Genome-wide Analysis of Fis Binding in Escherichia coli Indicates a Causative Role for A-/AT-tracts

Abstract

We determined the genome-wide distribution of the nucleoid-associated protein Fis in Escherichia coli using chromatin immunoprecipitation coupled with high-resolution whole genome-tiling microarrays. We identified 894 Fis-associated regions across the E. coli genome. A significant number of these binding sites were found within open reading frames (33%) and between divergently transcribed transcripts (5%). Analysis indicates that A-tracts and AT-tracts are an important signal for preferred Fis binding sites, and that A₆-tracts in particular constitute a high-affinity signal which dictates Fis phasing in stretches of DNA containing multiple and variably-spaced A-tracts and AT-tracts. Furthermore, we find evidence for an average of two Fis binding regions per supercoiling domain in the chromosome of exponentially growing cells. Transcriptome analysis shows approximately 21% of genes are affected by the deletion of fis; however, the changes in magnitude are small. To address the differential Fis-bindings under growth environment perturbation, ChIP-chip analysis was performed using cells grown under aerobic and anaerobic growth conditions. Interestingly, the Fis-binding regions are almost identical in aerobic and anaerobic growth conditions - indicating that E. coli genome topology mediated by Fis is superficially identical in the two conditions. These novel results provide new insight into how Fis modulates DNA topology at a genome scale, and so advance our understanding of the architectural bases of the E. coli nucleoid.

• ChIP-chip
• Fis
• nucleoid-associated protein
• supercoiling domains