You searched for subject:(Double strand break repair).
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Louisiana State University
1.
Li, Mingyang.
DNA Base Excision Repair and Double Strand Break Repair in Human Fibroblast.
Degree: PhD, Laboratory and Basic Science Research, 2017, Louisiana State University
URL: https://digitalcommons.lsu.edu/gradschool_dissertations/4186 
► In eukaryotes, DNA repair mechanisms detect and repair damaged DNA. DNA damage is primarily caused by a variety of exogenous and endogenous sources. Several…
(more)
▼ In eukaryotes, DNA repair mechanisms detect and repair damaged DNA. DNA damage is primarily caused by a variety of exogenous and endogenous sources. Several types of damage to DNA are repaired by different kinds of DNA repair pathways. This dissertation focused on repair of N-methylpurines (NMPs) and double-strand breaks (DSBs) in human fibroblasts.
NMPs, including N7-methylguanine (7MeG) and N3-methyladenine (3MeA), can be induced by environmental methylating agents (e.g. the soil fumigant methyl bromide), chemotherapeutics (e.g. nitrogen mustards), and natural cellular methyl donors like S-adenosylmethionine. In human cells, NMPs are repaired by the multi-step base excision repair pathway initiated by human alkyladenine glycosylase (hAAG). Repair of NMPs has been shown to be affected by DNA sequence contexts. However, the nature of the sequence contexts has been poorly understood. We developed a sensitive method, LAF-Seq (Lesion-Adjoining Fragment Sequencing), which allows nucleotide-resolution digital mapping of DNA damage and repair in multiple genomic fragments of interest in human cells. We also developed a strategy that allows accurate measurement of the excision kinetics of NMP bases in vitro. We demonstrate that 3MeAs are induced to a much lower level by the S<em>N</em>2 methylating agent dimethyl sulfate (DMS) and repaired much faster than 7MeGs in human fibroblasts. Induction of 7MeGs by DMS is affected by nearest-neighbor nucleotides, being enhanced at sites neighbored by a G or T on the 3’ side, but impaired at sites neighbored by a G on the 5’ side. Repair of 7MeGs is also affected by nearest-neighbor nucleotides, being slow if the lesions are between purines, especially Gs, and fast if the lesions are between pyrimidines, especially Ts. Excision of 7MeG bases from the DNA backbone by hAAG in vitro is similarly affected by nearest-neighbor nucleotides, suggesting that the effect of nearest-neighbor nucleotides on repair of 7MeGs in the cells is primarily achieved by modulating the initial step of the base excision repair process.
DSBs can be induced by hydrogen peroxide (H2O2), endonuclease I-PpoI and ionizing radiation. Senataxin is a putative RNA/DNA helicase. We demonstrate that senataxin facilitates repair of DSBs and modulates the activation of DNA damage response pathway of ATM-Chk2 and ATR-Chk1 upon DSB damage.
Subjects/Keywords: DNA repair; DNA damage; Base excision repair; Double-strand break repair
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APA (6th Edition):
Li, M. (2017). DNA Base Excision Repair and Double Strand Break Repair in Human Fibroblast. (Doctoral Dissertation). Louisiana State University. Retrieved from https://digitalcommons.lsu.edu/gradschool_dissertations/4186
Chicago Manual of Style (16th Edition):
Li, Mingyang. “DNA Base Excision Repair and Double Strand Break Repair in Human Fibroblast.” 2017. Doctoral Dissertation, Louisiana State University. Accessed April 12, 2021.
https://digitalcommons.lsu.edu/gradschool_dissertations/4186.
MLA Handbook (7th Edition):
Li, Mingyang. “DNA Base Excision Repair and Double Strand Break Repair in Human Fibroblast.” 2017. Web. 12 Apr 2021.
Vancouver:
Li M. DNA Base Excision Repair and Double Strand Break Repair in Human Fibroblast. [Internet] [Doctoral dissertation]. Louisiana State University; 2017. [cited 2021 Apr 12].
Available from: https://digitalcommons.lsu.edu/gradschool_dissertations/4186.
Council of Science Editors:
Li M. DNA Base Excision Repair and Double Strand Break Repair in Human Fibroblast. [Doctoral Dissertation]. Louisiana State University; 2017. Available from: https://digitalcommons.lsu.edu/gradschool_dissertations/4186
University of Rochester
2.
Nagarajan, Prabha.
Double strand break repair and genetic analyses of Rad27p
in the mitochondria of Saccharomyces cerevisiae.
Degree: PhD, 2015, University of Rochester
URL: http://hdl.handle.net/1802/30020
► Mitochondria contain their own genetic material, which is essential for energy production in eukaryotes. Similar to nuclear DNA, mitochondrial DNA (mtDNA) is also under constant…
(more)
▼ Mitochondria contain their own genetic material,
which is essential for energy production in eukaryotes. Similar to
nuclear DNA, mitochondrial DNA (mtDNA) is also under constant
mutagenic stress and the accumulation of mutations in this genome
has been associated with a wide range of metabolic and degenerative
diseases, certain types of cancer, and aging. Therefore,
maintaining the integrity of this genetic material is crucial for
cellular homeostasis. Several DNA repair pathways including
homologous recombination (HR) have been identified in this
organelle but the mechanistic details and the protein players
involved in these processes have remained elusive. To investigate
HR mechanisms and DNA repair proteins in mitochondria, we
engineered a system to induce a specific double strand break (DSB)
in the mtDNA of Saccharomyces cerevisiae and study its repair.
Using this system, we have determined that induced DSBs at a locus
flanked by repeat sequences are repaired by an erroneous HR
mechanism, which results in deletion of the region intervening the
repeats. Furthermore, DSB repair involves processing of DNA ends at
the break site, which produces single stranded recombinogenic
intermediates. Our results show that generation of deletions upon
DSB induction and DNA end resection requires the function of Rad27p
and Nuc1p. Both these proteins localize to the nucleus as well as
mitochondria but their precise function in the latter is poorly
understood.
</br>
To determine the roles of the
multifunctional Rad27p in mitochondria, we examined the mutagenic
effects of various nuclease deficient alleles of this protein in
this cellular compartment. Our results demonstrate that Rad27p
functions in more than one pathway in mitochondria, using its
multiple enzymatic activities. Furthermore, based on our findings,
we conclude that the yeast Rad27p uses a cryptic internal
mitochondrial-targeting signal, and an import mechanism that is
likely different from its mammalian homolog, FEN1.
Subjects/Keywords: DNA end resection; Double strand break repair; Mitochondrial DNA repair; Rad27
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APA (6th Edition):
Nagarajan, P. (2015). Double strand break repair and genetic analyses of Rad27p
in the mitochondria of Saccharomyces cerevisiae. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/30020
Chicago Manual of Style (16th Edition):
Nagarajan, Prabha. “Double strand break repair and genetic analyses of Rad27p
in the mitochondria of Saccharomyces cerevisiae.” 2015. Doctoral Dissertation, University of Rochester. Accessed April 12, 2021.
http://hdl.handle.net/1802/30020.
MLA Handbook (7th Edition):
Nagarajan, Prabha. “Double strand break repair and genetic analyses of Rad27p
in the mitochondria of Saccharomyces cerevisiae.” 2015. Web. 12 Apr 2021.
Vancouver:
Nagarajan P. Double strand break repair and genetic analyses of Rad27p
in the mitochondria of Saccharomyces cerevisiae. [Internet] [Doctoral dissertation]. University of Rochester; 2015. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1802/30020.
Council of Science Editors:
Nagarajan P. Double strand break repair and genetic analyses of Rad27p
in the mitochondria of Saccharomyces cerevisiae. [Doctoral Dissertation]. University of Rochester; 2015. Available from: http://hdl.handle.net/1802/30020
University of Alberta
3.
Dronyk, Ashley D.
New roles for B-cell lymphoma 10 in the nucleus.
Degree: MS, Department of Oncology, 2010, University of Alberta
URL: https://era.library.ualberta.ca/files/4q77fr43v
► Radiation therapy targets cancer cell death by overwhelming cells with harmful DNA damage. Understanding how cells repair radiation damage and in particular how they become…
(more)
▼ Radiation therapy targets cancer cell death by
overwhelming cells with harmful DNA damage. Understanding how cells
repair radiation damage and in particular how they become resistant
to radiation therapy is important for effective cancer treatment.
Our lab made the novel discovery that Bcl10, a cytoplasmic protein
important for NF-κB activation, localizes to endogenous γH2AX foci
in the nucleus of breast cancer cells. We determined that following
radiation treatment Bcl10 is recruited to ionizing
radiation-induced foci in a dose-dependent matter and that it is
important for the repair of radiation-induced DNA damage. We also
observed that breast cancer cells are extremely sensitive to Bcl10
knockdown, causing cellular senescence, while normal breast
epithelial cells are insensitive. Our findings identify Bcl10 as
potent anti-cancer target.
Subjects/Keywords: γH2AX; DNA repair; Bcl10; NF-κB; DNA double strand break
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APA (6th Edition):
Dronyk, A. D. (2010). New roles for B-cell lymphoma 10 in the nucleus. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/4q77fr43v
Chicago Manual of Style (16th Edition):
Dronyk, Ashley D. “New roles for B-cell lymphoma 10 in the nucleus.” 2010. Masters Thesis, University of Alberta. Accessed April 12, 2021.
https://era.library.ualberta.ca/files/4q77fr43v.
MLA Handbook (7th Edition):
Dronyk, Ashley D. “New roles for B-cell lymphoma 10 in the nucleus.” 2010. Web. 12 Apr 2021.
Vancouver:
Dronyk AD. New roles for B-cell lymphoma 10 in the nucleus. [Internet] [Masters thesis]. University of Alberta; 2010. [cited 2021 Apr 12].
Available from: https://era.library.ualberta.ca/files/4q77fr43v.
Council of Science Editors:
Dronyk AD. New roles for B-cell lymphoma 10 in the nucleus. [Masters Thesis]. University of Alberta; 2010. Available from: https://era.library.ualberta.ca/files/4q77fr43v
4.
Batenburg, Nicole.
Functional analysis of CSB in telomere maintenance and DNA double-strand break repair.
Degree: PhD, 2017, McMaster University
URL: http://hdl.handle.net/11375/22034
► Cockayne syndrome (CS) is a rare, segmental premature aging disorder in which the majority of cases are caused by mutations in the Cockayne syndrome group…
(more)
▼ Cockayne syndrome (CS) is a rare, segmental premature aging disorder in which the majority of cases are caused by mutations in the Cockayne syndrome group B protein (CSB). CSB is a multifunctional protein implicated in DNA repair, transcription and chromatin remodeling. The results presented here demonstrate that CSB plays an important role in telomere maintenance and DSB repair. We find that CS cells accumulate telomere doublets, have increased telomere-bound TRF1, decreased TERRA levels and a defect in telomerase-dependent telomere lengthening. These results imply that CS patients may be defective in telomere maintenance. We also uncover a novel and important role of CSB in DNA DSB repair. We show that CSB facilitates HR and supresses NHEJ during S and G2 phase. We find that CSB interacts with RIF1 and is recruited by RIF1 to DSBs in S phase. At DSBs, CSB remodels the chromatin extensively, which in turn limits RIF1 recruitment and promotes BRCA1 accumulation. The chromatin remodeling activity of CSB requires not only damage-induced phosphorylation on S10 by ATM but also cell cycle-dependent phosphorylation of S158 by cyclin A-CDK2. Both modifications are needed for the intramolecular interaction of CSB N-terminal domain with its ATPase domain. This intramolecular interaction has previously been reported to regulate the ATPase activity of CSB. Taken together, these results suggest that ATM and CDK2 control of CSB to promote chromatin remodeling, which in turn inhibits RIF1 in DNA DSB repair pathway choice.
Thesis
Doctor of Philosophy (PhD)
Advisors/Committee Members: Zhu, Xu-Dong, Biology.
Subjects/Keywords: Telomeres; Double-strand break repair; DNA damage; Aging; Cockayne syndrome; CSB
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APA ·
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APA (6th Edition):
Batenburg, N. (2017). Functional analysis of CSB in telomere maintenance and DNA double-strand break repair. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/22034
Chicago Manual of Style (16th Edition):
Batenburg, Nicole. “Functional analysis of CSB in telomere maintenance and DNA double-strand break repair.” 2017. Doctoral Dissertation, McMaster University. Accessed April 12, 2021.
http://hdl.handle.net/11375/22034.
MLA Handbook (7th Edition):
Batenburg, Nicole. “Functional analysis of CSB in telomere maintenance and DNA double-strand break repair.” 2017. Web. 12 Apr 2021.
Vancouver:
Batenburg N. Functional analysis of CSB in telomere maintenance and DNA double-strand break repair. [Internet] [Doctoral dissertation]. McMaster University; 2017. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/11375/22034.
Council of Science Editors:
Batenburg N. Functional analysis of CSB in telomere maintenance and DNA double-strand break repair. [Doctoral Dissertation]. McMaster University; 2017. Available from: http://hdl.handle.net/11375/22034
Texas Tech University
5.
-1773-2040.
Determination of structure of Mre11-Rad50 complex bound to DNA double strand break by NMR spectroscopy.
Degree: MS, Chemistry, 2018, Texas Tech University
URL: http://hdl.handle.net/2346/82067
► Our genomic DNA is exposed to a number of stress conditions such as reactive oxygen species, ionizing radiation, chemical agents and ultraviolet light which can…
(more)
▼ Our genomic DNA is exposed to a number of stress conditions such as reactive oxygen species, ionizing radiation, chemical agents and ultraviolet light which can result in DNA
double strand breaks (DSBs). Inefficiency of the proteins involved in the DNA damage response to
repair the damage might have tumorogenic potential. The initial complex involved in DNA DSB
repair is Mre11-Rad50-Nbs1 (MRN). It is thought to be involved in binding to and unwinding the damaged DNA
double helix, processing the DNA ends and recruiting other downstream proteins to
repair the damage. Advances in solution state NMR spectroscopy have enabled us to selectively label and study large protein complexes like MR (~200 kDa). We utilize side chain methyl labelling of Pyrococcus furiosus (Pf) Mre11 and Rad50 to study the structure and dynamics of the individual proteins and their complexes. Methyl groups are isotopically ILVM-labeled at isoleucine(Cδ1), leucine(Cδ), valine(Cγ) and methionine(Cε) for HMQC and NOESY experiments. The existing X-ray crystal structure of the Pf Mre11 nuclease and capping domains was used to help assign the labeled methyl groups in the NMR spectra leading to more than 80% assignments. We have made MR complex using ILVM-labeled Mre11 and deuterated Rad50 and have added a 15 bp DNA with a 2 nucleotide 3’ overhang, mimicking a DNA DSB substrate, to form the complete MR-DNA complex. HMQC spectra show significant changes in chemical shifts of various Mre11 methyl groups upon DNA binding, including M109 and M146, which is in agreement with the published Mre11-DNA crystal structure. We have looked at different DNA substrates bound to MR, such as ssDNA and a branched DNA to mimic a stalled replication fork. Distance restraints obtained from Paramagnetic Relaxation Enhancement (PRE) experiments and Chemical Shift Perturbations (CSPs) observed after DNA binding were used to dock the dsDNA molecules into MR structure. Together this data reveals the changes in the structure of the MR complex when it binds to DNA DSBs which will further enable us to study its role in DNA damage
repair.
Advisors/Committee Members: Latham, Michael (advisor), Wylie, Benjamin (committee member).
Subjects/Keywords: DNA double Strand Break repair; NMR spectroscopy; Mre11
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APA ·
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APA (6th Edition):
-1773-2040. (2018). Determination of structure of Mre11-Rad50 complex bound to DNA double strand break by NMR spectroscopy. (Masters Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/82067
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Chicago Manual of Style (16th Edition):
-1773-2040. “Determination of structure of Mre11-Rad50 complex bound to DNA double strand break by NMR spectroscopy.” 2018. Masters Thesis, Texas Tech University. Accessed April 12, 2021.
http://hdl.handle.net/2346/82067.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
MLA Handbook (7th Edition):
-1773-2040. “Determination of structure of Mre11-Rad50 complex bound to DNA double strand break by NMR spectroscopy.” 2018. Web. 12 Apr 2021.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Vancouver:
-1773-2040. Determination of structure of Mre11-Rad50 complex bound to DNA double strand break by NMR spectroscopy. [Internet] [Masters thesis]. Texas Tech University; 2018. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/2346/82067.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Council of Science Editors:
-1773-2040. Determination of structure of Mre11-Rad50 complex bound to DNA double strand break by NMR spectroscopy. [Masters Thesis]. Texas Tech University; 2018. Available from: http://hdl.handle.net/2346/82067
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
University of Edinburgh
6.
Cockram, Charlotte Anne.
Genomic analysis of RecA-DNA interactions during double-strand break repair in Escherichia coli.
Degree: PhD, 2014, University of Edinburgh
URL: http://hdl.handle.net/1842/17284
► Maintaining genomic integrity is crucial for cell survival. In Escherichia coli, Rec-Amediated homologous recombination (HR) plays an essential role in the repair of DNA double-strand…
(more)
▼ Maintaining genomic integrity is crucial for cell survival. In Escherichia coli, Rec-Amediated homologous recombination (HR) plays an essential role in the repair of DNA double-strand breaks (DSB) and the SOS response through a series of highly dynamic interactions with the chromosome. A greater understanding of the mechanism of homologous recombination requires quantitative analysis of genomic studies in live cells. The aim of this thesis was to investigate the dynamics of the RecA-DNA interactions in vivo following the induction of a site-specific DSB in the chromosome of E. coli. This DSB is caused by the cleavage of a DNA hairpin by the hairpin-specific endonuclease, SbcCD. The DNA hairpin is formed only on the lagging strand template of replication by a 246 bp-interrupted palindrome. As a result cleavage only occurs on one sister chromosome, leaving one unbroken chromosome to serve as a template for repair by HR. Here, this system has been used as a basis to develop a method that combines chromatin immunoprecipitation with quantitative PCR (ChIP-qPCR) and next-generation sequencing (ChIP-Seq) to quantify RecA protein binding during the active repair of a single chromosomal DSB. This study reports that DSB-dependent RecA binding is stimulated in response to the eight base DNA sequence Chi (5’-GCTGGTGG-3’). Increasing the number of Chi sites close to the DSB stimulates more RecA loading to DNA, with ChIP-Seq analysis also revealing a role for subsequent Chi sites in RecA binding during DSBR. If the Chi sites close to the DSB are removed then Chi-dependent RecA binding to DNA can be observed at distances greater than 100 kb from the DSB, suggesting that these subsequent Chi sites can be engaged in DSBR. Through collaboration, these in vivo data were combined with stochastic modeling to determine that, in vivo, Chi is recognised by the RecBCD complex with an efficiency of 20- 35%. The genomic analysis also revealed two unexpected aspects of RecA protein binding. First, ChIP-Seq analyses identified that following a DSB at lacZ there is RecA enrichment detected in the terminus region of the E. coli chromosome. This RecA binding is Chi-dependent, indicating a role for HR. Second, DSB-independent binding was observed at the RNA encoding genes dispersed throughout the chromosome. A temporal analysis of RecA dynamics was also performed. These analyses revealed that RecA binding to DNA near the DSB is extremely dynamic, cycling between periods of high RecA enrichment and periods of low RecA enrichment. This is the first in vivo study of DSB-dependent RecA-DNA distribution and dynamics in recombination proficient E. coli cells.
Subjects/Keywords: 572.8; DNA repair; recombination; double strand break; Chi; RecA
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APA (6th Edition):
Cockram, C. A. (2014). Genomic analysis of RecA-DNA interactions during double-strand break repair in Escherichia coli. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/17284
Chicago Manual of Style (16th Edition):
Cockram, Charlotte Anne. “Genomic analysis of RecA-DNA interactions during double-strand break repair in Escherichia coli.” 2014. Doctoral Dissertation, University of Edinburgh. Accessed April 12, 2021.
http://hdl.handle.net/1842/17284.
MLA Handbook (7th Edition):
Cockram, Charlotte Anne. “Genomic analysis of RecA-DNA interactions during double-strand break repair in Escherichia coli.” 2014. Web. 12 Apr 2021.
Vancouver:
Cockram CA. Genomic analysis of RecA-DNA interactions during double-strand break repair in Escherichia coli. [Internet] [Doctoral dissertation]. University of Edinburgh; 2014. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1842/17284.
Council of Science Editors:
Cockram CA. Genomic analysis of RecA-DNA interactions during double-strand break repair in Escherichia coli. [Doctoral Dissertation]. University of Edinburgh; 2014. Available from: http://hdl.handle.net/1842/17284
Brandeis University
7.
Wang, Ruoxi.
The Role of Chromosome Organization in DNA Double-Strand Break Repair.
Degree: 2016, Brandeis University
URL: http://hdl.handle.net/10192/32360
► 3D nuclear architecture is a key factor in regulating many cellular processes. Here, based on the published haploid yeast chromosome conformation capture data, we investigated…
(more)
▼ 3D nuclear architecture is a key factor in regulating many cellular processes. Here, based on the published haploid yeast chromosome conformation capture data, we investigated the role of chromosome organization in DNA double-strand break repair, mainly through gene conversion. By using both single-donor viability assay and two-donor competition assay, we found the repair efficiency of a homologous donor sequence is highly correlated with their reconstituted distances to the recipient DSB site, which was deduced from the Hi-C database. Such correlation still exists when the break is induced at another locus. We also demonstrated that increasing the length of homology, inserting an ectopic Recombination Enhancer (RE), slowing down resection by FUN30 deletion, and enhancing RPA protein abundance effectively increased the repair efficiency. In addition, intra-chromosomal gene conversion is more frequent than inter-chromosomal events, but it is still constrained by chromosome organization. Our data revealed the tethering of centromeres to the spindle pole body during homologous recombination process, which agrees with the RabI configuration of yeast chromosomes. The result also provided extensive data to validate the chromosome polymer folding model. Through this study, we hope to provide more insights in the structural-functional correlation in eukaryotic genomes.
Subjects/Keywords: chromosome conformation; double-strand break repair; homology search; homologous recombination
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APA (6th Edition):
Wang, R. (2016). The Role of Chromosome Organization in DNA Double-Strand Break Repair. (Thesis). Brandeis University. Retrieved from http://hdl.handle.net/10192/32360
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Ruoxi. “The Role of Chromosome Organization in DNA Double-Strand Break Repair.” 2016. Thesis, Brandeis University. Accessed April 12, 2021.
http://hdl.handle.net/10192/32360.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Ruoxi. “The Role of Chromosome Organization in DNA Double-Strand Break Repair.” 2016. Web. 12 Apr 2021.
Vancouver:
Wang R. The Role of Chromosome Organization in DNA Double-Strand Break Repair. [Internet] [Thesis]. Brandeis University; 2016. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/10192/32360.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang R. The Role of Chromosome Organization in DNA Double-Strand Break Repair. [Thesis]. Brandeis University; 2016. Available from: http://hdl.handle.net/10192/32360
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Edinburgh
8.
Azeroglu, Benura.
DNA synthesis during double-strand break repair in Escherichia coli.
Degree: PhD, 2015, University of Edinburgh
URL: http://hdl.handle.net/1842/16213
► Efficient and accurate repair of DNA double strand breaks (DSBs) is required to maintain genomic stability in both eukaryotes and prokaryotes. In Escherichia coli, DSBs…
(more)
▼ Efficient and accurate repair of DNA double strand breaks (DSBs) is required to maintain genomic stability in both eukaryotes and prokaryotes. In Escherichia coli, DSBs are repaired by homologous recombination (HR). During this process, DNA synthesis needs to be primed and templated from an intact homologous sequence to restore any information that may have been lost on the broken DNA molecule. Two critical late stages of the pathway are repair DNA synthesis and the processing of Holliday junctions (HJs). However, our knowledge of the detailed mechanisms of these steps is still limited. Our laboratory has developed a system that permits the induction of a site-specific DSB in the bacterial chromosome. This break forms in a replication dependent manner on one of the sister chromosomes, leaving the second sister chromosome intact for repair by HR. Unlike previously available systems, the repairable nature of these breaks has made it possible to physically investigate the different stages of DNA double-strand break repair (DSBR) in a chromosomal context. In this thesis, I have addressed some fundamental questions relating to repair DNA synthesis and processing of HJs by using a combination of mutants defective in specific biochemical reactions and an assay that I have developed to detect repair DNA synthesis, using a polar termination sequence (terB). First, by using terB sites located at different locations around the break point, it was shown that the DnaB-dependent repair forks are established in a coordinated manner, meaning that the collision of the repair forks occurs between two repair DNA synthesis initiation sites. Second, DSBR was shown to require the PriB protein known to transduce the DNA synthesis initiation signal from PriA protein to DnaT. Conversely, the PriC protein (known as an alternative to PriB in some reactions) was not required in this process. PriB was also shown to be required to establish DnaB-dependent repair synthesis using the terB assay. Third, the establishment and termination of repair DNA synthesis by collision of converging repair forks were shown to occur independently of HJ resolution. This conclusion results from the comparison of the viability of single and double mutants, deficient in either the establishment of DNA synthesis, HJ resolution or in both reactions, subjected to DSBs and from the study of the DNA intermediates that accumulated in these mutants as detected by two-dimensional gel electrophoresis. Fourth, the role of RecG protein during DSB repair was investigated. Solexa sequencing analyses showed that recG null mutant cells undergoing DSBs accumulate more DNA around the break point (Mawer and Leach, unpublished data). This phenomenon was further investigated by two different approaches. Using terB sites in different locations around the break point and ChIP-Seq analyses to investigate the distribution of RecA in a recG null mutant demonstrating that the establishment of repair forks depends on the presence of RecG. Further studies using PriA helicase-dead mutant showed…
Subjects/Keywords: 572.8; DNA synthesis; RecG; double-strand break repair; PriA; homologous recombination
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APA ·
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APA (6th Edition):
Azeroglu, B. (2015). DNA synthesis during double-strand break repair in Escherichia coli. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/16213
Chicago Manual of Style (16th Edition):
Azeroglu, Benura. “DNA synthesis during double-strand break repair in Escherichia coli.” 2015. Doctoral Dissertation, University of Edinburgh. Accessed April 12, 2021.
http://hdl.handle.net/1842/16213.
MLA Handbook (7th Edition):
Azeroglu, Benura. “DNA synthesis during double-strand break repair in Escherichia coli.” 2015. Web. 12 Apr 2021.
Vancouver:
Azeroglu B. DNA synthesis during double-strand break repair in Escherichia coli. [Internet] [Doctoral dissertation]. University of Edinburgh; 2015. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1842/16213.
Council of Science Editors:
Azeroglu B. DNA synthesis during double-strand break repair in Escherichia coli. [Doctoral Dissertation]. University of Edinburgh; 2015. Available from: http://hdl.handle.net/1842/16213
Delft University of Technology
9.
Verkooijen, Paul (author).
Predicting DNA repair-deficient genotypes based on Cas9-induced DNA repair products.
Degree: 2021, Delft University of Technology
URL: http://resolver.tudelft.nl/uuid:46282f1b-68b0-4b94-8e65-c648684a2713
► Double strand breaks are lesions to the DNA and can be fatal for cells. Therefore these breaks are repaired, primarily by one of the three…
(more)
▼ Double strand breaks are lesions to the DNA and can be fatal for cells. Therefore these breaks are repaired, primarily by one of the three major
repair pathways. Two of these pathways are non-homologous end-joining (NHEJ) and theta-mediated end-joining (TMEJ). These pathways leave genetic alterations in their
repair products, a form of DNA damage. DNA damage is linked to several diseases such as cancer. Understanding of these pathways is important and being able to recognize which pathways are active can be beneficial for research. In this work,
repair products are used to predict
repair-deficient genotypes using Cas9-induced
repair products. Ku80 and PolQ deficient genotypes are used, impairing NHEJ and TMEJ respectively. The ability to recognize a
repair-deficient genotype is tested using two predictive tasks. First statistical machine learning algorithms are used to predict the genotype where a
repair product can be found. This is done by only using a single
repair product as input. Secondly, a set of Cas9-induced
repair products from a single cell culture is used to predict the genotype of that cell culture. Results show that when given a single
repair products, models have difficulty predicting the correct genotype. However, results are modest and the best classifier achieved an AUC of 0.76. For predicting the genotype of a cell culture using multiple
repair products of that culture showed really promising results. When predicting on cell cultures with breaks induced on a target site which the model has seen in the training data, results are near perfect. Predicting on unseen target sites shows that there is room for improvement but the best performing models showed an average AUC of 0.879 across target sites. A Results show that Cas9-induced
repair products can be used to predict
repair-deficient genotypes.
Advisors/Committee Members: de Pinho Gonçalves, J.S. (mentor), Reinders, M.J.T. (graduation committee), Tijsterman, Marcel (graduation committee), Delft University of Technology (degree granting institution).
Subjects/Keywords: Machine Learning; double strand break; repair products; pathway deficiency
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APA (6th Edition):
Verkooijen, P. (. (2021). Predicting DNA repair-deficient genotypes based on Cas9-induced DNA repair products. (Masters Thesis). Delft University of Technology. Retrieved from http://resolver.tudelft.nl/uuid:46282f1b-68b0-4b94-8e65-c648684a2713
Chicago Manual of Style (16th Edition):
Verkooijen, Paul (author). “Predicting DNA repair-deficient genotypes based on Cas9-induced DNA repair products.” 2021. Masters Thesis, Delft University of Technology. Accessed April 12, 2021.
http://resolver.tudelft.nl/uuid:46282f1b-68b0-4b94-8e65-c648684a2713.
MLA Handbook (7th Edition):
Verkooijen, Paul (author). “Predicting DNA repair-deficient genotypes based on Cas9-induced DNA repair products.” 2021. Web. 12 Apr 2021.
Vancouver:
Verkooijen P(. Predicting DNA repair-deficient genotypes based on Cas9-induced DNA repair products. [Internet] [Masters thesis]. Delft University of Technology; 2021. [cited 2021 Apr 12].
Available from: http://resolver.tudelft.nl/uuid:46282f1b-68b0-4b94-8e65-c648684a2713.
Council of Science Editors:
Verkooijen P(. Predicting DNA repair-deficient genotypes based on Cas9-induced DNA repair products. [Masters Thesis]. Delft University of Technology; 2021. Available from: http://resolver.tudelft.nl/uuid:46282f1b-68b0-4b94-8e65-c648684a2713
University of Minnesota
10.
Kan, Yinan.
The Mechanism of Precise Genome Engineering in Human Cells.
Degree: PhD, Biochemistry, Molecular Bio, and Biophysics, 2015, University of Minnesota
URL: http://hdl.handle.net/11299/175533
► Genome engineering is the intentional alteration of the genetic information in living cells or organisms. Since Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated 9 (CRISPR/Cas9) was…
(more)
▼ Genome engineering is the intentional alteration of the genetic information in living cells or organisms. Since Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated 9 (CRISPR/Cas9) was repurposed for genome engineering, the “CRISPR Craze” is quickly bridging the genotype and phenotype worlds and transforming the biological, biomedical and biotechnological research. Interestingly, CRISRP/Cas9 does not perform precise genome engineering (PGE) by itself, but it only induces a targeted genomic lesion and invites the HDR pathways to introduce the desired modifications. Although PGE has a wide application in genome modification and gene therapy, the identity, property and hierarchy of the HDR pathways leading to the formation of PGE products remain obscure. In my doctorial dissertation, I demonstrated that double-strand DNA (dsDNA) donors with a sizable central heterology preferentially utilize the double-strand break repair (DSBR) pathway in the absence and presence of chromosomal double-strand breaks (DSBs). This pathway generates long, bidirectional conversion tracts with linear distribution. In contrast, single-strand oligonucleotide (ODN) donors utilize the synthesis-dependent strand annealing (SDSA) and single-strand DNA incorporation (ssDI) pathways, respectively, depending on the strandedness of the genomic lesions and ODN donors. These pathways produce short, unidirectional and bidirectional conversion tracts with Gaussian distributions. The SDSA pathway is preferentially utilized in the presence of compound genomic lesions such as DSBs and paired nicks. In summary, this work systematically determined the identity, property and hierarchy of the HDR pathways underlying PGE with definitive molecular evidence, and provided practical guidelines for the improvement of PGE.
Subjects/Keywords: CRISPR Cas9; Double strand break repair; Genome engineering; Homology directed repair; Single strand DNA incorporation; Synthesis dependent strand annealing
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APA (6th Edition):
Kan, Y. (2015). The Mechanism of Precise Genome Engineering in Human Cells. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/175533
Chicago Manual of Style (16th Edition):
Kan, Yinan. “The Mechanism of Precise Genome Engineering in Human Cells.” 2015. Doctoral Dissertation, University of Minnesota. Accessed April 12, 2021.
http://hdl.handle.net/11299/175533.
MLA Handbook (7th Edition):
Kan, Yinan. “The Mechanism of Precise Genome Engineering in Human Cells.” 2015. Web. 12 Apr 2021.
Vancouver:
Kan Y. The Mechanism of Precise Genome Engineering in Human Cells. [Internet] [Doctoral dissertation]. University of Minnesota; 2015. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/11299/175533.
Council of Science Editors:
Kan Y. The Mechanism of Precise Genome Engineering in Human Cells. [Doctoral Dissertation]. University of Minnesota; 2015. Available from: http://hdl.handle.net/11299/175533
University of Rochester
11.
Tian, Xiao.
Identification of longevity and cancer resistance
mechanisms in long-lived rodent species.
Degree: PhD, 2016, University of Rochester
URL: http://hdl.handle.net/1802/31700
► Aging is a universal biological process and the majority of age-associated diseases remain unsolved, especially cancer. However, aging proceeds at different rates between mammals, which…
(more)
▼ Aging is a universal biological process and the
majority of age-associated diseases remain unsolved, especially
cancer. However, aging proceeds at different rates between mammals,
which results in a huge diversity of lifespans. In the case of
rodent species, maximum lifespans range from 4 years to 32 years.
Strikingly, rodents also exhibit differential tumor susceptibility.
Cancer incidence in some mouse strains reaches 95%. In contrast,
naked mole rats (Heterocephalus glaber) and blind mole rats
(Nannospalax sp.) are extremely cancer resistant. This thesis
describes the results of several studies aiming to identify the
molecular mechanisms responsible for longevity and tumor resistance
in long-lived rodent species. The first two studies compared the
efficiencies of several DNA repair mechanisms which are critical to
maintain genomic stability. The next two studies focused on the
longest-lived rodent, the naked mole rat, and identified the
production of high-molecular-mass hyaluronan (HMM HA) as the
responsible mechanism for its cancer resistance. In addition to
the tumor suppression function, HMM HA synthesis inhibits mammalian
target of rapamycin (mTOR), which potentially contributes to naked
mole rats’ exceptional longevity.
</br>
Genomic
instability is a critical hallmark of aging. Genomic DNA relies on
DNA repair mechanisms to maintain its integrity. We therefore
investigated the impact of different DNA repair pathways on the
evolution of diverse lifespans. Nucleotide excision repair (NER) is
responsible for removal of lesions that distort DNA helical
structure, such as thymine dimers and 6,4 photoproducts produced by
UV exposure. Contradictory results were previously published on the
contribution of nucleotide excision repair (NER) in the evolution
of longevity. In the present study, we did not find a significant
correlation between NER efficiency and maximum lifespan in 19
rodent species. However, our study revealed that solar UV acts as
the major selection pressure in the evolution of NER, as there is a
strong positive correlation between NER efficiency and the level of
UV exposure.
</br>
DNA double-strand break (DSB)
repair is a critical genome maintenance mechanism, as it protects
against the most deleterious type of DNA damage. We identified a
strong positive correlation between DSB repair efficiency and
maximum lifespan of a species. Additionally, we identified Sirtuin
6 (SIRT6) as a key factor contributing to more efficient DSB repair
in long-lived species. By comparing SIRT6 in representative short-
and long-lived rodents, mouse and beaver, we identified the
amino-acid substitutions that are responsible for their
dramatically different DSB repair activities. Based on our results,
we propose that modulating SIRT6 activity is a potential strategy
in maintaining efficient DSB repair and genomic stability in aged
organisms.
</br>
The longest living rodent, the
naked mole rat, exhibits negligible senescence with advancing age,
and is highly resistant to neoplasia. In contrast, short-lived…
Subjects/Keywords: Aging; Cancer resistance; DNA double strand break repair; Heterocephalus glaber; Hyaluronan; Nucleotide excision repair
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APA ·
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Manager
APA (6th Edition):
Tian, X. (2016). Identification of longevity and cancer resistance
mechanisms in long-lived rodent species. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/31700
Chicago Manual of Style (16th Edition):
Tian, Xiao. “Identification of longevity and cancer resistance
mechanisms in long-lived rodent species.” 2016. Doctoral Dissertation, University of Rochester. Accessed April 12, 2021.
http://hdl.handle.net/1802/31700.
MLA Handbook (7th Edition):
Tian, Xiao. “Identification of longevity and cancer resistance
mechanisms in long-lived rodent species.” 2016. Web. 12 Apr 2021.
Vancouver:
Tian X. Identification of longevity and cancer resistance
mechanisms in long-lived rodent species. [Internet] [Doctoral dissertation]. University of Rochester; 2016. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1802/31700.
Council of Science Editors:
Tian X. Identification of longevity and cancer resistance
mechanisms in long-lived rodent species. [Doctoral Dissertation]. University of Rochester; 2016. Available from: http://hdl.handle.net/1802/31700
Temple University
12.
McDevitt, Shane.
Mechanistic Studies of Double-strand Break Repair Factors RAD52 and DNA Polymerase Theta.
Degree: PhD, 2018, Temple University
URL: http://digital.library.temple.edu/u?/p245801coll10,518019
► Biomedical Sciences
Small molecule disruption of RAD52 rings as a mechanism for precision medicine in BRCA deficient cancers Suppression of RAD52 causes synthetic lethality in…
(more)
▼ Biomedical Sciences
Small molecule disruption of RAD52 rings as a mechanism for precision medicine in BRCA deficient cancers Suppression of RAD52 causes synthetic lethality in BRCA deficient cells. Yet pharmacological inhibition of RAD52, which binds single-strand DNA (ssDNA) and lacks enzymatic activity, has not been demonstrated. Here, we identify the small molecule 6-hydroxy-DL-dopa (6-OH-dopa) as a major allosteric inhibitor of the RAD52 ssDNA binding domain. For example, we find that multiple small molecules bind to and completely transform RAD52 undecamer rings into dimers, which abolishes the ssDNA binding channel observed in crystal structures. 6-OH-dopa also disrupts RAD52 heptamer and undecamer ring superstructures, and suppresses RAD52 recruitment and recombination activity in cells with negligible effects on other double-strand break repair pathways. Importantly, we show that 6-OH-dopa selectively inhibits the proliferation of BRCA deficient cancer cells, including those obtained from leukemia patients. Taken together, these data demonstrate small molecule disruption of RAD52 rings as a promising mechanism for precision medicine in BRCA deficient cancers. How RNA transcripts coordinate DNA recombination and repair Genetic studies in yeast indicate that RNA transcripts facilitate homology-directed DNA repair in a manner that is dependent on RAD52. The molecular basis for so-called RNA-DNA repair, however, remains unknown. Using reconstitution assays, we demonstrate that RAD52 directly cooperates with RNA as a sequence-directed ribonucleoprotein complex to promote two related modes of RNA-DNA repair. In a RNA-bridging mechanism, RAD52 assembles recombinant RNA-DNA hybrids that coordinate synapsis and ligation of homologous DNA breaks. In a RNA-templated mechanism, RAD52 mediated RNA-DNA hybrids enable reverse transcription dependent RNA-to-DNA sequence transfer at DNA breaks that licenses subsequent DNA recombination. Notably, we show that both mechanisms of RNA-DNA repair are promoted by transcription of a homologous DNA template in trans. In summary, these data elucidate how RNA transcripts cooperate with RAD52 to coordinate homology-directed DNA recombination and repair in the absence of a DNA donor, and demonstrate a direct role for transcription in RNA-DNA repair. Characterization of DNA polymerase θ as a reverse transcriptase RNA-to-DNA sequence has been observed in human cells, but how the phenomena occurs remains unknown. Multiple lines of evidence suggest putative reverse transcriptase (RT) activity as a potential mechanism for how RNA sequence can alter chromosomal DNA, but the source of this RT remains unknown. Here, we have identified that the unique A-family DNA polymerase theta (Polθ) displays robust RT activity, a characteristic not found in any other human polymerase tested from the A, B, X, and Y families. We propose that Polθ may be responsible for the observed RT activity in human cells.
Temple University – Theses
Advisors/Committee Members: Pomerantz, Richard;, Tempera, Italo, Skorski, Tomasz, Johnson, Neil, Yan, Hong;.
Subjects/Keywords: Molecular biology; Biochemistry;
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APA (6th Edition):
McDevitt, S. (2018). Mechanistic Studies of Double-strand Break Repair Factors RAD52 and DNA Polymerase Theta. (Doctoral Dissertation). Temple University. Retrieved from http://digital.library.temple.edu/u?/p245801coll10,518019
Chicago Manual of Style (16th Edition):
McDevitt, Shane. “Mechanistic Studies of Double-strand Break Repair Factors RAD52 and DNA Polymerase Theta.” 2018. Doctoral Dissertation, Temple University. Accessed April 12, 2021.
http://digital.library.temple.edu/u?/p245801coll10,518019.
MLA Handbook (7th Edition):
McDevitt, Shane. “Mechanistic Studies of Double-strand Break Repair Factors RAD52 and DNA Polymerase Theta.” 2018. Web. 12 Apr 2021.
Vancouver:
McDevitt S. Mechanistic Studies of Double-strand Break Repair Factors RAD52 and DNA Polymerase Theta. [Internet] [Doctoral dissertation]. Temple University; 2018. [cited 2021 Apr 12].
Available from: http://digital.library.temple.edu/u?/p245801coll10,518019.
Council of Science Editors:
McDevitt S. Mechanistic Studies of Double-strand Break Repair Factors RAD52 and DNA Polymerase Theta. [Doctoral Dissertation]. Temple University; 2018. Available from: http://digital.library.temple.edu/u?/p245801coll10,518019
Université de Lorraine
13.
Hoff, Grégory.
Réparation des cassures double-brin et variabilité chromosomique chez Streptomyces : Double-strand break repair and chromosomal variability in Streptomyces.
Degree: Docteur es, Écotoxicologie, biodiversité, écosystèmes, 2016, Université de Lorraine
URL: http://www.theses.fr/2016LORR0288
► Rayons ionisants, dessiccation, ou encore métabolites secondaires exogènes sont autant de facteurs qui peuvent engendrer des dommages à l’ADN chez les bactéries du sol, notamment…
(more)
▼ Rayons ionisants, dessiccation, ou encore métabolites secondaires exogènes sont autant de facteurs qui peuvent engendrer des dommages à l’ADN chez les bactéries du sol, notamment en provoquant la formation de cassures
double-brin (DSB), préjudice majeur pour une cellule. Chez les procaryotes, l’évolution a sélectionné deux principaux mécanismes de réparation des DSB, à savoir la recombinaison homologue (RH) et le non-homologous end joining (NHEJ). La RH est un mécanisme quasi-ubiquiste dans le monde bactérien qui repose sur l’utilisation d’une copie intacte de la molécule endommagée comme matrice pour la réparation de la DSB. Contrairement à la RH, le NHEJ n’est présent que chez 20 à 25% des bactéries et est considéré comme un mécanisme mutagène puisque la réparation de la DSB se fait sans matrice homologue et peut entrainer l’ajout ou la délétion de nucléotides au site de cassure. Chez la bactérie modèle Mycobacterium, seuls deux acteurs sont nécessaires pour la réparation par NHEJ. Ainsi, un dimère de protéine Ku se fixe sur la cassure puis recrute la protéine multifonctionnelle LigD, qui catalyse le traitement puis la ligation des extrémités grâce à ses domaines polymérase, nucléase et ligase. Les mécanismes de réparation des DSB chez les Streptomyces étaient peu connus à l’initiation de ce travail. Cette bactérie présente des caractéristiques génomiques remarquables avec notamment un chromosome linéaire de grande taille (6 à 12 Mb). En ce qui concerne la RH, nous avons focalisé nos recherches sur les étapes tardives (post-synaptiques) et étudié le rôle du complexe RuvABC et de RecG impliqués chez Escherichia coli dans la migration de la croix de Holliday et de sa résolution. La construction de mutants simples et multiples a montré que bien que les gènes codant ces protéines soient très conservés chez les Streptomyces, leur déficience ne se traduit chez Streptomyces ambofaciens que par une faible baisse de la recombinaison suite à un événement de conjugaison. Aucune baisse de l’efficacité de recombinaison intrachromosomique n’a en revanche été observée. Ces résultats suggèrent que des acteurs alternatifs majeurs sont encore à découvrir chez les Streptomyces. Le décryptage du mécanisme de NHEJ chez S. ambofaciens constitue une première dans ce genre bactérien. Une étude génomique exhaustive a permis de révéler la très grande diversité du nombre d’acteurs potentiels de ce mécanisme (Ku, LigDom, PolDom, NucDom) et de l’organisation des gènes qui les codent.. L’analyse fonctionnelle a révélé que l’ensemble des acteurs étaient impliqués dans la réponse à l’exposition à un faisceau d’électrons accélérés, connus pour induire, entre autre, la formation de DSB. La génération de DSB, par coupure endonucléasique I-SceI, a par ailleurs permis de mettre en évidence au niveau moléculaire des réparations de type NHEJ (délétions ou insertions de quelques nucléotides, intégration de fragments d’ADN). Les cassures dans les régions terminales du chromosome sont accompagnées de grandes délétions (jusqu’à 2,1 Mb) et de réarrangements…
Advisors/Committee Members: Leblond, Pierre (thesis director), Thibessard, Annabelle (thesis director).
Subjects/Keywords: Streptomyces; NHEJ; Réparation de l’ADN; Cassure double-Brin; Streptomyces; NHEJ; DNA repair; Double-Strand break
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APA ·
Chicago ·
MLA ·
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Export
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Manager
APA (6th Edition):
Hoff, G. (2016). Réparation des cassures double-brin et variabilité chromosomique chez Streptomyces : Double-strand break repair and chromosomal variability in Streptomyces. (Doctoral Dissertation). Université de Lorraine. Retrieved from http://www.theses.fr/2016LORR0288
Chicago Manual of Style (16th Edition):
Hoff, Grégory. “Réparation des cassures double-brin et variabilité chromosomique chez Streptomyces : Double-strand break repair and chromosomal variability in Streptomyces.” 2016. Doctoral Dissertation, Université de Lorraine. Accessed April 12, 2021.
http://www.theses.fr/2016LORR0288.
MLA Handbook (7th Edition):
Hoff, Grégory. “Réparation des cassures double-brin et variabilité chromosomique chez Streptomyces : Double-strand break repair and chromosomal variability in Streptomyces.” 2016. Web. 12 Apr 2021.
Vancouver:
Hoff G. Réparation des cassures double-brin et variabilité chromosomique chez Streptomyces : Double-strand break repair and chromosomal variability in Streptomyces. [Internet] [Doctoral dissertation]. Université de Lorraine; 2016. [cited 2021 Apr 12].
Available from: http://www.theses.fr/2016LORR0288.
Council of Science Editors:
Hoff G. Réparation des cassures double-brin et variabilité chromosomique chez Streptomyces : Double-strand break repair and chromosomal variability in Streptomyces. [Doctoral Dissertation]. Université de Lorraine; 2016. Available from: http://www.theses.fr/2016LORR0288
14.
Smith, Cheryl Jacobs.
Mechanisms in Suppressing Chromosomal Translocations and Maintaining Genome Stability.
Degree: PhD, Human Genetics, 2014, University of Michigan
URL: http://hdl.handle.net/2027.42/108783
► Double strand breaks (DSBs) represent one of the most dangerous forms of DNA damage. DSBs are generated during normal metabolic processes, such as DNA replication,…
(more)
▼ Double strand breaks (DSBs) represent one of the most dangerous forms of DNA damage. DSBs are generated during normal metabolic processes, such as DNA replication, or upon exposure of cells to exogenous agents, such as ionizing radiation. In addition, DSBs are formed as intermediates during programmed DNA rearrangements that occur during early B and T lymphocyte development, a process known as V(D)J recombination. Unrepaired or mis-repaired DNA ends can engender detrimental outcomes for cells and organisms such as aberrant genomic events like chromosomal translocations. The classical nonhomologous end joining (cNHEJ) pathway is one of the major DNA DSB
repair pathways operative in mammalian cells and is required for both general DSB
repair and V(D)J recombination.
The studies of my dissertation investigate the functions of DNA nucleases in the
repair of
double strand breaks during V(D)J recombination. I have undertaken two independent, but related, lines of investigation to address this question. One project sought to elucidate the regulation of the ARTEMIS nuclease during V(D)J recombination. I examined the molecular mechanisms underlying tumorigenesis caused by an Artemis hypomorphic disease allele and identified that the ARTEMIS C-terminus suppresses tumorigenesis associated with misrepair of DNA DSBs generated during V(D)J recombination. My findings raise the possibility that particular defects in ARTEMIS that result in partial loss of function, can predispose to lymphoma, but not complete immunodeficiency.
The second project focused on determining the interplay between the ARTEMIS and MRE11 nuclease in facilitating normal and aberrant V(D)J rearrangements. My results indicate that mutation of the MRE11 complex prevents tumorigenesis associated with aberrant end joining of V(D)J loci, an in
turn, implicates the MRE11 complex in promoting tumorigenesis associated with DNA damage. Both projects have led to a greater understanding of the mechanisms underlying human lymphoma caused by impaired ARTEMIS nuclease activity, and additionally, identified the MRE11 complex as a possible chemotherapeutic target for improved treatment for lymphoid malignancies.
Advisors/Committee Members: Sekiguchi, Joann (committee member), Wilson, Thomas E. (committee member), Chan, Raymond C. (committee member), Dunnick, Wesley (committee member), Moran, John V. (committee member).
Subjects/Keywords: DNA Double Strand Break Repair and V(D)J Recombination; Lymphoma; Genetics; Health Sciences
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APA (6th Edition):
Smith, C. J. (2014). Mechanisms in Suppressing Chromosomal Translocations and Maintaining Genome Stability. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/108783
Chicago Manual of Style (16th Edition):
Smith, Cheryl Jacobs. “Mechanisms in Suppressing Chromosomal Translocations and Maintaining Genome Stability.” 2014. Doctoral Dissertation, University of Michigan. Accessed April 12, 2021.
http://hdl.handle.net/2027.42/108783.
MLA Handbook (7th Edition):
Smith, Cheryl Jacobs. “Mechanisms in Suppressing Chromosomal Translocations and Maintaining Genome Stability.” 2014. Web. 12 Apr 2021.
Vancouver:
Smith CJ. Mechanisms in Suppressing Chromosomal Translocations and Maintaining Genome Stability. [Internet] [Doctoral dissertation]. University of Michigan; 2014. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/2027.42/108783.
Council of Science Editors:
Smith CJ. Mechanisms in Suppressing Chromosomal Translocations and Maintaining Genome Stability. [Doctoral Dissertation]. University of Michigan; 2014. Available from: http://hdl.handle.net/2027.42/108783
Vanderbilt University
15.
Sowd, Gregory Alan.
DNA Damage Signaling Orchestrates SV40 Chromatin Replication.
Degree: PhD, Biological Sciences, 2013, Vanderbilt University
URL: http://hdl.handle.net/1803/13987
► The effects of DNA damage signaling on the DNA replication of the polyomavirus SV40 are examined in this dissertation. Infection of monkey cells with SV40…
(more)
▼ The effects of DNA damage signaling on the DNA replication of the polyomavirus SV40 are examined in this dissertation. Infection of monkey cells with SV40 results in large amounts of cellular DNA damage signaling through the cellular kinases ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR). Literature pertaining to DNA replication, DNA
repair, DNA damage signaling, and polyomaviral replication is first discussed. This is followed by a number of experiments testing the molecular mechanisms that necessitate DNA damage signaling by ATM and ATR during SV40 infection. Furthermore, the contribution of ATM and ATR to SV40-induced cell cycle arrest and
repair protein recruitment to viral DNA replication centers is explored. After an examination of how my experiments fit in with relevant manuscripts, I discuss the possible consequences of the aberrant products found upon inhibition of DNA damage signaling during SV40 DNA replication and how my current studies can be advanced. Additionally, the connection between DNA damage signaling and DNA
repair and the implications of my dissertation to cellular DNA replication are discussed.
Advisors/Committee Members: Ryoma Ohi (committee member), David Cortez (committee member), Terence Dermody (committee member), Ellen Fanning (committee member), Katherine Friedman (Committee Chair).
Subjects/Keywords: polyomavirus; Double Strand Break; Ku-55933; VE-821; ATR; ATM; DNA repair; DNA replication; SV40
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APA (6th Edition):
Sowd, G. A. (2013). DNA Damage Signaling Orchestrates SV40 Chromatin Replication. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/13987
Chicago Manual of Style (16th Edition):
Sowd, Gregory Alan. “DNA Damage Signaling Orchestrates SV40 Chromatin Replication.” 2013. Doctoral Dissertation, Vanderbilt University. Accessed April 12, 2021.
http://hdl.handle.net/1803/13987.
MLA Handbook (7th Edition):
Sowd, Gregory Alan. “DNA Damage Signaling Orchestrates SV40 Chromatin Replication.” 2013. Web. 12 Apr 2021.
Vancouver:
Sowd GA. DNA Damage Signaling Orchestrates SV40 Chromatin Replication. [Internet] [Doctoral dissertation]. Vanderbilt University; 2013. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1803/13987.
Council of Science Editors:
Sowd GA. DNA Damage Signaling Orchestrates SV40 Chromatin Replication. [Doctoral Dissertation]. Vanderbilt University; 2013. Available from: http://hdl.handle.net/1803/13987
Harvard University
16.
Zhang, Tingting.
Elucidating Mechanisms of IgH Class Switch Recombination Involving Switch Regions and Double Strand Break Joining.
Degree: PhD, Immunology, 2011, Harvard University
URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:10336910
► During IgH class switch recombination (CSR) in mature B lymphocytes, activation-induced cytidine deaminase (AID) initiates DNA double strand breaks (DSBs) within switch (S) regions flanking…
(more)
▼ During IgH class switch recombination (CSR) in mature B lymphocytes, activation-induced cytidine deaminase (AID) initiates DNA
double strand breaks (DSBs) within switch (S) regions flanking different sets of the IgH locus (IgH) constant ((C
H)) region exons. End-Joining of DSBs in the upstream donor S region (Sm) to DSBs in a downstream acceptor S region ((S
acc)) replaces the initial set of (C
H) exons, Cm, with a set of downstream (C
H) exons, leading to Ig class switching from IgM to another IgH class (e.g., IgG, IgE, or IgA). In addition to joining to DSBs within another S region, AID-induced DSBs within a given S region are often rejoined or joined to other DSBs in the same S region to form internal switch deletions (ISDs). ISDs were frequently observed in Sm but rarely in (S
accs), suggesting that AID targeting to (S
accs) requires prior recruitment to Sm. To test this hypothesis, we assessed CSR and ISDs in B cells lacking Sm and found that AID frequently targets downstream (S
accs) independently of Sm. These studies also led us to propose an alternative pathway of "downstream" IgE class switching that involves joining of DSBs within the downstream (Sγ1) and (Sε) regions as a first step before joining of (Sμ) to the hybrid downstream S region. To further elucidate the CSR mechanism, we addressed the long-standing question of whether S region DSBs during CSR involves a direction-specific mechanism similar to joining of RAG1/2 endonuclease-generated DSBs during V(D)J recombination. We used an unbiased high throughput method to isolate junctions between I-SceI meganuclease-generated DSBs at a target site that replaces the IgH (Sγ1) region and other genomic DSBs of endogenous origin. Remarkably, we found that the I-SceI-generated DSBs were joined to both upstream DSBs in (Sμ) and downstream DSBs in (Sε) predominantly in orientations associated with joining during productive CSR. This process required the DSB response factor 53BP1 to maintain the orientation-dependence, but not the overall levels, of joining between these widely separated IgH breaks. We propose that CSR exploits a mechanism involving 53BP1 to enhance directional joining of DSBs within IgH in an orientation that leads to productive CSR.
Advisors/Committee Members: Alt, Frederick W. (advisor), Notarangelo, Luigi (committee member), Lieberman, Judy (committee member), Scully, Ralph (committee member), Bassing, Craig (committee member).
Subjects/Keywords: 53BP1; class switch recombination; double strand break repair; IgH; switch regions; immunology
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APA (6th Edition):
Zhang, T. (2011). Elucidating Mechanisms of IgH Class Switch Recombination Involving Switch Regions and Double Strand Break Joining. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:10336910
Chicago Manual of Style (16th Edition):
Zhang, Tingting. “Elucidating Mechanisms of IgH Class Switch Recombination Involving Switch Regions and Double Strand Break Joining.” 2011. Doctoral Dissertation, Harvard University. Accessed April 12, 2021.
http://nrs.harvard.edu/urn-3:HUL.InstRepos:10336910.
MLA Handbook (7th Edition):
Zhang, Tingting. “Elucidating Mechanisms of IgH Class Switch Recombination Involving Switch Regions and Double Strand Break Joining.” 2011. Web. 12 Apr 2021.
Vancouver:
Zhang T. Elucidating Mechanisms of IgH Class Switch Recombination Involving Switch Regions and Double Strand Break Joining. [Internet] [Doctoral dissertation]. Harvard University; 2011. [cited 2021 Apr 12].
Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:10336910.
Council of Science Editors:
Zhang T. Elucidating Mechanisms of IgH Class Switch Recombination Involving Switch Regions and Double Strand Break Joining. [Doctoral Dissertation]. Harvard University; 2011. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:10336910
University of Adelaide
17.
Wang, Dong.
Chloroplast DNAs diversify nuclear and mitochondrial genomes in plants.
Degree: 2013, University of Adelaide
URL: http://hdl.handle.net/2440/83738
► Mitochondria and chloroplasts in eukaryotic cells originated more than a billion years ago when an ancestor of the nucleated cell engulfed two different prokaryotes in…
(more)
▼ Mitochondria and chloroplasts in eukaryotic cells originated more than a billion years ago when an ancestor of the nucleated cell engulfed two different prokaryotes in separate sequential events. Extant cytoplasmic organellar genomes contain very few genes compared with their candidate free-living ancestors, as most have functionally relocated to the nucleus. The first step in functional relocation involves the integration of cytoplasmic organllar DNA fragments into nuclear chromosomes and this process continues at high frequency with attendant genetic, genomic and evolutionary consequences. The frequency of DNA transposition from plastid (chloroplast) to nucleus has been measured experimentally in tobacco plants (Nicotiana tabacum) growing in ideal growth conditions. To monitor the effects of environmental stress on the rate of DNA transfer from plastid to nucleus, two different transplastomic tobacco lines were used and it was shown that DNA migration from chloroplasts to the nucleus was markedly increased by mild heat stress. In addition, manually induced DNA
double-
strand breaks (DSBs) were made using the rare-cutting endonuclease I-SceI in tobacco and Arabidopsis and this system was used to investigate the role of DSBs
repair during organellar DNA insertion into the nuclear genome. Integrants of none organelle DNA origin were found at the
break points when plants grown at normal temperature. In contrast, insertions of mitochondrial DNA fragments occurred during the
repair of induced DSBs were only observed in tobacco when plants were heat treated. This finding suggested that the frequency of mitochondrial DNA migration was also increased by mild heat stress. To further investigate whether the DSB
repair is involved in plastid DNA integration into the nuclear genome, 14 nuclear insertions of chloroplast DNA (nupts) that are unique to Oryza sativa subsp. indica were indentified. Comparisons with the nuclear pre-insertion loci (identified in the related subspecies, O. sativa subsp. Japonica which lacked these nupts) indicated that chloroplast DNA had integrated by non-homologous end joining. Combined with analyzing available DNase-seq data, this analysis also revealed that nupts were significantly more frequent in open chromatin regions of the nucleus. The generality of this insertion site preference was tested in the chimpanzee genome by comparing nuclear loci containing integrants of mitochondrial DNA (numts) with numt-lacking preinsertion sites in the human genome. Mitochondrial DNAs also tended to insert more frequently into regions of open chromatin revealed by human DNase-seq and FAIRE-seq databases. Chloroplast DNA movement is not limited to the nucleus and it is also found within the mitochondrial genome in most plants. However, the functions of these plastid-derived DNA tracts in mitochondrial genomes (also called mtpt for mitochondrial plastid DNA) have been considered to be limited to rare instances where plastid tRNA genes have replaced their mitochondrial counterparts, where short patches of…
Advisors/Committee Members: Timmis, Jeremy Newman (advisor), Adelson, David Louis (advisor), Da Silva, Jack (advisor), School of Molecular and Biomedical Science (school).
Subjects/Keywords: endosymbiotic gene transfer; open chromatin; double-strand break repair; chloroplast; mitochondrion; environmental stress
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APA ·
Chicago ·
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CSE |
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APA (6th Edition):
Wang, D. (2013). Chloroplast DNAs diversify nuclear and mitochondrial genomes in plants. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/83738
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Dong. “Chloroplast DNAs diversify nuclear and mitochondrial genomes in plants.” 2013. Thesis, University of Adelaide. Accessed April 12, 2021.
http://hdl.handle.net/2440/83738.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Dong. “Chloroplast DNAs diversify nuclear and mitochondrial genomes in plants.” 2013. Web. 12 Apr 2021.
Vancouver:
Wang D. Chloroplast DNAs diversify nuclear and mitochondrial genomes in plants. [Internet] [Thesis]. University of Adelaide; 2013. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/2440/83738.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang D. Chloroplast DNAs diversify nuclear and mitochondrial genomes in plants. [Thesis]. University of Adelaide; 2013. Available from: http://hdl.handle.net/2440/83738
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Colorado State University
18.
Nelson, Christopher Boulanger.
Telomeric double strand breaks undergo resection - but not repair - in G1 human cells.
Degree: PhD, Cell and Molecular Biology, 2017, Colorado State University
URL: http://hdl.handle.net/10217/184022
► Telomeres are specialized G-rich repetitive regions at the ends of eukaryotic chromosomes (TTAGGGn in mammalian cells). Telomeres function to prevent double strand break (DSB) repair…
(more)
▼ Telomeres are specialized G-rich repetitive regions at the ends of eukaryotic chromosomes (TTAGGGn in mammalian cells). Telomeres function to prevent
double strand break (DSB)
repair activities at chromosome ends, in order to avoid fusion events which result in lethal dicentric chromosomes. Telomeric repeats make up an appreciable amount of genomic DNA (1-15kb per chromosome end). Therefore, an interesting question becomes, how is the inevitable DSB occurring within a telomere dealt with by the cell? It has been suggested that DSBs within telomeric DNA may not be repaired at all, as DSB DNA damage response (DDR) foci at telomeres do not resolve following large amounts of global DNA damage (e.g. ionizing radiation). Such studies also suggest that telomere
repair may be inhibited specifically in G1, as the majority of surviving cells with unresolved telomere damage responses were senescent (a G1 phenotype). On the other hand, studies on the fragmentation of telomeric DNA following cutting with a telomere-targeted endonucleases indicate that
repair of telomere-specific DSBs involves Homologous Recombination (HR) and
Break-Induced Replication (BIR). However, a marker of telomeric DSB DDRs was only observed in cells with BrdU incorporation, in support of the view that
repair of telomeric DSBs is an S/G2-related process, which does not occur in G1. To follow up on these studies, we investigated telomeric DDRs and DSB
repair in individual G1 cells using ionizing radiation (IR) and a targeted telomere-cutting endonuclease. IR exposure could potentially induce loss of telomere function, such that persistent DDRs may not represent actual DSBs. To rule out this possibility, we evaluated whether persistent telomeric DDRs following IR occurred at telomeres that were critically short or lacking TRF2. We found that persistent telomeric DDRs occurred at telomeres of normal length and TRF2 status, in support of the conclusion that G1 telomeric DSBs are irreparable. Additionally, using the telomere-targeted endonuclease we observed that telomeric DSBs in G1 cells elicited a relatively conventional DSB DDR – with one important exception – G1 telomeric DDRs failed to recruit 53BP1, an event implicated in the completion of DSB
repair by most pathways, but especially, canonical non-homologous end joining (cNHEJ). Further, shRNA knockdown and kinase inhibition of the cNHEJ factor DNA-PKcs, provided evidence that cNHEJ is not responsible for
repair of telomeric DSBs, and that DNA-PKcs does not influence recruitment of 53BP1 to telomeric DSBs in G1. Partial deprotection of telomeres, achieved by siRNA depletion of TRF2, also failed to alleviate inhibition of 53BP1 recruitment to G1 telomeric DSBs, suggesting that 53BP1 recruitment to telomeric DSBs may require full deprotection of telomeres. However, as 53BP1 recruitment occurs at de-protected telomeres, this idea would be difficult to test. Most likely related to the lack of 53BP1 recruitment, an abundance of bidirectionally occurring single-stranded DNA was observed at G1 telomeric DSBs, a…
Advisors/Committee Members: Bailey, Susan (advisor), Argueso, Lucas (committee member), Kato, Takamitsu (committee member), Wiese, Claudia (committee member), Miller, Benjamin (committee member), Chicco, Adam (committee member).
Subjects/Keywords: DNA damage response; double strand break; telomeres; genomic stability; DNA repair; DNA damage
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APA ·
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CSE |
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Manager
APA (6th Edition):
Nelson, C. B. (2017). Telomeric double strand breaks undergo resection - but not repair - in G1 human cells. (Doctoral Dissertation). Colorado State University. Retrieved from http://hdl.handle.net/10217/184022
Chicago Manual of Style (16th Edition):
Nelson, Christopher Boulanger. “Telomeric double strand breaks undergo resection - but not repair - in G1 human cells.” 2017. Doctoral Dissertation, Colorado State University. Accessed April 12, 2021.
http://hdl.handle.net/10217/184022.
MLA Handbook (7th Edition):
Nelson, Christopher Boulanger. “Telomeric double strand breaks undergo resection - but not repair - in G1 human cells.” 2017. Web. 12 Apr 2021.
Vancouver:
Nelson CB. Telomeric double strand breaks undergo resection - but not repair - in G1 human cells. [Internet] [Doctoral dissertation]. Colorado State University; 2017. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/10217/184022.
Council of Science Editors:
Nelson CB. Telomeric double strand breaks undergo resection - but not repair - in G1 human cells. [Doctoral Dissertation]. Colorado State University; 2017. Available from: http://hdl.handle.net/10217/184022
University of New Mexico
19.
Wiest, Nathaniel E.
MAINTENANCE OF GENETIC AND EPIGENETIC STABILITY DURING DNA DOUBLE-STRAND BREAK REPAIR AND DNA REPLICATION.
Degree: Biomedical Sciences Graduate Program, 2019, University of New Mexico
URL: https://digitalrepository.unm.edu/biom_etds/191
► Eukaryotic genomes are assembled into a complex of DNA and proteins known as chromatin. The packaging of DNA into chromatin is the foundational strategy…
(more)
▼ Eukaryotic genomes are assembled into a complex of DNA and proteins known as chromatin. The packaging of DNA into chromatin is the foundational strategy that cells use to both compress genomic DNA into nuclei and regulate access to its contents. The basic repeating subunit of chromatin is the nucleosome, composed of an octamer of two copies of each of the core histone proteins H2A, H2B, H3, and H4 around which 146 bp of DNA are tightly wrapped. While the compaction of genomes into chromatin offers cells significant advantages, it also presents serious challenges to fundamental processes that maintain genome integrity, including DNA
repair and replication. Nucleosomes must be disrupted to allow access to damaged DNA by
repair factors. Additionally, the millions of nucleosomes that package genomic DNA are displaced during DNA replication. After their displacement, nucleosomes must be faithfully restored to preserve proper chromatin compaction and regulation of access to DNA that underlie transcriptional programs and cellular identity. Thus, the processes that maintain genome and epigenome stability are intricately linked.
In the first aim of this dissertation, I examined the role of the conserved SWI/SNF ATP-dependent nucleosome remodeler in the
repair of DNA
double-
strand breaks (DSBs) in yeast. I demonstrated that SWI/SNF facilitates the actions of the MRX complex at the DSB, including the eviction of KU, initiation of DNA end resection, recruitment of long-range resection factors, and activation of the DNA damage response. Furthermore, I showed that this activity of SWI/SNF is related to its role in the efficient eviction of nucleosomes near a DSB. This study contributes to an understanding of the roles of the clinically relevant SWI/SNF complex in mediating accurate
repair of DSBs in the context of chromatin.
In the second aim, I examined the role of DNA Ligase I (Lig1) in coordinating chromatin assembly and maturation on newly replicated DNA in mammalian cells. I accumulated preliminary data demonstrating that Lig1 may influence the deposition of the linker histone H1 on DNA during replication, and that that Lig1 may also contribute to the recruitment of DNA methylation machinery. These combined studies provide novel information on two critical processes that maintain genetic and epigenetic stability in eukaryotes.
Advisors/Committee Members: Alan E Tomkinson, PhD, Mary Ann Osley, PhD, Diane S Lidke, PhD, David Y Lee, MD/PhD.
Subjects/Keywords: Chromatin; SWI/SNF; Double-Strand Break Repair; DNA Replication; DNA Ligase; Genome Stability; Molecular Genetics
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APA (6th Edition):
Wiest, N. E. (2019). MAINTENANCE OF GENETIC AND EPIGENETIC STABILITY DURING DNA DOUBLE-STRAND BREAK REPAIR AND DNA REPLICATION. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biom_etds/191
Chicago Manual of Style (16th Edition):
Wiest, Nathaniel E. “MAINTENANCE OF GENETIC AND EPIGENETIC STABILITY DURING DNA DOUBLE-STRAND BREAK REPAIR AND DNA REPLICATION.” 2019. Doctoral Dissertation, University of New Mexico. Accessed April 12, 2021.
https://digitalrepository.unm.edu/biom_etds/191.
MLA Handbook (7th Edition):
Wiest, Nathaniel E. “MAINTENANCE OF GENETIC AND EPIGENETIC STABILITY DURING DNA DOUBLE-STRAND BREAK REPAIR AND DNA REPLICATION.” 2019. Web. 12 Apr 2021.
Vancouver:
Wiest NE. MAINTENANCE OF GENETIC AND EPIGENETIC STABILITY DURING DNA DOUBLE-STRAND BREAK REPAIR AND DNA REPLICATION. [Internet] [Doctoral dissertation]. University of New Mexico; 2019. [cited 2021 Apr 12].
Available from: https://digitalrepository.unm.edu/biom_etds/191.
Council of Science Editors:
Wiest NE. MAINTENANCE OF GENETIC AND EPIGENETIC STABILITY DURING DNA DOUBLE-STRAND BREAK REPAIR AND DNA REPLICATION. [Doctoral Dissertation]. University of New Mexico; 2019. Available from: https://digitalrepository.unm.edu/biom_etds/191
University of Edinburgh
20.
Parry, Frances Louise.
Identification of pre-synaptic processing proteins from Bacteroides fragilis.
Degree: PhD, 2011, University of Edinburgh
URL: http://hdl.handle.net/1842/5031
► The repair of DNA double-strand breaks (DSBs) is required for the survival of all organisms. In bacteria, DNA DSBs can occur during normal housekeeping processes…
(more)
▼ The repair of DNA double-strand breaks (DSBs) is required for the survival of all organisms. In bacteria, DNA DSBs can occur during normal housekeeping processes such as DNA replication or by exogenous damage due to chemicals or radiation. DSBs will compromise the integrity of the genome if left un-repaired, and can be fatal to an organism. Repair of DSBs by homologous recombination (HR) replicates missing chromosomal regions before joining of the separated DNA ends. In Escherichia coli the HR repair steps are; pre-synapsis, synapsis and post-synapsis. In the pre-synaptic stage a DSB is processed into a 3′ single-strand overhang, the substrate required for strand invasion in the synapsis stage and the eventual repair of the DSB. At present there are three identified pre-synapsis systems involved in recombination in bacteria; represented by the AdnAB, AddAB and the RecBCD protein complexes. Each system functions in a similar manner but differ in the physical composition of the machinery. This project investigated the pre-synaptic system of Bacteroides fragilis NCTC9343. Genes encoding putative pre-synapsis proteins were initially identified through analysis of the NCTC9343 genome. The function of these proteins was investigated in vivo by rescue of a repair-deficient strain of E. coli. This demonstrated that Bacteroides fragilis encodes a two component system, where both genes products are required to work in concert for pre-synaptic processing of DSBs. The identified genes were BF2192 and BF2191, and have been renamed addA and addB, respectively. To further examine the role of the AddAB proteins in DSB repair, a Bacteroides fragilis strain with a deletion of addAB was constructed and shown to be extremely sensitive to DNA damaging agents. The AddAB complex was purified and found to be an ATP-dependant helicase and exonuclease that acted on double-stranded DNA ends. In conclusion, this project has identified the proteins involved in pre-synaptic processing of DSBs in B. fragilis NCTC9343, consisting of AddAB homologues, and shown their protective role in repair of DNA damage.
Subjects/Keywords: 579; bacteroides fragilis; AddAB; double-strand break repair; RecBCD; pre-synaptic complex
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APA (6th Edition):
Parry, F. L. (2011). Identification of pre-synaptic processing proteins from Bacteroides fragilis. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/5031
Chicago Manual of Style (16th Edition):
Parry, Frances Louise. “Identification of pre-synaptic processing proteins from Bacteroides fragilis.” 2011. Doctoral Dissertation, University of Edinburgh. Accessed April 12, 2021.
http://hdl.handle.net/1842/5031.
MLA Handbook (7th Edition):
Parry, Frances Louise. “Identification of pre-synaptic processing proteins from Bacteroides fragilis.” 2011. Web. 12 Apr 2021.
Vancouver:
Parry FL. Identification of pre-synaptic processing proteins from Bacteroides fragilis. [Internet] [Doctoral dissertation]. University of Edinburgh; 2011. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1842/5031.
Council of Science Editors:
Parry FL. Identification of pre-synaptic processing proteins from Bacteroides fragilis. [Doctoral Dissertation]. University of Edinburgh; 2011. Available from: http://hdl.handle.net/1842/5031
Ohio University
21.
Khade, Nilesh V.
A Study of DNA Homologous Recombination Mechanism through
Biochemical Characterization of Rad52 and BRCA2 in Yeast and
Humans.
Degree: PhD, Biological Sciences (Arts and Sciences), 2015, Ohio University
URL: http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1437664889
► Homologous recombination (HR) is critical for double strand break repair and maintenance of genome stability. The recombination mediator proteins in HR play key roles by…
(more)
▼ Homologous recombination (HR) is critical for
double
strand break repair and maintenance of genome stability. The
recombination mediator proteins in HR play key roles by recruiting
RecA-family recombinases like Rad51 to single-stranded DNA. In
vitro, mediator proteins bind to their cognate Rad51 recombinases
and mediate their loading onto single-stranded DNA which catalyses
homology search and DNA
strand invasion, a unique and essential
process in HR. In yeast, the mediator function is characteristic of
the Rad52 (yRad52) protein which also promotes ssDNA annealing. In
humans, the breast cancer susceptibility protein (BRCA2) possess
the mediator function while the human Rad52 protein is thought to
anneal complementary single stranded DNA. However, the role of
human Rad52 (hRad52) in HR has remained elusive and no in vitro
mediator activity of human Rad52 has been reported. In this study,
the loss of mediator function in hRad52 was investigated by
examining interspecies interactions between the yeast and human
mediators with human Rad51 (hRad51) recombinase. Interestingly,
yRad52 successfully mediated loading of hRad51 recombinase onto the
single-stranded DNA complexed with yeast RPA in vitro. This
recombinase-loading activity was abolished when yeast RPA (E.coli
SSB homolog in yeast) was replaced with human RPA, suggesting that
species-specific interaction between Rad52 and RPA is important for
mediator activity. In this study, the hRad51 binding domain was
identified in the yRad52 C-terminus; deletion of the C-terminus
(yRad52NM) resulted in loss of mediator function. hRad52 was also
tested for mediator activity but it failed to mediate loading of
hRad51 in presence of either hRPA or yRPA. As yeast and human Rad52
share similarity between their N-terminal domains, the C-terminal
Rad51-binding domain of human Rad52 was replaced with BRC repeats
of BRCA2, which is known to interact with hRad51. In another
experiment, the hRad52 C-terminal domain was replaced with the
yRad52 C-terminal region. Unexpectedly, hRad52-BRC4 and
hRad52NM-y52C fusions did not attain mediator activity for human
Rad51. Mediator function was not present even when the yRad52
C-terminal domain was replaced with either multiple BRC4 repeats or
the BRC3-BRC4 repeat of BRCA2. Taken together, these results
indicate that BRC repeats cannot substitute the function of the
C-terminal Rad51-binding domain of human or yeast Rad52 and
furthermore, an intact yRad52 is required for hRad51 mediator
function. In addition, the yRad52 C-terminal domain was determined
to be required for efficient ssDNA annealing.
Advisors/Committee Members: Sugiyama, Tomohiko (Advisor).
Subjects/Keywords: Biochemistry; Biology; DNA Repair; Double Strand Break; Homologous Recombination; Mediator Activity; Annealing Activity; Rad52; BRCA2
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APA ·
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CSE |
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APA (6th Edition):
Khade, N. V. (2015). A Study of DNA Homologous Recombination Mechanism through
Biochemical Characterization of Rad52 and BRCA2 in Yeast and
Humans. (Doctoral Dissertation). Ohio University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1437664889
Chicago Manual of Style (16th Edition):
Khade, Nilesh V. “A Study of DNA Homologous Recombination Mechanism through
Biochemical Characterization of Rad52 and BRCA2 in Yeast and
Humans.” 2015. Doctoral Dissertation, Ohio University. Accessed April 12, 2021.
http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1437664889.
MLA Handbook (7th Edition):
Khade, Nilesh V. “A Study of DNA Homologous Recombination Mechanism through
Biochemical Characterization of Rad52 and BRCA2 in Yeast and
Humans.” 2015. Web. 12 Apr 2021.
Vancouver:
Khade NV. A Study of DNA Homologous Recombination Mechanism through
Biochemical Characterization of Rad52 and BRCA2 in Yeast and
Humans. [Internet] [Doctoral dissertation]. Ohio University; 2015. [cited 2021 Apr 12].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1437664889.
Council of Science Editors:
Khade NV. A Study of DNA Homologous Recombination Mechanism through
Biochemical Characterization of Rad52 and BRCA2 in Yeast and
Humans. [Doctoral Dissertation]. Ohio University; 2015. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1437664889
The Ohio State University
22.
Hu, Yiheng.
Functions of BRCA1, 53BP1 and SUMO isoforms in DNA
double-strand break repair in mammalian cells.
Degree: PhD, Molecular, Cellular and Developmental
Biology, 2014, The Ohio State University
URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1397756848
► In this dissertation study, we have investigated the protein functions in DNA double-strand break (DSB) repair of three important factors, BRCA1, 53BP1 and SUMO isoforms,…
(more)
▼ In this dissertation study, we have investigated the
protein functions in DNA
double-
strand break (DSB)
repair of three
important factors, BRCA1, 53BP1 and SUMO isoforms, at levels of
biochemical activity, protein dynamics and chromosomal DNA
repair.
Our work reveals novel mechanisms of these proteins functioning in
response to DSB damage, hence providing insights of where and how
they are actively involved in each subpathway of DSB
repair. In the
first part of our work, we studied BRCA1, a tumor suppressor
important for the maintenance of genomic stability including
centrosome control and DSB
repair, and found that a putative
enzymatic mutant of BRCA1— BRCA1(I26A), which had been thought to
disrupt its E3 ligase activity, was still functional in the
cellular processes of regulating centrosome number and homologous
recombination-dependent DSB
repair, thereby raising a question of
whether I26A mutant is indeed inert. Reevaluation of the
ubiquitination activity of this BRCA1(I26A) mutant revealed that it
is an active E3 ubiquitin ligase when associated with the
appropriate E2 factor. We then think that conclusions about the
dispensability of the BRCA1-dependent enzymatic activity in various
cellular processes should be reconsidered.Next we studied the
unique function of 53BP1, a known NHEJ factor for DSB
repair. We
found that 53BP1 specifically promotes the error-free
conservative-NHEJ (C-NHEJ) mechanism, dependent on its upstream
recruiters RNF8 and RNF168. 53BP1 has no effect on the highly
mutagenic and deletional alternative-NHEJ (Alt-NHEJ) pathway or on
homology-directed
repair (HDR), but it suppresses single-
strand
annealing (SSA). We discovered that the localization of 53BP1 at
sites of DSBs is accompanied by its bulk removal from the nucleus
except at sites of DNA damage. And the degradation of bulk 53BP1
upon DNA damage is due to each action of RNF8 and RNF168. Further,
we showed that failure to degrade bulk 53BP1 results in the failure
for its downstream effector RIF1 to localize appropriately to DNA
damage sites. These data provide a novel mechanism of 53BP1
responding to DSB damage. In the third part of our study, we
assessed SUMO isoforms in DSB
repair. We identified that SUMO
isoforms act differentially in DSB
repair pathways: SUMO1
stimulates all four subpathways while SUMO2/3 is only required for
C-NHEJ pathway. Strikingly, the single SUMO E2 enzyme, UBC9, was
required for C-NHEJ but not for HR or Alt-NHEJ. And the
conjugation-deficient SUMO1 mutant protein was competent for HR and
Alt-NHEJ
repair similar to the wild-type, but not for C-NHEJ. Our
data together reveal a novel role of SUMO1 as a free protein, not a
protein conjugate in homologous recombination and alternative-NHEJ.
Overall, we have identified biochemical steps at which these
factors are required for DSB
repair, as well as novel regulatory
mechanisms controlling the process.
Advisors/Committee Members: Parvin, Jeffrey (Advisor).
Subjects/Keywords: Molecular Biology; Double-strand break repair; BRCA1; 53BP1; SUMO; RNF8; RNF168; ionizing radiation
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APA (6th Edition):
Hu, Y. (2014). Functions of BRCA1, 53BP1 and SUMO isoforms in DNA
double-strand break repair in mammalian cells. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1397756848
Chicago Manual of Style (16th Edition):
Hu, Yiheng. “Functions of BRCA1, 53BP1 and SUMO isoforms in DNA
double-strand break repair in mammalian cells.” 2014. Doctoral Dissertation, The Ohio State University. Accessed April 12, 2021.
http://rave.ohiolink.edu/etdc/view?acc_num=osu1397756848.
MLA Handbook (7th Edition):
Hu, Yiheng. “Functions of BRCA1, 53BP1 and SUMO isoforms in DNA
double-strand break repair in mammalian cells.” 2014. Web. 12 Apr 2021.
Vancouver:
Hu Y. Functions of BRCA1, 53BP1 and SUMO isoforms in DNA
double-strand break repair in mammalian cells. [Internet] [Doctoral dissertation]. The Ohio State University; 2014. [cited 2021 Apr 12].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1397756848.
Council of Science Editors:
Hu Y. Functions of BRCA1, 53BP1 and SUMO isoforms in DNA
double-strand break repair in mammalian cells. [Doctoral Dissertation]. The Ohio State University; 2014. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1397756848
23.
Choudjaye, Jonathan.
Etude de l'organisation spatiale de la réparation des cassures double-brins de l'ADN : Study of the DNA double-strand break repair spatial organisation.
Degree: Docteur es, Biologie moléculaire, 2016, Université Toulouse III – Paul Sabatier
URL: http://www.theses.fr/2016TOU30390
► Les cassures Double-brin de l'ADN (DSBs) sont une menace majeure pour la stabilité du génome. Afin de se protéger des effets délétères de ces dommages,…
(more)
▼ Les cassures Double-brin de l'ADN (DSBs) sont une menace majeure pour la stabilité du génome. Afin de se protéger des effets délétères de ces dommages, les cellules activent une voie de réponse aux cassures double-brins (DDR) qui comprend des évènements qui conduisent à la reconnaissance et à la réparation de ces cassures ainsi qu'à un délai du cycle cellulaire. Cette DDR repose largement sur 2 membres de la famille des PI3K-like kinase, ataxia telangiectasia mutated (ATM) et DNA Protein Kinase (DNAPK) dont les fonctions respectives lors de la réparation restent controversées. Grâce à l'utilisation d'une lignée cellulaire contenant l'enzyme de restriction AsiSI combinée à de la cartographie par ChIP-chip, de l'analyse de la réparation de cassures séquence-spécifique ainsi qu'à de la microscopie haute résolution, j'ai pu, au cours de ma thèse mettre en évidence que aussi bien ATM que DNAPK sont recrutées sur une région confinée autour des DSBs. Cependant, une fois recrutées, elles présentent des fonctions non-redondantes que ce soit pour la ligation des cassures ou pour l'établissement des domaines yH2AX. Concernant la réparation, DNAPK est absolument requise pour la ligation des extrémités de la cassure alors que ATM est dispensable mais promeut la fidélité. En revanche, ATM est la principale kinase requise pour l'établissement des domaines yH2AX et ce quelque soit la cassure. J'ai aussi pu mettre en évidence le fait que plusieurs cassures induites par AsiSI sont capables de se regrouper au sein d'un "foyer de réparation" et ce de manière dépendante d'ATM et indépendante de DNAPK. Cette étude éclaircit les rôles respectifs des kinases ATM et DNAPK que ce soit pour la ligation des extrémités ou l'établissement des domaines yH2AX. Enfin elle a permis de mettre en évidence un nouveau rôle d'ATM dans l'organisation spatiale de la réparation et plus précisemment dans le regroupement de plusieurs DSBs au sein de "foyers de réparation" afin d'être réparées.
DNA Double Strand Breaks (DSBs) form a major threat to the genome stability. To circumvent the deleterious effects of DSBs, cells activate the DNA damage response (DDR), which comprises events that lead to detection and repair of these lesions, as well as a delay in cell cycle progression. This DDR largely rely on two members of the PI3K-like kinase family : ataxia telangiectasia mutated (ATM) and DNA Protein Kinase (DNAPK), whose respective functions during the DDR remains controversial. Using a cell line, expressing the AsiSI restriction enzyme, combined with high resolution ChIP-chip mapping, sequence-specific DSB repair kinetics analysis and advanced high resolution microscopy, we uncovered that both ATM and DNA-PK are recruited to a confined region surrounding DSBs. However, once present at the DSB site, they exhibit non-overlapping functions on end-joining and yH2AX domain establishment. At the repair level, DNAPK is absolutely required for end-joining while ATM is dispensable although promoting repair fidelity. By contrast, ATM is the main kinase required for…
Advisors/Committee Members: Legube, Gaëlle (thesis director).
Subjects/Keywords: Cassures double-brins; Réparation de l'ADN; ATM; DNAPK; Foyers de réparation; Double-strand break; DNA repair; ATM; DNAPK; Repair foci
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Record Details
Similar Records
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Choudjaye, J. (2016). Etude de l'organisation spatiale de la réparation des cassures double-brins de l'ADN : Study of the DNA double-strand break repair spatial organisation. (Doctoral Dissertation). Université Toulouse III – Paul Sabatier. Retrieved from http://www.theses.fr/2016TOU30390
Chicago Manual of Style (16th Edition):
Choudjaye, Jonathan. “Etude de l'organisation spatiale de la réparation des cassures double-brins de l'ADN : Study of the DNA double-strand break repair spatial organisation.” 2016. Doctoral Dissertation, Université Toulouse III – Paul Sabatier. Accessed April 12, 2021.
http://www.theses.fr/2016TOU30390.
MLA Handbook (7th Edition):
Choudjaye, Jonathan. “Etude de l'organisation spatiale de la réparation des cassures double-brins de l'ADN : Study of the DNA double-strand break repair spatial organisation.” 2016. Web. 12 Apr 2021.
Vancouver:
Choudjaye J. Etude de l'organisation spatiale de la réparation des cassures double-brins de l'ADN : Study of the DNA double-strand break repair spatial organisation. [Internet] [Doctoral dissertation]. Université Toulouse III – Paul Sabatier; 2016. [cited 2021 Apr 12].
Available from: http://www.theses.fr/2016TOU30390.
Council of Science Editors:
Choudjaye J. Etude de l'organisation spatiale de la réparation des cassures double-brins de l'ADN : Study of the DNA double-strand break repair spatial organisation. [Doctoral Dissertation]. Université Toulouse III – Paul Sabatier; 2016. Available from: http://www.theses.fr/2016TOU30390
University of Manchester
24.
Warmenhoven, John William.
Towards the Development of Double Strand Break Repair
Simulation in the Biological Stage of Geant4-DNA.
Degree: 2018, University of Manchester
URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315267
► Radiotherapy is used to deliver a lethal dose of radiation to a target tumour volume whilst sparing healthy tissue as much as possible. The physical…
(more)
▼ Radiotherapy is used to deliver a lethal dose of
radiation to a target tumour volume whilst sparing healthy tissue
as much as possible. The physical characteristics of protons make
them advantageous in this regards as they come to a full stop
within the patient at a depth determined by their initial energy.
However, it is known that there exists a difference between the
biological effect of the same dose delivered through photons
compared to that of protons. To understand this difference it is
not only important to investigate the differences between the
radiations but also how the cell responds to these different
challenges presented to it. These challenges are viewed by the cell
in terms of damage to its DNA, of which
double strand breaks are
the most significant. Various mechanisms exist within the cell
nucleus to
repair these
double strand breaks, ranging in complexity
from direct ligation through to use of homologous sections of DNA
to accurately reconstitute the damaged segment. These processes are
not fully characterised, with many challenges posed to both in
vitro or in vivo experimentation; not least of which is the
overwhelming complexity and interdependencies of the various
circuits in the nucleus. In this thesis an in silico approach is
presented to investigate these systems. Initially a model of the
non-homologous end joining
repair pathway is developed. Through
this model the compatibility of three experimentally supported
mechanisms is demonstrated by fitting the behaviour of the
resultant system to literature reported data. This work highlights
the importance of motion for correct determination of the overall
repair response. The model was then used in combination with track
structure damage simulations to investigate which parameters of the
physical beam are most impactful on the biological response of the
implemented pathway. This work reveals that, for the model detailed
in this thesis, the primary determinant of
repair fidelity is the
number of nearby interactive partners. Whilst the systems
implemented in these models are inherently simplified versions of
the processes in biological systems, they are still complex enough
that intrinsic assumptions and dependencies may go unnoticed. To
this end the damage model (developed separately) and the
repair
model (this work) were tested in combination with models developed
at other institutes. From this work we demonstrate that the
importance of motion and number of nearby neighbours are conserved
between these models despite large differences in their workings
and overall complexity. This demonstrates the utility of such
inter-comparative work, and to facilitate future collaborations
between other researchers in the field, the development of a
standard format for reporting DNA damage was initiated. The
University of Manchester John-William Warmenhoven Doctor of
Philosophy "Towards the Development of
Double Strand Break Repair
Simulation in the Biological Stage of Geant4-DNA" 30th March
2018
Advisors/Committee Members: MACKAY, RANALD RI, MERCHANT, MICHAEL M, Kirkby, Karen, Mackay, Ranald, Merchant, Michael.
Subjects/Keywords: Proton Therapy; Radiotherapy; DNA Repair; Non-homologous End Joining; Monte Carlo Simulation; Geant4-DNA; Double Strand Break Repair
Record Details
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Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Warmenhoven, J. W. (2018). Towards the Development of Double Strand Break Repair
Simulation in the Biological Stage of Geant4-DNA. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315267
Chicago Manual of Style (16th Edition):
Warmenhoven, John William. “Towards the Development of Double Strand Break Repair
Simulation in the Biological Stage of Geant4-DNA.” 2018. Doctoral Dissertation, University of Manchester. Accessed April 12, 2021.
http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315267.
MLA Handbook (7th Edition):
Warmenhoven, John William. “Towards the Development of Double Strand Break Repair
Simulation in the Biological Stage of Geant4-DNA.” 2018. Web. 12 Apr 2021.
Vancouver:
Warmenhoven JW. Towards the Development of Double Strand Break Repair
Simulation in the Biological Stage of Geant4-DNA. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2021 Apr 12].
Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315267.
Council of Science Editors:
Warmenhoven JW. Towards the Development of Double Strand Break Repair
Simulation in the Biological Stage of Geant4-DNA. [Doctoral Dissertation]. University of Manchester; 2018. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:315267
University of Oxford
25.
Somaiah, Navita.
Investigating the role of DNA double strand break repair in determining sensitivity to radiotherapy fraction size.
Degree: PhD, 2014, University of Oxford
URL: http://ora.ox.ac.uk/objects/uuid:8f941f8c-fa0d-4936-aac9-11549aaecb94
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596018
► The dose of curative radiotherapy (RT) for cancer is commonly limited by adverse effects presenting years later. Late reacting normal tissues are, on average, more…
(more)
▼ The dose of curative radiotherapy (RT) for cancer is commonly limited by adverse effects presenting years later. Late reacting normal tissues are, on average, more sensitive to the size of daily doses (fractions) than early reacting normal tissues and cancers. Clinical trials have shown breast cancers to be one exception to this rule, in that they are as sensitive to fraction size as the late reacting normal tissues. This has led to the adoption of hypofractionation (use of fractions >2.0 Gy) in the UK for the adjuvant therapy of women with early breast cancer. An understanding of the molecular basis of fraction size sensitivity is necessary to improve radiotherapy outcome. In this respect, it is relevant that late reacting normal tissues have lower proliferative indices than early reacting normal tissues and most cancers. Here, we test the hypothesis that tissue sensitivity to fraction size is determined by the DNA repair systems activated in response to DNA double strand breaks (DSB), and that these systems vary according to the proliferative status of the tissue. Clinical data suggest that sensitivity of epidermis to fraction size varies over a 5-week course of RT. It resembles a late reacting normal tissue in its sensitivity to fraction size in the first week of RT and loses fractionation sensitivity by weeks 4 & 5. We used this feature of human epidermis to test how fractionation sensitivity and DNA repair changed over 5 weeks of RT. Breast skin biopsies were collected 2 h after the 1st, 5th and last fractions from 30 breast cancer patients prescribed 50 Gy/25fractions/5weeks. Sections of epidermis were co-stained for Ki67, cyclin A, p21, RAD51, 53BP1 and β1-Integrin. After 5 weeks of radiotherapy, the mean basal Ki67 density increased from 5.72 to 15.46 cells per mm of basement membrane (p=0.002), of which the majority were in S/G2 phase as judged by cyclin A staining (p<0.0003). The p21 index rose from 2.8% to 87.4% (p<0.0001) after 25 fractions, indicating cell cycle arrest in the basal epidermis. By week 5, there was a 4-fold increase (p=0.0003) in the proportion of Ki67-positive cells showing RAD51 foci, confirming an association between activation of homologous recombination (HR) and loss of tissue fractionation sensitivity. Subsequently, CHO cell lines deficient in specific DNA repair genes were used to test molecular pathways involved in sensitivity to fraction size. We irradiated AA8 (WT), irs-1SF (XRCC3-), V3-3 (DNA-PK-) and EM9 (XRCC1-) with 16 Gy gamma-rays in 1 Gy daily fractions over 3 weeks or 16 Gy in 4 Gy daily fractions over 4 days, and studied clonogenic survival, DNA double-strand break (DSB) repair kinetics (RAD51 & 53BP1 staining) and cell cycle analysis using flow cytometry. We found that wild-type and DNA repair defective cells acquire resistance to fractionated radiotherapy by accumulation in the late S/G2 phase of the cell cycle and increased use of HR. In contrast, the irs1SF cells, defective in HR, failed to acquire radioresistance and remained equally sensitive to ionizing radiation…
Subjects/Keywords: 616.99; Medical Sciences; Oncology; Radiation; DNA double-strand break repair; cell cycle; DNA repair inhibitors; radiosensitisers; fractionated radiotherapy; fraction size sensitivity
Record Details
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Record Details
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« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Somaiah, N. (2014). Investigating the role of DNA double strand break repair in determining sensitivity to radiotherapy fraction size. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:8f941f8c-fa0d-4936-aac9-11549aaecb94 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596018
Chicago Manual of Style (16th Edition):
Somaiah, Navita. “Investigating the role of DNA double strand break repair in determining sensitivity to radiotherapy fraction size.” 2014. Doctoral Dissertation, University of Oxford. Accessed April 12, 2021.
http://ora.ox.ac.uk/objects/uuid:8f941f8c-fa0d-4936-aac9-11549aaecb94 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596018.
MLA Handbook (7th Edition):
Somaiah, Navita. “Investigating the role of DNA double strand break repair in determining sensitivity to radiotherapy fraction size.” 2014. Web. 12 Apr 2021.
Vancouver:
Somaiah N. Investigating the role of DNA double strand break repair in determining sensitivity to radiotherapy fraction size. [Internet] [Doctoral dissertation]. University of Oxford; 2014. [cited 2021 Apr 12].
Available from: http://ora.ox.ac.uk/objects/uuid:8f941f8c-fa0d-4936-aac9-11549aaecb94 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596018.
Council of Science Editors:
Somaiah N. Investigating the role of DNA double strand break repair in determining sensitivity to radiotherapy fraction size. [Doctoral Dissertation]. University of Oxford; 2014. Available from: http://ora.ox.ac.uk/objects/uuid:8f941f8c-fa0d-4936-aac9-11549aaecb94 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596018
University of Pennsylvania
26.
Jiang, Qinqin.
Molecular Recognition At Dna Damage Sites.
Degree: 2018, University of Pennsylvania
URL: https://repository.upenn.edu/edissertations/3051
► BRCA1 is frequently mutated in breast and ovarian cancer patients and it exerts its tumor suppressive function within several distinctive complexes by facilitating error-free DNA…
(more)
▼ BRCA1 is frequently mutated in breast and ovarian cancer patients and it exerts its tumor suppressive function within several distinctive complexes by facilitating error-free DNA repair via homologous recombination (HR) mechanism. The particular focus of this dissertation is the BRCA1-RAP80 ubiquitin recognition complex, which is composed of five core constituents (RAP80, Abraxas, MERIT40, BRCC45, and BRCC36) and targets BRCA1 to the chromatin flanking DNA damage sites. Although this complex is required for BRCA1 chromatin localization, its physiologic role has remained enigmatic, as has its relationship to canonical DNA repair mechanisms. Here we show that Merit40 (scaffolding protein of the RAP80 complex) deficient mice displayed marked hypersensitivity to DNA inter-strand crosslinks (ICLs), but not to whole body irradiation. Instead, Merit40 mutation exacerbated ICL induced chromosome instability in the context of concomitant Brca2 deficiency. These findings define specific functional interactions between the RAP80 complex dependent ubiquitin recognition and the FA-BRCA ICL repair network. As destabilization of the RAP80 complex is well tolerated in mice and could sensitive Brca2 mutant cells to frequently used chemotherapeutic agent mitomycin C (ICL-inducing agent), manipulating this complex might allow selective killing of Brca2 cancer cells. Moreover, inhibiting the enzymatic activity of the complex member BRCC36 was able to recapitulate Merit40 deficiency in cells and cause increased lethality in Brca2 mutant mice, indicating the RAP80 complex mediates ICL repair via the deubiquitinating (DUB) enzymatic activity of BRCC36. Mechanistically, we revealed that RAP80 is a substrate of BRCC36 and this deubiquitination process is essential to regulate the BRCA1-RAP80 chromatin localization. Additionally, to understand the specific chromatin environment that recruits the RAP80 complex to DNA damage sites, we devised a novel methodology to purify mono-nucleosomes bound by chromatin associated DNA repair proteins and employed mass spectrometry to quantitatively measure the abundance of individual post-translational modifications on these nucleosomes. This study allows us to assess the full spectrum of chromatin modifications that associate with different DNA repair pathways, and thus to direct DNA repair pathways by manipulating enzymes that are responsible for these modifications.
Subjects/Keywords: BRCA1 and BRCA2; Double strand break repair choice; Epigenetic; Fanconi Anemia; Interstrand crosslink repair; Ubiquitination; Biochemistry; Biology; Cell Biology
Record Details
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Jiang, Q. (2018). Molecular Recognition At Dna Damage Sites. (Thesis). University of Pennsylvania. Retrieved from https://repository.upenn.edu/edissertations/3051
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Jiang, Qinqin. “Molecular Recognition At Dna Damage Sites.” 2018. Thesis, University of Pennsylvania. Accessed April 12, 2021.
https://repository.upenn.edu/edissertations/3051.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Jiang, Qinqin. “Molecular Recognition At Dna Damage Sites.” 2018. Web. 12 Apr 2021.
Vancouver:
Jiang Q. Molecular Recognition At Dna Damage Sites. [Internet] [Thesis]. University of Pennsylvania; 2018. [cited 2021 Apr 12].
Available from: https://repository.upenn.edu/edissertations/3051.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Jiang Q. Molecular Recognition At Dna Damage Sites. [Thesis]. University of Pennsylvania; 2018. Available from: https://repository.upenn.edu/edissertations/3051
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Manchester
27.
Warmenhoven, John.
Towards the development of double strand break repair simulation in the biological stage of Geant4-DNA.
Degree: PhD, 2018, University of Manchester
URL: https://www.research.manchester.ac.uk/portal/en/theses/towards-the-development-of-double-strand-break-repair-simulation-in-the-biological-stage-of-geant4dna(fa31e136-61fd-4c12-ab46-7525408ceedb).html
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816251
► Radiotherapy is used to deliver a lethal dose of radiation to a target tumour volume whilst sparing healthy tissue as much as possible. The physical…
(more)
▼ Radiotherapy is used to deliver a lethal dose of radiation to a target tumour volume whilst sparing healthy tissue as much as possible. The physical characteristics of protons make them advantageous in this regards as they come to a full stop within the patient at a depth determined by their initial energy. However, it is known that there exists a difference between the biological effect of the same dose delivered through photons compared to that of protons. To understand this difference it is not only important to investigate the differences between the radiations but also how the cell responds to these different challenges presented to it. These challenges are viewed by the cell in terms of damage to its DNA, of which double strand breaks are the most significant. Various mechanisms exist within the cell nucleus to repair these double strand breaks, ranging in complexity from direct ligation through to use of homologous sections of DNA to accurately reconstitute the damaged segment. These processes are not fully characterised, with many challenges posed to both in vitro or in vivo experimentation; not least of which is the overwhelming complexity and interdependencies of the various circuits in the nucleus. In this thesis an in silico approach is presented to investigate these systems. Initially a model of the non-homologous end joining repair pathway is developed. Through this model the compatibility of three experimentally supported mechanisms is demonstrated by fitting the behaviour of the resultant system to literature reported data. This work highlights the importance of motion for correct determination of the overall repair response. The model was then used in combination with track structure damage simulations to investigate which parameters of the physical beam are most impactful on the biological response of the implemented pathway. This work reveals that, for the model detailed in this thesis, the primary determinant of repair fidelity is the number of nearby interactive partners. Whilst the systems implemented in these models are inherently simplified versions of the processes in biological systems, they are still complex enough that intrinsic assumptions and dependencies may go unnoticed. To this end the damage model (developed separately) and the repair model (this work) were tested in combination with models developed at other institutes. From this work we demonstrate that the importance of motion and number of nearby neighbours are conserved between these models despite large differences in their workings and overall complexity. This demonstrates the utility of such inter-comparative work, and to facilitate future collaborations between other researchers in the field, the development of a standard format for reporting DNA damage was initiated.
Subjects/Keywords: Geant4-DNA; Double Strand Break Repair; Monte Carlo Simulation; DNA Repair; Non-homologous End Joining; Radiotherapy; Proton Therapy
Record Details
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Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Warmenhoven, J. (2018). Towards the development of double strand break repair simulation in the biological stage of Geant4-DNA. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/towards-the-development-of-double-strand-break-repair-simulation-in-the-biological-stage-of-geant4dna(fa31e136-61fd-4c12-ab46-7525408ceedb).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816251
Chicago Manual of Style (16th Edition):
Warmenhoven, John. “Towards the development of double strand break repair simulation in the biological stage of Geant4-DNA.” 2018. Doctoral Dissertation, University of Manchester. Accessed April 12, 2021.
https://www.research.manchester.ac.uk/portal/en/theses/towards-the-development-of-double-strand-break-repair-simulation-in-the-biological-stage-of-geant4dna(fa31e136-61fd-4c12-ab46-7525408ceedb).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816251.
MLA Handbook (7th Edition):
Warmenhoven, John. “Towards the development of double strand break repair simulation in the biological stage of Geant4-DNA.” 2018. Web. 12 Apr 2021.
Vancouver:
Warmenhoven J. Towards the development of double strand break repair simulation in the biological stage of Geant4-DNA. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2021 Apr 12].
Available from: https://www.research.manchester.ac.uk/portal/en/theses/towards-the-development-of-double-strand-break-repair-simulation-in-the-biological-stage-of-geant4dna(fa31e136-61fd-4c12-ab46-7525408ceedb).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816251.
Council of Science Editors:
Warmenhoven J. Towards the development of double strand break repair simulation in the biological stage of Geant4-DNA. [Doctoral Dissertation]. University of Manchester; 2018. Available from: https://www.research.manchester.ac.uk/portal/en/theses/towards-the-development-of-double-strand-break-repair-simulation-in-the-biological-stage-of-geant4dna(fa31e136-61fd-4c12-ab46-7525408ceedb).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.816251
28.
Abello, Arthur.
Spécialisation de Ku80c dans le couplage entre coupure et réparation de l’ADN lors des réarrangements programmés du génome chez Paramecium tetraurelia : Specialization of Ku80c in the coupling between DNA break and repair during programmed genome rearrangements in Paramecium tetraurelia.
Degree: Docteur es, Sciences de la vie et de la santé, 2019, Université Paris-Saclay (ComUE)
URL: http://www.theses.fr/2019SACLS083
► Au cours de son cycle sexuel, le cilié Paramecium tetraurelia procède à de massifs réarrangements programmés de son génome (RPG). Ils consistent, entre autres choses,…
(more)
▼ Au cours de son cycle sexuel, le cilié Paramecium tetraurelia procède à de massifs réarrangements programmés de son génome (RPG). Ils consistent, entre autres choses, en l’excision de 45 000 séquences précisément délimitées, appelées IES (Internal Eliminated Sequences). La transposase domestiquée Piggymac (Pgm) introduit les cassures double-brin (CDB) à l’extrémité des IES. La réparation très précise de ces dommages est réalisée par la voie de réparation des extrémités non-homologues (NHEJ). Un des acteurs de cette voie est l’hétérodimère Ku70/Ku80. Suite à des duplications globales du génome, la paramécie possède trois gènes KU80, Un seul de ces gènes est induit lors des RPG (KU80c) et une expérience d’ARN interférence (ARNi) contre KU80c montre une complète inhibition de l’introduction des CDB. De plus, des expériences de Co-IP en système hétérologue montrent que Ku70/Ku80c interagit avec Pgm. Ces résultats prouvent le rôle essentiel de Ku dans l’introduction des CDB lors des RPG et soulèvent la question du mécanisme impliqué. Au cours de ma thèse j’ai caractérisé le couplage entre Ku et Pgm en analysant des expériences d’immunofluorescence avec ou sans pré-extraction, permettant de déterminer les interdépendances de ces protéines pour leur localisation et pour leur stabilité nucléaire. Ces approches ont permis de démontrer que Pgm requiert la présence de Ku pour être stablement localisé dans les noyaux lors des RPG. Ku80c partage 74% de sa séquence protéique avec Ku80a. Des expériences de complémentations fonctionnelles surexprimant Ku80a lors des RPG ont montré que Ku80a n’est pas capable ni de se localiser stablement dans les noyaux ni de participer à la stabilisation nucléaire de Pgm. De plus, les RPG sont inhibés. Ces résultats montrent que Ku80c s’est spécialisé dans le couplage avec Pgm pour l’introduction des CDB lors des RPG. L’utilisation de protéines chimériques a permis de déterminer que la spécialisation de Ku80c est portée par son domaine N-terminal ∝-β.
During its sexual cycle, the ciliate Paramecium tetraurelia undergoes massive Programmed Genome Rearrangements (PGR). They consist, among others, in excision of 45,000 precisely delimited sequences, called IES (Internal Eliminated Sequences). A domesticated transposase, PiggyMac (Pgm), introduces double-strand DNA breaks (DSB) at IES ends. The Non Homologous End Joining pathway (NHEJ) handles highly precise repair of DSB. One of the actors of this pathway is the heterodimer Ku70/Ku80. In P. tetraurelia, the KU80 gene is present in three paralogous copies. Only KU80c is specifically expressed during PGR and RNA interferences against KU80c showed a complete inhibition of DNA cleavage. Furthermore, a Co-IP experiment in a heterologous system showed that both Ku70/Ku80c interact with Pgm. These results provide evidence that Ku is an essential partner of Pgm for DSB introduction; raising the question of the activating mechanism involved. During my PhD, I characterized the coupling between Ku and Pgm by analyzing immunofluorescence experiments, with or…
Advisors/Committee Members: Bétermier, Mireille (thesis director).
Subjects/Keywords: NHEJ; Réparation; Cassure double-Brin; Couplage; Paramécie; Ciliés; NHEJ; Repair; Double strand break; Coupling; Paramecia; Ciliates
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APA (6th Edition):
Abello, A. (2019). Spécialisation de Ku80c dans le couplage entre coupure et réparation de l’ADN lors des réarrangements programmés du génome chez Paramecium tetraurelia : Specialization of Ku80c in the coupling between DNA break and repair during programmed genome rearrangements in Paramecium tetraurelia. (Doctoral Dissertation). Université Paris-Saclay (ComUE). Retrieved from http://www.theses.fr/2019SACLS083
Chicago Manual of Style (16th Edition):
Abello, Arthur. “Spécialisation de Ku80c dans le couplage entre coupure et réparation de l’ADN lors des réarrangements programmés du génome chez Paramecium tetraurelia : Specialization of Ku80c in the coupling between DNA break and repair during programmed genome rearrangements in Paramecium tetraurelia.” 2019. Doctoral Dissertation, Université Paris-Saclay (ComUE). Accessed April 12, 2021.
http://www.theses.fr/2019SACLS083.
MLA Handbook (7th Edition):
Abello, Arthur. “Spécialisation de Ku80c dans le couplage entre coupure et réparation de l’ADN lors des réarrangements programmés du génome chez Paramecium tetraurelia : Specialization of Ku80c in the coupling between DNA break and repair during programmed genome rearrangements in Paramecium tetraurelia.” 2019. Web. 12 Apr 2021.
Vancouver:
Abello A. Spécialisation de Ku80c dans le couplage entre coupure et réparation de l’ADN lors des réarrangements programmés du génome chez Paramecium tetraurelia : Specialization of Ku80c in the coupling between DNA break and repair during programmed genome rearrangements in Paramecium tetraurelia. [Internet] [Doctoral dissertation]. Université Paris-Saclay (ComUE); 2019. [cited 2021 Apr 12].
Available from: http://www.theses.fr/2019SACLS083.
Council of Science Editors:
Abello A. Spécialisation de Ku80c dans le couplage entre coupure et réparation de l’ADN lors des réarrangements programmés du génome chez Paramecium tetraurelia : Specialization of Ku80c in the coupling between DNA break and repair during programmed genome rearrangements in Paramecium tetraurelia. [Doctoral Dissertation]. Université Paris-Saclay (ComUE); 2019. Available from: http://www.theses.fr/2019SACLS083
University of Michigan
29.
Rogawski, Mary.
Regulation of ATM and CDK2 Kinases by the MRN Complex in DNA Damage Signaling and Cell Cycle Checkpoint Control.
Degree: PhD, Molecular & Cellular Pathology, 2018, University of Michigan
URL: http://hdl.handle.net/2027.42/143961
► Double-stranded breaks (DSBs) are toxic DNA lesions that if left unrepaired, lead to mutations, chromosomal aberrations, and oncogenesis. The DNA Damage Response (DDR) is a…
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▼ Double-stranded breaks (DSBs) are toxic DNA lesions that if left unrepaired, lead to mutations, chromosomal aberrations, and oncogenesis. The DNA Damage Response (DDR) is a complex network of signaling pathways designed to detect and
repair DNA breaks and thus acts as a critical anti-cancer barrier. The MRN complex, consisting of the proteins MRE11, RAD50, and NBS1, is a sensor of DSBs and has roles in facilitating activation of the ataxia-telangiectasia mutated (ATM) kinase, the master regulator of the DDR pathway. ATM phosphorylates a variety of proteins involved in initiating cellular responses important for safeguarding the genome, such as DNA
repair, cell cycle checkpoints, and if the damage is too catastrophic to be fixed, apoptosis. A second DNA DSB sensor exists called the KU70/KU80 heterodimer, which binds and activates the kinase DNA-dependent protein kinase, catalytic subunit (DNA-PKcs).
To investigate the apparently redundant roles of MRN and KU70/80 in DNA damage kinase signaling, we utilized cells derived from mouse models deficient in either MRN, KU, or both in conjunction with pharmacologic inhibitors for the respective kinases of each DNA damage sensor, ATM and DNA-PKcs. We found that when MRN is deficient, DNA-PKcs effectively substitutes for ATM. Surprisingly, in the absence of both MRN and KU, ATM is still recruited to the chromatin and can facilitate local chromatin responses, including phosphorylation of the histone variant H2AX and recruitment of MDC1. This data implies that MRN is not absolutely required for activation of ATM, as previously thought.
Our lab has previously described that the MRE11 C-terminus interacts with cyclin-dependent kinase 2 (CDK2), a kinase important for S-phase cell cycle progression, and that this interaction has roles for homology-directed DSB
repair in normally dividing cells. Interestingly, the MRE11 C-terminus is absent in an inherited patient allele causing ataxia-telangiectasia-like disorder 1 (ATLD1). To further understand roles of the MRE11-CDK2 interaction in the DDR, we treated cells with ionizing radiation (IR) to induce DSBs. We found that DNA damage disrupts this interaction in an ATM-dependent manner and causes a reduction in CDK2 catalytic activity. Next, we found that genetic disruption of the interaction in cells lacking either the MRN complex or the MRE11 C-terminus also led to decreased levels of CDK2 activity, mimicking IR-induced disruption of the interaction. Taken together, our data reveal a novel pathway of S-phase checkpoint regulation by the MRE11-CDK2 interaction.
To gain greater insight into roles of the MRN complex in cancer, we engineered a mouse model with B lymphocytes lacking MRN or MRN-nuclease activities. Both forms of MRN deficiency led to characteristics of cancer, including oncogenic translocations between C-MYC and the immunoglobulin locus. Surprisingly, these B lymphocytes did not progress to detectable B lineage lymphoma, even in the absence of p53. Moreover, MRE11-deficiencies prevented tumorigenesis in…
Advisors/Committee Members: Ferguson, David O (committee member), Ljungman, Mats E D (committee member), Canman, Christine E (committee member), Cierpicki, Tomasz (committee member), Wilson, Thomas E (committee member).
Subjects/Keywords: DNA double-strand break; DNA damage response; DNA repair; Cell cycle checkpoint; Cancer; Pathology; Science (General); Health Sciences; Science
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
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to Zotero / EndNote / Reference
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APA (6th Edition):
Rogawski, M. (2018). Regulation of ATM and CDK2 Kinases by the MRN Complex in DNA Damage Signaling and Cell Cycle Checkpoint Control. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/143961
Chicago Manual of Style (16th Edition):
Rogawski, Mary. “Regulation of ATM and CDK2 Kinases by the MRN Complex in DNA Damage Signaling and Cell Cycle Checkpoint Control.” 2018. Doctoral Dissertation, University of Michigan. Accessed April 12, 2021.
http://hdl.handle.net/2027.42/143961.
MLA Handbook (7th Edition):
Rogawski, Mary. “Regulation of ATM and CDK2 Kinases by the MRN Complex in DNA Damage Signaling and Cell Cycle Checkpoint Control.” 2018. Web. 12 Apr 2021.
Vancouver:
Rogawski M. Regulation of ATM and CDK2 Kinases by the MRN Complex in DNA Damage Signaling and Cell Cycle Checkpoint Control. [Internet] [Doctoral dissertation]. University of Michigan; 2018. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/2027.42/143961.
Council of Science Editors:
Rogawski M. Regulation of ATM and CDK2 Kinases by the MRN Complex in DNA Damage Signaling and Cell Cycle Checkpoint Control. [Doctoral Dissertation]. University of Michigan; 2018. Available from: http://hdl.handle.net/2027.42/143961
Texas Medical Center
30.
Pal, Sangita.
UNDERSTANDING THE MECHANISM OF GENOMIC INSTABILITY DURING REPLICATIVE AGING IN BUDDING YEAST.
Degree: PhD, 2017, Texas Medical Center
URL: https://digitalcommons.library.tmc.edu/utgsbs_dissertations/770
► Aging brings a gradual decline in molecular fidelity and biological functionality, resulting in age related phenotypes and diseases. Despite continued efforts to uncover the…
(more)
▼ Aging brings a gradual decline in molecular fidelity and biological functionality, resulting in age related phenotypes and diseases. Despite continued efforts to uncover the conserved aging pathways among eukaryotes, exact molecular causes of aging are still poorly understood. One of the most important hallmarks of aging is increased genomic instability. However, there remains much ambiguity as to the cause. I am studying the replicative life span (RLS) of the genetically tractable model organism Saccharomyces cerevisiae, or budding yeast using the innovative “mother enrichment program” as the method to isolate unparalleled numbers of aged yeast cells to investigate the molecular changes associated with aging. My goal is to determine the possible causes of loss of genomic integrity during replicative aging in budding yeast to gain potential insight into this vastly complex process.
In my work presented here, I uncovered a global loss of cohesion in mitotically aged yeast cells and this most likely serves as the cause of increased rDNA instability and/or ERC accumulation as observed during aging. These events, in turn, influence the global genomic integrity in replicatively aged cells. Furthermore, I discovered a profound defect in
double strand break (DSB)
repair with aging due to limiting levels of key components of the homologous recombination machinery. This DSB
repair defect in old cells limited the replicative lifespan, because restoration of DSB
repair by overexpressing key HR proteins ameliorated age-associated changes, to extend lifespan. We propose that the limiting levels of
repair factors and cohesin proteins impair the ability of the aged cells to counteract the increased burden of genomic damage accumulation coupled with chromosomal rearrangements and potentially chromosome loss, eventually to cross a threshold of genomic damage that is sensed by the cell to cause cessation of cell division marking the end of the replicative lifespan.
Advisors/Committee Members: Jessica K. Tyler, Ph.D., Pierre D. McCrea, Ph.D., Xiaobing Shi, Ph.D..
Subjects/Keywords: Replicative aging; Genomic instability; rDNA instability; Double-strand break repair; Cohesin; Biochemistry; Cell Biology; Molecular Biology; Molecular Genetics
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Record Details
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Pal, S. (2017). UNDERSTANDING THE MECHANISM OF GENOMIC INSTABILITY DURING REPLICATIVE AGING IN BUDDING YEAST. (Doctoral Dissertation). Texas Medical Center. Retrieved from https://digitalcommons.library.tmc.edu/utgsbs_dissertations/770
Chicago Manual of Style (16th Edition):
Pal, Sangita. “UNDERSTANDING THE MECHANISM OF GENOMIC INSTABILITY DURING REPLICATIVE AGING IN BUDDING YEAST.” 2017. Doctoral Dissertation, Texas Medical Center. Accessed April 12, 2021.
https://digitalcommons.library.tmc.edu/utgsbs_dissertations/770.
MLA Handbook (7th Edition):
Pal, Sangita. “UNDERSTANDING THE MECHANISM OF GENOMIC INSTABILITY DURING REPLICATIVE AGING IN BUDDING YEAST.” 2017. Web. 12 Apr 2021.
Vancouver:
Pal S. UNDERSTANDING THE MECHANISM OF GENOMIC INSTABILITY DURING REPLICATIVE AGING IN BUDDING YEAST. [Internet] [Doctoral dissertation]. Texas Medical Center; 2017. [cited 2021 Apr 12].
Available from: https://digitalcommons.library.tmc.edu/utgsbs_dissertations/770.
Council of Science Editors:
Pal S. UNDERSTANDING THE MECHANISM OF GENOMIC INSTABILITY DURING REPLICATIVE AGING IN BUDDING YEAST. [Doctoral Dissertation]. Texas Medical Center; 2017. Available from: https://digitalcommons.library.tmc.edu/utgsbs_dissertations/770
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Open Access Theses and Dissertations
