Sunlight-Induced DNA Lesions. Lesion Structure, Mutation Characteristics and Repair

The UV part of sunlight is known to induce a variety of genome defects. These lesions are the major cause of skin cancer development. In order to counter such toxic effects cells have developed a number of sophisticated DNA repair systems, like nucleotide excision repair and photoreactivation. The repair machinery is able to specifically recognize sunlight-induced DNA lesions and to subsequently remove this damage. Malfunctioning repair systems are responsible for the three rare genetic diseases Xeroderma pigmentosum, Cockayne's syndrome, and trichothiodystrophy. In this review article, the structure of the major sunlight-induced lesions will be discussed. An overview of the two major repair mechanisms, photoreactivation and excision repair, is given, and the effects of the DNA lesions on the p53 gene and on tumor genesis are discussed

Chemical investigation of light induced DNA bipyrimidine damage and repair

In all organisms, genetic information is stored in DNA and RNA. Both of these macromolecules are damaged by many exogenous and endogenous events, with UV irradiation being one of the major sources of damage. The major photolesions formed are the cyclobutane pyrimidine dimers (CPD), pyrimidine–pyrimidone-(6-4)-photoproducts, Dewar valence isomers and, for dehydrated spore DNA, 5-(a-thyminyl)-5,6-dihydrothymine (SP). In order to be able to investigate how nature’s repair and tolerance mechanisms protect the integrity of genetic information, oligonucleotides containing sequence and site-specific UV lesions are essential. This tutorial review provides an overview of synthetic procedures by which these oligonucleotides can be generated, either through phosphoramidite chemistry or direct irradiation of DNA. Moreover, a brief summary on their usage in analysing repair and tolerance processes as well as their biological effects is provided

Mitogenic signaling by Gq/11-coupled receptors

By binding to their cognate GPCRs, many potent mitogens such as neuropeptides, angiotensin II or lysophosphatidic acid stimulate cell proliferation via engaging the ERK/MAPK cascade. As mentioned before, agonists stimulating Gq/11-coupled receptors activate PLCb isoforms thereby activating PKCs and elevating [Ca2+]i. These two second messengers represent key molecules for coupling Gq/11 proteins to the ERK/MAPK cascade. In this work, by means of GnRH in gonadotropic aT3-1 cells and galanin or bradykinin in SCLC cells, different aspects of Gq/11-dependent mitogenic signaling pathways were revealed. Our findings together with previous reports underline the notion that signaling pathways emanating from Gq/11-coupled receptors are tightly regulated in a cell- and receptor-specific manner

Direct and Base Excision Repair-Mediated Regulation of a GC-Rich cis -Element in Response to 5-Formylcytosine and 5-Carboxycytosine

Stepwise oxidation of the epigenetic mark 5-methylcytosine and base excision repair (BER) of the resulting 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) may provide a mechanism for reactivation of epigenetically silenced genes; however, the functions of 5-fC and 5-caC at defined gene elements are scarcely explored. We analyzed the expression of reporter constructs containing either 2′-deoxy-(5-fC/5-caC) or their BER-resistant 2′-fluorinated analogs, asymmetrically incorporated into CG-dinucleotide of the GC box cis -element (5′-TGGGCGGAGC) upstream from the RNA polymerase II core promoter. In the absence of BER, 5-caC caused a strong inhibition of the promoter activity, whereas 5-fC had almost no effect, similar to 5-methylcytosine or 5-hydroxymethylcytosine. BER of 5-caC caused a transient but significant promoter reactivation, succeeded by silencing during the following hours. Both responses strictly required thymine DNA glycosylase (TDG); however, the silencing phase additionally demanded a 5′-endonuclease (likely APE1) activity and was also induced by 5-fC or an apurinic/apyrimidinic site. We propose that 5-caC may act as a repressory mark to prevent premature activation of promoters undergoing the final stages of DNA demethylation, when the symmetric CpG methylation has already been lost. Remarkably, the downstream promoter activation or repression responses are regulated by two separate BER steps, where TDG and APE1 act as potential switches

Third‐Generation Sequencing of Epigenetic DNA

The discovery of epigenetic bases has revolutionised the understanding of disease and development. Among the most studied epigenetic marks are cytosines covalently modified at the 5 position. In order to gain insight into their biological significance, the ability to determine their spatiotemporal distribution within the genome is essential. Techniques for sequencing on “next-generation” platforms often involve harsh chemical treatments leading to sample degradation. Third-generation sequencing promises to further revolutionise the field by providing long reads, enabling coverage of highly repetitive regions of the genome or structural variants considered unmappable by next generation sequencing technology. While the ability of third-generation platforms to directly detect epigenetic modifications is continuously improving, at present chemical or enzymatic derivatisation presents the most convenient means of enhancing reliability. This Review presents techniques available for the detection of cytosine modifications on third-generation platforms

The radical SAM enzyme spore photoproduct lyase employs a tyrosyl radical for DNA repair

The spore photoproduct lyase is a radical SAM enzyme, which repairs 5-(alpha-thyminyl)-5,6-dihydrothymidine. Here we show that the enzyme establishes a complex radical transfer cascade and creates a cysteine and a tyrosyl radical dyade to establish repair. This allows the enzyme to solve topological and energetic problems associated with the radical based repair reaction

Molecular mechanisms of xeroderma pigmentosum (XP) proteins

Nucleotide excision repair (NER) is a highly versatile and efficient DNA repair process, which is responsible for the removal of a large number of structurally diverse DNA lesions. Its extreme broad substrate specificity ranges from DNA damages formed upon exposure to ultraviolet radiation to numerous bulky DNA adducts induced by mutagenic environmental chemicals and cytotoxic drugs used in chemotherapy. Defective NER leads to serious diseases, such as xeroderma pigmentosum (XP). Eight XP complementation groups are known of which seven (XPA-XPG) are caused by mutations in genes involved in the NER process. The eighth gene, XPV, codes for the DNA polymerase., which replicates through DNA lesions in a process called translesion synthesis (TLS). Over the past decade, detailed structural information of these DNA repair proteins involved in eukaryotic NER and TLS have emerged. These structures allow us now to understand the molecular mechanism of the NER and TLS processes in quite some detail and we have begun to understand the broad substrate specificity of NER. In this review, we aim to highlight recent advances in the process of damage recognition and repair as well as damage tolerance by the XP proteins