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Topoisomerase II drug cleavage sites (no formaldehyde)

ABSTRACT: Topoisomerase II drug cleavage sites (no formaldehyde)

PROVIDER: PRJNA1180577 | ENA |

REPOSITORIES: ENA

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Topoisomerase II drug cleavage sites (no formaldehyde)

Project description:TOP2A and TOP2B bind and cleave genomic DNA. These enzymes are targeted by some anti-cancer drugs that stabilise the enzyme complexes on the DNA. Whole genome TOP2 ChIP-seq was carried out on human KG-1 cells in the presence and absence of the topoisomerase targeting drugs Etoposide and Mitoxantrone in the absence of formaldehyde.

2025-07-24 | GSE280809 | GEO

Genome-wide maps of Topoisomerase IV binding and cleavage sites in E. coli

Project description:We report binding of Topoisomerase IV on the E. coli genome. We report the cleavage sites of Topoisomerase IV on the E. coli genome

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Highly sensitive mapping of type II topoisomerase DNA cleavage sites with SHAN-seq

Project description:Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability, and a number of clinically important anticancer and antibacterial drugs, e.g., quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50 fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e., negative vs. positive supercoiling. SHAN-seq’s exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.

2024-08-06 | GSE267149 | GEO

Genome-wide strand-specific mapping of cleavage sites induced by topoisomerase I in E. coli

Project description:Cleavage sites induced by the EcTopoI G116S M320V topoisomerase mutant were identified in E. coli genome with a single-nucleotide resolution using Topo-Seq.

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Highly sensitive mapping of type II topoisomerase DNA cleavage sites with SHAN-seq

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Fluoroquinolone-induced gyrase cleavage sites

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Genome-wide strand-specific mapping of cleavage sites induced by topoisomerase I in E. coli

Project description:Genome-wide strand-specific mapping of cleavage sites induced by topoisomerase I in E. coli

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Genome-wide mapping of cleavage sites induced by topoisomerase IV in E. coli with a single-nucleotide resolution

Project description:Genome-wide mapping of cleavage sites induced by topoisomerase IV in E. coli with a single-nucleotide resolution

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Genome-wide mapping of cleavage sites induced by topoisomerase IV in E. coli with a single-nucleotide resolution

Project description:Topo IV cleavage sites induced by ciprofloxacin were identified in the E. coli genome with a single-nucleotide resolution using Topo-Seq.

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