ChAP-seq analysis to identify GoxR binding sites

Gene expression in the obligatory aerobic acetic acid bacterium Gluconobacter oxydans was shown to respond to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed the function of a transcriptional regulator named GoxR, which belongs to the FNR family. Here, we applied ChAP-seq analysis with a strep-tagged GoxR version to identify binding sites of this regulator in the genome of G. oxydans. For ChAP-seq the strain G. oxydans 621H::goxR-strep was constructed. This strain was cultivated aerobically. After harvesting of the cells, the pellet was treated with formaldehyde to perform cross-linking between bound proteins and the DNA. Afterwards, DNA bound to Strep-tagged GoxR was purified and submitted to sequencing.