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International Journal of Hyperthermia :... Feb 2008Heat shock is one of the most effective radiosensitizers known. As a result, combination of heat with ionizing radiation (IR) is considered a promising strategy in the... (Review)
Review
Heat shock is one of the most effective radiosensitizers known. As a result, combination of heat with ionizing radiation (IR) is considered a promising strategy in the management of human cancer. The mechanism of heat radiosensitization has been the subject of extensive work but a unifying mechanistic model is presently lacking. To understand the cause of excessive death in irradiated cells after heat exposure, it is necessary to characterize the lesion(s) underlying the effect and to determine which of the pathways processing this lesion are affected by heat. Since DNA double strand breaks (DSBs) are the main cause for IR-induced cell death, inhibition of DSB processing has long been considered a major candidate for heat radiosensitization. However, effective radiosensitization of mutants with defects in homologous recombination repair (HRR), or in DNA-PK dependent non-homologous end joining (D-NHEJ), the two primary pathways of DSB repair, has led to the formulation of models excluding DSBs as a cause for this phenomenon and attributing heat radiosensitization to inhibition of base damage processing. Since direct evidence for a major role of base damage in heat radiosensitization, or in IR-induced killing for that matter, is scarce and new insights in DSB repair allow alternative interpretations of existing data with repair mutants, we attempt here a re-evaluation of the role of DSBs and their repair in heat radiosensitization. First, we reanalyse data obtained with various DSB repair mutants on first principles and in the light of the recent recognition that alternative pathways of NHEJ, operating as backup (B-NHEJ), substantially contribute to DSB repair and thus probably also to heat radiosensitization. Second, we review aspects of combined action of heat and radiation, such as modulation in the cell-cycle-dependent variation in radiosensitivity to killing, as well as heat radiosensitization as a function of LET, and examine whether the observed effects are compatible with DSB repair inhibition. We conclude with a model reclaiming a central role for DSBs in heat radiosensitization.
Topics: Combined Modality Therapy; DNA Breaks, Double-Stranded; DNA Repair; Dose-Response Relationship, Radiation; Heat-Shock Response; Humans; Hyperthermia, Induced; Radiation Tolerance; Radiation-Sensitizing Agents
PubMed: 18214766
DOI: 10.1080/02656730701784782 -
Nature Communications Mar 2018Genetic 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...
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 an 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.
Topics: DNA Breaks, Double-Stranded; DNA Repair; RNA; Rad52 DNA Repair and Recombination Protein; Recombinational DNA Repair; Saccharomyces cerevisiae Proteins
PubMed: 29545568
DOI: 10.1038/s41467-018-03483-7 -
Nature Communications Sep 2022The RNA world is changing our views about sensing and resolution of DNA damage. Here, we develop single-molecule DNA/RNA analysis approaches to visualize how nascent RNA...
The RNA world is changing our views about sensing and resolution of DNA damage. Here, we develop single-molecule DNA/RNA analysis approaches to visualize how nascent RNA facilitates the repair of DNA double-strand breaks (DSBs). RNA polymerase II (RNAPII) is crucial for DSB resolution in human cells. DSB-flanking, RNAPII-generated nascent RNA forms RNA:DNA hybrids, guiding the upstream DNA repair steps towards favouring the error-free Homologous Recombination (HR) pathway over Non-Homologous End Joining. Specific RNAPII inhibitor, THZ1, impairs recruitment of essential HR proteins to DSBs, implicating nascent RNA in DNA end resection, initiation and execution of HR repair. We further propose that resection factor CtIP interacts with and helps re-activate RNAPII when paused by the RNA:DNA hybrids, collectively promoting faithful repair of chromosome breaks to maintain genomic integrity.
Topics: DNA Breaks, Double-Stranded; DNA End-Joining Repair; DNA Repair; Humans; RNA; RNA Polymerase II; Recombinational DNA Repair
PubMed: 36085345
DOI: 10.1038/s41467-022-33027-z -
Methods in Enzymology 2018Nicks are the most common form of DNA damage, but they have only recently been shown to initiate damage that requires repair. Analysis of the pathways of nick repair in...
Nicks are the most common form of DNA damage, but they have only recently been shown to initiate damage that requires repair. Analysis of the pathways of nick repair in human cells has benefited from the development of enzymes that target nicks to specific sites in the genome and of reporters that enable rapid analysis of homology-directed repair and mutagenic end joining. Nicks undergo efficient repair by single-stranded oligonucleotide donors complementary to either the nicked or intact DNA strand, via pathways that are normally suppressed by RAD51. Here we discuss the details of reporter assays that take advantage of the convenience and sensitivity of flow cytometry to analyze pathways of repair at targeted DNA nicks. These assays are readily carried out in 96-well format cell culture plates, enabling mechanistic questions to be addressed by determining the contributions of specific factors by depletion and/or ectopic expression.
Topics: DNA; DNA Breaks; DNA End-Joining Repair; DNA Repair; Genetic Techniques; Humans; Recombinational DNA Repair
PubMed: 29523243
DOI: 10.1016/bs.mie.2017.12.001 -
Carcinogenesis Jan 2010The reaction of DNA-damaging agents with the genome results in a plethora of lesions, commonly referred to as adducts. Adducts may cause DNA to mutate, they may... (Review)
Review
The reaction of DNA-damaging agents with the genome results in a plethora of lesions, commonly referred to as adducts. Adducts may cause DNA to mutate, they may represent the chemical precursors of lethal events and they can disrupt expression of genes. Determination of which adduct is responsible for each of these biological endpoints is difficult, but this task has been accomplished for some carcinogenic DNA-damaging agents. Here, we describe the respective contributions of specific DNA lesions to the biological effects of low molecular weight alkylating agents.
Topics: Alkylation; DNA; DNA Damage; DNA Repair; Mutagenesis
PubMed: 19875697
DOI: 10.1093/carcin/bgp262 -
Molecular and Cellular Biology Jan 2010Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is known to be involved in base excision DNA repair, acting as the major abasic... (Review)
Review
Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is known to be involved in base excision DNA repair, acting as the major abasic endonuclease; the protein also functions as a redox coactivator of several transcription factors that regulate gene expression. Recent findings highlight a novel role for APE1 in RNA metabolism. The new findings are as follows: (i) APE1 interacts with rRNA and ribosome processing protein NPM1 within the nucleolus; (ii) APE1 interacts with proteins involved in ribosome assembly (i.e., RLA0, RSSA) and RNA maturation (i.e., PRP19, MEP50) within the cytoplasm; (iii) APE1 cleaves abasic RNA; and (iv) APE1 cleaves a specific coding region of c-myc mRNA in vitro and influences c-myc mRNA level and half-life in cells. Such findings on the role of APE1 in the posttranscriptional control of gene expression could explain its ability to influence diverse biological processes and its relocalization to cytoplasmic compartments in some tissues and tumors. In addition, we propose that APE1 serves as a "cleansing" factor for oxidatively damaged abasic RNA, establishing a novel connection between DNA and RNA surveillance mechanisms. In this review, we introduce questions and speculations concerning the role of APE1 in RNA metabolism and discuss the implications of these findings in a broader evolutionary context.
Topics: Animals; DNA Repair; DNA-(Apurinic or Apyrimidinic Site) Lyase; Gene Expression; Humans; Metabolic Networks and Pathways; Nucleophosmin; RNA, Ribosomal; Transcription Factors
PubMed: 19901076
DOI: 10.1128/MCB.01174-09 -
Environmental and Molecular Mutagenesis Jul 2010Homologous recombination repair (HRR) encompasses mechanisms that employ homologous DNA sequences as templates for repair or tolerance of a wide range of DNA lesions... (Review)
Review
Homologous recombination repair (HRR) encompasses mechanisms that employ homologous DNA sequences as templates for repair or tolerance of a wide range of DNA lesions that inhibit DNA replication in S phase. Arguably the most imposing of these DNA lesions is that of the interstrand crosslink (ICL), consisting of a covalently attached chemical bridge between opposing DNA strands. ICL repair requires the coordinated activities of HRR and a number of proteins from other DNA repair and damage response systems, including nucleotide excision repair, base excision repair, mismatch repair, and translesion DNA synthesis (TLS). Interestingly, different organisms favor alternative methods of HRR in the ICL repair process. E. coli perform ICL repair using a homology-driven damage bypass mechanism analogous to daughter strand gap repair. Eukaryotes from yeast to humans initiate ICL repair primarily during DNA replication, relying on HRR activity to restart broken replication forks associated with double-strand break intermediates induced by nucleolytic activities of other excision repair factors. Higher eukaryotes also employ several additional factors, including members of the Fanconi anemia damage-response network, which further promote replication-associated ICL repair through the activation and coordination of various DNA excision repair, TLS, and HRR proteins. This review focuses on the proteins and general mechanisms of HRR associated with ICL repair in different model organisms.
Topics: Cross-Linking Reagents; DNA Repair; Humans; Recombination, Genetic; Sequence Homology, Nucleic Acid
PubMed: 20658649
DOI: 10.1002/em.20577 -
Journal of Toxicology and Environmental... 2011DNA repair is crucial to the integrity of the human genome since mammalian cells are continuously exposed to different chemical and physical genotoxic agents. To... (Review)
Review
DNA repair is crucial to the integrity of the human genome since mammalian cells are continuously exposed to different chemical and physical genotoxic agents. To counteract the lesions induced by these agents, organisms have developed a number of highly conserved repair mechanisms involving numerous protein complexes grouped in several different repair pathways. The importance of studying the individual capacity to repair DNA damage lies in the observation that deficient repair mechanisms of the genome have been linked to the presence of large number of diseases and cancer, and alterations in these mechanisms may also alter the susceptibility of individuals exposed to a particular mutagen. This review focused on the current knowledge of different assays developed to evaluate DNA repair capacity (DRC). These assays, which are grouped into five major categories, have been successfully applied in (1) in vitro studies, (2) epidemiological studies in patients with cancer or other different pathologies, and (3) environmentally or occupationally exposed populations. Nevertheless, some of the limitations include high interlaboratory variability and difficulty to implement the assays on a large scale. The selection of an adequate DRC assay needs to be made on the basis of the objective raised for its application and taking into account a number of determining factors, namely, (1) speed and cost, (2) type of DNA repair to be evaluated, and (3) sample availability.
Topics: Animals; DNA Damage; DNA Repair; Genetic Variation; Humans; Mutagenicity Tests; Mutagens
PubMed: 21707433
DOI: 10.1080/15287394.2011.582320 -
Genes Oct 2022In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and... (Review)
Review
In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and their disassembly within the proper time window are essential for genome integrity. However, how these membrane-less sub-compartments are formed, maintained and disassembled remains unclear. Recently, several studies across different model organisms proposed that DNA repair foci form via liquid phase separation. In this review, we discuss the current research investigating the physical nature of repair foci. First, we present the different models of condensates proposed in the literature, highlighting the criteria to differentiate them. Second, we discuss evidence of liquid phase separation at DNA repair sites and the limitations of this model to fully describe structures formed in response to DNA damage. Finally, we discuss the origin and possible function of liquid phase separation for DNA repair processes.
Topics: DNA-Binding Proteins; DNA Breaks, Double-Stranded; DNA Repair; DNA Damage; DNA
PubMed: 36292731
DOI: 10.3390/genes13101846 -
BioEssays : News and Reviews in... Sep 1994
Review
Topics: DNA Repair; Escherichia coli; Models, Genetic
PubMed: 7980490
DOI: 10.1002/bies.950160909