Genome-wide model for the normal eukaryotic DNA replication fork

To investigate DNA replication enzymology across the nuclear genome of budding yeast, deep sequencing was used to establish the pattern of uncorrected replication errors generated by an asymmetric mutator variant of DNA polymerase delta (Pol delta). Sequencing of 16 genomes identified 1,206-bp substitutions generated over 33 generations by L612M Pol delta in a mismatch repair defective strain. Alignment of sequences flanking these substitutions identified hotspot motifs for Pol delta replication errors. The substitutions were distributed evenly across all 16 chromosomes. The vast majority were transitions that occurred with a strand bias that varied in a predictable manner relative to known functional origins of replication. This strand bias strongly supports the idea that Pol delta is primarily a lagging strand polymerase during replication across the entire nuclear genome.