Major roles of cyclobutane pyrimidine dimers, nucleotide excision repair and ATR in the alternative splicing response to UV irradiation
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE85510 | GEO | 2017/04/17
SECONDARY ACCESSION(S): PRJNA338678
REPOSITORIES: GEO
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Project description:The majority of sunlight-associated melanomas carry a unique UV-related C to T mutation signature at dipyrimidine sites. UVB radiation is known to induce cyclobutane pyrimidine dimers (CPDs) as the major form of DNA damage, but the mechanism of how these DNA lesions lead to mutations is unknown. To map the genome-wide distribution of CPDs at single base resolution, we developed a new method, circle damage sequencing (circle-damage-seq). We found that in human cells CPDs form in a specific tetranucleotide sequence context (5’PyPy<>PyT/A), but this alone does not explain the mutation patterns. To test whether mutations arise at CPDs by cytosine deamination, we next applied a modification of circle-damage-seq and mapped UVB-induced cytosine-deaminated CPDs. We observed that the transcription start sites (TSS) are the sequences most protected from CPDs and deaminated CPDs. The strongest spike of CPDs and deaminated CPD lesions was found immediately upstream of the TSS, suggesting a mutation-promoting role of bound transcription factors. Most significantly, the genome-wide dinucleotide and trinucleotide sequence specificity of deaminated CPDs matched the prominent mutation signature found in melanomas. Our data identifies the cytosine-deaminated CPD as the leading premutagenic lesion responsible for the vast majority of mutations in sun-exposure-linked melanomas.
2020-10-22 | GSE159807 | GEO
Project description:Repair of UV damage from the transcribed strand (TS) of yeast genes is rapid due to the transcription coupled nucleotide excision repair (TC-NER) pathway. TC-NER is triggered when RNA polymerase stalls at UV damage, such as a UV-induced cyclobutane pyrimidine dimer (CPD). During transcription, the histone methyltransferase Set2 methylates histone H3K36, but it is not known if Set2 regulates TC-NER. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells lacking Set2.
2022-02-21 | GSE179794 | GEO
Project description:We characterized the role of H3K36 methylation in regulating repair of UV damage from the transcribed strand (TS) of yeast genes by the transcription coupled nucleotide excision repair (TC-NER) pathway. TC-NER is triggered when RNA polymerase stalls at UV damage, such as a UV-induced cyclobutane pyrimidine dimer (CPD). During transcription, the histone methyltransferase Set2 methylates histone H3K36, but it is not known if H3K36 methylation regulates TC-NER. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells containing mutants in histone H3K36 (or set2).
2022-02-21 | GSE194101 | GEO
Project description:To address CPD-dependent UVB activities, a model system was established in which transfection of keratinocytes with pseudouridine-modified mRNA (M-NM-(-mRNA) encoding CPD-photolyase resulted in 90% reduction of CPDs within 6 and 24 hours after UVB exposure. Microarray analysis of this model system demonstrated that more than 50 % of the gene expression altered by UVB were changed in a CPD-dependent manner. The expression of most of the CPD-dependent genes was changed at 6 h after UVB as compared to 24 h likely due to the higher CPD levels. Nine genes (ATF3, CCNE1, CDKN2B, EGR1, ID2, PTGS2, RUNX1, SNAI1, SNAI2) regulated by CPDs were selected for further investigation (qPCR, Western blot) based on the microarray data. Gene expression modulated by UVB irradiation in HaCaT keratinocytes was measured at 6 and 24 hours after the exposure to dose of 20 mJ/cm2 UVB. Three independent experiments were performed at each time (6 or 24 hours) using different passages for each experiment.
2015-01-16 | E-GEOD-65034 | biostudies-arrayexpress
Project description:We recently developed a high-resolution genome wide assay for mapping DNA excision repair named eXcision Repair-sequencing (XR-seq) (GEO accession: GSE67941) We have now used this assay to assay the effect of chromatin state on DNA repair. Here we report the results of a time-course of the repair of the UV induced damages cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts [(6-4)PPs] in normal human skin fibroblasts. Comparison of this data to histone modification and DNA-seq maps (ENCODE) revealed initial repair of both damages is enriched in open and active chromatin states, whereas repair in heterochromatic and repressed chromatin states is relatively low and persists to later time points. We performed XR-seq for two types of UV induced damages (CPD and (6-4)PP) at multiple time points after UV irradiation, in normal NHF1, and CS-B (CS1ANps3g2, GM16095) fibroblast cell lines. Two biological replicates were performed for each experiment in which independent independent cell populations were UV treated and subjected to XR-seq. For assaying CPD repair, cells were irradiated with 10J/m2 and for assaying (6-4)PP cells were irradiated with 20J/m2. Raw data for the 1h time points of (6-4)PP repair are the same as in GEO accession GSE67941).
2016-03-15 | E-GEOD-76391 | biostudies-arrayexpress
Project description:To address CPD-dependent UVB activities, a model system was established in which transfection of keratinocytes with pseudouridine-modified mRNA (Ψ-mRNA) encoding CPD-photolyase resulted in 90% reduction of CPDs within 6 and 24 hours after UVB exposure. Microarray analysis of this model system demonstrated that more than 50 % of the gene expression altered by UVB were changed in a CPD-dependent manner. The expression of most of the CPD-dependent genes was changed at 6 h after UVB as compared to 24 h likely due to the higher CPD levels. Nine genes (ATF3, CCNE1, CDKN2B, EGR1, ID2, PTGS2, RUNX1, SNAI1, SNAI2) regulated by CPDs were selected for further investigation (qPCR, Western blot) based on the microarray data.
2015-01-16 | GSE65034 | GEO
Project description:We developed a method for genome-wide mapping of DNA excision repair named XR-seq (eXcision Repair-seq). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating a ~30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells, cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts ((6-4)PPs). In wild-type cells, CPD repair was highly associated with transcription, specifically with the template strand. Experiments in cells defective in either transcription-coupled excision repair or general excision repair isolated the contribution of each pathway to the overall repair pattern, and showed that transcription-coupled repair of both photoproducts occurs exclusively on the template strand. XR-seq maps capture transcription-coupled repair at sites of divergent gene promoters and bi-directional eRNA production at enhancers. XR-seq data also uncovered the repair characteristics and novel sequence preferences of CPDs and (6-4)PPs. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells. We have performed XR-seq for two types of UV-induced damages (CPD and (6-4)PP) in three different cell lines: NHF1, XP-C (XP4PA-SV-EB, GM15983)), and CS-B (CS1ANps3g2, GM16095). Two biological replicates were performed for each experiment, in which independent cell populations were UV treated and subjected to XR-seq.
2015-04-19 | E-GEOD-67941 | biostudies-arrayexpress
Project description:The histone methyltransferase ASH1L, first discovered for its role in transcription, has been shown to accelerate the removal of ultraviolet (UV) light-induced cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair. Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C-containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C–>T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.
2024-06-02 | GSE260917 | GEO
Project description:Rad16 is required for global genomic nucleotide excision repair (GG-NER) of UV-induced CPD lesions. Here we have used a novel high-throughput sequencing method known as CPD-seq to map the repair of UV-induced cyclobutane pyrimidine dimers (CPDs) at single nucleotide resolution across the yeast genome in rad16 mutant cells. Analysis of CPD repair indicates that rad16 is generally required for CPD repair in the non-transcribed strand (NTS) of yeast genes and non-transcribed genomic regions.
2019-11-27 | GSE131101 | GEO
Project description:UV-induced DNA lesions are an important contributor to mutagenesis and cancer, but it is not fully understood how the chromosomal landscape influences UV lesion formation and repair. We have used a novel high-throughput sequencing method to precisely map UV-induced cyclobutane pyrimidine dimers (CPDs) at nucleotide resolution throughout the yeast genome. Analysis of CPD formation reveals that nucleosomal DNA having an inward rotational setting is protected from CPD lesions. In strongly positioned nucleosomes, this nucleosome 'photofootprint' overrides intrinsic dipyrimidine sequence preferences for CPD formation. CPD formation is also inhibited by DNA-bound transcription factors, in effect protecting important DNA elements from UV damage. Analysis of CPD repair revealed a clear signature of efficient transcription-coupled nucleotide excision repair. Repair was less efficient at translational positions near a nucleosome dyad and at heterochromatic regions in the yeast genome. These findings define the roles of nucleosomes and transcription factors in UV damage formation and repair. UV mapping data was analyzed for yeast cells irradiated with 125J/m2 and allowed to repair for 0hr (2 samples), 20 minutes, 1 hour, or 2 hours. Data is also included for naked DNA irradiated with UV 60 or 90 J/m2
2016-08-19 | E-GEOD-79977 | biostudies-arrayexpress