Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks Differently

ABSTRACT

Three DNA polymerases, polymerases α, δ, and ε (Pol α, Pol δ, and Pol ε), are responsible for eukaryotic genome duplication. When DNA replication stress is encountered, DNA synthesis stalls until the stress is ameliorated. However, it is not known whether there is a difference in the association of each polymerase with active and stalled replication forks. Here, we show that each DNA polymerase has a distinct pattern of association with active and stalled replication forks. Pol α is enriched at extending Okazaki fragments of active and stalled forks. In contrast, although Pol δ contacts the nascent lagging strands of active and stalled forks, it binds to only the matured (and not elongating) Okazaki fragments of stalled forks. Pol ε has greater contact with the nascent single-stranded DNA (ssDNA) of the leading strand on active forks than on stalled forks. We propose that the configuration of DNA polymerases at stalled forks facilitates the resumption of DNA synthesis after stress removal.

KEYWORDS:

• DNA replication
• replication stress
• DNA polymerase
• ChIP-ssSeq
• strand-specific sequencing

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at https://doi.org/10.1128/MCB.00190-17.

ACKNOWLEDGMENT

We thank Oscar Aparicio for yeast strains and plasmids, Steven Brill for the anti-RPA antibody, and June Oshiro for editing our manuscript.

We declare no competing financial interests.