, Cánepa ET. Chromatin relaxation-mediated induction of p19INK4d increases the ability of cells to repair damaged DNA. PLoS One 2013; 8:e61143. [PMID: 23593412 PMCID: PMC3625165 DOI: 10.1371/journal.pone.0061143] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/06/2013] [Indexed: 12/29/2022] Open
Abstract
The maintenance of genomic integrity is of main importance to the survival and health of organisms which are continuously exposed to genotoxic stress. Cells respond to DNA damage by activating survival pathways consisting of cell cycle checkpoints and repair mechanisms. However, the signal that triggers the DNA damage response is not necessarily a direct detection of the primary DNA lesion. In fact, chromatin defects may serve as initiating signals to activate those mechanisms. If the modulation of chromatin structure could initiate a checkpoint response in a direct manner, this supposes the existence of specific chromatin sensors. p19INK4d, a member of the INK4 cell cycle inhibitors, plays a crucial role in regulating genomic stability and cell viability by enhancing DNA repair. Its expression is induced in cells injured by one of several genotoxic treatments like cis-platin, UV light or neocarzinostatin. Nevertheless, when exogenous DNA damaged molecules are introduced into the cell, this induction is not observed. Here, we show that p19INK4d is enhanced after chromatin relaxation even in the absence of DNA damage. This induction was shown to depend upon ATM/ATR, Chk1/Chk2 and E2F activity, as is the case of p19INK4d induction by endogenous DNA damage. Interestingly, p19INK4d improves DNA repair when the genotoxic damage is caused in a relaxed-chromatin context. These results suggest that changes in chromatin structure, and not DNA damage itself, is the actual trigger of p19INK4d induction. We propose that, in addition to its role as a cell cycle inhibitor, p19INK4d could participate in a signaling network directed to detecting and eventually responding to chromatin anomalies.
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Affiliation(s)
- María F. Ogara
- Laboratorio de Biología Molecular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, Buenos Aires, Argentina
| | - Pablo F. Sirkin
- Laboratorio de Biología Molecular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, Buenos Aires, Argentina
| | - Abel L. Carcagno
- Laboratorio de Biología Molecular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, Buenos Aires, Argentina
| | - Mariela C. Marazita
- Laboratorio de Biología Molecular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, Buenos Aires, Argentina
| | - Silvina V. Sonzogni
- Laboratorio de Biología Molecular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, Buenos Aires, Argentina
| | - Julieta M. Ceruti
- Laboratorio de Biología Molecular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, Buenos Aires, Argentina
| | - Eduardo T. Cánepa
- Laboratorio de Biología Molecular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, Buenos Aires, Argentina
- * E-mail:
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48
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Zheng H, Chen L, Pledger WJ, Fang J, Chen J. p53 promotes repair of heterochromatin DNA by regulating JMJD2b and SUV39H1 expression. Oncogene 2013; 33:734-44. [PMID: 23376847 PMCID: PMC3912226 DOI: 10.1038/onc.2013.6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/12/2012] [Accepted: 12/09/2012] [Indexed: 12/26/2022]
Abstract
Constitutive heterochromatin is important for maintaining chromosome stability but also delays the repair of DNA double strand breaks (DSB). DSB repair in complex mammalian genomes involves a fast phase (2–6 hrs) where most of the breaks are rapidly repaired, and a slow phase (up to 24 hrs) where the remaining damages in heterochromatin are repaired. We found that p53 deficiency delays the slow phase DNA repair after ionizing irradiation. P53 deficiency prevents down regulation of histone H3K9 trimethylation at pericentric heterochromatin after DNA damage. Moreover, p53 directly induces expression of the H3 K9 demethylase JMJD2b through promoter binding. P53 activation also indirectly down regulates expression of the H3 K9 methytransferase SUV39H1. Depletion of JMJD2b or sustained expression of SUV39H1 delays the repair of heterochromatin DNA and reduces clonogenic survival after ionizing irradiation. The results suggest that by regulating JMJD2b and SUV39H1 expression, p53 not only controls transcription but also promotes heterochromatin relaxation to accelerate a rate-limiting step in the repair of complex genomes.
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Affiliation(s)
- H Zheng
- Molecular Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - L Chen
- Molecular Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - W J Pledger
- Molecular Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - J Fang
- Molecular Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - J Chen
- Molecular Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
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49
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Choi SY, Jang H, Roe JS, Kim ST, Cho EJ, Youn HD. Phosphorylation and ubiquitination-dependent degradation of CABIN1 releases p53 for transactivation upon genotoxic stress. Nucleic Acids Res 2013; 41:2180-90. [PMID: 23303793 PMCID: PMC3575827 DOI: 10.1093/nar/gks1319] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
CABIN1 acts as a negative regulator of p53 by keeping p53 in an inactive state on chromatin. Genotoxic stress causes rapid dissociation of CABIN1 and activation of p53. However, its molecular mechanism is still unknown. Here, we reveal the phosphorylation- and ubiquitination-dependent degradation of CABIN1 upon DNA damage, releasing p53 for transcriptional activation. The DNA-damage-signaling kinases, ATM and CHK2, phosphorylate CABIN1 and increase the degradation of CABIN1 protein. Knockdown or overexpression of these kinases influences the stability of CABIN1 protein showing that their activity is critical for degradation of CABIN1. Additionally, CABIN1 was found to undergo ubiquitin-dependent proteasomal degradation mediated by the CRL4DDB2 ubiquitin ligase complex. Both phosphorylation and ubiquitination of CABIN1 appear to be relevant for controlling the level of CABIN1 protein upon genotoxic stress.
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Affiliation(s)
- Soo-Youn Choi
- Department of Biomedical Sciences, Department of Biochemistry and Molecular Biology, National Creative Research Center for Epigenome Reprogramming Network, Seoul, Republic of Korea
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50
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Wang QE, Han C, Zhao R, Wani G, Zhu Q, Gong L, Battu A, Racoma I, Sharma N, Wani AA. p38 MAPK- and Akt-mediated p300 phosphorylation regulates its degradation to facilitate nucleotide excision repair. Nucleic Acids Res 2012; 41:1722-33. [PMID: 23275565 PMCID: PMC3561975 DOI: 10.1093/nar/gks1312] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Besides the primary histone acetyltransferase (HAT)-mediated chromatin remodeling function, co-transcriptional factor, p300, is also known to play a distinct role in DNA repair. However, the exact mechanism of p300 function in DNA repair has remained unclear and difficult to discern due to the phosphorylation and degradation of p300 in response to DNA damage. Here, we have demonstrated that p300 is only degraded in the presence of specific DNA lesions, which are the substrates of nucleotide excision repair (NER) pathway. In contrast, DNA double-strand breaks fail to degrade p300. Degradation is initiated by phosphorylation of p300 at serine 1834, which is catalyzed by the cooperative action of p38 mitogen-activated protein kinases and Akt kinases. In depth, functional analysis revealed that (i) p300 and CBP act redundantly in repairing ultraviolet (UV) lesions, (ii) the phosphorylation of p300 at S1834 is critical for efficient removal of UV-induced cyclobutane pyrimidine dimers and (iii) p300 is recruited to DNA damage sites located within heterochromatin. Taken together, we conclude that phosphorylated p300 initially acetylates histones to relax heterochromatin to allow damage recognition factors access to damage DNA. Thereupon, p300 is promptly degraded to allow the sequential recruitment of downstream repair proteins for successful execution of NER.
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Affiliation(s)
- Qi-En Wang
- Department of Radiology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA.
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