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Whole-genome analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans

ABSTRACT: Whole-genome analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans

PROVIDER: PRJNA1027326 | ENA |

REPOSITORIES: ENA

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Whole-genome analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans

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 (CPD) photoproducts in the Caenorhabditis elegans (C. elegans) genome. We focus on the C. elegans ortholog of the human XPC-deficient strain (xpc-1) and its exclusive use of transcription-coupled repair. We provide evidence demonstrating the utility of xpc-1 XR-seq as a remarkable tool for detecting nascent transcription and identifying new transcripts. The integration of epigenetic markers, chromatin states, and non-coding RNA annotations supports the robust detection of intergenic nascent transcription by XR-seq. Overall, our results provide a comprehensive view of the transcription-coupled repair landscape in C. elegans, highlighting their potential contributions to our understanding of DNA repair mechanisms and non-coding RNA biology.

2023-11-21 | GSE245181 | GEO

Drosophila, which Lacks Canonical Transcription-Coupled Repair Proteins, Performs Transcription-Coupled Repair

Project description:Drosophila, which Lacks Canonical Transcription-Coupled Repair Proteins, Performs Transcription-Coupled Repair

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Pervasive transcription-coupled DNA repair in E. coli

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Drosophila, which Lacks Canonical Transcription-Coupled Repair Proteins, Performs Transcription-Coupled Repair

Project description:Previous work with the classic T4 Endonuclease V digestion of irradiated Drosophila DNA followed by Southern hybridization led to the conclusion that Drosophila lacked transcription-coupled repair (TCR). This conclusion was reinforced by the Drosophila Genome Project which revealed that Drosophila lacked CSA, CSB, or UVSSA homologs, whose orthologs are present in eukaryotes that carry out TCR ranging from Arabidopsis to humans. A recently developed in vivo excision assay and the Excision Repair-sequencing (XR-seq) method have enabled genome-wide analysis of nucleotide excision repair in various organisms at single nucleotide resolution and strand-specific manner. Using these methods, we have discovered that Drosophila S2 cells carry out robust TCR comparable to that observed in mammalian cells. Our findings provide new insights into the mechanisms of TCR among various species.

2019-10-16 | GSE138846 | GEO

Pervasive transcription-coupled DNA repair in E. coli [CPD-seq]

Project description:Pervasive transcription-coupled DNA repair in E. coli [CPD-seq]

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CPD-seq mapping of transcription-coupled DNA repair in yeast

Project description:CPD-seq mapping of transcription-coupled DNA repair in yeast

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Role of Set2 in regulating transcription coupled-nucleotide excision repair

Project description:Role of Set2 in regulating transcription coupled-nucleotide excision repair

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Genome-wide distribution of transcription-coupled nucleotide excision repair and RNA polymerase II in DRB-treated XP-C cells after UV damage

Project description:The fate of RNAPII in the course of the transcription-coupled repair pathway is unclear. To address this problem we have used methods to control transcription, so as to initiate a discrete ‘wave’ of elongation complexes. We also used methods to identify where elongation complexes and transcription-repair coupling events are located in genes throughout the genome.

2017-12-21 | GSE106823 | GEO

CSB promotes transcription-coupled repair of DNA-protein crosslinks

Project description:PxP-MS (Purification of x-linked Proteins coupled to Mass Spectrometry) was used to assess the role of CSB in DNA-protein crosslink repair. The CSB protein is a sensor that can detect stalled RNA polymerases at sites of DNA damage, thereby triggering transcription-coupled repair mechanisms. DPCs were induced in WT and CSB knock-out RPE1 cells using a pulse of formaldehyde. To identify crosslinked proteins that specifically require CSB for repair, DNA-protein crosslinks were isolated from cells using PxP either directly after formaldehyde exposure or following a chase in drug-free media and identified by mass spectrometry.

2024-02-15 | PXD047668 | Pride

Role of Set2 in regulating transcription coupled-nucleotide excision repair

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

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