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

An alternative sigma factor (s32) recognizes the unique set of promoters upon heat shock. Here, we determined 54 s32 promoters at nucleotide resolution using ChIP-exo, enabling us to compare those with housekeeping s70 promoters. The results elucidated the overarching principles of promoter overlapping between the two s-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. Overall design: ChIP-exo profiles of sigH (30 ?), sigH (42 ?), RNAP beta (42 ?) were generated by deep sequencing in duplicates using Illumina MiSeq.