Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair

Abstract

DNA nicks are the most common form of DNA damage, and if unrepaired can give rise to genomic instability. In human cells, nicks are efficiently repaired via the single-strand break repair pathway, but relatively little is known about the fate of nicks not processed by that pathway. Here we show that homology-directed repair (HDR) at nicks occurs via a mechanism distinct from HDR at double-strand breaks (DSBs). HDR at nicks, but not DSBs, is associated with transcription and is eightfold more efficient at a nick on the transcribed strand than at a nick on the nontranscribed strand. HDR at nicks can proceed by a pathway dependent upon canonical HDR factors RAD51 and BRCA2; or by an efficient alternative pathway that uses either ssDNA or nicked dsDNA donors and that is strongly inhibited by RAD51 and BRCA2. Nicks generated by either I-AniI or the CRISPR/Cas9 D10A nickase are repaired by the alternative HDR pathway with little accompanying mutagenic end-joining, so this pathway may be usefully applied to genome engineering. These results suggest that alternative HDR at nicks may be stimulated in physiological contexts in which canonical RAD51/BRCA2-dependent HDR is compromised or down-regulated, which occurs frequently in tumors.NA nicks (single-strand breaks) are the most common form of DNA damage. Every day tens of thousands of DNA nicks occur and are repaired in each cell (1). Nicks can be caused by oxidative stress or ionizing radiation, which generates 30 nicks for every double-strand break (DSB). Reactive oxygen species (ROS), such as superoxide, hydrogen peroxide, and hydroxyl radicals, can damage a deoxyribose moiety to nick DNA directly, or modify DNA precursors (e.g., by converting guanine to 8-oxoguanine) and thereby overload downstream repair to create a burden of nicked DNA (1-4). Nicks are also intermediates in essential DNA metabolism and repair pathways, including base excision repair, nucleotide excision repair, mismatch repair, ribonucleoside monophosphate removal, and regulation of superhelicity by topoisomerases.Nicks are efficiently repaired by the single-strand break repair (SSBR) pathway, which assembles a repair complex at a nick in which X-ray repair cross-complementing protein 1 (XRCC1) is a critical but noncatalytic member (5-8). XRCC1 interacts with factors that clean up modified DNA ends to create a gap that is filled by polymerase POL β, or the replicative polymerases POL δ and e. LIG3 or other ligases then reseal the DNA backbone (5-7).Nicks can also initiate homology-directed repair (HDR) (9-12). This has drawn considerable interest as a strategy for gene therapy by targeted gene correction, because nicks cause less mutagenic end-joining (mutEJ) than do DSBs (13,14). However, the mechanism of HDR at nicks has not been defined, either in mammalian cells or in model organisms such as Saccharomyces cerevisiae. In particular, it is not known whether HDR at nicks proceeds via the canonical HDR pathway that has been characterized in detail at DNA DSBs, in which free single-stranded 3′ ends ...

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