Abstract
In mammalian cells, distinct replication domains (RDs) corresponding to structural units of chromosomes called topologically-associating domains (TADs) replicate at different times during S-phase1–4. Further, early/late replication of RDs corresponds to active/inactive chromatin interaction compartments5,6. Although replication origins are selected stochastically, such that each cell is using a different cohort of origins to replicate their genomes7–12, replication-timing is regulated independently and upstream of origin selection13. Moreover, cytogenetic evidence suggests that the same cohorts of RDs can replicate synchronously in consecutive cell cycles14. Hence, measuring the extent of cell-to-cell variation in replication timing is central to studies of chromosome structure and function. Here we devise a strategy to measure variation in single-cell replication timing using copy number variation. Our results detect a similar degree of stochastic variation in the temporal order of domain replication from cell-to-cell as within individual cells and between early vs. late replicating compartments. Finally, borders between replicated and un-replicated DNA were highly conserved between cells with domains replicating at similar times demarcating active and inactive compartments of the nucleus. These results demonstrate that the precise environment within each cell does not influence the extent of stochastic variation in replication timing.
