Replication program of a single-chromosome budding yeast strain

Nuclear architecture and chromosome folding are often speculated to influence genome replication. In yeasts, centromeres cluster close to the spindle pole body and telomeres position at the nuclear periphery. This 'Rabl configuration' spatially segregates the most early and late replicating parts of the genome, centromeres and telomeres, respectively, suggesting that origin position along the centromere-telomere axis may influence origin activity. Here, we investigated DNA replication in a wild-type, 16-chromosome Saccharomyces cerevisiae strain and in its single-chromosome counterpart engineered by chromosome fusion and elimination of all but two telomeres and one centromere, which strongly affects genome folding and abrogates the Rabl conformation. Using nanopore sequencing-based methods, we found that the DNA replication program of both strains was virtually indistinguishable, with the exception of origin inactivation next to deleted centromeres and changes in origin efficiency and fork direction at chromosome fusions, as anticipated from the known origin-regulation properties of centromeres and telomeres. Only a handful of replication changes, mostly due to local origin repression, were observed elsewhere. Fork speed was also unaffected except at deleted centromeres. In conclusion, the DNA replication program of budding yeast is remarkably resilient to perturbations of chromosome folding and loss of the Rabl conformation.