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Genome-wide maps of 8-oxodG in UV/NAC-treated MCF10A cells.

ABSTRACT: Genome-wide maps of 8-oxodG in UV/NAC-treated MCF10A cells.

PROVIDER: PRJNA798917 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17677052_1.fastq.gz	Fastqsanger.gz
	SRR17677052_2.fastq.gz	Fastqsanger.gz
	SRR17677053_1.fastq.gz	Fastqsanger.gz
	SRR17677053_2.fastq.gz	Fastqsanger.gz
	SRR17677054_1.fastq.gz	Fastqsanger.gz

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Genome-wide maps of 8-oxodG in UV/NAC-treated MCF10A cells.

Project description:8-oxodG accumulation within super-enhancers marks fragile CTCF-mediated chromatin loops.

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Dynamic Maps of UV Damage Formation and Repair for the Human Genome

Project description:UV-induced DNA damage is the major carcinogen of skin cancer. We developed HS-Damage-seq to map UV damage with unprecedented sensitivity and resolution in human cells. While the distribution of UV-induced damage are mainly determined by sequence context and essentially uniform throughout the genome, transcription factors can affect damage formation at specific positions. With time-course experiments, we observed changes in damage distribution at particular genomic loci and chromatin states, which reflects the nucleotide excision repair preferences and complements the repair maps by XR-seq. Our results demonstrated that while initial damage is uniformly distributed, they are heterogeneously repaired throughout the genome. The combination of damage and repair maps provides a holistic perspective of UV damage and repair in the human genome.

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Early Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC

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Genome-wide maps of UV damage repair by yeast CPD photolyase

Project description:Genome-wide maps of UV damage repair by yeast CPD photolyase

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Single-nucleotide resolution dynamic repair maps of UV damage in Saccharomyces cerevisiae genome

Project description:We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts [(6-4)PPs] in the Saccharomyces cerevisiae 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 21-27 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 (TS) at early time points followed by predominantly non-transcribed strand (NTS) repair at later stages. We have also characterized the excision repair level as a function of transcription level. The availability of high-resolution and dynamic repair maps should aid in future repair and mutagenesis studies in this model organism.

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Genome-wide maps of UV damage repair by yeast CPD photolyase

Project description:Here, we describe a genome-wide map of photoreactivation repair of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast (Saccharomyces cerevisiae) by the endogenous yeast CPD photolyase. CPDs were mapped at single nucleotide resolution across the yeast genome using the CPD-seq method immediately after UV radiation (0min) and following 30 or 60min photoreactivation with UVA light. Photoreactivation repair by photolyase was mapped in both wild-type yeast and rad14∆ cells deficient in nucleotide excision repair (NER). We used these data to analyze CPD repair by photolyase in yeast genes, nucleosomes, and transcription factor binding sites.

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Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

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.

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Transcription profiling of human 294T Cells treated with elesclomol alone or in combination with NAC compared to DMSO treated

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2008-06-18 | E-GEOD-11551 | biostudies-arrayexpress

Single-nucleotide resolution dynamic repair maps of UV damage in Saccharomyces cerevisiae genome

Project description:Single-nucleotide resolution dynamic repair maps of UV damage in Saccharomyces cerevisiae genome

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