RhlR-, C₄HSL-, and PqsE-dependent binding occupancy and gene expression of known QS regulated genes.

Genome browser depictions of ChIP-seq and RNA-seq profiles for WT PA14 (JPS0222) (black), ΔrhlR (JPS0151) (red), ΔrhlI (JPS0154) (blue), and ΔpqsE (JPS0561) (purple) strains at the (A) rhlA operon, (B) hcnA operon, and (C) phzA1 operon. ChIP-seq read counts per base were normalized to reads/100,000,000 reads. RNA-seq data were normalized as a part of genome alignment using Rockhopper. The data depicted for both ChIP- and RNA-seq are the average of biological replicates. D) MEME analysis was conducted on all 40 RhlR-bound sequences using default parameters, optionally looking for any number of repetitions [64].