Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis

Fis and H-NS are two well-known NAPs in proteobacteria which play crucial role in both genome organization and gene regulation. However, the global effects of Fis and H-NS on gene expression remain unclear. Here, to decipher transcriptional regulatory roles of Fis and H-NS we have performed RNA-sequencing to compare gene expression between the wild-type E. coli and its knockout mutants for fis and hns. We integrated our RNA-seq results with publically available ChIP-seq data to define direct and indirect regulation by Fis and H-NS. The regulatory networks thus provide a comprehensive view of coordinated regulatory roles for these important nucleoid-associated proteins. mRNA profiles of total six samples were generated using Illumina HiSeq 2500. Wild-type, fis mutant and hns mutant E. coli K-12 MG1655 strains were cultured in M9 minimal media at mid-exponential growth phase with biological duplicates.