ChIP-Seq of topoisomerase I in E. coli DY330

Distribution of topoisomerase I (EcTopoI) on genomic sites was studied for exponentially growing Escherichia coli in different conditions using ChIP-Seq. Overall design: DNA crosslinked with SPA-tagged EcTopoI was purified and sequenced from E. coli DY330 culture growing in LB medium (exponential phase, OD600=0.6). Cultures were either crosslinked with 1% formaldehyde untreated (i), or treated with 100 mkg/ml rifampicin for 20 min before crosslinking (ii, Rif), or EcTopoI 14-kDa CTD was overexpressed from pCA25 plasmid for 60 min before crosslinking (iii, CTD), or EcTopoI 14-kDa CTD was overexpressed from pCA25 plasmid for 60 min and then 100 mkg/ml rifampicin was added for 20 min before crosslinking (iv, CTD/Rif). Total DNA purified from a de-crosslinked cells lysate served as a Mock control. For each condition 3 biological replicates were processed and sequenced.