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

## TL;DR

This study shows that the error-prone DNA polymerase ζ is linked to replication timing and contributes to mutation patterns in the human genome.

## Contribution

The study identifies a strong link between polymerase ζ activity and replication timing, revealing its role in mutational heterogeneity.

## Key findings

- The GC->AA/TT mutational signature of polymerase ζ is the most frequent among dinucleotide mutations.
- The polymerase ζ signature increases with replication time in the human genome.
- The GC->TT DNM in the HRAS gene is associated with Costello syndrome and shows altered mutation rates near the site.

## Abstract

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 ζ (pol ζ), 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 ζ is strongly biased towards GC->AA/TT DNMs. Using primate divergence data, we show that the GC->AA/TT pol ζ 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 ζ signature drastically increases with the replication time in the human genome. Finally, the pol ζ 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 ζ activity. This study uncovers the genomic preferences of pol ζ, shedding light on a novel cause of mutational heterogeneity along the genome.