Exons and introns exhibit transcriptional strand asymmetry of dinucleotide distribution, damage formation and DNA repair

Abstract Recent cancer sequencing efforts have uncovered asymmetry in DNA damage induced mutagenesis between the transcribed and non-transcribed strands of genes. Here, we investigate the major type of damage induced by ultraviolet (UV) radiation, the cyclobutane pyrimidine dimers (CPDs), which are formed primarily in TT dinucleotides. We reveal that a transcriptional asymmetry already exists at the level of TT dinucleotide frequency and therefore also in CPD damage formation. This asymmetry is conserved in vertebrates and invertebrates and is completely reversed between introns and exons. We show the asymmetry in introns is linked to the transcription process itself, and is also found in enhancer elements. In contrast, the asymmetry in exons is not correlated to transcription, and is associated with codon usage preferences. Reanalysis of nucleotide excision repair, normalizing repair to the underlying TT frequencies, we show repair of CPDs is more efficient in exons compared to introns, contributing to the maintenance and integrity of coding regions. Our results highlight the importance of considering the primary sequence of the DNA in determining DNA damage sensitivity and mutagenic potential.

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Removal of Oxidative DNA Damage via FEN1-Dependent Long-Patch Base Excision Repair in Human Cell Mitochondria

Molecular and Cellular Biology ◽

10.1128/mcb.00457-08 ◽

2008 ◽

Vol 28 (16) ◽

pp. 4975-4987 ◽

Cited By ~ 145

Author(s):

Pingfang Liu ◽

Limin Qian ◽

Jung-Suk Sung ◽

Nadja C. de Souza-Pinto ◽

Li Zheng ◽

...

Keyword(s):

Dna Damage ◽

Base Excision Repair ◽

Oxidative Dna Damage ◽

Excision Repair ◽

Subcellular Fractionation ◽

Major Type ◽

Abasic Site ◽

Intact Cells ◽

Base Excision ◽

Extent Of Damage

ABSTRACT Repair of oxidative DNA damage in mitochondria was thought limited to short-patch base excision repair (SP-BER) replacing a single nucleotide. However, certain oxidative lesions cannot be processed by SP-BER. Here we report that 2-deoxyribonolactone (dL), a major type of oxidized abasic site, inhibits replication by mitochondrial DNA (mtDNA) polymerase γ and interferes with SP-BER by covalently trapping polymerase γ during attempted dL excision. However, repair of dL was detected in human mitochondrial extracts, and we show that this repair is via long-patch BER (LP-BER) dependent on flap endonuclease 1 (FEN1), not previously known to be present in mitochondria. FEN1 was retained in protease-treated mitochondria and detected in mitochondrial nucleoids that contain known mitochondrial replication and transcription proteins. Results of immunofluorescence and subcellular fractionation studies were also consistent with the presence of FEN1 in the mitochondria of intact cells. Immunodepletion experiments showed that the LP-BER activity of mitochondrial extracts was strongly diminished in parallel with the removal of FEN1, although some activity remained, suggesting the presence of an additional flap-removing enzyme. Biological evidence for a FEN1 role in repairing mitochondrial oxidative DNA damage was provided by RNA interference experiments, with the extent of damage greater and the recovery slower in FEN1-depleted cells than in control cells. The mitochondrial LP-BER pathway likely plays important roles in repairing dL lesions and other oxidative lesions and perhaps in normal mtDNA replication.

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Retracted: AKAP12 mediates PKA-induced phosphorylation of ATR to enhance nucleotide excision repair

Nucleic Acids Research ◽

10.1093/nar/gkw871 ◽

2016 ◽

Vol 44 (22) ◽

pp. 10711-10726 ◽

Cited By ~ 19

Author(s):

Stuart G. Jarrett ◽

Erin M. Wolf Horrell ◽

John A. D'Orazio

Keyword(s):

Dna Damage ◽

Nucleotide Excision Repair ◽

Nuclear Translocation ◽

Excision Repair ◽

Critical Role ◽

Loss Of Function ◽

Melanocortin 1 Receptor ◽

Nucleotide Excision ◽

Anchoring Protein ◽

Induced Mutagenesis

Abstract Loss-of-function in melanocortin 1 receptor (MC1R), a GS protein-coupled receptor that regulates signal transduction through cAMP and protein kinase A (PKA) in melanocytes, is a major inherited melanoma risk factor. Herein, we report a novel cAMP-mediated response for sensing and responding to UV-induced DNA damage regulated by A-kinase-anchoring protein 12 (AKAP12). AKAP12 is identified as a necessary participant in PKA-mediated phosphorylation of ataxia telangiectasia mutated and Rad3-related (ATR) at S435, a post-translational event required for cAMP-enhanced nucleotide excision repair (NER). Moreover, UV exposure promotes ATR-directed phosphorylation of AKAP12 at S732, which promotes nuclear translocation of AKAP12–ATR-pS435. This complex subsequently recruits XPA to UV DNA damage and enhances 5΄ strand incision. Preventing AKAP12's interaction with PKA or with ATR abrogates ATR-pS435 accumulation, delays recruitment of XPA to UV-damaged DNA, impairs NER and increases UV-induced mutagenesis. Our results define a critical role for AKAP12 as an UV-inducible scaffold for PKA-mediated ATR phosphorylation, and identify a repair complex consisting of AKAP12–ATR-pS435-XPA at photodamage, which is essential for cAMP-enhanced NER.

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UV- and Gamma-Radiation Sensitive Mutants of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/147.3.1401 ◽

1997 ◽

Vol 147 (3) ◽

pp. 1401-1409 ◽

Cited By ~ 1

Author(s):

C-Z Jiang ◽

C-N Yen ◽

K Cronin ◽

D Mitchell ◽

A B Britt

Keyword(s):

Dna Damage ◽

Gamma Radiation ◽

Excision Repair ◽

Repair Pathway ◽

Dark Repair ◽

Enhanced Sensitivity ◽

Pyrimidine Dimers ◽

Repair Mechanisms ◽

Repair Activity ◽

Base Excision

Arabidopsis seedlings repair UV-induced DNA damage via light-dependent and -independent pathways. The mechanism of the “dark repair” pathway is still unknown. To determine the number of genes required for dark repair and to investigate the substrate-specificity of this process we isolated mutants with enhanced sensitivity to UV radiation in the absence of photoreactivating light. Seven independently derived UV sensitive mutants were isolated from EMS-mutagenized population. These fell into six complementation groups, two of which (UVR1 and UVH1) have previously been defined. Four of these mutants are defective in the dark repair of UV-induced pyrimidine [6-4]pyrimidinone dimers. These four mutant lines are sensitive to the growth-inhibitory effects of gamma radiation, suggesting that this repair pathway is also involved in the repair of some type of gamma-induced DNA damage product. The requirement for the coordinate action of several different gene products for effective repair of pyrimidine dimers, as well as the nonspecific nature of the repair activity, is consistent with nucleotide excision repair mechanisms previously described in Saccharomyces cerevisiae and nonplant higher eukaryotes and inconsistent with substrate-specific base excision repair mechanisms found in some bacteria, bacteriophage, and fungi.

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Xeroderma Pigmentosum: Gene Variants and Splice Variants

Genes ◽

10.3390/genes12081173 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1173

Author(s):

Marie Christine Martens ◽

Steffen Emmert ◽

Lars Boeckmann

Keyword(s):

Dna Damage ◽

Xeroderma Pigmentosum ◽

Splice Variants ◽

Excision Repair ◽

Genetic Disorder ◽

Cyclobutane Pyrimidine Dimers ◽

Pyrimidine Dimers ◽

Damage Repair ◽

Nucleotide Excision ◽

Functional Relevance

The nucleotide excision repair (NER) is essential for the repair of ultraviolet (UV)-induced DNA damage, such as cyclobutane pyrimidine dimers (CPDs) and 6,4-pyrimidine-pyrimidone dimers (6,4-PPs). Alterations in genes of the NER can lead to DNA damage repair disorders such as Xeroderma pigmentosum (XP). XP is a rare autosomal recessive genetic disorder associated with UV-sensitivity and early onset of skin cancer. Recently, extensive research has been conducted on the functional relevance of splice variants and their relation to cancer. Here, we focus on the functional relevance of alternative splice variants of XP genes.

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UV light-induced DNA damage detection in the unicellular green alga Chlamydomonas reinhardtii

Biologia ◽

10.2478/s11756-008-0149-1 ◽

2008 ◽

Vol 63 (6) ◽

Cited By ~ 4

Author(s):

Alena Hercegová ◽

Andrea Ševčovičová ◽

Eliška Gálová

Keyword(s):

Dna Damage ◽

Chlamydomonas Reinhardtii ◽

Green Alga ◽

Excision Repair ◽

Biological Effects ◽

Pyrimidine Dimer ◽

Repair System ◽

Pyrimidine Dimers ◽

Unicellular Green Alga ◽

Mutant Strains

AbstractExposure of cells to ultraviolet radiation (UVR) is one of the best studied and most used model system for the examination of the biological effects of DNA damage, its repair and tolerance. The major product after UVR treatment is cyclobutane pyrimidine dimer (TT, TC, CC). Pyrimidine dimers are repaired by a direct reversal called photoreactivation or by excision of damage in a process of nucleotide excision repair. Several methods have been developed for the detection and quantification of pyrimidine dimers in DNA. The technique of Small and Greimann, in which DNA is incubated with the pyrimidine dimer-specific endonuclease, was used for the analysis of mutant strains with impaired excision repair system of the unicellular green alga Chlamydomonas reinhardtii. Another method is based on the binding of specific monoclonal antibodies to pyrimidine dimers. The aim of our work was to compare these two techniques with the use of mutant strains of C. reinhardtii — uvsX1 and uvsX2 which are assumed to be deficient in DNA damage recognition. One of their traits was sensitivity to UVR which could be caused by breakdown of the excision repair pathway. The results suggest that the immuno-approach is suitable for the detection of DNA damage induced by UVR.

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Functional impacts of the ubiquitin–proteasome system on DNA damage recognition in global genome nucleotide excision repair

Scientific Reports ◽

10.1038/s41598-020-76898-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Wataru Sakai ◽

Mayumi Yuasa-Sunagawa ◽

Masayuki Kusakabe ◽

Aiko Kishimoto ◽

Takeshi Matsui ◽

...

Keyword(s):

Dna Damage ◽

Nucleotide Excision Repair ◽

Excision Repair ◽

Proteasome Inhibitors ◽

Ubiquitin Proteasome System ◽

Damage Recognition ◽

Pyrimidine Dimers ◽

Nucleotide Excision ◽

Ubiquitin Proteasome ◽

Lesion Recognition

AbstractThe ubiquitin–proteasome system (UPS) plays crucial roles in regulation of various biological processes, including DNA repair. In mammalian global genome nucleotide excision repair (GG-NER), activation of the DDB2-associated ubiquitin ligase upon UV-induced DNA damage is necessary for efficient recognition of lesions. To date, however, the precise roles of UPS in GG-NER remain incompletely understood. Here, we show that the proteasome subunit PSMD14 and the UPS shuttle factor RAD23B can be recruited to sites with UV-induced photolesions even in the absence of XPC, suggesting that proteolysis occurs at DNA damage sites. Unexpectedly, sustained inhibition of proteasome activity results in aggregation of PSMD14 (presumably with other proteasome components) at the periphery of nucleoli, by which DDB2 is immobilized and sequestered from its lesion recognition functions. Although depletion of PSMD14 alleviates such DDB2 immobilization induced by proteasome inhibitors, recruitment of DDB2 to DNA damage sites is then severely compromised in the absence of PSMD14. Because all of these proteasome dysfunctions selectively impair removal of cyclobutane pyrimidine dimers, but not (6–4) photoproducts, our results indicate that the functional integrity of the proteasome is essential for the DDB2-mediated lesion recognition sub-pathway, but not for GG-NER initiated through direct lesion recognition by XPC.

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Rescue of cells from apoptosis increases DNA repair in UVB exposed cells: implications for the DNA damage response

Toxicology Research ◽

10.1039/c4tx00197d ◽

2015 ◽

Vol 4 (3) ◽

pp. 725-738 ◽

Cited By ~ 7

Author(s):

Mahsa Karbaschi ◽

Salvador Macip ◽

Vilas Mistry ◽

Hussein H. K. Abbas ◽

George J. Delinassios ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Nucleotide Excision Repair ◽

Dna Damage Response ◽

Excision Repair ◽

Cyclobutane Pyrimidine Dimers ◽

Pyrimidine Dimers ◽

Nucleotide Excision ◽

Damage Response ◽

Lengthy Process

Classically, the nucleotide excision repair (NER) of cyclobutane pyrimidine dimers (CPD) is a lengthy process (t1/2 > 48 h).

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Why Cockayne syndrome patients do not get cancer despite their DNA repair deficiency

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1610020113 ◽

2016 ◽

Vol 113 (36) ◽

pp. 10151-10156 ◽

Cited By ~ 26

Author(s):

Kate S. Reid-Bayliss ◽

Sarah T. Arron ◽

Lawrence A. Loeb ◽

Vladimir Bezrookove ◽

James E. Cleaver

Keyword(s):

Dna Damage ◽

Cultured Cells ◽

Excision Repair ◽

High Sensitivity ◽

Specific Protein ◽

Cockayne Syndrome ◽

Multiple Loci ◽

Dna Repair Deficiency ◽

Induced Mutagenesis ◽

Duplex Sequencing

Cockayne syndrome (CS) and xeroderma pigmentosum (XP) are human photosensitive diseases with mutations in the nucleotide excision repair (NER) pathway, which repairs DNA damage from UV exposure. CS is mutated in the transcription-coupled repair (TCR) branch of the NER pathway and exhibits developmental and neurological pathologies. The XP-C group of XP patients have mutations in the global genome repair (GGR) branch of the NER pathway and have a very high incidence of UV-induced skin cancer. Cultured cells from both diseases have similar sensitivity to UV-induced cytotoxicity, but CS patients have never been reported to develop cancer, although they often exhibit photosensitivity. Because cancers are associated with increased mutations, especially when initiated by DNA damage, we examined UV-induced mutagenesis in both XP-C and CS cells, using duplex sequencing for high-sensitivity mutation detection. Duplex sequencing detects rare mutagenic events, independent of selection and in multiple loci, enabling examination of all mutations rather than just those that confer major changes to a specific protein. We found telomerase-positive normal and CS-B cells had increased background mutation frequencies that decreased upon irradiation, purging the population of subclonal variants. Primary XP-C cells had increased UV-induced mutation frequencies compared with normal cells, consistent with their GGR deficiency. CS cells, in contrast, had normal levels of mutagenesis despite their TCR deficiency. The lack of elevated UV-induced mutagenesis in CS cells reveals that their TCR deficiency, although increasing cytotoxicity, is not mutagenic. Therefore the absence of cancer in CS patients results from the absence of UV-induced mutagenesis rather than from enhanced lethality.

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