Fig. 2: IHF binds the promoter regions of gafYZ and the GTA gene cluster to activate gene expression.

a, b anti-FLAG ChIP-seq profiles show the enrichment of FLAG-tagged IHFα and β in different genetic backgrounds. Profiles were plotted with the x-axis representing genomic positions and the y-axis representing the number of reads per base pair per million mapped reads (RPBPM). The positions and sequences of identified IHF-binding elements (IBE) are shown beneath the schematic diagram of genes (GTA-related genes are depicted as orange block arrows). The conserved TT nucleotides in IBEs were highlighted in bold, and were mutated to GG to eliminate IHF binding. Note that the GTA main gene cluster is on the minus strand, but was inverted to run from left to right for a presentation purpose only. ChIP-seq experiments were performed twice using biological replicates, and a representative profile is shown. MACS2-identified ChIP-seq peaks above IBE 1, 2, 3, and 6 are reproducible in both replicates and significant i.e., having Poisson distribution −log₁₀(p value) and false discovery rate −log₁₀(q value) > 1000 in both replicates. ChIP-seq peaks above IBE 4 and 5 were not reliably detected by MACS2 but have recognizable IHF-binding motif and were further characterized in Supplementary Fig. 2. c Relative gene expression of gafY (left panel) and gtaT (right panel) from indicated strains in stationary phase, as quantified by qRT-PCR (n = 2). d Total DNA extraction from indicated strains grown up to a stationary phase. Experiments were performed at least twice, and a representative image is shown. e Immunoblot of total cell lysates of indicated strains using a polyclonal anti-GtaL (GTA head-tail connector protein) antibody. A separate Coomassie-stained SDS-PAGE was loaded with the same volume of samples to serve as a loading control. Immunoblots were performed at least twice, and a representative image is shown. Source data are provided as a Source data file.