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Fonsêca TC, Abrantes TC, Fernandes PV, de Andrade BAB, Cabral MG, Romañach MJ, Agostini M, Abrahão AC. Immunohistochemical analysis of BRCA1 and acetyl-histone H3 in squamous cell carcinoma of the mobile tongue. Oral Surg Oral Med Oral Pathol Oral Radiol 2021; 132:320-326. [PMID: 34030994 DOI: 10.1016/j.oooo.2021.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/18/2021] [Accepted: 03/21/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE The objective of this study was to evaluate the immunoexpression profiles of breast cancer 1 (BRCA1) and acetyl-histone H3 (AcH3) in squamous cell carcinoma of the mobile tongue (SCC-MT) and their correlation with epidemiologic data and the histopathological grade of tumors. STUDY DESIGN Incisional biopsies of 43 SCC-MT were submitted to immunohistochemistry for AcH3 and BRCA1. Samples were microscopically graded as well differentiated (n = 21) or poorly differentiated (n = 22). Both groups were submitted to statistical analysis (P < .05) regarding the percentage of positive cells. RESULTS Thirty-nine cases were positive for AcH3 (91%), but no difference was observed for the histologic grading (P = .27). Positivity for BRCA1 was observed in all samples regardless of their cellular locations. Most cases in the poorly differentiated group presented with less than 10% nuclear staining (P < .01) and a predominance of cytoplasmic staining (P = .034). The well-differentiated group showed nuclear staining in most of the cases, with more than 50% of cells staining positive (P < .01). CONCLUSION AcH3 and BRCA1 were expressed in all samples. There was a significant decrease in cytoplasmic BRCA1 expression in the poorly differentiated group, suggesting BRCA1 as a possible prognostic marker for SCC-MT.
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Affiliation(s)
- T C Fonsêca
- Oral Pathology, Department of Oral Diagnosis and Pathology, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - T C Abrantes
- Oral Pathology, Department of Oral Diagnosis and Pathology, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - P V Fernandes
- Pathology Division, National Cancer Institute José Alencar Gomes da Silva (DIPAT/INCA), Rio de Janeiro, Brazil
| | - B A B de Andrade
- Oral Pathology, Department of Oral Diagnosis and Pathology, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M G Cabral
- Oral Pathology, Department of Oral Diagnosis and Pathology, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M J Romañach
- Oral Pathology, Department of Oral Diagnosis and Pathology, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M Agostini
- Oral Pathology, Department of Oral Diagnosis and Pathology, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A C Abrahão
- Oral Pathology, Department of Oral Diagnosis and Pathology, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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2
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Jain V, Hassan PA, Das B. Radiation-induced conformational changes in chromatin structure in resting human peripheral blood mononuclear cells. Int J Radiat Biol 2014; 90:1143-51. [PMID: 24844371 DOI: 10.3109/09553002.2014.925605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
UNLABELLED Abstract Background: Ionizing radiation induces a plethora of DNA damage including double-strand breaks (DSB) that may trigger a series of events such as transcription, DNA repair and alteration in the conformation of chromatin structure in human cells. We have made an attempt to study the conformational changes in chromatin fibers in irradiated human peripheral blood mononuclear cells (PBMC) using Dynamic Light Scattering (DLS) as a new tool. MATERIALS AND METHODS Venous blood samples were collected from 10 random, healthy individuals with written informed consent, approved by institutional ethics committee. PBMC were separated from blood, irradiated with different doses of gamma radiation from 0.25-1.0 Gy. Native chromatin was isolated from irradiated PBMC and changes in the hydrodynamic diameter of the chromatin fiber were measured using DLS. Both dose response and time kinetics was studied in order to see the chromatin changes. Radiation-induced DNA double-strand breaks were measured using gamma-H2AX (histone 2A member X) as a biomarker using flow cytometry and foci were visualized in confocal microscopy. RESULTS A significant alteration in hydrodynamic diameter of the chromatin fiber was observed at lower doses (0.25 and 0.50 Gy), whereas at higher dose (1.0 Gy), the size of the chromatin fiber was comparable to unirradiated control. Among the 10 individuals studied, five individuals showed significant increase (p ≤ 0.002) in hydrodynamic size at 0.25 Gy whereas four individuals showed significant decrease (p ≤ 0.009) at 0.25 Gy. One individual did not show any significant difference as compared to control. However, dose-dependent increase in gamma-H2AX fluorescence signals as well as foci number was observed. Increased fragmentation of chromatin fiber was also observed using Atomic Force Microscopy at higher doses. CONCLUSION Radiation-induced DNA damage response can lead to individual specific conformational changes in chromatin structure at lower doses (0.25 Gy and 0.50 Gy) which can be detected using dynamic light scattering method in resting human PBMC.
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Affiliation(s)
- Vinay Jain
- Low Level Radiation Research Section, Radiation Biology and Health Sciences Division, Bio Science Group, Bhabha Atomic Research Centre , Trombay, Mumbai-400 085 , India
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LeGresley SE, Wilt J, Antonik M. DNA damage may drive nucleosomal reorganization to facilitate damage detection. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:032708. [PMID: 24730875 DOI: 10.1103/physreve.89.032708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Indexed: 06/03/2023]
Abstract
One issue in genome maintenance is how DNA repair proteins find lesions at rates that seem to exceed diffusion-limited search rates. We propose a phenomenon where DNA damage induces nucleosomal rearrangements which move lesions to potential rendezvous points in the chromatin structure. These rendezvous points are the dyad and the linker DNA between histones, positions in the chromatin which are more likely to be accessible by repair proteins engaged in a random search. The feasibility of this mechanism is tested by considering the statistical mechanics of DNA containing a single lesion wrapped onto the nucleosome. We consider lesions which make the DNA either more flexible or more rigid by modeling the lesion as either a decrease or an increase in the bending energy. We include this energy in a partition function model of nucleosome breathing. Our results indicate that the steady state for a breathing nucleosome will most likely position the lesion at the dyad or in the linker, depending on the energy of the lesion. A role for DNA binding proteins and chromatin remodelers is suggested based on their ability to alter the mechanical properties of the DNA and DNA-histone binding, respectively. We speculate that these positions around the nucleosome potentially serve as rendezvous points where DNA lesions may be encountered by repair proteins which may be sterically hindered from searching the rest of the nucleosomal DNA. The strength of the repositioning is strongly dependent on the structural details of the DNA lesion and the wrapping and breathing of the nucleosome. A more sophisticated evaluation of this proposed mechanism will require detailed information about breathing dynamics, the structure of partially wrapped nucleosomes, and the structural properties of damaged DNA.
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Affiliation(s)
- Sarah E LeGresley
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| | - Jamie Wilt
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| | - Matthew Antonik
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
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4
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Giudice FS, Pinto DS, Nör JE, Squarize CH, Castilho RM. Inhibition of histone deacetylase impacts cancer stem cells and induces epithelial-mesenchyme transition of head and neck cancer. PLoS One 2013; 8:e58672. [PMID: 23527004 PMCID: PMC3603970 DOI: 10.1371/journal.pone.0058672] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/05/2013] [Indexed: 12/30/2022] Open
Abstract
The genome is organized and packed into the nucleus through interactions with core histone proteins. Emerging evidence suggests that tumors are highly responsive to epigenetic alterations that induce chromatin-based events and dynamically influence tumor behavior. We examined chromatin organization in head and neck squamous cell carcinoma (HNSCC) using acetylation levels of histone 3 as a marker of chromatin compaction. Compared to control oral keratinocytes, we found that HNSCC cells are hypoacetylated and that microenvironmental cues (e.g., microvasculature endothelial cells) induce tumor acetylation. Furthermore, we found that chemical inhibition of histone deacetylases (HDAC) reduces the number of cancer stem cells (CSC) and inhibits clonogenic sphere formation. Paradoxically, inhibition of HDAC also induced epithelial-mesenchymal transition (EMT) in HNSCC cells, accumulation of BMI-1, an oncogene associated with tumor aggressiveness, and expression of the vimentin mesenchymal marker. Importantly, we observed co-expression of vimentin and acetylated histone 3 at the invasion front of human HNSCC tumor tissues. Collectively, these findings suggest that environmental cues, such as endothelial cell-secreted factors, modulate tumor plasticity by limiting the population of CSC and inducing EMT. Therefore, inhibition of HDAC may constitute a novel strategy to disrupt the population of CSC in head and neck tumors to create a homogeneous population of cancer cells with biologically defined signatures and predictable behavior.
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Affiliation(s)
- Fernanda S. Giudice
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Decio S. Pinto
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Jacques E. Nör
- Department of Cariology, Restorative Sciences and Endodontics, School of Dentistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
| | - Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
- * E-mail:
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Fachinetti D, Bermejo R, Cocito A, Minardi S, Katou Y, Kanoh Y, Shirahige K, Azvolinsky A, Zakian VA, Foiani M. Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol Cell 2010; 39:595-605. [PMID: 20797631 DOI: 10.1016/j.molcel.2010.07.024] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 05/05/2010] [Accepted: 06/08/2010] [Indexed: 01/19/2023]
Abstract
Chromosome replication initiates at multiple replicons and terminates when forks converge. In E. coli, the Tus-TER complex mediates polar fork converging at the terminator region, and aberrant termination events challenge chromosome integrity and segregation. Since in eukaryotes, termination is less characterized, we used budding yeast to identify the factors assisting fork fusion at replicating chromosomes. Using genomic and mechanistic studies, we have identified and characterized 71 chromosomal termination regions (TERs). TERs contain fork pausing elements that influence fork progression and merging. The Rrm3 DNA helicase assists fork progression across TERs, counteracting the accumulation of X-shaped structures. The Top2 DNA topoisomerase associates at TERs in S phase, and G2/M facilitates fork fusion and prevents DNA breaks and genome rearrangements at TERs. We propose that in eukaryotes, replication fork barriers, Rrm3, and Top2 coordinate replication fork progression and fusion at TERs, thus counteracting abnormal genomic transitions.
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Affiliation(s)
- Daniele Fachinetti
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare (IFOM-IEO Campus), Via Adamello 16, 20139 Milan, Italy
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6
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Bermejo R, Capra T, Gonzalez-Huici V, Fachinetti D, Cocito A, Natoli G, Katou Y, Mori H, Kurokawa K, Shirahige K, Foiani M. Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription. Cell 2009; 138:870-84. [DOI: 10.1016/j.cell.2009.06.022] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 04/10/2009] [Accepted: 06/10/2009] [Indexed: 12/18/2022]
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7
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Conde F, Refolio E, Cordón-Preciado V, Cortés-Ledesma F, Aragón L, Aguilera A, San-Segundo PA. The Dot1 histone methyltransferase and the Rad9 checkpoint adaptor contribute to cohesin-dependent double-strand break repair by sister chromatid recombination in Saccharomyces cerevisiae. Genetics 2009; 182:437-46. [PMID: 19332880 PMCID: PMC2691753 DOI: 10.1534/genetics.109.101899] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 03/26/2009] [Indexed: 12/20/2022] Open
Abstract
Genomic integrity is threatened by multiple sources of DNA damage. DNA double-strand breaks (DSBs) are among the most dangerous types of DNA lesions and can be generated by endogenous or exogenous agents, but they can arise also during DNA replication. Sister chromatid recombination (SCR) is a key mechanism for the repair of DSBs generated during replication and it is fundamental for maintaining genomic stability. Proper repair relies on several factors, among which histone modifications play important roles in the response to DSBs. Here, we study the role of the histone H3K79 methyltransferase Dot1 in the repair by SCR of replication-dependent HO-induced DSBs, as a way to assess its function in homologous recombination. We show that Dot1, the Rad9 DNA damage checkpoint adaptor, and phosphorylation of histone H2A (gammaH2A) are required for efficient SCR. Moreover, we show that Dot1 and Rad9 promote DSB-induced loading of cohesin onto chromatin. We propose that recruitment of Rad9 to DSB sites mediated by gammaH2A and H3K79 methylation contributes to DSB repair via SCR by regulating cohesin binding to damage sites. Therefore, our results contribute to an understanding of how different chromatin modifications impinge on DNA repair mechanisms, which are fundamental for maintaining genomic stability.
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8
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Alberghina L, Coccetti P, Orlandi I. Systems biology of the cell cycle of Saccharomyces cerevisiae: From network mining to system-level properties. Biotechnol Adv 2009; 27:960-978. [PMID: 19465107 DOI: 10.1016/j.biotechadv.2009.05.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Following a brief description of the operational procedures of systems biology (SB), the cell cycle of budding yeast is discussed as a successful example of a top-down SB analysis. After the reconstruction of the steps that have led to the identification of a sizer plus timer network in the G1 to S transition, it is shown that basic functions of the cell cycle (the setting of the critical cell size and the accuracy of DNA replication) are system-level properties, detected only by integrating molecular analysis with modelling and simulation of their underlying networks. A detailed network structure of a second relevant regulatory step of the cell cycle, the exit from mitosis, derived from extensive data mining, is constructed and discussed. To reach a quantitative understanding of how nutrients control, through signalling, metabolism and transcription, cell growth and cycle is a very relevant aim of SB. Since we know that about 900 gene products are required for cell cycle execution and control in budding yeast, it is quite clear that a purely systematic approach would require too much time. Therefore lines for a modular SB approach, which prioritises molecular and computational investigations for faster cell cycle understanding, are proposed. The relevance of the insight coming from the cell cycle SB studies in developing a new framework for tackling very complex biological processes, such as cancer and aging, is discussed.
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Affiliation(s)
- Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milano, Italy.
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milano, Italy
| | - Ivan Orlandi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milano, Italy
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Misri S, Pandita S, Kumar R, Pandita TK. Telomeres, histone code, and DNA damage response. Cytogenet Genome Res 2009; 122:297-307. [PMID: 19188699 DOI: 10.1159/000167816] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2008] [Indexed: 12/30/2022] Open
Abstract
Genomic stability is maintained by telomeres, the end terminal structures that protect chromosomes from fusion or degradation. Shortening or loss of telomeric repeats or altered telomere chromatin structure is correlated with telomere dysfunction such as chromosome end-to-end associations that could lead to genomic instability and gene amplification. The structure at the end of telomeres is such that its DNA differs from DNA double strand breaks (DSBs) to avoid nonhomologous end-joining (NHEJ), which is accomplished by forming a unique higher order nucleoprotein structure. Telomeres are attached to the nuclear matrix and have a unique chromatin structure. Whether this special structure is maintained by specific chromatin changes is yet to be thoroughly investigated. Chromatin modifications implicated in transcriptional regulation are thought to be the result of a code on the histone proteins (histone code). This code, involving phosphorylation, acetylation, methylation, ubiquitylation, and sumoylation of histones, is believed to regulate chromatin accessibility either by disrupting chromatin contacts or by recruiting non-histone proteins to chromatin. The histone code in which distinct histone tail-protein interactions promote engagement may be the deciding factor for choosing specific DSB repair pathways. Recent evidence suggests that such mechanisms are involved in DNA damage detection and repair. Altered telomere chromatin structure has been linked to defective DNA damage response (DDR), and eukaryotic cells have evolved DDR mechanisms utilizing proficient DNA repair and cell cycle checkpoints in order to maintain genomic stability. Recent studies suggest that chromatin modifying factors play a critical role in the maintenance of genomic stability. This review will summarize the role of DNA damage repair proteins specifically ataxia-telangiectasia mutated (ATM) and its effectors and the telomere complex in maintaining genome stability.
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Affiliation(s)
- S Misri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
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No attenuation of the ATM-dependent DNA damage response in murine telomerase-deficient cells. DNA Repair (Amst) 2008; 8:347-53. [PMID: 19071232 DOI: 10.1016/j.dnarep.2008.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Revised: 11/02/2008] [Accepted: 11/10/2008] [Indexed: 12/19/2022]
Abstract
Inactivation of mammalian telomerase leads to telomere attrition, eventually culminating in uncapped telomeres, which elicit a DNA damage response and cell cycle arrest or death. In some instances, telomerase modulation evokes a response not obviously attributable to changes in telomere length. One such example is the suppression of the DNA damage response (DDR) and changes in histone modification that occur upon repression of the telomerase reverse transcriptase, TERT, in human primary cells [K. Masutomi, R. Possemato, J.M. Wong, J.L. Currier, Z. Tothova, J.B. Manola, S. Ganesan, P.M. Lansdorp, K. Collins and W.C. Hahn, The telomerase reverse transcriptase regulates chromatin state and DNA damage responses, Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 8222-8227]. Here, we evaluate the contribution of TERT to the DDR in murine Tert(-/-) cells without critically shortened telomeres. We treated mTert(-/-) embryonic stem (ES) cells and murine embryonic fibroblasts (MEFs) with etoposide and irradiation, and assessed the status of p53(pS15), 53BP1, ATM(pS1981), SMC1(pS957), and gammaH2AX by indirect immunofluorescence or western blotting. In four independently derived mTert(-/-) ES cell lines, there was no significant difference in the induction of gammaH2AX, 53BP1 foci, or the phosphorylation of ATM targets (ATM, SMC1, p53) between wildtype and mTert(-/-) ES cells and MEFs. A slight difference in post-translational modification of histones H3 and H4 was observed in a subset of mTert(-/-) ES cells, however this difference was reflected in the cellular levels of H3 and H4. Thus, in contrast to previous studies in human cells, the absence of Tert does not overtly affect the ATM-dependent response to DNA damage in murine cells.
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Role of Dot1 in the response to alkylating DNA damage in Saccharomyces cerevisiae: regulation of DNA damage tolerance by the error-prone polymerases Polzeta/Rev1. Genetics 2008; 179:1197-210. [PMID: 18562671 DOI: 10.1534/genetics.108.089003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Maintenance of genomic integrity relies on a proper response to DNA injuries integrated by the DNA damage checkpoint; histone modifications play an important role in this response. Dot1 methylates lysine 79 of histone H3. In Saccharomyces cerevisiae, Dot1 is required for the meiotic recombination checkpoint as well as for chromatin silencing and the G(1)/S and intra-S DNA damage checkpoints in vegetative cells. Here, we report the analysis of the function of Dot1 in the response to alkylating damage. Unexpectedly, deletion of DOT1 results in increased resistance to the alkylating agent methyl methanesulfonate (MMS). This phenotype is independent of the dot1 silencing defect and does not result from reduced levels of DNA damage. Deletion of DOT1 partially or totally suppresses the MMS sensitivity of various DNA repair mutants (rad52, rad54, yku80, rad1, rad14, apn1, rad5, rad30). However, the rev1 dot1 and rev3 dot1 mutants show enhanced MMS sensitivity and dot1 does not attenuate the MMS sensitivity of rad52 rev3 or rad52 rev1. In addition, Rev3-dependent MMS-induced mutagenesis is increased in dot1 cells. We propose that Dot1 inhibits translesion synthesis (TLS) by Polzeta/Rev1 and that the MMS resistance observed in the dot1 mutant results from the enhanced TLS activity.
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Lazzaro F, Sapountzi V, Granata M, Pellicioli A, Vaze M, Haber JE, Plevani P, Lydall D, Muzi-Falconi M. Histone methyltransferase Dot1 and Rad9 inhibit single-stranded DNA accumulation at DSBs and uncapped telomeres. EMBO J 2008; 27:1502-12. [PMID: 18418382 PMCID: PMC2328446 DOI: 10.1038/emboj.2008.81] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Accepted: 03/26/2008] [Indexed: 01/01/2023] Open
Abstract
Cells respond to DNA double-strand breaks (DSBs) and uncapped telomeres by recruiting checkpoint and repair factors to the site of lesions. Single-stranded DNA (ssDNA) is an important intermediate in the repair of DSBs and is produced also at uncapped telomeres. Here, we provide evidence that binding of the checkpoint protein Rad9, through its Tudor domain, to methylated histone H3-K79 inhibits resection at DSBs and uncapped telomeres. Loss of DOT1 or mutations in RAD9 influence a Rad50-dependent nuclease, leading to more rapid accumulation of ssDNA, and faster activation of the critical checkpoint kinase, Mec1. Moreover, deletion of RAD9 or DOT1 partially bypasses the requirement for CDK1 in DSB resection. Interestingly, Dot1 contributes to checkpoint activation in response to low levels of telomere uncapping but is not essential with high levels of uncapping. We suggest that both Rad9 and histone H3 methylation allow transmission of the damage signal to checkpoint kinases, and keep resection of damaged DNA under control influencing, both positively and negatively, checkpoint cascades and contributing to a tightly controlled response to DNA damage.
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Affiliation(s)
- Federico Lazzaro
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita' degli Studi di Milano, Milano, Italy
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Bermejo R, Doksani Y, Capra T, Katou YM, Tanaka H, Shirahige K, Foiani M. Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activation. Genes Dev 2007; 21:1921-36. [PMID: 17671091 PMCID: PMC1935030 DOI: 10.1101/gad.432107] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 06/21/2007] [Indexed: 11/25/2022]
Abstract
DNA topoisomerases solve topological problems during chromosome metabolism. We investigated where and when Top1 and Top2 are recruited on replicating chromosomes and how their inactivation affects fork integrity and DNA damage checkpoint activation. We show that, in the context of replicating chromatin, Top1 and Top2 act within a 600-base-pair (bp) region spanning the moving forks. Top2 exhibits additional S-phase clusters at specific intergenic loci, mostly containing promoters. TOP1 ablation does not affect fork progression and stability and does not cause activation of the Rad53 checkpoint kinase. top2 mutants accumulate sister chromatid junctions in S phase without affecting fork progression and activate Rad53 at the M-G1 transition. top1 top2 double mutants exhibit fork block and processing and phosphorylation of Rad53 and gamma H2A in S phase. The exonuclease Exo1 influences fork processing and DNA damage checkpoint activation in top1 top2 mutants. Our data are consistent with a coordinated action of Top1 and Top2 in counteracting the accumulation of torsional stress and sister chromatid entanglement at replication forks, thus preventing the diffusion of topological changes along large chromosomal regions. A failure in resolving fork-related topological constrains during S phase may therefore result in abnormal chromosome transitions, DNA damage checkpoint activation, and chromosome breakage during segregation.
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MESH Headings
- Cell Cycle
- Cell Cycle Proteins/metabolism
- Checkpoint Kinase 2
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- Consensus Sequence
- DNA Damage
- DNA Replication
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/metabolism
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- Genes, Fungal
- Models, Biological
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- Protein Serine-Threonine Kinases/metabolism
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Rodrigo Bermejo
- Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology Foundation (IFOM-IEO Campus) and DSBB-Università degli Studi di Milano, 20139 Milan, Italy
| | - Ylli Doksani
- Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology Foundation (IFOM-IEO Campus) and DSBB-Università degli Studi di Milano, 20139 Milan, Italy
| | - Thelma Capra
- Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology Foundation (IFOM-IEO Campus) and DSBB-Università degli Studi di Milano, 20139 Milan, Italy
| | - Yuki-Mori Katou
- Laboratory of Genome Structure and Function, Division for Gene Research, Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan
| | - Hirokazu Tanaka
- Laboratory of Genome Structure and Function, Division for Gene Research, Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Division for Gene Research, Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan
| | - Marco Foiani
- Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology Foundation (IFOM-IEO Campus) and DSBB-Università degli Studi di Milano, 20139 Milan, Italy
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14
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Ghosal G, Muniyappa K. The characterization of Saccharomyces cerevisiae Mre11/Rad50/Xrs2 complex reveals that Rad50 negatively regulates Mre11 endonucleolytic but not the exonucleolytic activity. J Mol Biol 2007; 372:864-882. [PMID: 17698079 DOI: 10.1016/j.jmb.2007.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 07/04/2007] [Accepted: 07/09/2007] [Indexed: 12/29/2022]
Abstract
The evolutionarily conserved heterotrimeric Mre11/Rad50/Xrs2 (Nbs1) (MRX/N) complex plays a central role in an array of cellular responses involving DNA damage, telomere length homeostasis, cell-cycle checkpoint control and meiotic recombination. The underlying biochemical functions of MRX/N complex, or each of its individual subunits, at telomeres and the importance of complex formation are poorly understood. Here, we show that the Saccharomyces cerevisiae MRX complex, or its subunits, display an overwhelming preference for G-quadruplex DNA than for telomeric single-stranded or double-stranded DNA implicating the possible existence of this DNA structure in vivo. Although these alternative DNA substrates failed to affect Rad50 ATPase activity, kinetic analyses revealed that interaction of Rad50 with Xrs2 and/or Mre11 led to a twofold increase in the rates of ATP hydrolysis. Significantly, we show that Mre11 displays sequence-specific double-stranded DNA endonuclease activity, and Rad50, but not Xrs2, abrogated endonucleolytic but not the exonucleolytic activity. This repression was alleviated upon ATP hydrolysis by Rad50, suggesting that complex formation between Rad50 and Mre11 might be important for blocking the inappropriate cleavage of genomic DNA. Mre11 alone, or in the presence of ATP, MRX, MR or MX sub-complexes cleaved at the 5' end of an array of G residues in single-stranded DNA, at G quartets in G4 DNA, and at the center of TGTG repeats in duplex DNA. We propose that negative regulation of Mre11 endonuclease activity by Rad50 might be important for native as well as de novo telomere length homeostasis.
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Affiliation(s)
- Gargi Ghosal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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15
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Ricaud L, Proux C, Renou JP, Pichon O, Fochesato S, Ortet P, Montané MH. ATM-mediated transcriptional and developmental responses to gamma-rays in Arabidopsis. PLoS One 2007; 2:e430. [PMID: 17487278 PMCID: PMC1855986 DOI: 10.1371/journal.pone.0000430] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 04/19/2007] [Indexed: 11/19/2022] Open
Abstract
ATM (Ataxia Telangiectasia Mutated) is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT). To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT) and homozygous ATM-deficient mutants challenged with a dose of γ-rays (IR) that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of prolonged S-G2 phases that coincided with cell proliferation delay, or an anticipated subsequent auxin increase, accelerated cell differentiation or death, was used to link IR-regulated hallmark functions and tissue phenotypes after IR. The transcription burst was almost exclusively AtATM-dependent or weakly AtATR-dependent, and followed two major trends of expression in atm: (i)-loss or severe attenuation and delay, and (ii)-inverse and/or stochastic, as well as specific, enabling one to distinguish IR/ATM pathway constituents. Our data provide a large resource for studies on the interaction between plant checkpoints of the cell cycle, development, hormone response, and DNA repair functions, because IR-induced transcriptional changes partially overlap with the response to environmental stress. Putative connections of ATM to stem cell maintenance pathways after IR are also discussed.
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Affiliation(s)
- Lilian Ricaud
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Caroline Proux
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Jean-Pierre Renou
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Olivier Pichon
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Sylvain Fochesato
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Philippe Ortet
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Marie-Hélène Montané
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
- * To whom correspondence should be addressed. E-mail:
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16
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Ataian Y, Krebs JE. Five repair pathways in one context: chromatin modification during DNA repair. Biochem Cell Biol 2007; 84:490-504. [PMID: 16936822 DOI: 10.1139/o06-075] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The eukaryotic cell is faced with more than 10 000 various kinds of DNA lesions per day. Failure to repair such lesions can lead to mutations, genomic instability, or cell death. Therefore, cells have developed 5 major repair pathways in which different kinds of DNA damage can be detected and repaired: homologous recombination, nonhomologous end joining, nucleotide excision repair, base excision repair, and mismatch repair. However, the efficient repair of DNA damage is complicated by the fact that the genomic DNA is packaged through histone and nonhistone proteins into chromatin, a highly condensed structure that hinders DNA accessibility and its subsequent repair. Therefore, the cellular repair machinery has to circumvent this natural barrier to gain access to the damaged site in a timely manner. Repair of DNA lesions in the context of chromatin occurs with the assistance of ATP-dependent chromatin-remodeling enzymes and histone-modifying enzymes, which allow access of the necessary repair factors to the lesion. Here we review recent studies that elucidate the interplay between chromatin modifiers / remodelers and the major DNA repair pathways.
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Affiliation(s)
- Yeganeh Ataian
- Department of Biological Sciences, University of AK Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
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17
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Abstract
In Saccharomyces cerevisiae, H3 methylation at lysine 4 (H3K4) is mediated by Set1. Set1 is a large protein bearing a conserved RNA recognition motif in addition to its catalytic C-terminal SET domain. The SET and RRM domains are conserved in Set1 orthologs from yeast to humans. Set1 belongs to a complex of 8 proteins, also showing a striking conservation, most subunits being required to efficiently catalyze methylation of H3K4. The deletion of SET1 is not lethal but has pleiotropic phenotypes. It affects growth, transcriptional activation, repression and elongation, telomere length regulation, telomeric position effect, rDNA silencing, meiotic differentiation, DNA repair, chromosome segregation, and cell wall organization. In this review, we discuss the regulation of H3K4 methylation and try to link Set1 activity with the multiple phenotypes displayed by cells lacking Set1. We also suggest that Set1 may have multiple targets.
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Affiliation(s)
- Pierre-Marie Dehé
- Instabilité du Génome et Cancerogénèse (IGC), CNRS, 31 chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
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18
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Zhang P, Dilley C, Mattson MP. DNA damage responses in neural cells: Focus on the telomere. Neuroscience 2007; 145:1439-48. [PMID: 17207936 PMCID: PMC1924472 DOI: 10.1016/j.neuroscience.2006.11.052] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Revised: 11/20/2006] [Accepted: 11/22/2006] [Indexed: 01/24/2023]
Abstract
Postmitotic neurons must survive for the entire life of the organism and be able to respond adaptively to adverse conditions of oxidative and genotoxic stress. Unrepaired DNA damage can trigger apoptosis of neurons which is typically mediated by the ataxia telangiectasia mutated (ATM)-p53 pathway. As in all mammalian cells, telomeres in neurons consist of TTAGGG DNA repeats and several associated proteins that form a nucleoprotein complex that prevents chromosome ends from being recognized as double strand breaks. Proteins that stabilize telomeres include TRF1 and TRF2, and proteins known to play important roles in DNA damage responses and DNA repair including ATM, Werner and the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs). We have been performing studies of developing and adult neurons aimed at understanding the effects of global and telomere-directed DNA damage responses in neuronal plasticity and survival in the contexts of aging and neurodegenerative disorders. Deficits in specific DNA repair proteins, including DNA-PKcs and uracil DNA glycosylase (UDG), render neurons vulnerable to adverse conditions of relevance to the pathogenesis of neurodegenerative disorders such as Alzheimer's disease and stroke. Similarly, early postmitotic neurons with reduced telomerase activity exhibit accentuated responses to DNA damage and are prone to apoptosis demonstrating a pivotal role for telomere maintenance in both mitotic cells and postmitotic neurons. Our recent findings suggest key roles for TRF2 in regulating the differentiation and survival of neurons. TRF2 affects cell survival and differentiation by modulating DNA damage pathways, and gene expression. A better understanding of the molecular mechanisms by which neurons respond to global and telomere-specific DNA damage may reveal novel strategies for prevention and treatment of neurodegenerative disorders. Indeed, work in this and other laboratories has shown that dietary folic acid can protect neurons against Alzheimer's disease by keeping homocysteine levels low and thereby minimizing the misincorporation of uracil into DNA in neurons.
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Affiliation(s)
- P Zhang
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
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Dellaire G, Ching RW, Ahmed K, Jalali F, Tse KCK, Bristow RG, Bazett-Jones DP. Promyelocytic leukemia nuclear bodies behave as DNA damage sensors whose response to DNA double-strand breaks is regulated by NBS1 and the kinases ATM, Chk2, and ATR. ACTA ACUST UNITED AC 2006; 175:55-66. [PMID: 17030982 PMCID: PMC2064496 DOI: 10.1083/jcb.200604009] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The promyelocytic leukemia (PML) nuclear body (NB) is a dynamic subnuclear compartment that is implicated in tumor suppression, as well as in the transcription, replication, and repair of DNA. PML NB number can change during the cell cycle, increasing in S phase and in response to cellular stress, including DNA damage. Although topological changes in chromatin after DNA damage may affect the integrity of PML NBs, the molecular or structural basis for an increase in PML NB number has not been elucidated. We demonstrate that after DNA double-strand break induction, the increase in PML NB number is based on a biophysical process, as well as ongoing cell cycle progression and DNA repair. PML NBs increase in number by a supramolecular fission mechanism similar to that observed in S-phase cells, and which is delayed or inhibited by the loss of function of NBS1, ATM, Chk2, and ATR kinase. Therefore, an increase in PML NB number is an intrinsic element of the cellular response to DNA damage.
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Affiliation(s)
- Graham Dellaire
- The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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20
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Roscic A, Möller A, Calzado MA, Renner F, Wimmer VC, Gresko E, Lüdi KS, Schmitz ML. Phosphorylation-dependent control of Pc2 SUMO E3 ligase activity by its substrate protein HIPK2. Mol Cell 2006; 24:77-89. [PMID: 17018294 DOI: 10.1016/j.molcel.2006.08.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 07/04/2006] [Accepted: 08/04/2006] [Indexed: 11/24/2022]
Abstract
Sumoylation serves to control key cellular functions, but the regulation of SUMO E3 ligase activity is largely unknown. Here we show that the polycomb group protein Pc2 binds to and colocalizes with homeodomain interacting protein kinase 2 (HIPK2) and serves as a SUMO E3 ligase for this kinase. DNA damage-induced HIPK2 directly phosphorylates Pc2 at multiple sites, which in turn controls Pc2 sumoylation and intranuclear localization. Inducible phosphorylation of Pc2 at threonine 495 is required for its ability to increase HIPK2 sumoylation in response to DNA damage, thereby establishing an autoregulatory feedback loop between a SUMO substrate and its cognate E3 ligase. Sumoylation enhances the ability of HIPK2 to mediate transcriptional repression, thus providing a mechanistic link for DNA damage-induced transcriptional silencing.
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Affiliation(s)
- Ana Roscic
- Institute of Biochemistry, Medical Faculty, Friedrichstrasse 24, Justus-Liebig-University, D-35392 Giessen, Germany
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21
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Costelloe T, Fitzgerald J, Murphy NJ, Flaus A, Lowndes NF. Chromatin modulation and the DNA damage response. Exp Cell Res 2006; 312:2677-86. [PMID: 16893724 DOI: 10.1016/j.yexcr.2006.06.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 06/19/2006] [Indexed: 11/22/2022]
Abstract
The ability to sense and respond appropriately to genetic lesions is vitally important to maintain the integrity of the genome. Emerging evidence indicates that various modulations to chromatin structure are centrally important to many aspects of the DNA damage response (DDR). Here, we discuss recently described roles for specific post-translational covalent modifications to histone proteins, as well as ATP-dependent chromatin remodelling, in DNA damage signalling and repair of DNA double strand breaks.
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Affiliation(s)
- Thomas Costelloe
- Genome Stability Laboratory, Department of Biochemistry and National Centre for Biomedical Engineering Science, National University of Ireland, Galway
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