Variation_of_DNA_damage_and_repair_along_a_bacterial_genome

We have developed a protocol similar to certain MEDIP-seq protocols to identify genomic regions containing 8-oxoguanine bases. To develop this protocol, we are using a simple experimental design on E.coli. Briefly, cells are exposed to high but sublethal doses of oxidative damage (5mM H2O2 for 20 min). Then DNA is extracted immediately after treatment to minimise the action of DNA repair (condition 1) or cells are incubated for 1h to allow substantial DNA repair (condition 2). The comparison of these two conditions with an unexposed control population will allow us to quantify the extent of DNA damage at different parts of a genome, before and after substantial DNA repair. Three biological replicates have been produced for each of the three conditions (9 samples in total). The use of E.coli is ideal to develop this technology as it allows us to obtain high coverage data at a dramatically lower sequencing cost. Further, we have extensive RNA-sequencing and methylation data for the same strain under comparable conditions, which will allow us to demonstrate the potential of this technology to shed light on the interplay of DNA mutagenesis and DNA repair with genome organisation, transcription and epigenetics.