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ABSTRACT: Caffeine is a widely used inhibitor of the protein kinases that play a central role in the DNA damage response. We used chemical inhibitors and genetically deficient mouse embryonic stem cell lines to study the role of DNA damage response in stable integration of the transfected DNA and found that caffeine rapidly, efficiently and reversibly inhibited homologous integration of the transfected DNA as measured by several homologous recombination-mediated gene-targeting assays. Biochemical and structural biology experiments revealed that caffeine interfered with a pivotal step in homologous recombination, homologous joint molecule formation, through increasing interactions of the RAD51 nucleoprotein filament with non-homologous DNA. Our results suggest that recombination pathways dependent on extensive homology search are caffeine-sensitive and stress the importance of considering direct checkpoint-independent mechanisms in the interpretation of the effects of caffeine on DNA repair.
Nucleic Acids Research 05/2013; · 8.03 Impact Factor
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Arjan F Theil,
Julie Nonnekens,
Barbara Steurer,
Pierre-Olivier Mari,
Jan de Wit,
Charlène Lemaitre,
Jurgen A Marteijn,
Anja Raams,
Alex Maas,
Marcel Vermeij, Jeroen Essers,
Jan H J Hoeijmakers,
Giuseppina Giglia-Mari,
Wim Vermeulen
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ABSTRACT: The ten-subunit transcription factor IIH (TFIIH) plays a crucial role in transcription and nucleotide excision repair (NER). Inactivating mutations in the smallest 8-kDa TFB5/TTDA subunit cause the neurodevelopmental progeroid repair syndrome trichothiodystrophy A (TTD-A). Previous studies have shown that TTDA is the only TFIIH subunit that appears not to be essential for NER, transcription, or viability. We studied the consequences of TTDA inactivation by generating a Ttda knock-out (Ttda(-/-) ) mouse-model resembling TTD-A patients. Unexpectedly, Ttda(-/-) mice were embryonic lethal. However, in contrast to full disruption of all other TFIIH subunits, viability of Ttda(-/-) cells was not affected. Surprisingly, Ttda(-/-) cells were completely NER deficient, contrary to the incomplete NER deficiency of TTD-A patient-derived cells. We further showed that TTD-A patient mutations only partially inactivate TTDA function, explaining the relatively mild repair phenotype of TTD-A cells. Moreover, Ttda(-/-) cells were also highly sensitive to oxidizing agents. These findings reveal an essential role of TTDA for life, nucleotide excision repair, and oxidative DNA damage repair and identify Ttda(-/-) cells as a unique class of TFIIH mutants.
PLoS Genetics 04/2013; 9(4):e1003431. · 8.69 Impact Factor
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Judith W J Bergs,
Przemek M Krawczyk,
Tijana Borovski,
Rosemarie Ten Cate,
Hans M Rodermond,
Jan Stap,
Jan Paul Medema,
Jaap Haveman, Jeroen Essers,
Chris van Bree,
Lukas J A Stalpers,
Roland Kanaar,
Jacob A Aten,
Nicolaas A P Franken
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ABSTRACT: In S and G2 phase mammalian cells DNA double strand breaks (DSBs) can potentially be repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ). Results of several studies suggest that these two mechanistically distinct repair pathways can compete for DNA ends. Because HR and NHEJ differ with respect to error susceptibility, generation of chromosome rearrangements, which are potentially carcinogenic products of DSB repair, may depend on the pathway choice. To investigate this hypothesis, the influence of HR and NHEJ inhibition on the frequencies of chromosome aberrations in G2 phase cells was investigated. SW-1573 and RKO cells were treated with mild (41°C) hyperthermia in order to disable HR and/or NU7441/cisplatin to inactivate NHEJ and frequencies of chromosomal fragments (resulting from unrepaired DSBs) and translocations (products of erroneous DSB rejoining) were studied using premature chromosome condensation (PCC) combined with fluorescence in situ hybridization (FISH). It is shown here that temporary inhibition of HR by hyperthermia results in increased frequency of ionizing-radiation (IR)-induced chromosomal translocations and that this effect is abrogated by NU7441- or cisplatin-mediated inhibition of NHEJ. The results suggest that in the absence of HR, DSB repair is shifted to the error-prone NHEJ pathway resulting in increased frequencies of chromosomal rearrangements. These results might be of consequence for clinical cancer treatment approaches that aim at inhibition of one or more DSB repair pathways.
DNA repair 12/2012; · 4.20 Impact Factor
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Adva Levy-Barda,
Yaniv Lerenthal,
Anthony J Davis,
Young Min Chung, Jeroen Essers,
Zhengping Shao,
Nicole van Vliet,
David J Chen,
Mickey C-T Hu,
Roland Kanaar,
Yael Ziv,
Yosef Shiloh
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ABSTRACT: The DNA damage response (DDR) is a complex signaling network that leads to damage repair while modulating numerous cellular processes. DNA double-strand breaks (DSBs), a highly cytotoxic DNA lesion, activate this system most vigorously. The DSB response network is orchestrated by the ATM protein kinase, which phosphorylates key players in its various branches. Proteasome-mediated protein degradation plays an important role in the proteome dynamics following DNA damage induction. Here, we identify the nuclear proteasome activator PA28γ (REGγ; PSME3) as a novel DDR player. PA28γ depletion leads to cellular radiomimetic sensitivity and a marked delay in DSB repair. Specifically, PA28γ deficiency abrogates the balance between the two major DSB repair pathways--nonhomologous end-joining and homologous recombination repair. Furthermore, PA28γ is found to be an ATM target, being recruited to the DNA damage sites and required for rapid accumulation of proteasomes at these sites. Our data reveal a novel ATM-PA28γ-proteasome axis of the DDR that is required for timely coordination of DSB repair.
Cell cycle (Georgetown, Tex.) 12/2011; 10(24):4300-10. · 5.36 Impact Factor
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Reinier A Boon,
Timon Seeger,
Susanne Heydt,
Ariane Fischer,
Eduard Hergenreider,
Anton J G Horrevoets,
Manlio Vinciguerra,
Nadia Rosenthal,
Sergio Sciacca,
Michele Pilato,
Paula van Heijningen, Jeroen Essers,
Ralf P Brandes,
Andreas M Zeiher,
Stefanie Dimmeler
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ABSTRACT: Aging represents a major risk factor for coronary artery disease and aortic aneurysm formation. MicroRNAs (miRs) have emerged as key regulators of biological processes, but their role in age-associated vascular pathologies is unknown.
We aim to identify miRs in the vasculature that are regulated by age and play a role in age-induced vascular pathologies.
Expression profiling of aortic tissue of young versus old mice identified several age-associated miRs. Among the significantly regulated miRs, the increased expression of miR-29 family members was associated with a profound downregulation of numerous extracellular matrix (ECM) components in aortas of aged mice, suggesting that this miR family contributes to ECM loss, thereby sensitizing the aorta for aneurysm formation. Indeed, miR-29 expression was significantly induced in 2 experimental models for aortic dilation: angiotensin II-treated aged mice and genetically induced aneurysms in Fibulin-4(R/R) mice. More importantly, miR-29b levels were profoundly increased in biopsies of human thoracic aneurysms, obtained from patients with either bicuspid (n=79) or tricuspid aortic valves (n=30). Finally, LNA-modified antisense oligonucleotide-mediated silencing of miR-29 induced ECM expression and inhibited angiotensin II-induced dilation of the aorta in mice.
In conclusion, miR-29-mediated downregulation of ECM proteins may sensitize the aorta to the formation of aneurysms in advanced age. Inhibition of miR-29 in vivo abrogates aortic dilation in mice, suggesting that miR-29 may represent a novel molecular target to augment matrix synthesis and maintain vascular wall structural integrity.
Circulation Research 09/2011; 109(10):1115-9. · 9.49 Impact Factor
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ABSTRACT: Ultraviolet (UV) radiation-induced DNA lesions can be efficiently repaired by nucleotide excision repair (NER). However, NER is less effective during replication of UV-damaged chromosomes. In contrast, translesion DNA synthesis (TLS) and homologous recombination (HR) are capable of dealing with lesions in replicating DNA. The core HR protein in mammalian cells is the strand exchange protein RAD51, which is aided by numerous proteins, including RAD54. We used RAD54 as a cellular marker for HR to study the response of mammalian embryonic stem (ES) cells to UV irradiation. In contrast to yeast, ES cells lacking RAD54 are not UV sensitive. Here we show that the requirement for mammalian RAD54 is masked by active NER. By genetically inactivating NER and HR through disruption of the Xpa and Rad54 genes, respectively, we demonstrate the contribution of HR to chromosomal integrity upon UV irradiation. We demonstrate using chromosome fiber analysis at the individual replication fork level, that HR activity is important for the restart of DNA replication after induction of DNA damage by UV-light in NER-deficient cells. Furthermore, our data reveal RAD54-dependent and -independent contributions of HR to the cellular sensitivity to UV-light, and they uncover that RAD54 can compensate for the loss of TLS polymerase η with regard to UV-light sensitivity. In conclusion, we show that HR is important for the progression of UV-stalled replication forks in ES cells, and that protection of the fork is an interplay between HR and TLS.
DNA repair 08/2011; 10(11):1095-105. · 4.20 Impact Factor
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ABSTRACT: Thoracic aortic aneurysms (TAAs) are a potential life-threatening disease with limited pharmacological treatment options. Current treatment options are aimed at lowering aortic hemodynamic stress, predominantly with β-adrenoceptor blockers. Increasing evidence supports a role for the renin-angiotensin system (RAS) in aneurysm development. RAS blockade would not only lower blood pressure, but might also target the molecular pathways involved in aneurysm formation, in particular the transforming growth factor-β and extracellular signal-regulated kinase 1/2 pathways. Indeed, the angiotensin II type 1 (AT₁) receptor blocker losartan was effective in lowering aortic root growth in mice and patients with Marfan's syndrome. RAS inhibition (currently possible at 3 levels, i.e. renin, ACE and the AT₁ receptor) is always accompanied by a rise in renin due to interference with the negative feedback loop between renin and angiotensin II. Only during AT₁ receptor blockade will this result in stimulation of the non-blocked angiotensin II type 2 (AT₂) receptor. This review summarizes the clinical aspects of TAAs, provides an overview of the current mouse models for TAAs, and focuses on the RAS as a new target for TAA treatment, discussing in particular the possibility that AT₂ receptor stimulation might be crucial in this regard. If true, this would imply that AT₁ receptor blockers (and not ACE inhibitors or renin inhibitors) should be the preferred treatment option for TAAs.
Pharmacology [?] Therapeutics 07/2011; 131(1):50-60. · 8.56 Impact Factor
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Przemek M Krawczyk,
Berina Eppink, Jeroen Essers,
Jan Stap,
Hans Rodermond,
Hanny Odijk,
Alex Zelensky,
Chris van Bree,
Lukas J Stalpers,
Marrije R Buist,
Thomas Soullié,
Joost Rens,
Hence J M Verhagen,
Mark J O'Connor,
Nicolaas A P Franken,
Timo L M Ten Hagen,
Roland Kanaar,
Jacob A Aten
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ABSTRACT: Defective homologous recombination (HR) DNA repair imposed by BRCA1 or BRCA2 deficiency sensitizes cells to poly (ADP-ribose) polymerase (PARP)-1 inhibition and is currently exploited in clinical treatment of HR-deficient tumors. Here we show that mild hyperthermia (41-42.5 °C) induces degradation of BRCA2 and inhibits HR. We demonstrate that hyperthermia can be used to sensitize innately HR-proficient tumor cells to PARP-1 inhibitors and that this effect can be enhanced by heat shock protein inhibition. Our results, obtained from cell lines and in vivo tumor models, enable the design of unique therapeutic strategies involving localized on-demand induction of HR deficiency, an approach that we term induced synthetic lethality.
Proceedings of the National Academy of Sciences 06/2011; 108(24):9851-6. · 9.68 Impact Factor
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ABSTRACT: Rad54, a member of the SWI/SNF protein family of DNA-dependent ATPases, repairs DNA double-strand breaks (DSBs) through homologous recombination. Here we demonstrate that Rad54 is required for the timely accumulation of the homologous recombination proteins Rad51 and Brca2 at DSBs. Because replication protein A and Nbs1 accumulation is not affected by Rad54 depletion, Rad54 is downstream of DSB resection. Rad54-mediated Rad51 accumulation does not require Rad54's ATPase activity. Thus, our experiments demonstrate that SWI/SNF proteins may have functions independent of their ATPase activity. However, quantitative real-time analysis of Rad54 focus formation indicates that Rad54's ATPase activity is required for the disassociation of Rad54 from DNA and Rad54 turnover at DSBs. Although the non-DNA-bound fraction of Rad54 reversibly interacts with a focus, independent of its ATPase status, the DNA-bound fraction is immobilized in the absence of ATP hydrolysis by Rad54. Finally, we show that ATP hydrolysis by Rad54 is required for the redistribution of DSB repair sites within the nucleus.
The Journal of Cell Biology 02/2011; 192(5):735-50. · 10.26 Impact Factor
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Els Moltzer,
Luuk te Riet,
Sigrid M A Swagemakers,
Paula M van Heijningen,
Marcel Vermeij,
Richard van Veghel,
Angelique M Bouhuizen,
Joep H M van Esch,
Stephanie Lankhorst,
Natasja W M Ramnath,
Monique C de Waard,
Dirk J Duncker,
Peter J van der Spek,
Ellen V Rouwet,
A H Jan Danser, Jeroen Essers
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ABSTRACT: Medial degeneration is a key feature of aneurysm disease and aortic dissection. In a murine aneurysm model we investigated the structural and functional characteristics of aortic wall degeneration in adult fibulin-4 deficient mice and the potential therapeutic role of the angiotensin (Ang) II type 1 (AT(1)) receptor antagonist losartan in preventing aortic media degeneration. Adult mice with 2-fold (heterozygous Fibulin-4(+/R)) and 4-fold (homozygous Fibulin-4(R/R)) reduced expression of fibulin-4 displayed the histological features of cystic media degeneration as found in patients with aneurysm or dissection, including elastin fiber fragmentation, loss of smooth muscle cells, and deposition of ground substance in the extracellular matrix of the aortic media. The aortic contractile capacity, determined by isometric force measurements, was diminished, and was associated with dysregulation of contractile genes as shown by aortic transcriptome analysis. These structural and functional alterations were accompanied by upregulation of TGF-β signaling in aortas from fibulin-4 deficient mice, as identified by genome-scaled network analysis as well as by immunohistochemical staining for phosphorylated Smad2, an intracellular mediator of TGF-β. Tissue levels of Ang II, a regulator of TGF-β signaling, were increased. Prenatal treatment with the AT(1) receptor antagonist losartan, which blunts TGF-β signaling, prevented elastic fiber fragmentation in the aortic media of newborn Fibulin-4(R/R) mice. Postnatal losartan treatment reduced haemodynamic stress and improved lifespan of homozygous knockdown fibulin-4 animals, but did not affect aortic vessel wall structure. In conclusion, the AT(1) receptor blocker losartan can prevent aortic media degeneration in a non-Marfan syndrome aneurysm mouse model. In established aortic aneurysms, losartan does not affect aortic architecture, but does improve survival. These findings may extend the potential therapeutic application of inhibitors of the renin-angiotensin system to the preventive treatment of aneurysm disease.
PLoS ONE 01/2011; 6(8):e23411. · 4.09 Impact Factor
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ABSTRACT: MOTIVATION: Complete, accurate and reproducible analysis of intracellular foci from fluorescence microscopy image sequences of live cells requires full automation of all processing steps involved: cell segmentation and tracking followed by foci segmentation and pattern analysis. Integrated systems for this purpose are lacking. RESULTS: Extending our previous work in cell segmentation and tracking, we developed a new system for performing fully automated analysis of fluorescent foci in single cells. The system was validated by applying it to two common tasks: intracellular foci counting (in DNA damage repair experiments) and cell-phase identification based on foci pattern analysis (in DNA replication experiments). Experimental results show that the system performs comparably to expert human observers. Thus, it may replace tedious manual analyses for the considered tasks, and enables high-content screening. Availability and implementation: The described system was implemented in MATLAB (The MathWorks, Inc., USA) and compiled to run within the MATLAB environment. The routines together with four sample datasets are available at http://celmia.bigr.nl/. The software is planned for public release, free of charge for non-commercial use, after publication of this article.
Bioinformatics 10/2010; 26(19):2424-30. · 5.47 Impact Factor
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Eric L Kaijzel,
Paula M van Heijningen,
Piotr A Wielopolski,
Marcel Vermeij,
Gerben A Koning,
Wiggert A van Cappellen,
Ivo Que,
Alan Chan,
Jouke Dijkstra,
Natasja W M Ramnath,
Lukas J A C Hawinkels,
Monique R Bernsen,
Clemens W G M Löwik, Jeroen Essers
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ABSTRACT: We imaged the protease activity of matrix metalloproteinases (MMPs) upregulated during aneurysm formation, using protease-activatable near-infrared fluorescence probes. We tested whether these protease-activatable sensors can directly report the in vivo activity of the key biomarkers in aneurysm, using our genetically modified fibulin-4 mouse models for aneurysm formation. Mice homozygous for the fibulin-4 reduced-expression allele (fibulin-4(R/R)) show dilatation of the ascending aorta and a tortuous, stiffened aorta resulting from disorganized elastic fiber networks. Strikingly, even a moderate reduction in expression of fibulin-4 in the heterozygous fibulin-4(+/R) mice occasionally results in modest aneurysm formation.
Aorta transcriptome and protein expression analysis of fibulin-4(+/R) and fibulin-4(R/R) animals identified excessive transforming growth factor-β signaling as the critical event in the pathogenesis of aneurysm formation. To determine whether a perturbed elastin lamellar structure arose from induction of transforming growth factor-β-regulated MMPs, we performed gelatin zymography and used a protease-activatable near-infrared fluorescence probe to monitor and quantify MMP upregulation in animals, using various in vivo optical imaging modules and coregistration of the fluorescence signal with CT images of the same animals. Gelatin zymography demonstrated a significant increase in the presence of the active form of MMP-9 in the aortic arch of fibulin-4(R/R) mice. In vivo analysis of MMP upregulation using the near-infrared fluorescence probe and subsequent isosurface concentration mapping from reconstructed tomographic images from fibulin-4(+/R) and fibulin-4(R/R) mice revealed a graded increase in activation of MMPs within the aneurysmal lesions.
We aimed to develop molecular imaging procedures for faster, earlier, and easier recognition of aortic aneurysms. We show that in vivo coregistration of MMP activity by noninvasive tomographic imaging methods allows the detection of increased MMP activity, even before the aneurysm has actually formed.
Circulation Cardiovascular Imaging 09/2010; 3(5):567-77. · 5.94 Impact Factor
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IEEE transactions on medical imaging 06/2010; 29(6):1331. · 3.54 Impact Factor
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ABSTRACT: Cell segmentation and tracking in time-lapse fluorescence microscopy images is a task of fundamental importance in many biological studies on cell migration and proliferation. In recent years, level sets have been shown to provide a very appropriate framework for this purpose, as they are well suited to capture topological changes occurring during mitosis, and they easily extend to higher dimensional image data. This model evolution approach has also been extended to deal with many cells concurrently. Notwithstanding its high potential, the multiple-level-set method suffers from a number of shortcomings, which limit its applicability to a larger variety of cell biological imaging studies. In this paper, we propose several modifications and extensions to the coupled-active-surfaces algorithm, which considerably improve its robustness and applicability. Our algorithm was validated by comparing it to the original algorithm and two other cell segmentation algorithms. For the evaluation, four real fluorescence microscopy image datasets were used, involving different cell types and labelings that are representative of a large range of biological experiments. Improved tracking performance in terms of precision (up to 11%), recall (up to 8%), ability to correctly capture all cell division events, and computation time (up to nine times reduction) is achieved.
IEEE transactions on medical imaging. 03/2010; 29(3):852-67.
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ABSTRACT: Non-homologous end-joining (NHEJ) and homologous recombination repair (HRR), contribute to repair ionizing radiation (IR)-induced DNA double-strand breaks (DSBs). Mre11 binding to DNA is the first step for activating HRR and Ku binding to DNA is the first step for initiating NHEJ. High-linear energy transfer (LET) IR (such as high energy charged particles) killing more cells at the same dose as compared with low-LET IR (such as X or gamma rays) is due to inefficient NHEJ. However, these phenomena have not been demonstrated at the animal level and the mechanism by which high-LET IR does not affect the efficiency of HRR remains unclear. In this study, we showed that although wild-type and HRR-deficient mice or DT40 cells are more sensitive to high-LET IR than to low-LET IR, NHEJ deficient mice or DT40 cells are equally sensitive to high- and low-LET IR. We also showed that Mre11 and Ku respond differently to shorter DNA fragments in vitro and to the DNA from high-LET irradiated cells in vivo. These findings provide strong evidence that the different DNA DSB binding properties of Mre11 and Ku determine the different efficiencies of HRR and NHEJ to repair high-LET radiation induced DSBs.
Nucleic Acids Research 02/2010; 38(10):3245-51. · 8.03 Impact Factor
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IEEE Trans. Med. Imaging. 01/2010; 29:852-867.
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ABSTRACT: When DNA is damaged in cells progressing through S phase, replication blockage can be avoided by TLS (Translesion DNA synthesis). This is an auxiliary replication mechanism that relies on the function of specialized polymerases that accomplish DNA damage bypass. Intriguingly, recent evidence has linked TLS polymerases to processes that can also take place outside S phase such as nucleotide excision repair (NER). Here we show that Pol eta is recruited to UV-induced DNA lesions in cells outside S phase including cells permanently arrested in G(1). This observation was confirmed by different strategies including global UV irradiation, local UV irradiation and local multi-photon laser irradiation of single nuclei in living cells. The potential connection between Pol eta recruitment to DNA lesions outside S phase and NER was further evaluated. Interestingly, the recruitment of Pol eta to damage sites outside S phase did not depend on active NER, as UV-induced focus formation occurred normally in XPA, XPG and XPF deficient fibroblasts. Our data reveals that the re-localization of the TLS polymerase Pol eta to photo-lesions might be temporally and mechanistically uncoupled from replicative DNA synthesis and from DNA damage processing.
Cell cycle (Georgetown, Tex.) 10/2009; 8(20):3340-8. · 5.36 Impact Factor
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ABSTRACT: Nijmegen breakage syndrome (NBS) is characterized by genome instability and cancer predisposition. NBS patients contain a mutation in the NBS1 gene, which encodes the NBS1 component of the DNA double-strand break (DSB) response complex MRE11/RAD50/NBS1. To investigate the NBS phenotype in more detail, we combined the mouse mimic of the most common patient mutation (Nbs1(Delta B/DeltaB)) with a Rad54 null mutation, which diminishes homologous recombination. Double mutant cells were particularly sensitive to treatments that cause single strand breaks (SSBs), presumably because these SSBs can be converted into detrimental DSBs upon passage of a replication fork. The persistent presence of nuclear RAD51 foci and increased levels of chromatid type breaks in metaphase spreads indicated that replication-associated DSBs are repaired inefficiently in the double mutant cells. We conclude that Nbs1 and Rad54 function cooperatively, but in separate pathways to counteract this type of DNA damage and discuss mechanistic implications of these findings.
DNA repair 09/2009; 8(12):1363-70. · 4.20 Impact Factor
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Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, USA, June 28 - July 1, 2009; 01/2009
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ABSTRACT: Ataxia-telangiectasia is a pleiotropic genomic instability disorder caused by lack or inactivation of the ATM protein kinase and characterized by progressive ataxia, immunodeficiency, ionizing radiation sensitivity and cancer predisposition. ATM mobilizes the cellular response to DNA double strand breaks by phosphorylating key players in this response. Double strand breaks are repaired by either nonhomologous end-joining or homologous recombination (HR) in which the Rad54 and Rad54B paralogs function. Here, we investigated the functional relationships between Atm and the Rad54 proteins by constructing compound genotypes in mice. Mouse strains were generated that combined inactivation of the Atm, Rad54 and Rad54B genes. All mutant genotypes were viable, but obtained at sub-Mendelian ratios. Double mutants for Atm and each Rad54 paralog exhibited reduced body weight and shorter lifespan, but no distinct neurological phenotype. Concomitant inactivation of ATM and Rad54 did not increase IR sensitivity; however, the triple Atm/Rad54/Rad54B mutant exhibited a significant IR hypersensitivity compared to the other genotypes. Interestingly, Atm-/- animals also exhibited hypersensitivity to the crosslinking agent mitomycin C, which was increased by deficiency of either one of the Rad54 paralogs. Our results reveal a differential interaction of the ATM-mediated DNA damage response and Rad54 paralog-mediated HR depending on the DNA damaging agent that initiates the response.
DNA Repair 01/2009; 8(2):253-61. · 4.14 Impact Factor
