Fig. 3: 3D-seq maps DNA–protein interactions for P. aeruginosa transcription factors with multiple binding sites. | Nature Microbiology

Fig. 3: 3D-seq maps DNA–protein interactions for P. aeruginosa transcription factors with multiple binding sites.

From: Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase

Fig. 3

a–g, Moving average (n = 4, 75 bp window) of C•G-to-T•A transition frequencies at genomic locations encompassing known binding sites upstream of the indicated genes for GacA and FleQ. Points calculated from filtered 3D-seq data derived from P. aeruginosa strains expressing GacA–DddA (a–d) or FleQ–DddA (e–g) grown with 0.0005% w/v arabinose for induction of DddAI–F. The genetic background of strains employed are noted where applicable (a–d). h, Abundance of transcripts encoding the indicated genes downstream of FleQ DPI sites discovered herein by 3D-seq. Mean ± s.d. are shown; n = 6 biologically independent samples. *P < 0.05, two-tailed paired t-test comparing ΔfleQ and WT expression for each gene (PA2869, P = 0.0022; PA3340, P = 0.0015; yfiR, P = 0.035).

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