In vivo probing of promoter overlapping between σ-factors in Escherichia coli (ChIP-exo)

An alternative sigma factor (σ32) recognizes the unique set of promoters upon heat shock. Here, we determined 54 σ32 promoters at nucleotide resolution using ChIP-exo, enabling us to compare those with housekeeping σ70 promoters. The results elucidated the overarching principles of promoter overlapping between the two σ-factors, which are sequence-specific non-, half-, and full-shared modes with a perfect sequence conservativeness of −35 element as a key determinant of full-shared mode. ChIP-exo profiles of sigH (30 ℃), sigH (42 ℃), RNAP beta (42 ℃) were generated by deep sequencing in duplicates using Illumina MiSeq.