Replication program of a single-chromosome budding yeast strain
Genome replication is influenced by many factors including nuclear architecture and 3D chromosome folding. In yeasts, centromeres cluster close to the spindle pole body and telomeres position away at the nuclear periphery. This "Rabl configuration" spatially segregates the most early and late replicating parts of the genome, centromeres and telomeres, respectively. It has been proposed that replication timing is driven by origin position along the centromere-telomere axis. To address this, we have investigated DNA replication in a single-chromosome yeast strain, in which all but two telomeres and one centromere have been eliminated, which strongly affects the 3D-folding of the genome and eliminates the Rabl conformation. We used recent nanopore-sequencing based techniques to map DNA replication at the single-molecule level in this strain and its wild-type counterpart. We observed, as expected, inactivation of origins next to deleted centromeres and changes in fork direction and origin efficiency at chromosome fusions. However, only few and weaker replication changes, mostly due to  local origin repression, were observed away from the rearranged loci. The prevalence of dispersive initiation events and the speed of fork progression were unchanged between the two strains except at deleted centromeres and a handful of other loci. In conclusion, the DNA replication program of budding yeast is remarkably resilient to the loss of the Rabl conformation of chromosomes.