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Pervasive transcription-coupled DNA repair in E. coli [RNA-seq 2]

ABSTRACT: Pervasive transcription-coupled DNA repair in E. coli [RNA-seq 2]

PROVIDER: PRJNA721484 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14225278_1.fastq.gz	Fastqsanger.gz
	SRR14225278_2.fastq.gz	Fastqsanger.gz
	SRR14225279_1.fastq.gz	Fastqsanger.gz
	SRR14225279_2.fastq.gz	Fastqsanger.gz
	SRR14225280_1.fastq.gz	Fastqsanger.gz

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Pervasive transcription-coupled DNA repair in E. coli

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Pervasive transcription-coupled DNA repair in E. coli [RNA-seq 1]

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

Project description:Global Genomic Repair (GGR) and Transcription-Coupled Repair (TCR) have been viewed, respectively, as major and minor sub-pathways of the nucleotide excision repair (NER) process that removes bulky lesions from the genome. Here we applied a next generation sequencing assay, CPD-seq, in E. coli to measure the levels of cyclobutane pyrimidine dimer (CPD) lesions before, during, and after UV-induced genotoxic stress, and, therefore, to determine the rate of genomic recovery by NER at a single nucleotide resolution. We find that active transcription is necessary for the repair of not only the template strand (TS), but also the non-template strand (NTS), and that the bulk of TCR is independent of Mfd – a DNA translocase that is thought to be necessary and sufficient for TCR in bacteria. We further show that repair of both TS and NTS is enhanced by increased readthrough past Rho-dependent terminators. We demonstrate that UV-induced genotoxic stress promotes global antitermination so that TCR is more accessible to the antisense, intergenic, and other low transcribed regions. Overall, our data suggests that GGR and TCR are essentially the same process required for complete repair of the bacterial genome.

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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 [RNA-seq 2]

2022-02-05 | GSE171971 | GEO

Pervasive transcription-coupled DNA repair in E. coli [RNA-seq 1]

2022-02-05 | GSE171970 | GEO

Genome-wide Transcription-coupled Repair in E.coli is Mediated by the Mfd Protein

Project description:Transcription-coupled DNA repair is widespread in nature having been found in organisms from E. coli to yeast to humans. In E. coli, the transcription-repair coupling factor (TRCF) encoded by the mfd gene recognizes RNA polymerase (RNAP) stalled at a damage site and recruits the excision repair proteins to the stalled RNAP and promotes damage recognition while displacing RNAP and the truncated transcript from the damage site and in doing so, enhances the rate of repair of the transcribed strand (TS). Recently, it has been reported that there are other E. coli proteins that mediate transcription-coupled repair (TCR) independently of the Mfd protein. To understand the relative contributions of various proteins to and mechanisms of TCR we used the recently developed nucleotide excision repair sequencing (XR-seq) method for genome-wide analysis of excision repair to generate excision repair maps of entire genomes of various E. coli strains with deletions of genes implicated in TCR. Our data show that the Mfd protein catalyzes TCR throughout the genome.

2017-02-08 | GSE92734 | GEO

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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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

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