Genomic analysis of the binding of IHF and HU to the chromosome of E. coli K12 MG1655

Two nucleoid associated proteins (NAP) in E. coli, IHF and HU, are composed of two homologous subunits each (IhfA and IhfB; HupA and HupB). They are both members of the DNABII family of DNA-binding proteins and are strikingly similar to each other in sequence and in their unique structural fold. However, similarities end there: they differ in their sequence specificity, with IHF being sequence-specific and HU binding uniformly along the chromosome. Whereas binding of each subunit of HU in the form of homodimers to the DNA is relatively well established, there are conflicting data for such binding for IHF. Moreover, the two proteins differ in the degree of conservation across bacteria: whereas at least one subunit of HU is found across most bacterial genomes making it the most conserved NAP, IHF has a more restricted occurrence. Their functions include regulation of transcription, replication and recombination via DNA binding and extend to the control of translation initiation by HU via protein-RNA interactions. Here we present a genome-scale study of the binding characteristics of HU and IHF to the E. coli K12 chromosome, at four different time-points during batch growth in LB, using chromatin-immunoprecipitation coupled to high-throughput sequencing (ChIP-seq). We also perform microarray analysis of gene expression in single and double deletion mutants of each protein, to identify their regulons. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms.