scholarly journals Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin

2020 ◽  
Author(s):  
Albino Bacolla ◽  
Shiladitya Sengupta ◽  
Zu Ye ◽  
Chunying Yang ◽  
Joy Mitra ◽  
...  
Keyword(s):  
Genome Stability ◽  
High Throughput Sequencing ◽  
Excision Repair ◽  
Essential Gene ◽  
Atmospheric Oxygen ◽  
Super Resolution ◽  
Population Variation ◽  
Mutation Rates ◽  
Open Chromatin ◽  
Base Excision

Abstract Human genome stability requires efficient repair of oxidized bases, which is initiated via damage recognition and excision by NEIL1 and other base excision repair (BER) pathway DNA glycosylases (DGs). However, the biological mechanisms underlying detection of damaged bases among the million-fold excess of undamaged bases remain enigmatic. Indeed, mutation rates vary greatly within individual genomes, and lesion recognition by purified DGs in the chromatin context is inefficient. Employing super-resolution microscopy and co-immunoprecipitation assays, we find that acetylated NEIL1 (AcNEIL1), but not its non-acetylated form, is predominantly localized in the nucleus in association with epigenetic marks of uncondensed chromatin. Furthermore, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) revealed non-random AcNEIL1 binding near transcription start sites of weakly transcribed genes and along highly transcribed chromatin domains. Bioinformatic analyses revealed a striking correspondence between AcNEIL1 occupancy along the genome and mutation rates, with AcNEIL1-occupied sites exhibiting fewer mutations compared to AcNEIL1-free domains, both in cancer genomes and in population variation. Intriguingly, from the evolutionarily conserved unstructured domain that targets NEIL1 to open chromatin, its damage surveillance of highly oxidation-susceptible sites to preserve essential gene function and to limit instability and cancer likely originated ∼500 million years ago during the buildup of free atmospheric oxygen.

scholarly journals XRCC1 Prevents Replication Fork Instability during Misincorporation of the DNA Demethylation Bases 5-Hydroxymethyl-2′-Deoxycytidine and 5-Hydroxymethyl-2′-Deoxyuridine

2022 ◽  
Vol 23 (2) ◽  
pp. 893
Author(s):  
María José Peña-Gómez ◽  
Marina Suárez-Pizarro ◽  
Iván V. Rosado
Keyword(s):  
Genomic Instability ◽  
Base Excision Repair ◽  
Replication Fork ◽  
Genome Stability ◽  
Excision Repair ◽  
Embryonic Stem ◽  
Dna Demethylation ◽  
Dna Bases ◽  
Stem Cell Pluripotency ◽  
Base Excision

Whilst avoidance of chemical modifications of DNA bases is essential to maintain genome stability, during evolution eukaryotic cells have evolved a chemically reversible modification of the cytosine base. These dynamic methylation and demethylation reactions on carbon-5 of cytosine regulate several cellular and developmental processes such as embryonic stem cell pluripotency, cell identity, differentiation or tumourgenesis. Whereas these physiological processes are well characterized, very little is known about the toxicity of these cytosine analogues when they incorporate during replication. Here, we report a role of the base excision repair factor XRCC1 in protecting replication fork upon incorporation of 5-hydroxymethyl-2′-deoxycytosine (5hmC) and its deamination product 5-hydroxymethyl-2′-deoxyuridine (5hmU) during DNA synthesis. In the absence of XRCC1, 5hmC exposure leads to increased genomic instability, replication fork impairment and cell lethality. Moreover, the 5hmC deamination product 5hmU recapitulated the genomic instability phenotypes observed by 5hmC exposure, suggesting that 5hmU accounts for the observed by 5hmC exposure. Remarkably, 5hmC-dependent genomic instability and replication fork impairment seen in Xrcc1−/− cells were exacerbated by the trapping of Parp1 on chromatin, indicating that XRCC1 maintains replication fork stability during processing of 5hmC and 5hmU by the base excision repair pathway. Our findings uncover natural epigenetic DNA bases 5hmC and 5hmU as genotoxic nucleosides that threaten replication dynamics and genome integrity in the absence of XRCC1.

scholarly journals Oxidative stress triggers the preferential assembly of base excision repair complexes on open chromatin regions

2010 ◽  
Vol 38 (9) ◽  
pp. 2878-2890 ◽  
Author(s):  
Rachel Amouroux ◽  
Anna Campalans ◽  
Bernd Epe ◽  
J. Pablo Radicella
Keyword(s):  
Oxidative Stress ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Open Chromatin ◽  
Base Excision

scholarly journals The Multiple Cellular Roles of SMUG1 in Genome Maintenance and Cancer

2021 ◽  
Author(s):  
Sripriya Raja ◽  
Bennett Van Houten
Keyword(s):  
Genome Stability ◽  
Excision Repair ◽  
Critical Role ◽  
Multiple Roles ◽  
Genome Maintenance ◽  
Uracil Dna Glycosylase ◽  
Damage Recognition ◽  
Base Excision ◽  
Cellular Phenotypes ◽  
Moonlighting Functions

Single-stand selective monofunctional uracil DNA glycosylase 1 (SMUG1) works to remove uracil and certain oxidized bases from DNA during base excision repair (BER). This review provides a historical characterization of SMUG1 and 5-hydroxymethyl-2'-deoxyuridine (5-hmdU) one important substrate of this enzyme. Biochemical and structural analyses provide remarkable insight into the mechanism of this glycosylase revealing SMUG1 has a unique helical wedge which influences damage recognition during repair. Rodent studies suggest that, while SMUG1 shares substrate specificity with another uracil glycosylase UNG2, loss of SMUG1 can have unique cellular phenotypes. This review highlights the multiple roles SMUG1 may play in preserving genome stability, and how the loss of SMUG1 activity may promote cancer. Finally, we discuss recent studies indicating SMUG1 has moonlighting functions beyond BER, playing a critical role in RNA processing including the RNA component of telomerase.

scholarly journals Role of DNA polymerase β oxidized nucleotide insertion in DNA ligation failure

2017 ◽  
Vol 58 (5) ◽  
pp. 603-607 ◽  
Author(s):  
Melike Çağlayan ◽  
Samuel H Wilson
Keyword(s):  
Dna Polymerase ◽  
Genome Stability ◽  
Excision Repair ◽  
Cancer Therapeutics ◽  
Repair System ◽  
Dna Polymerase Β ◽  
Dna Base Excision Repair ◽  
Dna Base ◽  
Nucleotide Insertion ◽  
Base Excision

Abstract Production of reactive oxygen and nitrogen species (ROS), such as hydrogen peroxide, superoxide and hydroxyl radicals, has been linked to cancer, and these oxidative molecules can damage DNA. Base excision repair (BER), a major repair system maintaining genome stability over a lifespan, has an important role in repairing oxidatively induced DNA damage. Failure of BER leads to toxic consequences in ROS-exposed cells, and ultimately can contribute to the pathobiology of disease. In our previous report, we demonstrated that oxidized nucleotide insertion by DNA polymerase β (pol β) impairs BER due to ligation failure and leads to formation of a cytotoxic repair intermediate. Biochemical and cytotoxic effects of ligation failure could mediate genome stability and influence cancer therapeutics. In this review, we discuss the importance of coordination between pol β and DNA ligase I during BER, and how this could be a fundamental mechanism underlying human diseases such as cancer and neurodegeneration. A summary of this work was presented in a symposium at the International Congress of Radiation Research 2015 in Kyoto, Japan.

scholarly journals Nucleophosmin modulates stability, activity, and nucleolar accumulation of base excision repair proteins

2014 ◽  
Vol 25 (10) ◽  
pp. 1641-1652 ◽  
Author(s):  
Mattia Poletto ◽  
Lisa Lirussi ◽  
David M. Wilson ◽  
Gianluca Tell
Keyword(s):  
Dna Damage Response ◽  
Base Excision Repair ◽  
Genome Stability ◽  
Excision Repair ◽  
Multifunctional Protein ◽  
Protein Levels ◽  
Exact Function ◽  
Damage Response ◽  
Base Excision ◽  
Representative Protein

Nucleophosmin (NPM1) is a multifunctional protein that controls cell growth and genome stability via a mechanism that involves nucleolar–cytoplasmic shuttling. It is clear that NPM1 also contributes to the DNA damage response, yet its exact function is poorly understood. We recently linked NPM1 expression to the functional activation of the major abasic endonuclease in mammalian base excision repair (BER), apurinic/apyrimidinic endonuclease 1 (APE1). Here we unveil a novel role for NPM1 as a modulator of the whole BER pathway by 1) controlling BER protein levels, 2) regulating total BER capacity, and 3) modulating the nucleolar localization of several BER enzymes. We find that cell treatment with the genotoxin cisplatin leads to concurrent relocalization of NPM1 and BER components from nucleoli to the nucleoplasm, and cellular experiments targeting APE1 suggest a role for the redistribution of nucleolar BER factors in determining cisplatin toxicity. Finally, based on the use of APE1 as a representative protein of the BER pathway, our data suggest a function for BER proteins in the regulation of ribogenesis.

scholarly journals Genetic Analysis of Transcription-Associated Mutation in Saccharomyces cerevisiae

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 109-120 ◽  
Author(s):  
Natalie J Morey ◽  
Christopher N Greene ◽  
Sue Jinks-Robertson
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Mutation Rates ◽  
Base Pairs ◽  
Genetic Studies ◽  
Dna Damage And Repair ◽  
Nucleotide Excision ◽  
Translesion Bypass ◽  
Base Excision

Abstract High levels of transcription are associated with elevated mutation rates in yeast, a phenomenon referred to as transcription-associated mutation (TAM). The transcription-associated increase in mutation rates was previously shown to be partially dependent on the Rev3p translesion bypass pathway, thus implicating DNA damage in TAM. In this study, we use reversion of a pGAL-driven lys2ΔBgl allele to further examine the genetic requirements of TAM. We find that TAM is increased by disruption of the nucleotide excision repair or recombination pathways. In contrast, elimination of base excision repair components has only modest effects on TAM. In addition to the genetic studies, the lys2ΔBgl reversion spectra of repair-proficient low and high transcription strains were obtained. In the low transcription spectrum, most of the frameshift events correspond to deletions of AT base pairs whereas in the high transcription strain, deletions of GC base pairs predominate. These results are discussed in terms of transcription and its role in DNA damage and repair.

scholarly journals The Response to Oxidative DNA Damage in Neurons: Mechanisms and Disease

2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Laura Narciso ◽  
Eleonora Parlanti ◽  
Mauro Racaniello ◽  
Valeria Simonelli ◽  
Alessio Cardinale ◽  
...  
Keyword(s):  
Dna Damage ◽  
Genome Stability ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Age Related ◽  
Neurological Alterations ◽  
Base Excision ◽  
And Function

There is a growing body of evidence indicating that the mechanisms that control genome stability are of key importance in the development and function of the nervous system. The major threat for neurons is oxidative DNA damage, which is repaired by the base excision repair (BER) pathway. Functional mutations of enzymes that are involved in the processing of single-strand breaks (SSB) that are generated during BER have been causally associated with syndromes that present important neurological alterations and cognitive decline. In this review, the plasticity of BER during neurogenesis and the importance of an efficient BER for correct brain function will be specifically addressed paying particular attention to the brain region and neuron-selectivity in SSB repair-associated neurological syndromes and age-related neurodegenerative diseases.

scholarly journals Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells

2021 ◽  
Author(s):  
Philip S Robinson ◽  
Laura E. Thomas ◽  
Federico Abascal ◽  
Hyunchul Jung ◽  
Luke Harvey ◽  
...  
Keyword(s):  
Excision Repair ◽  
Functional Decline ◽  
Fold Increase ◽  
Colorectal Adenomas ◽  
Mutation Rates ◽  
Base Substitution ◽  
Intestinal Epithelial ◽  
Mutational Signatures ◽  
Base Excision ◽  
Cellular Dna

Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequenced normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 5-fold in all individuals, except for one showing a 33-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C>A changes. Different mutation rates and signatures between individuals were likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.

scholarly journals Identification of a Chemotherapeutic Lead Molecule for the Potential Disruption of the FAM72A-UNG2 Interaction to Interfere with Genome Stability, Centromere Formation, and Genome Editing

Cancers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 5870
Author(s):  
Senthil Renganathan ◽  
Subrata Pramanik ◽  
Rajasekaran Ekambaram ◽  
Arne Kutzner ◽  
Pok-Son Kim ◽  
...  
Keyword(s):  
Genome Stability ◽  
Excision Repair ◽  
Sequence Similarity ◽  
Genome Integrity ◽  
Therapeutic Approaches ◽  
In Silico Screening ◽  
Uracil Dna Glycosylase ◽  
Base Excision ◽  
Molecular Docking And Dynamics ◽  
Cell Signaling Pathways

Family with sequence similarity 72 A (FAM72A) is a pivotal mitosis-promoting factor that is highly expressed in various types of cancer. FAM72A interacts with the uracil-DNA glycosylase UNG2 to prevent mutagenesis by eliminating uracil from DNA molecules through cleaving the N-glycosylic bond and initiating the base excision repair pathway, thus maintaining genome integrity. In the present study, we determined a specific FAM72A-UNG2 heterodimer protein interaction using molecular docking and dynamics. In addition, through in silico screening, we identified withaferin B as a molecule that can specifically prevent the FAM72A-UNG2 interaction by blocking its cell signaling pathways. Our results provide an excellent basis for possible therapeutic approaches in the clinical treatment of cancer.

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