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Proceedings of the National Academy of... Oct 2019Mutational signatures can reveal properties of underlying mutational processes and are important when assessing signals of selection in cancer. Here, we describe the...
Mutational signatures can reveal properties of underlying mutational processes and are important when assessing signals of selection in cancer. Here, we describe the sequence characteristics of mutations induced by ultraviolet (UV) light, a major mutagen in several human cancers, in terms of extended (longer than trinucleotide) patterns as well as variability of the signature across chromatin states. Promoter regions display a distinct UV signature with reduced TCG > TTG transitions, and genome-wide mapping of UVB-induced DNA photoproducts (pyrimidine dimers) showed that this may be explained by decreased damage formation at hypomethylated promoter CpG sites. Further, an extended signature model encompassing additional information from longer contextual patterns improves modeling of UV mutations, which may enhance discrimination between drivers and passenger events. Our study presents a refined picture of the UV signature and underscores that the characteristics of a single mutational process may vary across the genome.
Topics: Cell Line, Tumor; Computational Biology; DNA Damage; DNA Methylation; Genetic Variation; Genome, Human; Humans; Melanoma; Mutation; Promoter Regions, Genetic; Pyrimidine Dimers; Ultraviolet Rays
PubMed: 31548379
DOI: 10.1073/pnas.1909021116 -
Journal of Bacteriology Nov 1983In Deinococcus radiodurans, the genes uvsC, uvsD, uvsE, and mtcA are all involved in the single-strand incision of UV-irradiated DNA, and mutations in at least two of...
In Deinococcus radiodurans, the genes uvsC, uvsD, uvsE, and mtcA are all involved in the single-strand incision of UV-irradiated DNA, and mutations in at least two of them were required to produce an incisionless strain. One mutation must be in mtcA and one in uvsC, uvsD, or uvsE. Strains carrying single mutations in any one of the genes can incise DNA to the same extent as the wild-type strain. Neither the presence of EDTA nor the absence of protein synthesis affected the incision step. Strains deficient in DNA incision have greatly reduced DNA degradation after UV irradiation, and upon addition of chloramphenicol to the postirradiation medium, they do not undergo excessive DNA degradation as is seen in the wild-type strain and strains singly mutant in uvsC, uvsD, or uvsE. The strain singly mutant in mtcA also lacked chloramphenicol-enhanced DNA degradation and loss of viability but behaved similarly to the wild-type strain with respect to resumption of DNA synthesis and DNA degradation in the absence of chloramphenicol. It is proposed that two constitutive, cation-independent UV endonucleases are present in D. radiodurans: UV endonuclease alpha (the product of the mtcA gene), which incises in response to pyrimidine dimers, mitomycin C cross-links, bromomethylbenzanthracene adducts, and other alkylation damage, and UV endonuclease beta (the product of the uvsC, uvsD, and uvsE genes), which incises only in response to pyrimidine dimers. Both endonucleases have associated exonuclease activity. The exonucleolytic activity associated with UV endonuclease alpha requires a UV-induced protein to terminate (or control) its activity, whereas the exonucleolytic activity associated with UV endonuclease beta is slower acting and does not require the inducible terminator.
Topics: Bacterial Proteins; Chloramphenicol; DNA Repair; Genes; Genes, Bacterial; Kinetics; Micrococcus; Mutation; Pyrimidine Dimers; Ultraviolet Rays
PubMed: 6313608
DOI: 10.1128/jb.156.2.576-583.1983 -
DNA Repair Oct 2008Xeroderma pigmentosum variant (XPV) patients carry germ-line mutations in DNA polymerase eta (poleta), a major translesion DNA synthesis (TLS) polymerase, and exhibit...
Reduced efficiency and increased mutagenicity of translesion DNA synthesis across a TT cyclobutane pyrimidine dimer, but not a TT 6-4 photoproduct, in human cells lacking DNA polymerase eta.
Xeroderma pigmentosum variant (XPV) patients carry germ-line mutations in DNA polymerase eta (poleta), a major translesion DNA synthesis (TLS) polymerase, and exhibit severe sunlight sensitivity and high predisposition to skin cancer. Using a quantitative TLS assay system based on gapped plasmids we analyzed TLS across a site-specific TT CPD (thymine-thymine cyclobutane pyrimidine dimer) or TT 6-4 PP (thymine-thymine 6-4 photoproduct) in three pairs of poleta-proficient and deficient human cells. TLS across the TT CPD lesion was reduced by 2.6-4.4-fold in cells lacking poleta, and exhibited a strong 6-17-fold increase in mutation frequency at the TT CPD. All targeted mutations (74%) in poleta-deficient cells were opposite the 3'T of the CPD, however, a significant fraction (23%) were semi-targeted to the nearest nucleotides flanking the CPD. Deletions and insertions were observed at a low frequency, which increased in the absence of poleta, consistent with the formation of double strand breaks due to defective TLS. TLS across TT 6-4 PP was about twofold lower than across CPD, and was marginally reduced in poleta-deficient cells. TLS across TT 6-4 PP was highly mutagenic (27-63%), with multiple mutations types, and no significant difference between cells with or without poleta. Approximately 50% of the mutations formed were semi-targeted, of which 84-93% were due to the insertion of an A opposite the template G 5' to the 6-4 PP. These results, which are consistent with the UV hyper-mutability of XPV cells, highlight the critical role of poleta in error-free TLS across CPD in human cells, and suggest a potential involvement, although minor, of poleta in TLS across 6-4 PP under some conditions.
Topics: Cells, Cultured; DNA; DNA-Directed DNA Polymerase; Fibroblasts; Humans; Mutagenesis; Plasmids; Pyrimidine Dimers; Sequence Analysis, DNA; Xeroderma Pigmentosum
PubMed: 18634905
DOI: 10.1016/j.dnarep.2008.06.008 -
American Journal of Botany May 2014•
UNLABELLED
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PREMISE OF THE STUDY
Although ultraviolet radiation (UV) is known to have negative effects on plant growth, there has been no direct evidence that plants growing at higher elevations are more severely affected by ultraviolet-B (UV-B) radiation, which is known to increase with elevation. We examined damage to DNA, a primary target of UV-B, in the widespread species Polygonum sachalinense (Fallopia sachalinensis) and Plantago asiatica at two elevations.•
METHODS
We sampled leaves of both species at 300 and 1700 m above sea level every 2 h for 11 d across the growing season and determined the level of cyclobutane pyrimidine dimer (CPD), a major product of UV damage to DNA.•
KEY RESULTS
The CPD level was significantly influenced by the time of day, date, elevation, and their interactions in both species. The CPD level tended to be higher at noon or on sunny days. DNA damage was more severe at 1700 m than at 300 m: on average, 8.7% greater at high elevation in P. asiatica and 7.8% greater in P. sachalinense Stepwise multiple regression analysis indicated that the CPD level was explained mainly by UV-B and had no significant relationship with other environmental factors such as temperature and photosynthetically active radiation.•
CONCLUSIONS
UV-induced DNA damage in plants is greater at higher elevations.
Topics: Altitude; DNA Damage; Plant Leaves; Plantago; Polygonum; Pyrimidine Dimers; Sunlight; Ultraviolet Rays
PubMed: 24748608
DOI: 10.3732/ajb.1400010 -
Molecular Vision 2013Little is known about DNA damage in human pterygium, and no data about DNA damage involvement as a potential angiogenic factor are available. We studied, with...
PURPOSE
Little is known about DNA damage in human pterygium, and no data about DNA damage involvement as a potential angiogenic factor are available. We studied, with immunohistochemistry, the presence and localization of thymine dimers in the epithelial and stromal components of the human primary pterygium and its recurrences with a special emphasis on the vascular network and its interactions with the p53 tumor suppressor gene protein.
METHODS
Thirty-five primary human pterygium, three recurrences, and three normal bulbar conjunctiva were included in the present study. Formalin-fixed, paraffin-embedded tissues were submitted for immunohistochemical analysis with antithymine dimers and p53 antibodies. Thymine dimer and p53 nuclear staining was assessed in the epithelial and stromal components of pterygial tissues and normal counterparts.
RESULTS
Thymine dimers were present in the epithelial and stromal components of human pterygium and its recurrences. The thymine dimers were detected in the epithelial component of the human pterygium with a higher density and intensity in the basal layer of the epithelium. Small blood vessels' endothelial cells showed positive reaction for antithymine dimer antibodies together with isolated positive expression found in the nuclei of perivascular cells. For the recurrent pterygium, dimer expression was found only in the subepithelial fibrovascular layer components and in scattered cells from the basal layer of the epithelium. P53 expression was positive in 38.5% of the cases in the epithelial compartment, and in two cases, scattered p53 positive endothelial, fibroblast-like, and perivascular cells were detected in the fibrovascular compartment.
CONCLUSIONS
Thymine dimers in human pterygium and its recurrences suggest that DNA damage is involved not only in pterygium epithelial and fibrous proliferation but also in angiogenesis and lymphangiogenesis from this ocular lesion in a still incomplete elucidated pathogenic mechanism.
Topics: Adult; Conjunctiva; DNA Damage; Epithelium; Female; Humans; Immunohistochemistry; Lymphangiogenesis; Male; Middle Aged; Neovascularization, Pathologic; Pterygium; Pyrimidine Dimers; Recurrence; Stromal Cells; Tumor Suppressor Protein p53
PubMed: 23401662
DOI: No ID Found -
Nucleic Acids Research Jul 2019Failure in repairing ultraviolet radiation-induced DNA damage can lead to mutations and cancer. Among UV-lesions, the pyrimidine-pyrimidone (6-4) photoproduct (6-4PP) is...
Failure in repairing ultraviolet radiation-induced DNA damage can lead to mutations and cancer. Among UV-lesions, the pyrimidine-pyrimidone (6-4) photoproduct (6-4PP) is removed from the genome much faster than the cyclobutane pyrimidine dimer (CPD), owing to the more efficient recognition of 6-4PP by XPC-RAD23B, a key initiator of global-genome nucleotide excision repair (NER). Here, we report a crystal structure of a Rad4-Rad23 (yeast XPC-Rad23B ortholog) bound to 6-4PP-containing DNA and 4-μs molecular dynamics (MD) simulations examining the initial binding of Rad4 to 6-4PP or CPD. This first structure of Rad4/XPC bound to a physiological substrate with matched DNA sequence shows that Rad4 flips out both 6-4PP-containing nucleotide pairs, forming an 'open' conformation. The MD trajectories detail how Rad4/XPC initiates 'opening' 6-4PP: Rad4 initially engages BHD2 to bend/untwist DNA from the minor groove, leading to unstacking and extrusion of the 6-4PP:AA nucleotide pairs towards the major groove. The 5' partner adenine first flips out and is captured by a BHD2/3 groove, while the 3' adenine extrudes episodically, facilitating ensuing insertion of the BHD3 β-hairpin to open DNA as in the crystal structure. However, CPD resists such Rad4-induced structural distortions. Untwisting/bending from the minor groove may be a common way to interrogate DNA in NER.
Topics: DNA; DNA Repair; DNA-Binding Proteins; Molecular Dynamics Simulation; Nucleic Acid Conformation; Protein Binding; Protein Domains; Pyrimidine Dimers; Saccharomyces cerevisiae Proteins
PubMed: 31106376
DOI: 10.1093/nar/gkz359 -
Nature Communications Jul 2017HBO1, a histone acetyl transferase, is a co-activator of DNA pre-replication complex formation. We recently reported that HBO1 is phosphorylated by ATM and/or ATR and...
HBO1, a histone acetyl transferase, is a co-activator of DNA pre-replication complex formation. We recently reported that HBO1 is phosphorylated by ATM and/or ATR and binds to DDB2 after ultraviolet irradiation. Here, we show that phosphorylated HBO1 at cyclobutane pyrimidine dimer (CPD) sites mediates histone acetylation to facilitate recruitment of XPC at the damaged DNA sites. Furthermore, HBO1 facilitates accumulation of SNF2H and ACF1, an ATP-dependent chromatin remodelling complex, to CPD sites. Depletion of HBO1 inhibited repair of CPDs and sensitized cells to ultraviolet irradiation. However, depletion of HBO1 in cells derived from xeroderma pigmentosum patient complementation groups, XPE, XPC and XPA, did not lead to additional sensitivity towards ultraviolet irradiation. Our findings suggest that HBO1 acts in concert with SNF2H-ACF1 to make the chromosome structure more accessible to canonical nucleotide excision repair factors.
Topics: Adenosine Triphosphatases; Ataxia Telangiectasia Mutated Proteins; Chromosomal Proteins, Non-Histone; DNA Damage; DNA Repair; DNA-Binding Proteins; Histone Acetyltransferases; Humans; Phosphorylation; Pyrimidine Dimers; Transcription Factors; Ultraviolet Rays
PubMed: 28719581
DOI: 10.1038/ncomms16102 -
Nature Jul 2019Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex...
Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced pyrimidine dimers throughout the genome; however, it remains unknown how these lesions are recognized in chromatin, in which nucleosomes restrict access to DNA. Here we report cryo-electron microscopy structures of UV-DDB bound to nucleosomes bearing a 6-4 pyrimidine-pyrimidone dimer or a DNA-damage mimic in various positions. We find that UV-DDB binds UV-damaged nucleosomes at lesions located in the solvent-facing minor groove without affecting the overall nucleosome architecture. In the case of buried lesions that face the histone core, UV-DDB changes the predominant translational register of the nucleosome and selectively binds the lesion in an accessible, exposed position. Our findings explain how UV-DDB detects occluded lesions in strongly positioned nucleosomes, and identify slide-assisted site exposure as a mechanism by which high-affinity DNA-binding proteins can access otherwise occluded sites in nucleosomal DNA.
Topics: Cryoelectron Microscopy; DNA; DNA Damage; DNA-Binding Proteins; Histones; Humans; Models, Molecular; Nucleosomes; Pyrimidine Dimers; Thermodynamics; Ultraviolet Rays
PubMed: 31142837
DOI: 10.1038/s41586-019-1259-3 -
Proceedings of the National Academy of... Apr 2018We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers...
We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers and (6-4) pyrimidine-pyrimidone photoproducts in the genome. We find that these photoproducts are removed from the genome primarily by incisions 13-18 nucleotides 5' and 6-7 nucleotides 3' to the UV damage that generate 21- to 27-nt-long excision products. Analyses of the excision repair kinetics both in single genes and at the genome-wide level reveal strong transcription-coupled repair of the transcribed strand at early time points followed by predominantly nontranscribed strand repair at later stages. We have also characterized the excision repair level as a function of the transcription level. The availability of high-resolution and dynamic repair maps should aid in future repair and mutagenesis studies in this model organism.
Topics: DNA Damage; DNA Repair; DNA, Fungal; Genome, Fungal; Pyrimidine Dimers; Saccharomyces cerevisiae; Transcription, Genetic; Ultraviolet Rays
PubMed: 29581276
DOI: 10.1073/pnas.1801687115 -
International Journal of Molecular... Dec 2021DNA polymerase η (Polη) is a translesion synthesis polymerase that can bypass different DNA lesions with varying efficiency and fidelity. Its most well-known function...
DNA polymerase η (Polη) is a translesion synthesis polymerase that can bypass different DNA lesions with varying efficiency and fidelity. Its most well-known function is the error-free bypass of ultraviolet light-induced cyclobutane pyrimidine dimers. The lack of this unique ability in humans leads to the development of a cancer-predisposing disease, the variant form of . Human Polη can insert rNTPs during DNA synthesis, though with much lower efficiency than dNTPs, and it can even extend an RNA chain with ribonucleotides. We have previously shown that Mn is a specific activator of the RNA synthetic activity of yeast Polη that increases the efficiency of the reaction by several thousand-fold over Mg. In this study, our goal was to investigate the metal cofactor dependence of RNA synthesis by human Polη. We found that out of the investigated metal cations, only Mn supported robust RNA synthesis. Steady state kinetic analysis showed that Mn activated the reaction a thousand-fold compared to Mg, even during DNA damage bypass opposite 8-oxoG and TT dimer. Our results revealed a two order of magnitude higher affinity of human Polη towards ribonucleotides in the presence of Mn compared to Mg. It is noteworthy that activation occurred without lowering the base selectivity of the enzyme on undamaged templates, whereas the fidelity decreased across a TT dimer. In summary, our data strongly suggest that, like with its yeast homolog, Mn is the proper metal cofactor of hPolη during RNA chain extension, and selective metal cofactor utilization contributes to switching between its DNA and RNA synthetic activities.
Topics: Adenosine Triphosphate; Cytidine Triphosphate; DNA; DNA Damage; DNA Repair; DNA-Directed DNA Polymerase; Guanosine Triphosphate; Humans; Kinetics; Manganese; Pyrimidine Dimers; Uridine Triphosphate
PubMed: 35008656
DOI: 10.3390/ijms23010230