Genome-wide binding of FliA.

(A) Genome-wide binding of FliA (green) determined by ChIP-seq. Gray boxes represent gene in the MG1655 genome. (B) ChIP-qPCR enrichment at one well-known (fliC) and 13 novel FliA binding sites (n = 3, * p<0.05, ** p<0.01). Gene names in parentheses indicate that the binding site occurs within that gene. (C) FliA motif derived in this study (all binding sites). (D) Motif derived from binding sites with FAT scores ≤4. Motifs in C and D were generated using MEME [52]. (E) Distribution of motifs relative to ChIP-seq peak centers. Motifs cluster ∼25 nt upstream of the peak center, relative to the orientation of the motif.