Differential Roles of positive and negative supercoiling in compacting theE. coligenome

Abstract

AbstractThis study aims to explore whether and how positive and negative supercoiling contribute to the three-dimensional (3D) spatial organization of the bacterial genome. We used recently published GapR ChIP-seq and Topo-seq data, which marks positive and negative supercoiling sites, respectively, to study how GapR and TopoI binding sites correlate with the corresponding contact frequencies obtained from the Hi-C data of theE. colichromosome. We found that chromosomal loci enriched with GapR or TopoI binding sites have overall higher Hi-C contact frequencies than sites that do not contain the corresponding binding sites, with GapR peaks corresponding to higher spatial contacts than TopoI peaks. Additionally, we found that Hi-C contact frequencies alone could identify GapR, but not TopoI, binding sites with high accuracy. Finally, we found that majority of positive and negative supercoils coincides with highly active transcription units, with a minor group likely associated with replication. Our results suggest that both positive and negative supercoiling enhance chromosomal interactions, but the positive supercoils contribute significantly more than the negative supercoils to bring distant chromosomal loci closer in space.