DNA polymerase zeta can efficiently replicate structures formed by AT/TA repeat sequences and prevent their deletion.

Long AT repeat tracts form non-B DNA structures that stall DNA replication and cause chromosomal breakage. AT repeats are abundant in human common fragile sites (CFSs), genomic regions that undergo breakage under replication stress. Using an in vivo yeast model system containing AT-rich repetitive elements from human CFS FRA16D, we find that DNA polymerase zeta (Pol ζ) is required to prevent breakage and subsequent deletions at hairpin and cruciform forming (AT/TA)n sequences, with little to no role at an (A/T)28 repeat or a control non-structure forming sequence. DNA polymerase eta is not protective for deletions at AT-rich structures, while DNA polymerase delta is protective, but not in a repeat-specific manner. Using purified replicative holoenzymes in vitro, we show that hairpin structures are most inhibitory to yeast DNA polymerase epsilon, whereas yeast and human Pol ζ efficiently synthesize these regions in a stepwise manner. A requirement for the Rev1 protein and the modifiable lysine 164 of proliferating cell nuclear antigen to prevent deletions at AT/TA repeats suggests a mechanism for Pol ζ recruitment. Our results reveal a novel role for Pol ζ in replicating through AT-rich hairpins and suggest a role for Pol ζ in rescue of stalled replication forks caused by DNA structures.