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

Topo IV cleavage sites induced by ciprofloxacin were identified in the E. coli genome with a single-nucleotide resolution using Topo-Seq. Overall design: To stabilizie cleavage complexes, exponentially growing E. coli DY330 parC-SPA or E. coli DY330 parC-SPA gyrA-S83L cells were treated with 10 mkM ciprofloxacin. Topo IV cleavage complexes with DNA were enriched by immunoprecipitation and obtained DNA fragments were sequenced. Non-treated samples and samples without the immunoprecipitation step served as controls. 3 biological replicates were processed and sequenced.