Conformational asymmetry of replicated human chromosomes

DNA replication generates sister chromatids with identical sequence, yet its mechanism is fundamentally asymmetric: Chromatids inherit strands of opposite orientation, whereas forks synthesize new strands by distinct leading- and lagging-strand mechanisms. How this replication asymmetry affects chromosome organization is unknown. Using sister chromatid-sensitive conformation analysis, we found that human sister chromatids are consistently misaligned in the 5'→3' direction of inherited DNA strands. This shift persisted without cohesin-mediated loop extrusion but was lost upon disruption of cohesion. Polymer modeling showed that modest directional misalignment of cohesive cohesins can explain the observed shift, and we propose two models for how such misalignment could originate from replication fork asymmetry. This register shift between sister chromatids has implications for homology search during DNA repair.