Relevant bibliographies by topics / Human DNA repair and recombination pathways

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
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Academic literature on the topic 'Human DNA repair and recombination pathways'

Author: Grafiati
Published: 14 March 2023

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Journal articles on the topic "Human DNA repair and recombination pathways"

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Zhao, Lei, Chengyu Bao, Yuxuan Shang, Xinye He, Chiyuan Ma, Xiaohua Lei, Dong Mi, and Yeqing Sun. "The Determinant of DNA Repair Pathway Choices in Ionising Radiation-Induced DNA Double-Strand Breaks." BioMed Research International 2020 (August 25, 2020): 1–12. http://dx.doi.org/10.1155/2020/4834965.

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Ionising radiation- (IR-) induced DNA double-strand breaks (DSBs) are considered to be the deleterious DNA lesions that pose a serious threat to genomic stability. The major DNA repair pathways, including classical nonhomologous end joining, homologous recombination, single-strand annealing, and alternative end joining, play critical roles in countering and eliciting IR-induced DSBs to ensure genome integrity. If the IR-induced DNA DSBs are not repaired correctly, the residual or incorrectly repaired DSBs can result in genomic instability that is associated with certain human diseases. Although many efforts have been made in investigating the major mechanisms of IR-induced DNA DSB repair, it is still unclear what determines the choices of IR-induced DNA DSB repair pathways. In this review, we discuss how the mechanisms of IR-induced DSB repair pathway choices can operate in irradiated cells. We first briefly describe the main mechanisms of the major DNA DSB repair pathways and the related key repair proteins. Based on our understanding of the characteristics of IR-induced DNA DSBs and the regulatory mechanisms of DSB repair pathways in irradiated cells and recent advances in this field, We then highlight the main factors and associated challenges to determine the IR-induced DSB repair pathway choices. We conclude that the type and distribution of IR-induced DSBs, chromatin state, DNA-end structure, and DNA-end resection are the main determinants of the choice of the IR-induced DNA DSB repair pathway.
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Jalan, Manisha, Juber Patel, Kyrie S. Olsen, Sana Ahmed-Seghir, Daniel S. Higginson, Jorge S. Reis-Filho, Nadeem Riaz, and Simon N. Powell. "Abstract 5688: RNA-mediated DNA repair: A novel repair pathway in homologous recombination-deficient cancers." Cancer Research 82, no. 12_Supplement (June 15, 2022): 5688. http://dx.doi.org/10.1158/1538-7445.am2022-5688.

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Abstract Genome instability has long been considered the primary driver of most cancer types. A double strand break (DSB) in DNA can have deleterious consequences for a cell, which if not repaired faithfully, can lead to mutations and chromosomal rearrangements, or even cell death. DSBs can be processed by several DNA repair pathways, of which homologous recombination (HR) is the preferred method due to its error-free nature. HR uses an intact homologous DNA sequence as a template for recovering the information lost at the break site. A significant proportion of all cancers, especially triple-negative breast, ovarian pancreatic and prostate cancers, have loss of function alterations affecting genes involved in HR-mediated DNA repair. Alternate repair pathways operate when HR is defective in tumors, but the pathways operative in this context remain a matter of contention. Previous work in vivo in yeast and in vitro systems has established a new role of RNA in DNA repair. Owing to its abundance in the cell and its sequence similarity to parental DNA, we sought to define whether RNA can act as a template for the repair of DSBs in human cells. We developed a novel high throughput assay to test if DNA breaks can be repaired using RNA as an alternative template in mammalian cells. Human cells were transfected with a guide RNA cloned in a Cas9 expression vector to generate a site-specific DSB at the AAVS1 locus, a safe harbour, in the human genome. Furthermore, a donor template in the form of DNA or RNA (homologous to the DSB locus) containing a unique mutational signature was provided at the time of transfection. The unique mutational signature enables us to determine if the donor has been utilized as a template for DNA repair. Using this assay, we demonstrate that cells can use a spliced RNA transcript as a functional template to repair a DSB. We have identified that Rev3L, a key component of the translesion synthesis polymerase Pol Zeta (ζ), has a novel reverse-transcriptase activity in human cells and can help repair the DSB using RNA as a template. Further characterization of this repair pathway and its associated mutational scar will provide new insights into the mutational signatures seen in HR-defective cancers, enabling a better understanding of the DNA repair pathways upregulated in these tumours. The proposed studies could help prioritize novel therapeutic approaches by exploiting synthetic lethality in HR-deficient cancers as well as HR-proficient cancers when used in combinatorial cancer therapy. Citation Format: Manisha Jalan, Juber Patel, Kyrie S Olsen, Sana Ahmed-Seghir, Daniel S Higginson, Jorge S Reis-Filho, Nadeem Riaz, Simon N Powell. RNA-mediated DNA repair: A novel repair pathway in homologous recombination-deficient cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5688.
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Kennedy, Richard D., and Alan D. D'Andrea. "DNA Repair Pathways in Clinical Practice: Lessons From Pediatric Cancer Susceptibility Syndromes." Journal of Clinical Oncology 24, no. 23 (August 10, 2006): 3799–808. http://dx.doi.org/10.1200/jco.2005.05.4171.

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Human cancers exhibit genomic instability and an increased mutation rate due to underlying defects in DNA repair. Cancer cells are often defective in one of six major DNA repair pathways, namely: mismatch repair, base excision repair, nucleotide excision repair, homologous recombination, nonhomologous endjoining and translesion synthesis. The specific DNA repair pathway affected is predictive of the kinds of mutations, the tumor drug sensitivity, and the treatment outcome. The study of rare inherited DNA repair disorders, such as Fanconi anemia, has yielded new insights to drug sensitivity and treatment of sporadic cancers, such as breast or ovarian epithelial tumors, in the general population. The Fanconi anemia pathway is an example of how DNA repair pathways can be deregulated in cancer cells and how biomarkers of the integrity of these pathways could be useful as a guide to cancer management and may be used in the development of novel therapeutic agents.
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Guo, Yingying, Linda L. Breeden, Helmut Zarbl, Bradley D. Preston, and David L. Eaton. "Expression of a Human Cytochrome P450 in Yeast Permits Analysis of Pathways for Response to and Repair of Aflatoxin-Induced DNA Damage." Molecular and Cellular Biology 25, no. 14 (July 2005): 5823–33. http://dx.doi.org/10.1128/mcb.25.14.5823-5833.2005.

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ABSTRACT Aflatoxin B1 (AFB1) is a human hepatotoxin and hepatocarcinogen produced by the mold Aspergillus flavus. In humans, AFB1 is primarily bioactivated by cytochrome P450 1A2 (CYP1A2) and 3A4 to a genotoxic epoxide that forms N7-guanine DNA adducts. A series of yeast haploid mutants defective in DNA repair and cell cycle checkpoints were transformed with human CYP1A2 to investigate how these DNA adducts are repaired. Cell survival and mutagenesis following aflatoxin B1 treatment was assayed in strains defective in nucleotide excision repair (NER) (rad14), postreplication repair (PRR) (rad6, rad18, mms2, and rad5), homologous recombinational repair (HRR) (rad51 and rad54), base excision repair (BER) (apn1 apn2), nonhomologous end-joining (NHEJ) (yku70), mismatch repair (MMR) (pms1), translesion synthesis (TLS) (rev3), and checkpoints (mec1-1, mec1-1 rad53, rad9, and rad17). Together our data suggest the involvement of homologous recombination and nucleotide excision repair, postreplication repair, and checkpoints in the repair and/or tolerance of AFB1-induced DNA damage in the yeast model. Rev3 appears to mediate AFB1-induced mutagenesis when error-free pathways are compromised. The results further suggest unique roles for Rad5 and abasic endonuclease-dependent DNA intermediates in regulating AFB1-induced mutagenicity.
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Wang, Xuejie, Yang Dong, Xiaocong Zhao, Jinbao Li, Jordan Lee, Zhenxin Yan, Shuangshuang Yang, et al. "Rtt105 promotes high-fidelity DNA replication and repair by regulating the single-stranded DNA-binding factor RPA." Proceedings of the National Academy of Sciences 118, no. 25 (June 17, 2021): e2106393118. http://dx.doi.org/10.1073/pnas.2106393118.

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Single-stranded DNA (ssDNA) covered with the heterotrimeric Replication Protein A (RPA) complex is a central intermediate of DNA replication and repair. How RPA is regulated to ensure the fidelity of DNA replication and repair remains poorly understood. Yeast Rtt105 is an RPA-interacting protein required for RPA nuclear import and efficient ssDNA binding. Here, we describe an important role of Rtt105 in high-fidelity DNA replication and recombination and demonstrate that these functions of Rtt105 primarily depend on its regulation of RPA. The deletion of RTT105 causes elevated spontaneous DNA mutations with large duplications or deletions mediated by microhomologies. Rtt105 is recruited to DNA double-stranded break (DSB) ends where it promotes RPA assembly and homologous recombination repair by gene conversion or break-induced replication. In contrast, Rtt105 attenuates DSB repair by the mutagenic single-strand annealing or alternative end joining pathway. Thus, Rtt105-mediated regulation of RPA promotes high-fidelity replication and recombination while suppressing repair by deleterious pathways. Finally, we show that the human RPA-interacting protein hRIP-α, a putative functional homolog of Rtt105, also stimulates RPA assembly on ssDNA, suggesting the conservation of an Rtt105-mediated mechanism.
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Giot, Loïc, Roland Chanet, Michel Simon, Céline Facca, and Gérard Faye. "Involvement of the Yeast DNA Polymerase δ in DNA Repair in Vivo." Genetics 146, no. 4 (August 1, 1997): 1239–51. http://dx.doi.org/10.1093/genetics/146.4.1239.

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The POL3 encoded catalytic subunit of DNA polymerase δ possesses a highly conserved C-terminal cysteine-rich domain in Saccharomyces cerevisiae. Mutations in some of its cysteine codons display a lethal phenotype, which demonstrates an essential function of this domain. The thermosensitive mutant pol3-13, in which a serine replaces a cysteine of this domain, exhibits a range of defects in DNA repair, such as hypersensitivity to different DNA-damaging agents and deficiency for induced mutagenesis and for recombination. These phenotypes are observed at 24°, a temperature at which DNA replication is almost normal; this differentiates the functions of POL3 in DNA repair and DNA replication. Since spontaneous mutagenesis and spontaneous recombination are efficient in pol3-13, we propose that POL3 plays an important role in DNA repair after irradiation, particularly in the error-prone and recombinational pathways. Extragenic suppressors of pol3-13 are allelic to sdp5-1, previously identified as an extragenic suppressor of pol3-11. SDP5, which is identical to HYS2, encodes a protein homologous to the p50 subunit of bovine and human DNA polymerase δ. SDP5 is most probably the p55 subunit of Polδ of S. cerevisiae and seems to be associated with the catalytic subunit for both DNA replication and DNA repair.
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Priest, Shelby J., Marco A. Coelho, Verónica Mixão, Shelly Applen Clancey, Yitong Xu, Sheng Sun, Toni Gabaldón, and Joseph Heitman. "Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans." PLOS Genetics 17, no. 1 (January 19, 2021): e1008871. http://dx.doi.org/10.1371/journal.pgen.1008871.

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Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in prokaryotes and eukaryotes is the mismatch repair pathway, which blocks recombination between divergent DNA sequences. Previous studies illuminated the role of the mismatch repair component Msh2 in blocking genetic recombination between divergent DNA during meiosis. Loss of Msh2 results in increased interspecific genetic recombination in bacterial and yeast models, and increased viability of progeny derived from yeast hybrid crosses. Hybrid isolates of two pathogenic fungalCryptococcusspecies,Cryptococcus neoformansandCryptococcus deneoformans, are isolated regularly from both clinical and environmental sources. In the present study, we sought to determine if loss of Msh2 would relax the species boundary betweenC.neoformansandC.deneoformans. We found that crosses between these two species in which both parents lack Msh2 produced hybrid progeny with increased viability and high levels of aneuploidy. Whole-genome sequencing revealed few instances of recombination among hybrid progeny and did not identify increased levels of recombination in progeny derived from parents lacking Msh2. Several hybrid progeny produced structures associated with sexual reproduction when incubated alone on nutrient-rich medium in light, a novel phenotype inCryptococcus. These findings represent a unique, unexpected case where rendering the mismatch repair system defective did not result in increased meiotic recombination across a species boundary. This suggests that alternative pathways or other mismatch repair components limit meiotic recombination between homeologous DNA and enforce species boundaries in the basidiomyceteCryptococcusspecies.
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Costantino, Lorenzo, Sotirios K. Sotiriou, Juha K. Rantala, Simon Magin, Emil Mladenov, Thomas Helleday, James E. Haber, George Iliakis, Olli P. Kallioniemi, and Thanos D. Halazonetis. "Break-Induced Replication Repair of Damaged Forks Induces Genomic Duplications in Human Cells." Science 343, no. 6166 (December 5, 2013): 88–91. http://dx.doi.org/10.1126/science.1243211.

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In budding yeast, one-ended DNA double-strand breaks (DSBs) and damaged replication forks are repaired by break-induced replication (BIR), a homologous recombination pathway that requires the Pol32 subunit of DNA polymerase delta. DNA replication stress is prevalent in cancer, but BIR has not been characterized in mammals. In a cyclin E overexpression model of DNA replication stress, POLD3, the human ortholog of POL32, was required for cell cycle progression and processive DNA synthesis. Segmental genomic duplications induced by cyclin E overexpression were also dependent on POLD3, as were BIR-mediated recombination events captured with a specialized DSB repair assay. We propose that BIR repairs damaged replication forks in mammals, accounting for the high frequency of genomic duplications in human cancers.
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De Falco, Mariarosaria, and Mariarita De Felice. "Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea." International Journal of Molecular Sciences 22, no. 24 (December 10, 2021): 13296. http://dx.doi.org/10.3390/ijms222413296.

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All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.
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Symington, Lorraine S. "Role of RAD52 Epistasis Group Genes in Homologous Recombination and Double-Strand Break Repair." Microbiology and Molecular Biology Reviews 66, no. 4 (December 2002): 630–70. http://dx.doi.org/10.1128/mmbr.66.4.630-670.2002.

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SUMMARY The process of homologous recombination is a major DNA repair pathway that operates on DNA double-strand breaks, and possibly other kinds of DNA lesions, to promote error-free repair. Central to the process of homologous recombination are the RAD52 group genes (RAD50, RAD51, RAD52, RAD54, RDH54/TID1, RAD55, RAD57, RAD59, MRE11, and XRS2), most of which were identified by their requirement for the repair of ionizing-radiation-induced DNA damage in Saccharomyces cerevisiae. The Rad52 group proteins are highly conserved among eukaryotes, and Rad51, Mre11, and Rad50 are also conserved in prokaryotes and archaea. Recent studies showing defects in homologous recombination and double-strand break repair in several human cancer-prone syndromes have emphasized the importance of this repair pathway in maintaining genome integrity. Although sensitivity to ionizing radiation is a universal feature of rad52 group mutants, the mutants show considerable heterogeneity in different assays for recombinational repair of double-strand breaks and spontaneous mitotic recombination. Herein, I provide an overview of recent biochemical and structural analyses of the Rad52 group proteins and discuss how this information can be incorporated into genetic studies of recombination.
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Dissertations / Theses on the topic "Human DNA repair and recombination pathways"

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KATIA, CAPITANI. "Genome editing for clinically relevant mutations in genetic diseases and cancer." Doctoral thesis, Università di Siena, 2022. http://hdl.handle.net/11365/1211914.

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The present thesis concerns of two sections. The first one focuses on the application of Cluster Regularly Interspaced Short Palindromic Repeats (CRISPR) system as a tool for precise genome targeting and genome editing; the association between specific endonuclease and RNA guides complementary to the DNA target allows its targeting with single-nucleotide precision. CRISPR/Cas is able to perform Double-Strand Breaks (DSBs) at a target site which are soon repaired by cellular repairing mechanism, non-homologous end joining (NHEJ) or homology-directed repair (HDR). The first part of my project aims to explore and demonstrate the efficacy of a personalized therapeutic approach based on the CRISPR/Cas9 technology associated with adeno-associated viral vectors (AAVs)s, a mutation-specific gene therapy to restore mutated genes in genetic diseases to their original sequence trough the HDR-mediated correction. I developed an mCherry/EGFP reporter cassette where the reporter gene bears a mutation-specific target. It connects the mCherry and the EGFP (out of frame) coding sequences. Due to a frameshift, the reactivation of the EGFP allows the visualization of cells in which Cas9 had targeted the mutation-specific sequence leading to the production of Indels. I worked to edit mutations involved in specific genetic diseases such as mutations in FOXG1 or in MECP2, which are responsible for Rett syndrome, in the IQSEC2 gene that causes an intellectual disability clinically related to the Rett syndrome and in COL4A3 and COL4A5 causing Alport syndrome. In the second part of my study, I worked on developing a gene editing system aims to selective targeting to cancer cells while preserving the genetic integrity of normal cells. To this aim, I plan to exploit microhomology-mediated end joining (MMEJ) through Cas12a, an RNA-directed endonuclease that causes double-strand breaks with staggered ends, to insert in-frame the Herpes Simplex Virus –Thymidine Kinase suicide gene to trigger cell death. I designed and developed a construct to target a patient-specific single nucleotide variant within a coding sequence of the TP53 gene, from a patient with Chronic Lymphocytic Leukemia characterized by clonal expansion of clones bearing this TP53 mutation. I am able to detect the proper integration of the suicide gene sequence by analyzing the treated cells by fluorescence-activated cell sorting (FACS). Indeed, a green fluorescent protein (EGFP) sequence is linked to the TK by a 2A peptide system, thus green fluorescent cells are also the one expressing for the TK gene. The second section of my thesis concerns the COVID-19 pandemic global crisis and the need to understand how best to study and treat COVID-19. A key focus is sharing and analyzing data to learn about the genetic determinants of COVID-19 susceptibility, severity, and outcomes. In particular, my work has been focused on the TLR7 gene that has been involved as an important pattern recognition receptor for the ssRNA of SARS-CoV-2. We demonstrate that rare loss-of-function variants in the TLR7 gene in young men with severe COVID-19 and with no prior history of major chronic diseases were associated with impaired TLR7 signaling and type I and II IFN responses.
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Cukras, Scott. "Promoting Genome Stability via Multiple DNA Repair Pathways." Scholar Commons, 2015. https://scholarcommons.usf.edu/etd/5470.

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Maintaining genome integrity is indispensible for cells to prevent and limit accruement of deleterious mutations and to promote viable cell growth and proliferation. Cells possess a myriad of mechanisms to detect, prevent and repair incurred cellular damage. Here we discuss various proteins and their accompanying cellular pathways that promote genome stability. We first investigate the NEDD8 protein and its role in promoting homologous recombination repair via multiple Cullin E3 ubiquitin ligases. We provide specific mechanisms through which, UBE2M, an E2 conjugating enzyme, neddylates various Cullin ligases to render them catalytically active to degrade their substrates by the proteasome. We show that CUL1, CUL2 and CUL4 are important in regulating various steps in the DNA damage response. Our data indicates that UBE2M and the neddylation pathway are important for genome stability. Our second topic discusses the role of the USP1- UAF1 deubiquitinating enzyme in promoting homologous recombination. We show that USP1-UAF1 interact with and stabilize RAD51AP1 (RAD51- Associated Protein 1). RAD51AP1 has previously been reported to promote homologous recombination by facilitating recombinase activity of RAD51, an essential protein involved in homologous recombination repair. We show that USP1, UAF1 and RAD51AP1 depletion leads to genome instability. Our data demonstrates the importance of these proteins in promoting genome integrity via homologous recombination.
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Braybrooke, Jeremy P. "Characterisation of human homologues of the RAD51 protein." Thesis, Oxford Brookes University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340870.

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Tay, Ye Dee. "The analysis of homologous recombination pathways in Saccharomyces cerevisiae." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:2832c80a-202d-4b92-9685-5570c25f7386.

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Homologous recombination (HR) is essential for the repair of DNA doublestrand breaks (DSBs) and damaged replication forks. However, HR can also cause gross chromosomal rearrangements (GCRs) by producing crossovers (COs), resulting in the reciprocal exchange of sequences between non-sister chromatids. Therefore, HR-mediated GCRs are suppressed via the promotion of HR pathways that favour noncrossover (NCO) formation, such as the synthesis-dependent strand annealing (SDSA) and dissolution pathways, which are modulated by Mph1 and Sgs1 helicases, respectively. The mismatch repair (MMR) pathway is intricately associated with HR via its roles in repairing mismatches on heteroduplex DNA that can arise during HR and in preventing homeologous recombination. Using a plasmid break-repair assay, we have revealed a novel, MMR-independent role of MutSα in promoting the formation of a subset of COs that is specifically supressible by Mph1, during HR between two completely homologous sequences. In contrast, the MMR-dependent function of MutSα, together with Mph1 and Sgs1, was shown to be required for the suppression of CO formation during homeologous recombination. These data indicate that Mph1 can both antagonise and promote the functions of MutSα during DSB repair, depending on the levels of homology between the two recombining sequences. COs are generated by the resolution of Holliday junction (HJ) intermediates formed at the terminal stages of HR. Several S.cerevisiae proteins such as Yen1, Mus81, Slx1 and Rad1 have been implicated in HJ resolution. However, the in vivo roles of these proteins in HJ resolution remain to be confirmed. To directly and quantitatively monitor in vivo HJ resolution in S.cerevisiae, a transformation-based HJ resolution assay using a plasmid-borne HJ substrate has been developed. Using this system, we have demonstrated an in vivo HJ resolution function of Yen1, which acts redundantly with Mus81. Moreover, these redundant activities of Yen1 and Mus81 are essential for survival during replication stress, but are dispensable for DSB repair. An Slx4 and Rad1-dependent in vivo HJ resolution activity was also observed in the absence of Yen1 and Mus81 that was suppressed by presence of Slx1. Models describing how the nucleases interact to process HJs in vivo will be discussed.
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McCulloch, Scott D. "IDENTIFICATION AND CHARACTERIZATION OF MULTIPLE DNA LOOP REPAIR PATHWAYS IN HUMAN CELLS." UKnowledge, 2002. http://uknowledge.uky.edu/gradschool_diss/465.

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The stability of DNA is a critical factor for several diseases, the most prevalent of which is cancer. Several neurodegenerative and accelerated aging diseases are also characterized by genomic instability. The number and complexity of DNA repair pathways that human cells possess underscores the importance of genomic stability. These pathways ensure that damaged DNA is repaired and that a cells complement of DNA remains stable upon cell division. How one particular type of DNA alteration, a DNA loop, is processed in human cells was the focus of this study. We have employed an in vitro system to study defined DNA loop substrates by human nuclear extracts. The influence of either a 5 or 3 nick, the range of loop sizes processed, and the role of DNA mismatch repair, DNA nucleotide excision repair, and the Werner Syndrome helicase proteins were variables tested. The results indicate tha t DNA loops containing between 5 to 12 nucleotides are processed in a strand - specific manner when either a 5 or 3 nick is present , with repair being targeted solely to the nicked strand . This repair occurs by both mismatch repair dependent and independent pathways. The processing of DNA loops containing 30 nucleotides in length is directed either by a 5 nick, or by the loop itself, but not by a 3 nick. The nick independent pathway results solely in loop removal. The large loop pathway is independent of mismatch repair, nucleotide excision repair, and the WRN helicase/exonuclease protein. Both of the 5 nick directed pathways occur by excision that initiates at the pre- existing nick and proceeds towards the loop along the shortest path between the nick and loop. DNA resynthesis occurs using either DNA polymerase , , or and also initiates at the pre-existing 5 nick. The 3 nick directed intermediate loop repair pathway proceeds in a similar fashion, likely after a nick is made 5 to the loop region on the strand that contained the pre-existing nick. DNA synthesis inhibition has only a minor affect on the nick independent loop removal pathway as only a short tract of DNA surrounding the loop site is processed. In total, the results point to at least 3 novel pathways that process DNA loops that likely contribute to total genomic stability.
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Cataldi, Marcela Patricia. "Diverse Effects of DNA Repair Pathways on the Outcome of Recombinant Adeno-Associated Virus (rAAV) Vector Gene Delivery." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1303842573.

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Amunugama, Ravindra Bandara. "Insights into Regulation of Human RAD51 Nucleoprotein Filament Activity During Homologous Recombination." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1321984760.

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Drew, Yvette Claire. "The potential of the PARP-1 inhibitor, AGO14699, in human cancers defective in homologous recombination DNA repair." Thesis, University of Newcastle upon Tyne, 2012. http://hdl.handle.net/10443/1551.

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The aims of this study were to undertake the first comprehensive in vitro, in vivo and clinical investigation into the effects of the PARP-1 inhibitor, AG014699, in human cancers defective in homologous recombination (HR) DNA double strand break (DSB) repair. HR deficient cells were 9-fold more sensitive to AG014699 than HR proficient cells (mean LC50 = 3.26 μM vs. 29.68; P < 0.0001), confirming the theory of synthetic lethality. BRCA1 methylated UACC3199 breast cancer cells were also sensitive to AG014699 with mean LC50 significantly lower than the HR proficient cells (7.6 μM vs. 29.68; P = 0.002). AG014699 inhibited PARP activity by > 95% and induced DNA DSBs in all 11 cell lines studied. Evidence of HR (by Rad51 foci) was observed only in cells with functional BRCA1/2. A prolonged schedule of AG014699 (10 mg/kg daily for five days of a seven-day cycle for six cycles) more effectively delayed the growth of BRCA2 mutated xenografts than a ten day AG014699 schedule (tumour growth delay (TGD) = 27.5 vs. 12.5 days; P = 0.02). AG014699 significantly delayed UACC3199 tumour growth compared to untreated controls (mean time to relative tumour volume 5 = 35.8 vs. 25.2 days; P = 0.05); confirming in vitro findings that BRCA1 methylated cancer cells are sensitive to PARP inhibition. Clinical trial data from 38 patients demonstrated that AG014699 is non-toxic and efficacious with a clinical benefit rate of 34%. Higher baseline PARP-1 activity was associated with response to AG014699. The major findings of these studies are: the confirmation of the selective cytotoxicity of PARP inhibitors in BRCA mutated cancers; the results in UACC3199 cells which suggest that cancers with other HR defects could benefit from single agent PARP inhibitors, and finally the concept that length of exposure to (not just degree of) PARP inhibition is important for single agent anti-tumour activity. Furthermore, these data have formed the basis for a major amendment to the clinical trial; the result of which is eagerly awaited.
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Stults, Dawn Michelle. "Human ribosomal RNA gene clusters are recombinational hotspots in cancer." Lexington, Ky. : [University of Kentucky Libraries], 2009. http://hdl.handle.net/10225/1122.

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Thesis (M.S.)--University of Kentucky, 2009.
Title from document title page (viewed on May 6, 2009). Document formatted into pages; contains: v, 27 p. : ill. Includes abstract and vita. Includes bibliographical references (p. 25-26).
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Stults, Dawn Michelle. "STRUCTURAL INSTABILITY OF HUMAN RIBOSOMAL RNA GENE CLUSTERS." UKnowledge, 2010. http://uknowledge.uky.edu/gradschool_diss/68.

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The human ribosomal RNA genes are critically important for cell metabolism and viability. They code for the catalytic RNAs which, encased in a housing of more than 80 ribosomal proteins, link together amino acids by peptide bonds to generate all cellular proteins. Because the RNAs are not repeatedly translated, as is the case with messenger RNAs, multiple copies are required. The genes which code for the human ribosomal RNAs (rRNAs) are arranged as clusters of tandemly repeated sequences. Three of four catalytic RNAs are spliced from a single transcript. The genes are located on the short arms of the five acrocentric chromosomes (13, 14, 15, 21, and 22). The genes for the fourth rRNA are on chromosome 1q42, also arranged as a cluster of tandem repeats. The repeats are extremely similar in sequence, which makes them ideal for misalignment, non‐allelic homologous recombination (NAHR), and genomic destabilization during meiosis , replication, and damage repair. In this dissertation, I have used pulse‐field gel electrophoresis and in‐blot Southern hybridization to explore the physical structure of the human rRNA genes and determine their stability and heritability in normal, healthy individuals. I have also compared their structure in solid tumors compared to normal, healthy tissue from the same patient to determine whether dysregulated homologous recombination is an important means of genomic destabilization in cancer progression. Finally, I used the NCI‐60 panel of human cancer cell lines to compare the results from the pulsed‐field analysis, now called the gene cluster instability (GCI) assay, to two other indicators of homologous‐recombination-mediated genomic instability: sister chromatid exchange, and 5‐hydroxymethyl‐2’deoxyuridine sensitivity.
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Book chapters on the topic "Human DNA repair and recombination pathways"

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Masuda, Yuji, Fumio Hanaoka, and Chikahide Masutani. "Translesion DNA Synthesis and Damage Tolerance Pathways." In DNA Replication, Recombination, and Repair, 249–304. Tokyo: Springer Japan, 2016. http://dx.doi.org/10.1007/978-4-431-55873-6_11.

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Thompson, Larry H., Christine A. Weber, and Nigel J. Jones. "Human DNA Repair and Recombination Genes." In DNA Repair Mechanisms and Their Biological Implications in Mammalian Cells, 547–61. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-1327-4_44.

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Tricarico, Rossella, and Alfonso Bellacosa. "Active DNA Demethylation in Development, Human Disease, and Cancer." In DNA Replication, Recombination, and Repair, 517–48. Tokyo: Springer Japan, 2016. http://dx.doi.org/10.1007/978-4-431-55873-6_21.

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Sutherland, Betsy M., Haim Hacham, Richard W. Gange, Daniel Maytum, and John C. Sutherland. "DNA Damage and Repair in Human Skin: Pathways and Questions." In DNA Damage and Repair in Human Tissues, 149–60. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4613-0637-5_12.

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Lopez, Bernard, and Jacques Coppey. "Duplex-Duplex Homologous Recombination Catalysed by a Human Nuclear Extract. Involvement in Double-Strand Break Repair." In DNA Repair Mechanisms and Their Biological Implications in Mammalian Cells, 221–31. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-1327-4_21.

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Goodenow, Donna, Kiran Lalwani, and Christine Richardson. "DNA Damage and Repair Mechanisms Triggered by Exposure to Bioflavonoids and Natural Compounds." In DNA - Damages and Repair Mechanisms. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.95453.

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Eukaryotic cells use homologous recombination (HR), classical end-joining (C-NHEJ), and alternative end-joining (Alt-EJ) to repair DNA double-strand breaks (DSBs). Repair pathway choice is controlled by the activation and activity of pathways specific proteins in eukaryotes. Activity may be regulated by cell cycle stage, tissue type, and differentiation status. Bioflavonoids and other environmental agents such as pesticides have been shown to biochemically act as inhibitors of topoisomerase II (Top2). In cells, bioflavonoids directly lead to DNA double-strand breaks through both Top2-dependent and independent mechanisms, as well as induce DNA damage response (DDR) signaling, and promote alternative end-joining and chromosome alterations. This chapter will present differences in expression and activity of proteins in major DNA repair pathways, findings of Top2 inhibition by bioflavonoids and cellular response, discuss how these compounds trigger alternative end-joining, and conclude with implications for genome instability and human disease.
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Adachi, Kei, and Hiroyuki Nakai. "The Role of DNA Repair Pathways in Adeno-Associated Virus Infection and Viral Genome Replication / Recombination / Integration." In DNA Repair and Human Health. InTech, 2011. http://dx.doi.org/10.5772/24265.

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D’Andrea, Alan D. "DNA Repair Pathways and Human Cancer." In The Molecular Basis of Cancer, 47–66. Elsevier, 2015. http://dx.doi.org/10.1016/b978-1-4557-4066-6.00004-4.

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D'Andrea, Alan D. "DNA Repair Pathways and Human Cancer." In The Molecular Basis of Cancer, 39–55. Elsevier, 2008. http://dx.doi.org/10.1016/b978-141603703-3.10004-4.

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M., Gordon, and Stephan Gasser. "Integration of the DNA Damage Response with Innate Immune Pathways." In DNA Repair and Human Health. InTech, 2011. http://dx.doi.org/10.5772/24735.

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Conference papers on the topic "Human DNA repair and recombination pathways"

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Galvin, David J., Tin H. Thin, Jean-Paul Truman, Larissa Shenker, Richard Kolesnick, Zvi Fuks, and Adriana Haimovitz-Friedman. "Abstract 1406: Involvement of DNA repair pathways in DAG-lactone radiosensitization of human LNCaP cells." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-1406.

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Qin, Qin, Hong Xie, Amie L. Holmes, Sandy S. Wise, and John P. Wise. "Abstract 2118: Particulate chromate induces persistent DNA double strand breaks resulting in disruption of homologous recombination repair in human lung cells." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-2118.

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Ratnaparkhe, Manasi, John Wong, Pei-Chi Wei, Mario Hlevnjak, Paul Northcott, David T. Jones, Marcel Kool, et al. "Abstract 1352: Inactivation of factors of DNA double-strand break repair by homologous recombination or non-homologous end-joining leads to frequent catastrophic genomic events in murine and human tumors." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-1352.

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Riaz, N., P. Blecua, RS Lim, R. Shen, DS Higginson, N. Weinhold, L. Norton, B. Weigelt, SN Powell, and JS Reis-Filho. "Abstract PD8-09: Bi-allelic alterations in homologous recombination (HR) DNA repair-related genes as the basis for HR defects in human cancers: A pan-cancer genomics and functional analysis." In Abstracts: 2017 San Antonio Breast Cancer Symposium; December 5-9, 2017; San Antonio, Texas. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.sabcs17-pd8-09.

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Reports on the topic "Human DNA repair and recombination pathways"

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Sigurdsson, Stefan. Functions of Human Rad51 and Other Recombination Factors in DNA Double-Strand Break Repair. Fort Belvoir, VA: Defense Technical Information Center, June 2002. http://dx.doi.org/10.21236/ada407420.

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Sigurdsson, Stefan. Functions of Human Rad51 and Other Recombination Factors in DNA Double-Strand Break Repair. Fort Belvoir, VA: Defense Technical Information Center, June 2004. http://dx.doi.org/10.21236/ada426820.

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Obringer, John W., Steve Phipps, and Martin D. Johnson. Near Infrared, High Energy, Ultrashort Pulse Laser-Light Exposure Genetically Induces p53, a Gene in the DNA Repair and Cell Suicide Pathways in Cultured Human Cells. Fort Belvoir, VA: Defense Technical Information Center, November 1999. http://dx.doi.org/10.21236/ada381797.

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Wilson, Thomas E., Avraham A. Levy, and Tzvi Tzfira. Controlling Early Stages of DNA Repair for Gene-targeting Enhancement in Plants. United States Department of Agriculture, March 2012. http://dx.doi.org/10.32747/2012.7697124.bard.

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Gene targeting (GT) is a much needed technology as a tool for plant research and for the precise engineering of crop species. Recent advances in this field have shown that the presence of a DNA double-strand break (DSB) in a genomic locus is critical for the integration of an exogenous DNA molecule introduced into this locus. This integration can occur via either non-homologous end joining (NHEJ) into the break or homologous recombination (HR) between the broken genomic DNA and the introduced vector. A bottleneck for DNA integration via HR is the machinery responsible for homology search and strand invasion. Important proteins in this pathway are Rad51, Rad52 and Rad54. We proposed to combine our respective expertise: on the US side, in the design of zincfinger nucleases (ZFNs) for the induction of DNA DSBs at any desired genomic locus and in the integration of DNA molecules via NHEJ; and on the Israeli side in the HR events, downstream of the DSB, that lead to homology search and strand invasion. We sought to test three major pathways of targeted DNA integration: (i) integration by NHEJ into DSBs induced at desired sites by specially designed ZFNs; (ii) integration into DSBs induced at desired sites combined with the use of Rad51, Rad52 and Rad54 proteins to maximize the chances for efficient and precise HR-mediated vector insertion; (iii) stimulation of HR by Rad51, Rad52 and Rad54 in the absence of DSB induction. We also proposed to study the formation of dsT-DNA molecules during the transformation of plant cells. dsT-DNA molecules are an important substrate for HR and NHEJ-mediatedGT, yet the mode of their formation from single stranded T-DNA molecules is still obscure. In addition we sought to develop a system for assembly of multi-transgene binary vectors by using ZFNs. The latter may facilitate the production of binary vectors that may be ready for genome editing in transgenic plants. ZFNs were proposed for the induction of DSBs in genomic targets, namely, the FtsH2 gene whose loss of function can easily be identified in somatic tissues as white sectors, and the Cruciferin locus whose targeting by a GFP or RFP reporter vectors can give rise to fluorescent seeds. ZFNs were also proposed for the induction of DSBs in artificial targets and for assembly of multi-gene vectors. We finally sought to address two important cell types in terms of relevance to plant transformation, namely GT of germinal (egg) cells by floral dipping, and GT in somatic cells by root and leave transformation. To be successful, we made use of novel optimized expression cassettes that enable coexpression of all of the genes of interest (ZFNs and Rad genes) in the right tissues (egg or root cells) at the right time, namely when the GT vector is delivered into the cells. Methods were proposed for investigating the complementation of T-strands to dsDNA molecules in living plant cells. During the course of this research, we (i) designed, assembled and tested, in vitro, a pair of new ZFNs capable of targeting the Cruciferin gene, (ii) produced transgenic plants which expresses for ZFN monomers for targeting of the FtsH2 gene. Expression of these enzymes is controlled by constitutive or heat shock induced promoters, (iii) produced a large population of transgenic Arabidopsis lines in which mutated mGUS gene was incorporated into different genomic locations, (iv) designed a system for egg-cell-specific expression of ZFNs and RAD genes and initiate GT experiments, (v) demonstrated that we can achieve NHEJ-mediated gene replacement in plant cells (vi) developed a system for ZFN and homing endonuclease-mediated assembly of multigene plant transformation vectors and (vii) explored the mechanism of dsTDNA formation in plant cells. This work has substantially advanced our understanding of the mechanisms of DNA integration into plants and furthered the development of important new tools for GT in plants.
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Wright, Adam, Marija Milacic, Karen Rothfels, Joel Weiser, Quang Trinh, Bijay Jassal, Robin Haw, and Lincoln Stein. Evaluating the Predictive Accuracy of Reactome's Curated Biological Pathways. Reactome, November 2022. http://dx.doi.org/10.3180/poster/20221109wright.

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Reactome is a database of human biological pathways manually curated from the primary literature and peer-reviewed by experts. To evaluate the utility of Reactome pathways for predicting functional consequences of genetic perturbations, we compared predictions of perturbation effects based on Reactome pathways against published empirical observations. Ten cancer-relevant Reactome pathways, representing diverse biological processes such as signal transduction, cell division, DNA repair, and transcriptional regulation, were selected for testing. For each pathway, root input nodes and key pathway outputs were defined. We then used pathway-diagram-derived logic graphs to predict, either by inspection by biocurators or using a novel algorithm MP-BioPath, the effects of bidirectional perturbations (upregulation/activation or downregulation/inhibition) of single root inputs on the status of key outputs. These predictions were then compared to published empirical tests.
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