Summary The Escherichia coli structural maintenance of chromosomes complex, MukBEF, forms axial cores to chromosomes that determine their spatio-temporal organization. Here, we show that axial cores direct chromosome arms to opposite poles and generate the translational symmetry between newly replicated sister chromosomes. MatP, a replication terminus ( ter ) binding protein prevents chromosome rotation around the longitudinal cell axis by displacing MukBEF from ter , thereby maintaining the linear shape of axial cores. During DNA replication, MukBEF action directs lagging strands towards the cell center, marked by accumulation of DNA-bound β 2 -clamps in the wake of replisomes, in a process necessary for the translational symmetry of sister chromosomes. Finally, the ancestral (‘immortal’) template DNA strand, propagated from previous generations, is preferentially inherited by the cell forming at the old pole, dependent on MukBEF-MatP. The work demonstrates how chromosome organization-segregation can foster non-random inheritance of genetic material and provides a framework for understanding how chromosome conformation and dynamics shape subcellular organization.