An extended sequence specificity for UV-induced DNA damage

Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering

Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.

UV irradiation remodels the specificity landscape of transcription factors

Somatic mutations are highly enriched at transcription factor (TF) binding sites, with the strongest trend being observed for ultraviolet light (UV)-induced mutations in melanomas. One of the main mechanisms proposed for this hypermutation pattern is the inefficient repair of UV lesions within TF-binding sites, caused by competition between TFs bound to these lesions and the DNA repair proteins that must recognize the lesions to initiate repair. However, TF binding to UV-irradiated DNA is poorly characterized, and it is unclear whether TFs maintain specificity for their DNA sites after UV exposure. We developed UV-Bind, a high-throughput approach to investigate the impact of UV irradiation on protein-DNA binding specificity. We applied UV-Bind to ten TFs from eight structural families, and found that UV lesions significantly altered the DNA-binding preferences of all the TFs tested. The main effect was a decrease in binding specificity, but the precise effects and their magnitude differ across factors. Importantly, we found that despite the overall reduction in DNA-binding specificity in the presence of UV lesions, TFs can still compete with repair proteins for lesion recognition, in a manner consistent with their specificity for UV-irradiated DNA. In addition, for a subset of TFs, we identified a surprising but reproducible effect at certain nonconsensus DNA sequences, where UV irradiation leads to a high increase in the level of TF binding. These changes in DNA-binding specificity after UV irradiation, at both consensus and nonconsensus sites, have important implications for the regulatory and mutagenic roles of TFs in the cell.

Sequence-dependent thymine dimerization and lifetimes of the photoexcited state of oligonucleotides

DNA-sequence-dependent thymine-thymine (TT) dimerization was investigated from the perspective of the UV-induced charge transfer state. Steady-state and transient absorption measurements suggest that the relatively small oxidation potential and long-lived charge transfer state at the neighboring nucleobases of the TT site may reduce DNA lesion accumulation.

Role of mitochondria on UV-induced skin damage and molecular mechanisms of active chemical compounds targeting mitochondria

Mitochondria are the principal place of energy metabolism and ROS production, leading to mtDNA being especially sensitive to the impacts of oxidative stress. Our review aims to elucidate and update the mechanisms of mitochondria in UV-induced skin damage. The mitochondrial deteriorative response to UV manifests morphological and functional alterations, including mitochondrial fusion and fission, mitochondrial biogenesis, mitochondrial energy metabolism and mitophagy. Additionally, we conclude the effect and molecular mechanisms of active chemical components to protect skin from UV-induced damage via mitochondrial protection which have been described in the last five years, showing prospective prospects in cosmetics as new therapeutic targets.

The influence of DNA methylation on the sequence specificity of UVB- and UVC-induced DNA damage

Ultraviolet light (UV) is one of the most common DNA damaging agents in the human environment. This paper examined the influence of DNA methylation on the level of UVB- and UVC-induced DNA damage. A purified DNA sequence containing CpG dinucleotides was methylated with a CpG methylase. We employed the linear amplification technique and the end-labelling approach followed by capillary electrophoresis with laser-induced fluorescence to investigate the sequence specificity of UV-induced DNA damage. The linear amplification technique mainly detects cyclobutane pyrimidine dimer (CPD) adducts, while the end-labelling approach mainly detects 6-4 photoproduct (6-4PP) lesions. The levels of CPD and 6-4PP adducts detected in methylated/unmethylated labelled sequences were analysed. The comparison showed that 5-methyl-cytosine significantly reduced the level of both CPD and 6-4PP adducts after UVB (308 nm) and UVC (254 nm) irradiation compared with the non-methylated counterpart.

Formation and Recognition of UV-Induced DNA Damage within Genome Complexity

Ultraviolet (UV) light is a natural genotoxic agent leading to the formation of photolesions endangering the genomic integrity and thereby the survival of living organisms. To prevent the mutagenetic effect of UV, several specific DNA repair mechanisms are mobilized to accurately maintain genome integrity at photodamaged sites within the complexity of genome structures. However, a fundamental gap remains to be filled in the identification and characterization of factors at the nexus of UV-induced DNA damage, DNA repair, and epigenetics. This review brings together the impact of the epigenomic context on the susceptibility of genomic regions to form photodamage and focuses on the mechanisms of photolesions recognition through the different DNA repair pathways.

The Intercontinental phylogeography of neustonic daphniids

Organisms that live at the freshwater surface layer (the neuston) occupy a high energy habitat that is threatened by human activities. Daphniids of the genera Scapholeberis and Megafenestra are adapted to the neuston but are poorly studied for biogeography and diversity. Here we assess the global phylogeography of neustonic daphniids. We obtained 402 new multigene sequences from the 12S rRNA, 16S rRNA, and tRNA (val) regions of the mitochondrial genomes of daphniids from 186 global sites. We assessed the intercontinental origins and boundaries of mitochondrial lineages and the relative rates of evolution in neustonic and planktonic daphniids. We identified 17 divergent lineages in the neustonic daphniids that were associated with biogeographic regions. Six of these lineages had intercontinental ranges – four of these were Transberingian. Patagonian populations of Scapholeberis rammneri were monophyletic and nested within a closely related clade of western North American haplotypes, suggesting an introduction from the Western Nearctic to South America. The Eastern Palearctic was more diverse than other regions, containing eight of the major lineages detected in the Scapholeberinae. The Genus Scapholeberis had high levels of divergence compared to non-neustonic daphniids. Neustonic daphniids have more divergent biogeographic lineages than previously appreciated.

Intragenomic variability and extended sequence patterns in the mutational signature of ultraviolet light

Mutational signatures have emerged as essential tools in cancer genomics, providing clinically relevant insights as well as accurate background models needed when assessing signals of selection in cancer. Here, we observe that the mutational signature of ultraviolet (UV) light varies across chromatin states, highlighting a previously unappreciated aspect of mutational signatures. Our results imply that locally derived, rather than genome-wide or exome-wide, signatures are more accurate, which is of relevance in situations such as cancer driver gene detection, where correct modelling of signatures and expected mutation rates is critical. We also show that incorporation of longer contextual patterns into the signature further improves modeling of UV mutations.

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.

Capture and "self-release" of circulating tumor cells using metal-organic framework materials

Capturing circulating tumor cells (CTCs) from peripheral blood for subsequent analyses has shown potential in precision medicine for cancer patients. Broad as the prospect is, there are still some challenges that hamper its clinical applications. One of the challenges is to maintain the viability of the captured cells during the capturing and releasing processes. Herein, we have described a composite material that could encapsulate a magnetic Fe3O4 core in a MIL-100 shell (MMs), which could respond to pH changes and modify the anti-EpCAM antibody (anti-EpCAM-MMs) on the surface of MIL-100. After the anti-EpCAM-MMs captured the cells, there was no need for additional conditions but with the acidic environment during the cell culture process, MIL-100 could realize automatic degradation, leading to cell self-release. This self-release model could not only improve the cell viability, but could also reduce the steps of the release process and save human and material resources simultaneously. In addition, we combined clinical patients' case diagnosis with the DNA sequencing and next generation of RNA sequencing technologies in the hope of precision medicine for patients in the future.

The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence

The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons.