Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA358485 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5125160.fastq.gz | Fastqsanger.gz | |||
| SRR5125161.fastq.gz | Fastqsanger.gz | |||
| SRR5125162.fastq.gz | Fastqsanger.gz | |||
| SRR5125163.fastq.gz | Fastqsanger.gz | |||
| SRR5125164.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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Project description:We uncovered evidence for an expanded role of transcription-coupled repair factor Mfd in Escherichia coli. In mfd knockout cells, expression of 75 genes was significantly increased while that of 18 genes was diminished. GO term analysis revealed that the affected genes were disproportionately from certain functional groups. RNA levels in the knockout deviated from wild type beginning at transcription start sites, arguing against premature termination as the cause. RNA-seq analysis in cells overexpressing Mfd revealed dramatic deviation of gene expression in the chromosome terminus region. Taken together, our data support a novel role for Mfd in transcription regulation.
2017-05-01 | GSE81584 | GEO
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
Project description:Mfd alters global transcription patterns in undamaged Escherichia coli cells
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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.
2022-02-05 | GSE171969 | GEO
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.
2022-02-05 | GSE171970 | GEO
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.
2022-02-05 | GSE171971 | GEO
Project description:We measured the mRNA abundance in E.coli using RNAseq to calculate mRNA lifetimes. The data is used in support of a larger paper on the proteome and transcriptome of E.coli.
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Project description:Transcriptional profiling of E.coli O157:H7 cells comparing control untreated cells with PEG8000treated cells
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