Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli

Counting DNA reads using whole genome sequencing is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyse the genomic consequences of DSBR. RecA binding to the chromosome of two E. coli strains was analysed by RecA-ChIP. Two biological repeats were carried out for each of the two strains. One strain experienced an induced DNA double strand break (DL4184) and one did not (DL4201). Both strains were recombination proficient.