Genome wide identification of BysR binding sites in Burkholderia sp. JP2-270

To verify genes that are directly regulated by BysR, we used DNA affinity purification sequencing analysis (DAP-seq) for genome-wide recognition of BysR binding sites in vitro. The HALO-fusion BysR protein was successfully expressed and purified. After affinity purification and sequencing, at least 22 million double-end reads per sample were generated and with > 99 % of reads uniquely mapped to the JP2-270 genome. A total of 470 enriched common peaks of two replicates with –log10(P-value) = 2 were called . The mean width of DAP-seq peaks was < 1,000. In total, 367 (78%) of these peaks were found to locate in the -1 kbp to 1 kbp regions by the analysis of peak summit positions relative to the start codons of JP2-270 open reading frames. Overall design: Identification of the binding sites of BysR in vitro in the genom of Burkholderia sp. JP2-270.