In E. coli, Topoisomerase IV is responsible for the untangling of catenanes that are formed during the replication of the chromosome and has been shown to play an essential role in nucleoid segregation. Previous studies have shown that alterations in Topo IV result in a prolonged interaction between sister chromosomes leading to poor chromosome segregation and a loss in cell viability. Using chromosome conformation capture (Hi-C) and fluorescence microscopy, we have shown that the alteration of Topo IV affects the organization of the entire chromosome. As this phenotype only occurs in circular chromosome replicative cells, we hypothesized that this is due to an accumulation of precatenanes throughout the chromosome, allowing loci on different sister chromosomes to interact (inter-chromosomal contacts). We further showed that the butterfly wing positions are dependent on both matS and MatP, and that MukB defines the length and density of the butterfly wings. We thereby hypothesized that the matS-MatP complex and these Topo IV sites define a decatenation hub where unresolved precatenanes would be “pulled” toward this hub, to be decatenated prior to cell.