Relevant bibliographies by topics / DNA double-strand breaks, Sae2

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Academic literature on the topic 'DNA double-strand breaks, Sae2'

Author: Grafiati
Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "DNA double-strand breaks, Sae2"

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Yu, Tai-Yuan, Michael T. Kimble, and Lorraine S. Symington. "Sae2 antagonizes Rad9 accumulation at DNA double-strand breaks to attenuate checkpoint signaling and facilitate end resection." Proceedings of the National Academy of Sciences 115, no. 51 (December 3, 2018): E11961—E11969. http://dx.doi.org/10.1073/pnas.1816539115.

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The Mre11-Rad50-Xrs2NBS1 complex plays important roles in the DNA damage response by activating the Tel1ATM kinase and catalyzing 5′–3′ resection at DNA double-strand breaks (DSBs). To initiate resection, Mre11 endonuclease nicks the 5′ strands at DSB ends in a reaction stimulated by Sae2CtIP. Accordingly, Mre11-nuclease deficient (mre11-nd) and sae2Δ mutants are expected to exhibit similar phenotypes; however, we found several notable differences. First, sae2Δ cells exhibit greater sensitivity to genotoxins than mre11-nd cells. Second, sae2Δ is synthetic lethal with sgs1Δ, whereas the mre11-nd sgs1Δ mutant is viable. Third, Sae2 attenuates the Tel1-Rad53CHK2 checkpoint and antagonizes Rad953BP1 accumulation at DSBs independent of Mre11 nuclease. We show that Sae2 competes with other Tel1 substrates, thus reducing Rad9 binding to chromatin and to Rad53. We suggest that persistent Sae2 binding at DSBs in the mre11-nd mutant counteracts the inhibitory effects of Rad9 and Rad53 on Exo1 and Dna2-Sgs1–mediated resection, accounting for the different phenotypes conferred by mre11-nd and sae2Δ mutations. Collectively, these data show a resection initiation independent role for Sae2 at DSBs by modulating the DNA damage checkpoint.
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Fu, Qiong, Julia Chow, Kara A. Bernstein, Nodar Makharashvili, Sucheta Arora, Chia-Fang Lee, Maria D. Person, Rodney Rothstein, and Tanya T. Paull. "Phosphorylation-Regulated Transitions in an Oligomeric State Control the Activity of the Sae2 DNA Repair Enzyme." Molecular and Cellular Biology 34, no. 5 (December 16, 2013): 778–93. http://dx.doi.org/10.1128/mcb.00963-13.

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In the DNA damage response, many repair and signaling molecules mobilize rapidly at the sites of DNA double-strand breaks. This network of immediate responses is regulated at the level of posttranslational modifications that control the activation of DNA processing enzymes, protein kinases, and scaffold proteins to coordinate DNA repair and checkpoint signaling. Here we investigated the DNA damage-induced oligomeric transitions of the Sae2 protein, an important enzyme in the initiation of DNA double-strand break repair. Sae2 is a target of multiple phosphorylation events, which we identified and characterizedin vivoin the budding yeastSaccharomyces cerevisiae. Both cell cycle-dependent and DNA damage-dependent phosphorylation sites in Sae2 are important for the survival of DNA damage, and the cell cycle-regulated modifications are required to prime the damage-dependent events. We found that Sae2 exists in the form of inactive oligomers that are transiently released into smaller active units by this series of phosphorylations. DNA damage also triggers removal of Sae2 through autophagy and proteasomal degradation, ensuring that active Sae2 is present only transiently in cells. Overall, this analysis provides evidence for a novel type of protein regulation where the activity of an enzyme is controlled dynamically by posttranslational modifications that regulate its solubility and oligomeric state.
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Yu, Tai-Yuan, Valerie E. Garcia, and Lorraine S. Symington. "CDK and Mec1/Tel1-catalyzed phosphorylation of Sae2 regulate different responses to DNA damage." Nucleic Acids Research 47, no. 21 (September 25, 2019): 11238–49. http://dx.doi.org/10.1093/nar/gkz814.

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Abstract Sae2 functions in the DNA damage response by controlling Mre11-Rad50-Xrs2 (MRX)-catalyzed end resection, an essential step for homology-dependent repair of double-strand breaks (DSBs), and by attenuating DNA damage checkpoint signaling. Phosphorylation of Sae2 by cyclin-dependent kinase (CDK1/Cdc28) activates the Mre11 endonuclease, while the physiological role of Sae2 phosphorylation by Mec1 and Tel1 checkpoint kinases is not fully understood. Here, we compare the phenotype of sae2 mutants lacking the main CDK (sae2-S267A) or Mec1 and Tel1 phosphorylation sites (sae2-5A) with sae2Δ and Mre11 nuclease defective (mre11-nd) mutants. The phosphorylation-site mutations confer DNA damage sensitivity, but not to the same extent as sae2Δ. The sae2-S267A mutation is epistatic to mre11-nd for camptothecin (CPT) sensitivity and synergizes with sgs1Δ, whereas sae2-5A synergizes with mre11-nd and exhibits epistasis with sgs1Δ. We find that attenuation of checkpoint signaling by Sae2 is mostly independent of Mre11 endonuclease activation but requires Mec1 and Tel1-dependent phosphorylation of Sae2. These results support a model whereby CDK-catalyzed phosphorylation of Sae2 activates resection via Mre11 endonuclease, whereas Sae2 phosphorylation by Mec1 and Tel1 promotes resection by the Dna2-Sgs1 and Exo1 pathways indirectly by dampening the DNA damage response.
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Cannavo, Elda, Giordano Reginato, and Petr Cejka. "Stepwise 5′ DNA end-specific resection of DNA breaks by the Mre11-Rad50-Xrs2 and Sae2 nuclease ensemble." Proceedings of the National Academy of Sciences 116, no. 12 (February 28, 2019): 5505–13. http://dx.doi.org/10.1073/pnas.1820157116.

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To repair DNA double-strand breaks by homologous recombination, the 5′-terminated DNA strands must first be resected to produce 3′ overhangs. Mre11 fromSaccharomyces cerevisiaeis a 3′ → 5′ exonuclease that is responsible for 5′ end degradation in vivo. Using plasmid-length DNA substrates and purified recombinant proteins, we show that the combined exonuclease and endonuclease activities of recombinant MRX-Sae2 preferentially degrade the 5′-terminated DNA strand, which extends beyond the vicinity of the DNA end. Mechanistically, Rad50 restricts the Mre11 exonuclease in an ATP binding-dependent manner, preventing 3′ end degradation. Phosphorylated Sae2, along with stimulating the MRX endonuclease as shown previously, also overcomes this inhibition to promote the 3′ → 5′ exonuclease of MRX, which requires ATP hydrolysis by Rad50. Our results support a model in which MRX-Sae2 catalyzes 5′-DNA end degradation by stepwise endonucleolytic DNA incisions, followed by exonucleolytic 3′ → 5′ degradation of the individual DNA fragments. This model explains how both exonuclease and endonuclease activities of Mre11 functionally integrate within the MRX-Sae2 ensemble to resect 5′-terminated DNA.
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Chen, Huan, Roberto A. Donnianni, Naofumi Handa, Sarah K. Deng, Julyun Oh, Leonid A. Timashev, Stephen C. Kowalczykowski, and Lorraine S. Symington. "Sae2 promotes DNA damage resistance by removing the Mre11–Rad50–Xrs2 complex from DNA and attenuating Rad53 signaling." Proceedings of the National Academy of Sciences 112, no. 15 (March 23, 2015): E1880—E1887. http://dx.doi.org/10.1073/pnas.1503331112.

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The Mre11–Rad50–Xrs2/NBS1 (MRX/N) nuclease/ATPase complex plays structural and catalytic roles in the repair of DNA double-strand breaks (DSBs) and is the DNA damage sensor for Tel1/ATM kinase activation. Saccharomyces cerevisiae Sae2 can function with MRX to initiate 5′-3′ end resection and also plays an important role in attenuation of DNA damage signaling. Here we describe a class of mre11 alleles that suppresses the DNA damage sensitivity of sae2Δ cells by accelerating turnover of Mre11 at DNA ends, shutting off the DNA damage checkpoint and allowing cell cycle progression. The mre11 alleles do not suppress the end resection or hairpin-opening defects of the sae2Δ mutant, indicating that these functions of Sae2 are not responsible for DNA damage resistance. The purified MP110LRX complex shows reduced binding to single- and double-stranded DNA in vitro relative to wild-type MRX, consistent with the increased turnover of Mre11 from damaged sites in vivo. Furthermore, overproduction of Mre11 causes DNA damage sensitivity only in the absence of Sae2. Together, these data suggest that it is the failure to remove Mre11 from DNA ends and attenuate Rad53 kinase signaling that causes hypersensitivity of sae2Δ cells to clastogens.
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Nicolette, Matthew L., Kihoon Lee, Zhi Guo, Mridula Rani, Julia M. Chow, Sang Eun Lee, and Tanya T. Paull. "Mre11–Rad50–Xrs2 and Sae2 promote 5′ strand resection of DNA double-strand breaks." Nature Structural & Molecular Biology 17, no. 12 (November 21, 2010): 1478–85. http://dx.doi.org/10.1038/nsmb.1957.

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Rattray, Alison J., Carolyn B. McGill, Brenda K. Shafer, and Jeffrey N. Strathern. "Fidelity of Mitotic Double-Strand-Break Repair in Saccharomyces cerevisiae: A Role for SAE2/COM1." Genetics 158, no. 1 (May 1, 2001): 109–22. http://dx.doi.org/10.1093/genetics/158.1.109.

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Abstract Errors associated with the repair of DNA double-strand breaks (DSBs) include point mutations caused by misincorporation during repair DNA synthesis or novel junctions made by nonhomologous end joining (NHEJ). We previously demonstrated that DNA synthesis is ∼100-fold more error prone when associated with DSB repair. Here we describe a genetic screen for mutants that affect the fidelity of DSB repair. The substrate consists of inverted repeats of the trp1 and CAN1 genes. Recombinational repair of a site-specific DSB within the repeat yields TRP1 recombinants. Errors in the repair process can be detected by the production of canavanine-resistant (can1) mutants among the TRP1 recombinants. In wild-type cells the recombinational repair process is efficient and fairly accurate. Errors resulting in can1 mutations occur in <1% of the TRP1 recombinants and most appear to be point mutations. We isolated several mutant strains with altered fidelity of recombination. Here we characterize one of these mutants that revealed an ∼10-fold elevation in the frequency of can1 mutants among TRP1 recombinants. The gene was cloned by complementation of a coincident sporulation defect and proved to be an allele of SAE2/COM1. Physical analysis of the can1 mutants from sae2/com1 strains revealed that many were a novel class of chromosome rearrangement that could reflect break-induced replication (BIR) and NHEJ. Strains with either the mre11s-H125N or rad50s-K81I alleles had phenotypes in this assay that are similar to that of the sae2/com1Δ strain. Our data suggest that Sae2p/Com1p plays a role in ensuring that both ends of a DSB participate in a recombination event, thus avoiding BIR, possibly by regulating the nuclease activity of the Mre11p/Rad50p/Xrs2p complex.
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Akamatsu, Yufuko, Yasuto Murayama, Takatomi Yamada, Tomofumi Nakazaki, Yasuhiro Tsutsui, Kunihiro Ohta, and Hiroshi Iwasaki. "Molecular Characterization of the Role of the Schizosaccharomyces pombe nip1+/ctp1+ Gene in DNA Double-Strand Break Repair in Association with the Mre11-Rad50-Nbs1 Complex." Molecular and Cellular Biology 28, no. 11 (March 31, 2008): 3639–51. http://dx.doi.org/10.1128/mcb.01828-07.

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ABSTRACT The Schizosaccharomyces pombe nip1 +/ctp1 + gene was previously identified as an slr (synthetically lethal with rad2) mutant. Epistasis analysis indicated that Nip1/Ctp1 functions in Rhp51-dependent recombinational repair, together with the Rad32 (spMre11)-Rad50-Nbs1 complex, which plays important roles in the early steps of DNA double-strand break repair. Nip1/Ctp1 was phosphorylated in asynchronous, exponentially growing cells and further phosphorylated in response to bleomycin treatment. Overproduction of Nip1/Ctp1 suppressed the DNA repair defect of an nbs1-s10 mutant, which carries a mutation in the FHA phosphopeptide-binding domain of Nbs1, but not of an nbs1 null mutant. Meiotic DNA double-strand breaks accumulated in the nip1/ctp1 mutant. The DNA repair phenotypes and epistasis relationships of nip1/ctp1 are very similar to those of the Saccharomyces cerevisiae sae2/com1 mutant, suggesting that Nip1/Ctp1 is a functional homologue of Sae2/Com1, although the sequence similarity between the proteins is limited to the C-terminal region containing the RHR motif. We found that the RxxL and CxxC motifs are conserved in Schizosaccharomyces species and in vertebrate CtIP, originally identified as a cofactor of the transcriptional corepressor CtBP. However, these two motifs are not found in other fungi, including Saccharomyces and Aspergillus species. We propose that Nip1/Ctp1 is a functional counterpart of Sae2/Com1 and CtIP.
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Mimitou, Eleni P., and Lorraine S. Symington. "Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing." Nature 455, no. 7214 (September 21, 2008): 770–74. http://dx.doi.org/10.1038/nature07312.

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Marsella, Antonio, Elisa Gobbini, Corinne Cassani, Renata Tisi, Elda Cannavo, Giordano Reginato, Petr Cejka, and Maria Pia Longhese. "Sae2 and Rif2 regulate MRX endonuclease activity at DNA double-strand breaks in opposite manners." Cell Reports 34, no. 13 (March 2021): 108906. http://dx.doi.org/10.1016/j.celrep.2021.108906.

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Dissertations / Theses on the topic "DNA double-strand breaks, Sae2"

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GOBBINI, ELISA. "A screen for synthetic phenotypes reveals new Sae2 functions and interactions in the repair of DNA double-strand breaks." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2016. http://hdl.handle.net/10281/102381.

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Genome instability is one of the most pervasive characteristics of cancer cells and can be due to DNA repair defects and failure to arrest the cell cycle. Among the many types of DNA damage, the DNA double strand break (DSB) is one of the most severe, because it can cause mutations and chromosomal rearrangements. Generation of DSBs triggers a highly conserved mechanism, known as DNA damage checkpoint, which arrests the cell cycle until DSBs are repaired. DSBs can be repaired by homologous recombination (HR), which requires the DSB ends to be nucleolytically processed (resected) to generate single-strand DNA. In Saccharomyces cerevisiae, initiation of DSB resection requires the conserved MRX/MRN complex (Mre11-Rad50-Xrs2 in yeast; Mre11-Rad50-Nbs1 in mammals) that, together with Sae2 (CtIP in mammals), catalyzes an endonucleolytic cleavage of the 5’ strands. More extensive resection depends on two pathways: one catalyzed by the exonuclease Exo1, and a second requiring the nuclease Dna2 with the helicase Sgs1. The absence of Sae2 not only impairs DSB resection, but also causes prolonged MRX binding at the DSBs that leads to persistent Tel1 (ATM in humans)- and Rad53-dependent DNA damage checkpoint activation and cell cycle arrest. Whether this enhanced checkpoint signaling contributes to the DNA damage sensitivity and/or the resection defect of sae2∆ cells is not known. sae2∆ cells are sensitive to the alkylating agent methyl methanesulfonate (MMS) and camptothecin (CPT), which traps covalent topoisomerase I (Top1)-DNA cleavable complexes and induces DNA replication-dependent cell death. Since this sensitivity has been shown to be due to resection defect, we searched for extragenic suppressors of the sae2∆ sensitivity to CPT and MMS. By performing a genetic screen, we identify three mutant alleles (SGS1-ss, rad53-ss and tel1-ss) that suppress both the DNA damage hypersensitivity and the resection defect of sae2∆ cells. We show that Sgs1-ss mediated suppression depends on the Dna2 nuclease but not on Exo1. Furthermore, not only Sgs1-ss suppresses the resection defect of sae2∆ cells but it also increases resection efficiency compared to wild type cells. The checkpoint protein Rad9 limits the action of Sgs1/Dna2 in DSB resection by inhibiting Sgs1 binding/persistence at the DSB ends. When inhibition by Rad9 is abolished by the Sgs1‐ss mutant variant or by deletion of RAD9, the requirement for Sae2 and functional MRX in DSB resection is reduced. rad53-ss and tel1-ss mutant alleles, but also the kinase defective alleles (rad53-kd and tel1-kd), suppress both the DNA damage hypersensitivity and the resection defect of sae2∆ cells through an Sgs1-Dna2-dependent mechanism. These suppression events do not involve escaping the checkpoint-mediated cell cycle arrest. Rather, defective Rad53 or Tel1 signaling bypasses Sae2 function at DSBs by decreasing the amount of Rad9 bound at DSBs. As a consequence, reduced Rad9 association to DNA ends relieves inhibition of Sgs1-Dna2 activity, which can then compensate for the lack of Sae2 in DSB resection and DNA damage resistance. We propose that persistent Tel1 and Rad53 checkpoint signaling in cells lacking Sae2 cause DNA damage hypersensitivity and defective DSB resection by increasing the amount of Rad9 bound at the DSBs, which in turn inhibits the Sgs1-Dna2 resection machinery.
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Wardrope, Laura. "Repair of double-strand DNA breaks in Escherichia coli." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/13208.

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Double-strand DNA breaks (DSBs) occur during normal cell metabolism and are lethal unless repaired. E. coli repairs DSBs using a pathway that involves homologous recombination. The mechanisms involved in this process were investigated by manipulating the EcoKI restriction-modification system of E. coli so that the restriction activity cleaves chromosomes to produce DSBs. The viability of recombination and repair mutants was measured following the induction of DSBs. The results show that RecG and RuvABC facilitate the survival of DSBs. Surprisingly, RuvABC was able to promote survival even when recombination could not be initiated. Pulsed field gel electrophoresis (PFGE) was carried out on the genomic DNA of mutants exposed to DSBs. This allowed Holliday junctions (HJs) linking the chromosomes of strains lacking RuvABC to be detected. Most significantly, the PFGE phenotype of a recG mutant mirrored that of the wild-type, suggesting that the RecG protein is not involved in the resolution of HJs. The outcome of HJ resolution to form crossover or non-crossover products was also investigated in mutants exposed to DSBs by measuring the effect on viability of inactivating the XerCD/dif system that is involved in chromosome dimer resolution. The deleterious effect of xerC mutations on recG and ruvAC mutants was approximately 10-fold greater than on wild-type. These results prompted an interesting discussion as to how the functions of the products of these genes interact in the cell. Finally, the theory that the product of the essential yqgF gene is an alternative HJ resolvase was investigated. yqgF was placed under the control of an inducible promoter and the effect of depleting YqgF levels on survival of DSBs was measured. No evidence to suggest that YqgF can resolve HJs was found.
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Liu, Nan. "Hypersensitivity of ataxia telangiectasia cells to DNA double strand breaks." Thesis, University of St Andrews, 1994. http://hdl.handle.net/10023/13905.

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Cells of ataxia telangiectasia (AT) individuals are hypersensitive to a variety of DNA damaging agents such as ionizing radiation and bleomycin, presumed to be due to an intrinsic defect in repair of DNA damage. The nature of the DNA lesion(s) to which AT cells are abnormally sensitive, and the defect in DNA repair are presently unclear. The major part of this project aimed at investigating the sensitivity of AT cells to DNA double-strand breaks (dsb) generated by restriction endonucleases (RE), thereby verifying the hypothesis that AT cells are deficient in the processing of dsb. AT lymphoblastoid cell lines (AT-PA and AT-KM) used in this study were initially characterized and found to be approximately 3 times more sensitive to ionizing radiation in the induction of micronuclei (Mn) and chromosomal aberrations (CA) compared with a normal lymphoblastoid cell line (N-SW). Other cellular characteristics were observed in AT-PA cells following-irradiation such as normal induction and rejoining of dsb and reduced inhibition of DNA synthesis. By using SLO poration, RE were introduced into the AT and normal cell lines and the yield of CA resulting from RE-induced dsb were subsequently investigated. The frequencies of CA induced by Pvu II were 2 - 4 fold higher in AT-PA than in N-SW cells at both 5 h and 24 h sampling times. The enhanced frequency of CA in AT cells treated with Pvu II was principally a result of an increase of chromatid aberrations, rather than chromosome aberrations at 24 h. higher frequencies of chromatid exchanges appeared in AT-PA than in N-SW cells. The results suggest that AT cells are characterized by a defect in dsb processing that converts a higher number of dsb into CA than in the normal cell line. With respect to the different end-structures of RE-induced dsb, cohesive-ended dsb generated by BamH I and Pst I were found to induce lower frequencies of CA than blunt-ended dsb generated by Pvu II and EcoR V in both the AT cell lines and the normal cell line. The results support the previous observations that cohesive-ended dsb are less clastogenic than blunt-ended dsb (Bryant 1984). Although inducing lower frequencies of CA than Pvu II and EcoR V, BamH I and Pst I induced higher number of CA in both AT-PA and AT-KM cells when compared with N-SW cells, again indicating a defect in processing cohesive-ended dsb exists in AT cells. A potent DNA repair inhibitor, Ara A, was found to potentiate the production of CA by RE in AT and normal cells. The enhancement ratios (by ara A) for CA induced by Pvu II and Pst 1 were higher in N-SW cells than in AT-PA and AT-KM cells. Ara A appeared to have no effect on the frequencies of CA induced by BamH I in any of the cell lines tested. Based on these findings, a mechanism for the rejoining of RE-induced dsb in which DNA repair synthesis may be involved is proposed, and it is postulated that dsb in AT cells are subjected to greater end degradation. Inhibition of DNA synthesis was observed in normal cells after treatment with Pvu II and EcoR V, while EcoR I and BamH I had only minor effect. AT-PA cells were found to be resistant to RE-induced inhibition of DNA synthesis, as in the case of ionizing radiation. This result suggests that RE-induced blunt-ended dsb mimic radiation-induced lesions in supressing DNA synthesis in normal cells and that AT cells respond to RE-induced dsb in a similar way to damage induced by ionizing radiation. Finally, when a nuclear extract from N-SW cells was introduced into Pvu Il-treated AT-PA cells, it was able to confer a normal frequency of CA. In contrast, neither whole cell nor nuclear extracts from normal cells influenced the production of CA induced by y-rays. These findings provide evidence for the presence of factor(s) in normal nuclear extract which complements the defect in processing of RE-induced dsb in AT cells.
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Krietsch, Jana. "PARP-1 activation regulates the DNA damage response to DNA double-strand breaks." Thesis, Université Laval, 2014. http://www.theses.ulaval.ca/2014/30722/30722.pdf.

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Les cassures double-brin de l'ADN, lorsque incorrectement réparées, peuvent avoir des conséquences fatales telles que des délétions et des réarrangements chromosomiques, favorisant la carcinogenèse. La poly(ADP-ribosyl)ation réalisée par la protéine poly(ADP-ribose) polymérase-1 (PARP-1) est l'une des premières modifications post-traductionnelles qui se produisent en réponse aux dommages à l'ADN. La PARP-1 utilise la nicotinamide pour générer un polymère chargé négativement, nommé poly(ADP-ribose) polymère (PAR), lequel est attaché en majorité à la PARP-1 elle-même ainsi qu'à d'autres protéines cibles. Le PAR a récemment été reconnu comme un signal de recrutement pour certaines protéines de réparation aux sites de dommages à l'ADN, mais un débat est en cours quant au rôle précis de la PARP-1 et du PAR dans la réponse aux dommages de l'ADN. Au cours de mon projet de doctorat, nous avons pu confirmer que les protéines qui se retrouvent en complexe avec le PAR immédiatement après les dommages à l'ADN sont principalement des facteurs de réparation. Étonnamment, les complexes protéiques associés au PAR pendant la période de récupération suite aux dommages sont enrichis en facteurs de liaison à l'ARN. Toutefois, la protéine liant l'ARN la plus abondante que nous avons détectée dans l'interactome du PAR, soit NONO, ne suit pas cette dernière cinétique puisqu'elle est fortement enrichie immédiatement après les dommages à l'ADN. Notre étude subséquente de NONO dans la réponse aux cassures double-brin de l'ADN a étonnamment révélé une implication directe de celle-ci par le mécanismede réparation de jonction des extrémités non-homologues. En plus, nous avons constaté que NONO se lie fortement et spécifiquement au PAR via son motif 1 de la reconnaissance de l'ARN, soulignant la compétition entre les PAR et l'ARN pour le même site de liaison. Fait intéressant, le recrutement in vivo de NONO aux sites de dommages de l'ADN dépend entièrement du PAR et nécessite le motif 1 de la reconnaissance de l'ARN. En conclusion, nos résultats établissent NONO comme une nouvelle protéine impliquée dans la réponse aux cassures double-brin de l'ADN et plus généralement démontrent un autre niveau de complexité supplémentaire dans l'interdépendance de la biologie de l'ARN et la réparation de l'ADN.
DNA double-strand breaks are potentially lethal lesions, which if not repaired correctly, can have harmful consequences such as carcinogenesis promoted by chromosome deletions and rearrangements. Poly(ADP-ribosyl)ation carried out by poly(ADP-ribose) polymerase 1 (PARP-1) is one of the first posttranslational modifications occurring in response to DNA damage. In brief, PARP-1 uses nicotinamide to generate a negatively charged polymer called poly(ADP-ribose) polymer (PAR), that can be attached to acceptor proteins, which is to a large extent PARP-1 itself. PAR has recently been recognized as a recruitment signal for key DNA repair proteins to sites of DNA damage but the precise role of PARP-1 and its catalytic product PAR in the DNA damage response are still a matter of ongoing debate. Throughout my doctoral work, we confirmed that the proteins in complex with PAR promptly after DNA damage are mostly DNA repair proteins, whereas during the period of recovery from DNA damage, the PAR interactome is highly enriched with RNA processing factors. Interestingly, one of the most abundant RNA-binding proteins detected in the PAR interactome, namely NONO, did not follow these kinetics as it was highly enriched immediately after DNA damage in the DNA repair protein complexes centered on PAR. Our subsequent investigation of NONO in the DNA damage response to double-strand breaks strikingly revealed a direct implication for NONO in repair by nonhomologous end joining (NHEJ). Moreover, we found that NONO strongly and specifically binds to PAR through its RNA-recognition motif 1 (RRM1), highlighting competition between PAR and RNA for the same binding site. Remarkably, the in vivo recruitment of NONO to DNA damage sites completely depends on PAR and requires the RRM1 motif. In conclusion, our results establish NONO as a new protein implicated in the DNA damage response to double-strand break and in broader terms add another layer of complexity to the cross-talk between RNA-biology and DNA repair.
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Ma, Yue. "Double-strand breaks (DSBs) and structure transition on genome-sized DNA." Thesis, https://doors.doshisha.ac.jp/opac/opac_link/bibid/BB13097333/?lang=0, 2018. https://doors.doshisha.ac.jp/opac/opac_link/bibid/BB13097333/?lang=0.

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DNA中の二本鎖切断(DSB)に対するアスコルビン酸(AA)およびDMSOの保護効果を、蛍光顕微鏡による巨大DNA(T4 DNA; 166kbp)の単分子観察によって評価した。凍結／解凍の状態に対して3つの異なる形態の放射源、可視光、γ線、および超音波の環境下にさらした。1‐プロパノールと2‐プロパノールの間で異なる効果が表れた。ゲノムDNA分子の高次構造の変化は、1−プロパノールを用いると、長軸長が濃度60％で最小を示し、次にアルコール含有量の増加と共に増加する傾向があることを見出した。一方、2−プロパノールを用いると、長軸長はアルコール含有量の増加と共にほぼ単調な減少を示した。
The protective effect of ascorbic acid (AA) and DMSO against double-strand breaks (DSBs) in DNA was evaluated by single-molecule observation of giant DNA (T4 DNA; 166kbp) through fluorescence microscopy. Samples were exposed to three different forms of radiation: visible light, γ-ray, and ultrasound or freeze/thawing. The change of the higher-order structure of genomic DNA molecules in the presence of alcohols by use of single DNA observation with fluorescence microscopy, by focusing our attention to unveil the different effect between 1-propanol and 2-propanol.
博士(工学)
Doctor of Philosophy in Engineering
同志社大学
Doshisha University
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Khalil, Ashraf. "ATM-Dependent ERK Signaling in Response to DNA Double Strand Breaks." VCU Scholars Compass, 2006. http://scholarscompass.vcu.edu/etd/760.

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Ionizing radiation (IR) triggers many signaling pathways stemming from DNA damage, and, independently, from extra-nuclear events. To generate radio-mimetic DNA double-strand breaks (DSBs) without and minimizing the effects on extra-nuclear radiation targets, human (p53+) glioma and carcinoma cells containing bromodeoxyuridine (BrdU)- substituted DNA were treated with Hoechst 33258 followed by long wave-length UV (UV-A) (BrdU photolysis). BrdU photolysis resulted in well-controlled, dose-dependent generation of DSBs equivalent to 0.2 - 20 Gy of IR, as detected by pulse-field gel electrophoresis, accompanied by dose-dependent H2AX phosphorylation at ser-139 and ATM phosphorylation at ser-1981, indicating ATM activation. Furthermore, BrdU photolysis increased phosphorylation of Chk2 (at thr-68) and p53 (at ser-15). p53 phosphorylation was reduced by the ATM inhibitor caffeine, and H2AX phosphorylation was greatly reduced in AT cells, confirming that phosphorylation was primarily ATM-dependent. We also examined the effects of BrdU photolysis on the major cellular signaling ERK pathways. Interestingly, low-dose (≤ 2 Gy-equivalents) BrdU photolysis stimulated ERK1/2 phosphorylation whereas higher doses (≥ 5 Gy eq.) resulted in Em1/2 dephosphorylation. ERK1/2 phosphorylation was ATM-dependent, whereas dephosphorylation was ATM-independent and DSBs dose-dependent. Thus ERK1/2 appear to be both positively and negatively regulated by ATM depending on the severity of the insult to DNA. In summary, few DSBs trigger ATM-dependent ERK1/2 pro-survival signals whereas more DSBs result in ERK1/2 dephosphorylation consistent with a switch from pro-survival to anti-survival signaling that might affect DSBs repair.
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MARSELLA, ANTONIO. "Functions and regulation of the MRX complex at DNA double strand breaks." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2021. http://hdl.handle.net/10281/310478.

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Le rotture del doppio filamento del DNA (DSB) sono tra le lesioni del DNA le più gravi. Se non adeguatamente riparati, i DSB potrebbero portare alla perdita di informazioni genetiche e all'instabilità del genoma, che è uno dei tratti distintivi delle cellule tumorali. Le cellule eucariotiche riparano i DSB mediante il non-homologous end joining (NHEJ), che ricongiunge direttamente le estremità rotte del DNA e la ricombinazione omologa (HR), che utilizza la sequenza di DNA omologa per riparare il DSB. L'HR richiede una degradazione nucleolitica delle estremità, in un processo chiamato resection. In Saccharomyces cerevisiae, il complesso MRX (Mre11, Rad50 e Xrs2), aiutato da Sae2, avvia il processamento delle estremità del DSB eseguendo un taglio sulle estremità 5'. Questo taglio, catalizzato dalla subunità Mre11, consente l'accesso alle nucleasi Exo1 e Dna2. Nel NHEJ, le due estremità devono essere collegate per consentire la loro corretta riparazione. Questa funzione, chiamata end tethering, dipende dalla subunità Rad50, che lega e idrolizza l'ATP. Una transizione da uno stato legato all'ATP a uno stato di taglio post-idrolisi regola le attività di associazione e processamento del DNA di MRX. Il complesso MRX è essenziale anche nell'attivazione del checkpoint perché recluta la chinasi del checkpoint Tel1 al DSB. In questa tesi, abbiamo studiato le funzioni e la regolazione del complesso MRX nella riparazione dei DSB. Abbiamo trovato degli alleli mre11 che sopprimono l'ipersensibilità delle cellule sae2Δ agli agenti genotossici. Le mutazioni nell'N-terminale di Mre11 sopprimono il difetto di resection delle cellule sae2Δ riducendo l'associazione di MRX e Tel1 al DSB. La ridotta persistenza di Tel1 potenzia l'attività di resection di Dna2 diminuendo l'associazione di Rad9 al DSB. Al contrario, le mutazioni di mre11 localizzate nel C-terminale non necessitano di Sae2 nel tethering ma non nella resection, possibilmente destabilizzando la conformazione aperta di Mre11 - Rad50. Questi risultati mostrano l'esistenza di domini Mre11 strutturalmente distinti che supportano la resistenza agli agenti genotossici mediando diversi processi. L'attivazione di Tel1 in vitro da parte di MRX richiede il legame dell'ATP a Rad50. In questa tesi, descriviamo due alleli, mre11-S499P e rad50-A78T, che influenzano l'attivazione di Tel1 senza compromettere le funzioni MRX nella riparazione DSB. Queste due varianti riducono l'interazione Tel1-MRX portando a una bassa associazione Tel1 ai DSB che ne riduce l'attivazione. Le simulazioni di dinamica molecolare mostrano che il sub-complesso MR wild-type legato all'ATP rimane in una conformazione 'chiusa', mentre la presenza di ADP porta alla destabilizzazione del dimero Rad50 e dell'associazione Mre11-Rad50, entrambi gli eventi sono richiesti per la transizione conformazionale MR ad uno stato aperto. Al contrario, MRA78T provoca un'apertura del complesso anche se legato all'ATP, indicando che il difetto di attivazione di Tel1 causato da MRA78T risulta dalla destabilizzazione dello stato conformazionale legato all'ATP. La mancanza di Sae2 aumenta la persistenza di MRX ai DSB e all'attivazione dei checkpoint. In questa tesi, dimostriamo anche che la proteina telomerica Rif2, che stimola l'idrolisi dell'ATP da parte di Rad50, inibisce l'attività dell'endonucleasi Mre11 ed è responsabile dell’aumento di MRX ai DSB nelle cellule sae2Δ. Abbiamo identificato un residuo di Rad50 che è importante per l'interazione Rad50-Rif2 e l'inibizione mediata da Rif2 della nucleasi Mre11. Questo residuo altera l'interazione Mre11-Rad50. Proponiamo che Sae2 stimoli l'attività endonucleasica di MRX stabilizzando lo stato di taglio, mentre Rif2 lo inibisce antagonizzando il legame di Sae2 e stabilizzando una conformazione di MR che non è adatta al taglio.
DNA double strand breaks (DSBs) are among the most severe DNA lesions. If not properly repaired, DSBs could lead to loss of genetic information and genome instability, which is one of the hallmarks of cancer cells. Eukaryotic cells repair DSBs by non-homologous end joining (NHEJ), which directly re-ligates the DNA broken ends, and homologous recombination (HR), which uses the intact homologous DNA sequence as a template to repair the DSB. HR requires a nucleolytic degradation of the broken DNA ends, in a process called resection. In Saccharomyces cerevisiae, the MRX (Mre11, Rad50 and Xrs2) complex, aided by Sae2, initiates resection of the DSB ends by performing an endonucleolytic cleavage on the 5’-ended strands. This cleavage, catalyzed by the Mre11 subunit, allows the access of Exo1 and Dna2 nucleases that elongate the ssDNA ends. In NHEJ, the two broken ends need to be physically connected to allow their correct religation. This function, called end tethering, depends on the Rad50 subunit, which binds and hydrolyses ATP. A transitions between an ATP-bound state to a post-hydrolysis cutting state regulates MRX DNA binding and processing activities. The MRX complex is also essential in DNA damage checkpoint activation because it recruits the checkpoint kinase Tel1 at the break site. In this thesis, we studied functions and regulation of the MRX complex in DSB repair. We found mre11 alleles that suppress the hypersensitivity of sae2Δ cells to genotoxic agents. The mutations in the Mre11 N-terminus suppress the resection defect of sae2Δ cells by lowering MRX and Tel1 association to DSBs. The diminished Tel1 persistence potentiates Dna2 resection activity by decreasing Rad9 association to DSBs. By contrast, the mre11 mutations localized at the C-terminus bypass Sae2 function in end-tethering but not in DSB resection, possibly by destabilizing the Mre11–Rad50 open conformation. These findings unmask the existence of structurally distinct Mre11 domains that support resistance to genotoxic agents by mediating different processes. In vitro Tel1 activation by MRX requires ATP binding to Rad50, suggesting a role for the MR subcomplex in Tel1 activation. In this thesis, we describe two separation-of-functions alleles, mre11-S499P and rad50-A78T, which we show to specifically affect Tel1 activation without impairing MRX functions in DSB repair. Both Mre11-S499P and Rad50-A78T reduce Tel1–MRX interaction leading to low Tel1 association at DSBs that reduces Tel1 activation. Molecular dynamics simulations show that the wild type MR subcomplex bound to ATP lingers in a tightly ‘closed’ conformation, while ADP presence leads to the destabilization of Rad50 dimer and of Mre11–Rad50 association, both events being required for MR conformational transition to an open state. By contrast, MRA78T undertakes complex opening even if Rad50 is bound to ATP, indicating that defective Tel1 activation caused by MRA78T results from destabilization of the ATP- bound conformational state. The lack of Sae2 increases MRX persistence at DSBs and checkpoint activation. In this thesis, we also show that the telomeric protein Rif2, which stimulates ATP hydrolysis by Rad50, inhibits the Mre11 endonuclease activity and is responsible for the increased MRX retention at DSBs in sae2Δ cells. We identified a Rad50 residue that is important for Rad50-Rif2 interaction and Rif2-mediated inhibition of Mre11 nuclease. This residue is located nearby a Rad50 surface that binds Sae2 and is important to stabilize the Mre11-Rad50 interaction in the cutting state. We propose that Sae2 stimulates MRX endonuclease activity by stabilizing the cutting state, whereas Rif2 inhibits it by antagonizing Sae2 binding to Rad50 and stabilizing a MR conformation that is not competent for DNA cleavage. The results described in this PhD thesis contribute to the understanding of the molecular mechanisms supporting functions and regulation of the MRX complex at DSBs.
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Tentner, Andrea R. (Andrea Ruth). "Quantitative measurement and modeling of the DNA damage signaling network : DNA double-strand breaks." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/61234.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2009.
"September 2009." Cataloged from PDF version of thesis.
Includes bibliographical references (p. 218-229).
DNA double-strand breaks (DSB) are one of the major mediators of chemotherapy-induced cytotoxicity in tumors. Cells that experience DNA damage can initiate a DNA damage-mediated cell-cycle arrest, attempt to repair the damage and, if successful, resume the cell-cycle (arrest/repair/resume). Cells can also initiate an active cell-death program known as apoptosis. However, it is not known what "formula" a cell uses to integrate protein signaling molecule activities to determine which of these paths it will take, or what protein signaling-molecules are essential to the execution of that decision. A better understanding of how these cellular decisions are made and mediated on a molecular level is essential to the improvement of existing combination and targeted chemotherapies, and to the development of novel targeted and personalized therapies. Our goal has been to gain an understanding of how cells responding to DSB integrate protein signaling-molecule activities across distinct signaling networks to make and execute binary cell-fate decisions, under conditions relevant to tumor physiology and treatment. We created a quantitative signal-response dataset, measuring signals that widely sample the response of signaling networks activated by the induction of DSB, and the associated cellular phenotypic responses, that together reflect the dynamic cellular responses that follow the induction of DSB. We made use of mathematical modeling approaches to systematically discover signal-response relationships within the DSB-responsive protein signaling network. The structure and content of the signal-response dataset is described, and the use of mathematical modeling approaches to analyze the dataset and discover specific signal-response relationships is illustrated. As a specific example, we selected a particularly strong set of identified signal-response correlations between ERK1/2 activity and S phase cell-cycle phenotype, identified in the mathematical data analysis, to posit a causal relationship between ERK1/2 and S phase cell cycle phenotype. We translated this posited causal relationship into an experimental hypothesis and experimentally test this hypothesis. We describe the validation of an experimental hypothesis based upon model-derived signal response relationships, and demonstrate a dual role for ERK1/2 in mediating cell-cycle arrest and apoptosis following DNA damage. Directions for the extension of the signal-response dataset and mathematical modeling approaches are outlined.
by Andrea R. Tentner.
Ph.D.
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VILLA, MATTEO. "Regulation of DNA-end resection at DNA double strand breaks and stalled replication forks." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2018. http://hdl.handle.net/10281/198950.

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L’instabilità genomica è una delle principali caratteristiche delle cellule tumorali e può essere generata da danni al DNA o da stress replicativi. Le rotture della doppia elica di DNA, Double Strand Breaks-DSBs, sono tra i danni più pericolosi che le cellule devono affrontare. In risposta ai DSBs, le cellule attivano un meccanismo molto conservato noto come checkpoint da danno al DNA, il cui effetto primario è quello di bloccare il ciclo cellulare fino a quando la rottura non è stata riparata. L’attivazione del checkpoint è dovuta alle chinasi apicali Tel1 e Mec1 che fosforilano e attivano le chinasi effettrici Rad53 e Chk1. I DSBs possono essere riparati mediante la ricombinazione omologa che inizia con la degradazione nucleolitica-resection- dell’estremità della rottura catalizzata dal complesso MRX e da Sae2. In seguito, le nucleasi Exo1 e Dna2, insieme all’elicasi Sgs1, catalizzano la formazione di lunghi tratti di DNA a singolo filamento. La resection è controllata negativamente dal complesso Ku, che inibisce Exo1, e dalla proteina di checkpoint Rad9, il cui meccanismo di regolazione non è noto. In lievito, l’assenza di Sae2 genera un difetto di resection che è responsabile dell’attivazione persistente del checkpoint dipendente da Tel1 e da Rad53. Per via di questo difetto, mutanti sae2 sono sensibili ad agenti genotossici che inducono DSBs. Tuttavia, la causa del difetto di resection e come l’attivazione incontrollata del checkpoint contribuiscano al fenotipo di sensibilità non è ancora noto. Per questo abbiamo cercato altri meccanismi che regolano l’inizio della resection, identificando mutazioni extrageniche in grado di sopprimere le sensibilità di cellule sae2. Abbiamo quindi isolato tre alleli SGS1-G1298R, rad53-Y88H e tel1-N2021D, in grado di sopprimere non solo le sensibilità ma anche il difetto di resection di mutanti sae2. La soppressione mediata da Sgs1-G1298R dipende da Dna2 e non da Exo1. Inoltre, l’azione di Sgs1-G1298R non solo sopprime il difetto di resection di cellule sae2 ma aumenta anche l’efficienza del processo rispetto ad un ceppo selvatico, a causa della resistenza all’inibizione mediata da Rad9. Infatti, Rad9 regola negativamente il reclutamento di Sgs1 alle estremità della lesione. Quando l’azione inibitoria di Rad9 viene meno, la richiesta del complesso MRX e di Sae2 nell’inizio della resection è ridotta. Rad53-Y88H e Tel1-N2021 sono varianti con perdita di funzione in grado di sopprimere le sensibilità di cellule sae2, in maniera dipendente da Sgs1-Dna2. Inoltre, anche l’assenza dell’attività chinasica di Rad53 e Tel1 permette di ottenere lo stesso fenotipo di soppressione che, tuttavia, non è dovuto al ruolo delle stesse nel blocco del ciclo cellulare. Infatti, queste mutazioni diminuiscono la quantità di Rad9 legato al DSB. Ciò facilita l’azione dell’elicasi Sgs1 e della nucleasi Dna2, sopprimendo così il difetto di resection di cellule sae2. Tali dati portano ad ipotizzare che l’attivazione persistente del checkpoint Tel1 e Rad53 dipendente causi un aumento del reclutamento dell’inibitore Rad9 nell’intorno della lesione che, a sua volta, è responsabile del difetto di resection e delle sensibilità di cellule sae2. Gli stress replicativi inducono il blocco della forca di replicazione e il processo di resection può essere un valido meccanismo per risolverlo. A questo proposito, abbiamo dimostrato che l’assenza dell’inibizione mediata da Rad9 compromette la risposta agli stress replicativi di cellule difettive nell’attività chinasica di Mec1, attraverso la degradazione delle forche bloccate in maniera dipendente da Sgs1 e Dna2. Tale funzione protettiva di Rad9 è indipendente dalla sua funzione nel checkpoint ma dipende principalmente dall’interazione di Rad9 con la proteina Dpb11. Per questo, abbiamo ipotizzato che Rad9 sia in grado di regolare la resection non solo al DSB ma anche alle forche di replicazione bloccate.
Genome instability is an hallmark of cancer cells and can be due to DNA damage or replication stress. DNA double strand breaks (DSBs) are the most dangerous type of damage that cells have to manage. In response to DSBs, cells activate an highly conserved mechanism known as DNA damage checkpoint (DDC), whose primary effect is to halt the cell cycle until the damage is repaired. DDC is activated by the apical kinases Tel1/ATM and Mec1/ATR, which phosphorylate and activate the effector kinases Rad53/CHK2 and Chk1/CHK1. The Homologous Recombination (HR)-mediated repair of a DSB starts with the nucleolytic degradation (resection) of the 5’ ends to create long ssDNA tails. In Saccharomyces cerevisiae, resection starts with an endonucleolytic cleavage catalyzed by the MRX complex together with Sae2. More extensive resection relies on two parallel pathways that involve the nucleases Exo1 and Dna2, together with the helicase Sgs1. Resection must be tightly controlled to avoid excessive ssDNA creation. The Ku complex and the checkpoint protein Rad9 negatively regulate resection. While Ku inhibits Exo1, Rad9 restrains nucleolytic degradation by an unknown mechanism. The absence of Sae2 impairs DSB resection and causes prolonged MRX binding at DSB that leads to persistent Tel1 and Rad53-dependent DNA damage checkpoint. SAE2 deleted strains are sensitive to DSBs inducing agents, like camptothecin (CPT). This sensitivity has been associated to the resection defect of sae2∆ cells, but what causes this resection defect and if the enhanced checkpoint signaling contributes to the DNA damage sensitivity of sae2∆ cells is unknown. For these reasons, we tried to identify other possible mechanisms regulating MRX/Sae2 requirement in DSB resection by searching extragenic mutations that suppressed the sensitivity to DNA damaging agents of sae2Δ cells. We identified three mutant alleles (SGS1-G1298R, rad53-Y88H and tel1-N2021D) that suppress both the DNA damage hypersensitivity and the resection defect of sae2∆ cells. We show that Sgs1-G1298R-mediated suppression depends on Dna2 but not on Exo1. Furthermore, not only Sgs1-G1298R suppresses the resection defect of sae2∆ cells but also increases resection efficiency even in a wild type context by escaping Rad9-mediated inhibition. In fact, Rad9 negatively regulates the binding/persistence of Sgs1 at the DSB ends. When inhibition by Rad9 is abolished by the Sgs1-G1298R mutant variant, the requirement for MRX/Sae2 in DSBs resection is reduced. Rad53-Y88H and Tel1-N2021 are loss of function mutant variants that suppress sae2∆ cells sensitivity in a Sgs1-Dna2 dependent manner. Furthermore, abolishing Rad53 and Tel1 kinase activity results in a similar suppression phenotype which does not involve the escape from the checkpoint mediated cell cycle arrest. Rather, defective Rad53 or Tel1 signaling bypasses Sae2 function in DSBs resection by decreasing the amount of Rad9 bound at DSBs. This increases the Sgs1-Dna2 activity that, in turn, can compensate for the lack of Sae2. We propose that persistent Tel1 and Rad53 checkpoint signaling in sae2∆ cells causes DNA damage hypersensitivity and defective DSB resection by increasing the amount of Rad9 that, in turn, inhibits Sgs1-Dna2. Replication stress can induce fork stalling and controlled resection can be a relevant mechanism to allow repair/restart of stalled replication forks. We show that loss of the inhibition that Rad9 exerts on resection exacerbates the sensitivity to replication stress of Mec1 defective yeast cells by exposing stalled replication forks to Dna2-dependent degradation. This Rad9 protective function is independent of checkpoint activation and relies mainly on Rad9-Dpb11 interaction. We propose that Rad9 not only regulates the action of Sgs1-Dna2 at DSBs but also at stalled replication forks, supporting cell viability when the S-phase checkpoint is not fully functional.
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North, Matthew Howard. "The formation and repair of DNA double-strand breaks in saccaromyces cerevisiae." Thesis, University of Sheffield, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.489352.

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Books on the topic "DNA double-strand breaks, Sae2"

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Al-Zain, Amr M. Mutagenic Repair Outcomes of DNA Double-Strand Breaks. [New York, N.Y.?]: [publisher not identified], 2021.

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Yoshikawa, Kenichi, and Fuyuhiko Tamanoi. DNA Damage and Double Strand Breaks. Elsevier Science & Technology, 2022.

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MITOCHONDRIAL DNA DOUBLE-STRAND BREAKS: IN REPLICATION AND IN REPAIR. Shreveport, Louisiana, USA: Louisiana State University Health Sciences Center-Shreveport, Louisiana, USA, 2017.

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Diaz, Robert L. Reduction of DNA double-strand breaks in S. cerevisiae does not change crossover frequency and reveals a novel phenomenon: Crossover homeostasis. 2003.

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Stauropoulos, Dimitrios James. An analysis of the interplay between telomeric factors and DNA repair proteins, in the human ALT pathway and cellular response to genomic double strand breaks. 2005.

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Book chapters on the topic "DNA double-strand breaks, Sae2"

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Falk, Martin, Emilie Lukasova, and Stanislav Kozubek. "Repair of DNA Double-Strand Breaks." In Radiation Damage in Biomolecular Systems, 329–57. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-2564-5_20.

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Chadwick, K. H. "DNA Double Strand Breaks and Chromosomal Aberrations." In Understanding Radiation Biology, 65–84. Names: Chadwick, K. H. (Kenneth Helme), 1937- author.Title: Understanding radiation biology : from DNA damage to cancer and radiation risk / by Kenneth Chadwick. Description: Boca Raton: CRC Press, [2020]: CRC Press, 2019. http://dx.doi.org/10.1201/9780429288197-4.

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Chadwick, K. H. "The Molecular Model and DNA Double Strand Breaks." In Understanding Radiation Biology, 3–20. Names: Chadwick, K. H. (Kenneth Helme), 1937- author.Title: Understanding radiation biology : from DNA damage to cancer and radiation risk / by Kenneth Chadwick. Description: Boca Raton: CRC Press, [2020]: CRC Press, 2019. http://dx.doi.org/10.1201/9780429288197-1.

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IIiakis, George, and Nge Cheong. "In Vitro Rejoining of Double-Strand Breaks in Genomic DNA." In DNA Repair Protocols, 473–85. Totowa, NJ: Humana Press, 1999. http://dx.doi.org/10.1007/978-1-4612-1608-7_39.

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Barone, F., M. Belli, E. Rongoni, O. Sapora, and M. A. Tabocchini. "X-Ray-Induced DNA Double Strand Breaks in Polynucleosomes." In Radiation Carcinogenesis and DNA Alterations, 293–96. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5269-3_19.

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Chadwick, K. H., H. P. Leenhouts, E. Wijngaard, and M. J. Sijsma. "DNA Double-Strand Breaks and their Relation to Cytoxicity." In Quantitative Mathematical Models in Radiation Biology, 147–58. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-46656-4_14.

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Hendzel, Michael J., and Hilmar Strickfaden. "DNA Repair Foci Formation and Function at DNA Double-Strand Breaks." In The Functional Nucleus, 219–37. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-38882-3_10.

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Frankenberg-Schwager, M., and D. Frankenberg. "Rejoining of Radiation-Induced DNA Double-Strand Breaks in Yeast." In Advances in Mutagenesis Research, 1–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76232-1_1.

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Ferdousi, Leyla Vahidi, and Miria Ricchetti. "Repair of DNA Double-Strand Breaks in Adult Stem Cells." In Stem Cell Biology and Regenerative Medicine, 59–82. New York: River Publishers, 2022. http://dx.doi.org/10.1201/9781003339601-4.

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Ferdousi, Leyla Vahidi, Haser Hasan Sutcu, and Miria Ricchetti. "Repair of DNA Double-Strand Breaks in Adult Stem Cells." In Stem Cell Biology and Regenerative Medicine, 71–105. 2nd ed. New York: River Publishers, 2022. http://dx.doi.org/10.1201/9781003339618-3.

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Conference papers on the topic "DNA double-strand breaks, Sae2"

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Xu, Fei, Lili Yan, Jianrong Wang, and Jinming Yang. "Abstract 2491: Beclin1 promotes DNA double-strand breaks repair." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-2491.

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Durocher, Daniel. "Abstract SY07-03: The ubiquitin-based response to DNA double-strand breaks." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-sy07-03.

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Kenmotmsu, Takahiro, Naoki Ogawa, Rinko Kubota, Kenji Yoshida, Yukihiro Kagawa, Yoshiaki Watanabe, Yuko Yoshikawa, and Kenich Yoshikawa. "Double-strand breaks on a genomic DNA caused by ultrasound: Evaluation by single DNA observation." In 2013 International Symposium on Micro-NanoMechatronics and Human Science (MHS). IEEE, 2013. http://dx.doi.org/10.1109/mhs.2013.6710461.

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Puts, Gemma S., Stuart G. Jarrett, Devin Snyder, Richard Vincent, Ying Wang, Katie Leonard, Ben Portney, Feyruz Rassool, Michal Zalzman, and David M. Kaetzel. "Abstract 4846: The metastasis suppressor NME1 is recruited to DNA double strand breaks." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-4846.

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Li, Xueyuan, Weiwei Li, Jinxin Kong, Yongmei Qi, and Dejun Huang. "The protective effect of reduced glutathione on cadmium-induced DNA double-strand breaks." In International conference on Human Health and Medical Engineering. Southampton, UK: WIT Press, 2014. http://dx.doi.org/10.2495/hhme130521.

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Orthwein, Alexandre, and Daniel Durocher. "Abstract IA12: Regulation of the RNF168-dependent response to DNA double-strand breaks." In Abstracts: AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; January 29-February 1, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.cansusc14-ia12.

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WEI, LEIZHEN, and NATSUKO CHIBA. "ANALYSIS OF BRCA1 ACCUMULATION AT DNA DOUBLE-STRAND BREAKS USING A MOLECULAR IMAGING TECHNIQUE." In Proceedings of the Tohoku University Global Centre of Excellence Programme. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2009. http://dx.doi.org/10.1142/9781848163539_0049.

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Luczak, Michal W., and Anatoly Zhitkovich. "Abstract 1754: Monoubiquitinated γ-H2AX - a more specific biomarker of DNA double-strand breaks." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-1754.

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Luczak, Michal W., and Anatoly Zhitkovich. "Abstract 1754: Monoubiquitinated γ-H2AX - a more specific biomarker of DNA double-strand breaks." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-1754.

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Ishfaq, Talia, Zaain Ahmad, Nourhan Mohamed, Milica Janosevic, Ziyad Abdelrahim, Jessica Georgopulos, and James Fackenthal. "Abstract 4724: DNA demethylation and double-strand breaks affect levels of theBRCA2Δ3 alternate splicing isoform." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-4724.

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Reports on the topic "DNA double-strand breaks, Sae2"

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Deininger, Prescott L. The Human L1 Element Causes DNA Double-Strand Breaks in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, August 2006. http://dx.doi.org/10.21236/ada474882.

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Aneva, Nevena, and Gergana Savova. Impact of Different Types Photon Radiation on DNA Double-strand Breaks Repair Process in Microglial Cells. "Prof. Marin Drinov" Publishing House of Bulgarian Academy of Sciences, November 2021. http://dx.doi.org/10.7546/crabs.2021.11.14.

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Zafar, Faria, Sara B. Seidler, Amy Kronenberg, David Schild, and Claudia Wiese. Homologous recombination contributes to the repair of DNA double-strand breaks induced by high-energy iron ions. Office of Scientific and Technical Information (OSTI), June 2010. http://dx.doi.org/10.2172/983115.

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Pawlowski, Wojtek P., and Avraham A. Levy. What shapes the crossover landscape in maize and wheat and how can we modify it. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600025.bard.

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Meiotic recombination is a process in which homologous chromosomes engage in the exchange of DNA segments, creating gametes with new genetic makeup and progeny with new traits. The genetic diversity generated in this way is the main engine of crop improvement in sexually reproducing plants. Understanding regulation of this process, particularly the regulation of the rate and location of recombination events, and devising ways of modifying them, was the major motivation of this project. The project was carried out in maize and wheat, two leading crops, in which any advance in the breeder’s toolbox can have a huge impact on food production. Preliminary work done in the USA and Israeli labs had established a strong basis to address these questions. The USA lab pioneered the ability to map sites where recombination is initiated via the induction of double-strand breaks in chromosomal DNA. It has a long experience in cytological analysis of meiosis. The Israeli lab has expertise in high resolution mapping of crossover sites and has done pioneering work on the importance of epigenetic modifications for crossover distribution. It has identified genes that limit the rates of recombination. Our working hypothesis was that an integrative analysis of double-strand breaks, crossovers, and epigenetic data will increase our understanding of how meiotic recombination is regulated and will enhance our ability to manipulate it. The specific objectives of the project were: To analyze the connection between double-strand breaks, crossover, and epigenetic marks in maize and wheat. Protocols developed for double-strand breaks mapping in maize were applied to wheat. A detailed analysis of existing and new data in maize was conducted to map crossovers at high resolution and search for DNA sequence motifs underlying crossover hotspots. Epigenetic modifications along maize chromosomes were analyzed as well. Finally, a computational analysis tested various hypotheses on the importance of chromatin structure and specific epigenetic modifications in determining the locations of double-strand breaks and crossovers along chromosomes. Transient knockdowns of meiotic genes that suppress homologous recombination were carried out in wheat using Virus-Induced Gene Silencing. The target genes were orthologs of FANCM, DDM1, MET1, RECQ4, and XRCC2.
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Weil, Clifford F., Anne B. Britt, and Avraham Levy. Nonhomologous DNA End-Joining in Plants: Genes and Mechanisms. United States Department of Agriculture, July 2001. http://dx.doi.org/10.32747/2001.7585194.bard.

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Repair of DNA breaks is an essential function in plant cells as well as a crucial step in addition of modified DNA to plant cells. In addition, our inability to introduce modified DNA to its appropriate locus in the plant genome remains an important hurdle in genetically engineering crop species.We have taken a combined forward and reverse genetics approach to examining DNA double strand break repair in plants, focusing primarily on nonhomologous DNA end-joining. The forward approach utilizes a gamma-plantlet assay (miniature plants that are metabolically active but do not undergo cell division, due to cell cycle arrest) and has resulted in identification of five Arabidopsis mutants, including a new one defective in the homolog of the yeast RAD10 gene. The reverse genetics approach has identified knockouts of the Arabidopsis homologs for Ku80, DNA ligase 4 and Rad54 (one gene in what proves to be a gene family involved in DNA repair as well as chromatin remodeling and gene silencing)). All these mutants have phenotypic defects in DNA repair but are otherwise healthy and fertile. Additional PCR based screens are in progress to find knockouts of Ku70, Rad50, and Mre11, among others. Two DNA end-joining assays have been developed to further our screens and our ability to test candidate genes. One of these involves recovering linearized plasmids that have been added to and then rejoined in plant cells; plasmids are either recovered directly or transformed into E. coli and recovered. The products recovered from various mutant lines are then compared. The other assay involves using plant transposon excision to create DNA breaks in yeast cells and then uses the yeast cell as a system to examine those genes involved in the repair and to screen plant genes that might be involved as well. This award supported three graduate students, one in Israel and two in the U.S., as well as a technician in the U.S., and is ultimately expected to result directly in five publications and one Masters thesis.
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