Polymerase ζ activity is linked to replication timing in humans: evidence from mutational signatures

Replication timing is an important determinant of germline mutation patterns, with a higher rate of point mutations in late replicating regions. Mechanisms underlying this association remain elusive. One of the suggested explanations is the activity of error-prone DNA polymerases in late-replicating regions. Polymerase {zeta} (pol {zeta}), an essential error-prone polymerase biased towards transversions, also has a tendency to produce dinucleotide mutations (DNMs), complex mutational events that simultaneously affect two adjacent nucleotides. Experimental studies have shown that pol {zeta} is strongly biased towards GC->AA/TT DNMs. Using primate divergence data, we show that the GC->AA/TT pol {zeta} mutational signature is the most frequent among DNMs, and its rate exceeds the mean rate of other DNM types by a factor of ~10. Unlike the overall rate of DNMs, the pol {zeta} signature drastically increases with the replication time in the human genome. Finally, the pol {zeta} signature is enriched in transcribed regions, and there is a strong prevalence of GC->TT over GC->AA DNMs on the non-template strand, indicating association with transcription. A recurrently occurring GC->TT DNM in HRAS gene causes the Costello syndrome; we find a 2-fold increase in the mutation rate, and a 2-fold decrease in the transition/transversion ratio, at distances of up to 1 kb from the DNM, suggesting a link between the Costello syndrome and pol {zeta} activity. This study uncovers the genomic preferences of pol {zeta}, shedding light on a novel cause of mutational heterogeneity along the genome.