Mapping of PhoP binding sites in the <i>M. tuberculosis</i> chromosome by ChIP-seq.

<p><b>A.</b> UCSC genome browser view showing PhoP binding regions across the <i>M. tuberculosis</i> genome. Peak height correlates with sequence reads and consequently with PhoP binding affinity. The use of a <i>phoP</i> mutant in this experiment (bottom panel) allows identification of false positive signals. <b>B.</b> PhoP and RNA polymerase (RNApol) ChIP-seq profiles for selected genes. Note that the PhoP binding site lies upstream that of RNApol for <i>lipF</i>, <i>narK1</i>, <i>pks2</i> and <i>pks3</i>, known to be transcriptionally activated by PhoP. The position of the PhoP binding region lies downstream that of RNApol for the <i>PE8</i> gene. PhoP binding at the 3′-end of <i>hddA</i> is shown as an example of non-canonical target. <b>C.</b> Bar diagram showing distance (in bp) between the PhoP binding sites and the start codon of adjacent ORFs. <b>D.</b> Bar diagram showing distance between the position of the PhoP binding site and the summit of the RNApol peak calculated from ChIP-seq data. <b>E.</b> Sequence logo showing the consensus sequence derived from the PhoP binding sites identified by ChIP-seq.