Transcription-coupled nucleotide excision repair: New insights revealed by genomic approaches

Duan, Mingrui; Speer, Rachel M.; Ulibarri, Jenna; Liu, Ke Jian; Mao, Peng

doi:10.1016/j.dnarep.2021.103126

Cited by 29 publications

(20 citation statements)

References 75 publications

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“…Compared to BER, which is predominant for the processing small base modifications, such as alkylation, deamination, and base oxidation, nucleotide excision repair (NER) pathways remove many diverse helix-distorting lesions and crosslinks caused by UV radiation, chemical agents, and some types of oxidative lesions, cyclopurines, thymine glycol, as well as malondialdehyde and ethylene adducts, for instance (Izumi and Mellon, 2021 ). Notably, these DNA lesions are not only the substrates for NER but have also been found to block transcription (Duan et al, 2021 ). NER consists of two subpathways: global genome (GG-NER) and transcription-coupled NER (TC-NER).…”

Section: Dna Repair Pathways That Are Activated In Postmitotic Neuronsmentioning

confidence: 99%

“…NER consists of two subpathways: global genome (GG-NER) and transcription-coupled NER (TC-NER). GG-NER repairs general helix-distorting lesions anywhere in the genome, whereas TC-NER deals with the damages that block transcription and is initiated by stalling of RNA polymerase II (Duan et al, 2021 ). Since the aim of DNA repair in neurons was to remove all obstacles to transcription and translation, TC-NER is of significant importance to neurons.…”

Section: Dna Repair Pathways That Are Activated In Postmitotic Neuronsmentioning

confidence: 99%

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Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases

Cao

Liu

et al. 2022

Front. Cell. Neurosci.

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Most of the neurodegenerative diseases and aging are associated with reactive oxygen species (ROS) or other intracellular damaging agents that challenge the genome integrity of the neurons. As most of the mature neurons stay in G0/G1 phase, replication-uncoupled DNA repair pathways including BER, NER, SSBR, and NHEJ, are pivotal, efficient, and economic mechanisms to maintain genomic stability without reactivating cell cycle. In these progresses, polymerases are prominent, not only because they are responsible for both sensing and repairing damages, but also for their more diversified roles depending on the cell cycle phase and damage types. In this review, we summarized recent knowledge on the structural and biochemical properties of distinct polymerases, including DNA and RNA polymerases, which are known to be expressed and active in nervous system; the biological relevance of these polymerases and their interactors with neuronal degeneration would be most graphically illustrated by the neurological abnormalities observed in patients with hereditary diseases associated with defects in DNA repair; furthermore, the vicious cycle of the trinucleotide repeat (TNR) and impaired DNA repair pathway is also discussed. Unraveling the mechanisms and contextual basis of the role of the polymerases in DNA damage response and repair will promote our understanding about how long-lived postmitotic cells cope with DNA lesions, and why disrupted DNA repair contributes to disease origin, despite the diversity of mutations in genes. This knowledge may lead to new insight into the development of targeted intervention for neurodegenerative diseases.

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Section: Dna Repair Pathways That Are Activated In Postmitotic Neuronsmentioning

confidence: 99%

Section: Dna Repair Pathways That Are Activated In Postmitotic Neuronsmentioning

confidence: 99%

Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases

Cao

Liu

et al. 2022

Front. Cell. Neurosci.

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“…These repair pathways have been extensively reviewed elsewhere, [8][9][10][11][12] but we briefly summarized these in what follows. NER is responsible for the removal of lesions caused by ultraviolet (UV) rays and other environmental carcinogens.…”

Section: Dna Repair and Genome Stability Pathwaysmentioning

confidence: 99%

Peripheral neuropathies associated with DNA repair disorders

et al. 2022

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Repair of genomic DNA is a fundamental housekeeping process that quietly maintains the health of our genomes. The consequences of a genetic defect affecting a component of this delicate mechanism are quite harmful, characterized by a cascade of premature aging that injures a variety of organs, including the nervous system. One part of the nervous system that is impaired in certain DNA repair disorders is the peripheral nerve. Chronic motor, sensory, and sensorimotor polyneuropathies have all been observed in affected individuals, with specific physiologies associated with different categories of DNA repair disorders. Cockayne syndrome has classically been linked to demyelinating polyneuropathies, whereas xeroderma pigmentosum has long been associated with axonal polyneuropathies. Three additional recessive DNA repair disorders are associated with neuropathies, including trichothiodystrophy, Werner syndrome, and ataxia‐telangiectasia. Although plausible biological explanations exist for why the peripheral nerves are specifically vulnerable to impairments of DNA repair, specific mechanisms such as oxidative stress remain largely unexplored in this context, and bear further study. It is also unclear why different DNA repair disorders manifest with different types of neuropathy, and why neuropathy is not universally present in those diseases. Longitudinal physiological monitoring of these neuropathies with serial electrodiagnostic studies may provide valuable noninvasive outcome data in the context of future natural history studies, and thus the responses of these neuropathies may become sentinel outcome measures for future clinical trials of treatments currently in development such as adeno‐associated virus gene replacement therapies.

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“…Within genes, particular regions may be favoured, such as the 5′ portion of the DHFR gene [ 137 ], although the molecular basis for such differential repair across genes remains subject to speculation. This strand bias is now very well established, with transcription coupled-NER (TC-NER) being perhaps the most obvious example of a process leading to the biased removal of lesions [ 138 ], contributing to the heterogeneous distribution of damage and mutational, strand asymmetry in the cancer genome [ 139 ]. In the case of UVR, chromatin structure and accessibility alter following exposure [ 140 ].…”

Section: Factors Influencing the Distribution Of Dna Damagementioning

confidence: 99%

Genome-wide mapping of genomic DNA damage: methods and implications

Amente

Scala

Majello

et al. 2021

Cell. Mol. Life Sci.

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Exposures from the external and internal environments lead to the modification of genomic DNA, which is implicated in the cause of numerous diseases, including cancer, cardiovascular, pulmonary and neurodegenerative diseases, together with ageing. However, the precise mechanism(s) linking the presence of damage, to impact upon cellular function and pathogenesis, is far from clear. Genomic location of specific forms of damage is likely to be highly informative in understanding this process, as the impact of downstream events (e.g. mutation, microsatellite instability, altered methylation and gene expression) on cellular function will be positional—events at key locations will have the greatest impact. However, until recently, methods for assessing DNA damage determined the totality of damage in the genomic location, with no positional information. The technique of “mapping DNA adductomics” describes the molecular approaches that map a variety of forms of DNA damage, to specific locations across the nuclear and mitochondrial genomes. We propose that integrated comparison of this information with other genome-wide data, such as mutational hotspots for specific genotoxins, tumour-specific mutation patterns and chromatin organisation and transcriptional activity in non-cancerous lesions (such as nevi), pre-cancerous conditions (such as polyps) and tumours, will improve our understanding of how environmental toxins lead to cancer. Adopting an analogous approach for non-cancer diseases, including the development of genome-wide assays for other cellular outcomes of DNA damage, will improve our understanding of the role of DNA damage in pathogenesis more generally.

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Transcription-coupled nucleotide excision repair: New insights revealed by genomic approaches

Cited by 29 publications

References 75 publications

Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases

Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases

Peripheral neuropathies associated with DNA repair disorders

Genome-wide mapping of genomic DNA damage: methods and implications

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