Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair Luther Davisa,b and Nancy Maizelsa,b,c,d,1 Departments of aImmunology, cBiochemistry, and dPathology, University of Washington School of Medicine, Seattle, WA 98195; and bNorthwest Genome Engineering Consortium, Seattle, WA 98195 Edited by James E. Haber, Brandeis University, Waltham, MA, and approved January 21, 2014 (received for review January 6, 2014) DNA nicks are the most common form of DNA damage, and if Here we compare frequencies of HDR at DNA nicks and DSBs unrepaired can give rise to genomic instability. In human cells, in human cells, using both dsDNA and ssDNA donors for repair. nicks are efficiently repaired via the single-strand break repair We show that HDR at nicks, but not DSBs, is associated with pathway, but relatively little is known about the fate of nicks not transcription and occurs more efficiently at a nick on the tran- processed by that pathway. Here we show that homology-directed scribed strand than at a nick on the nontranscribed strand. We repair (HDR) at nicks occurs via a mechanism distinct from HDR at further show that two distinct pathways can promote HDR at double-strand breaks (DSBs). HDR at nicks, but not DSBs, is associated nicks. One pathway resembles canonical HDR at DSBs and re- with transcription and is eightfold more efficient at a nick on the quires RAD51 and BRCA2 and primarily uses dsDNA donors. transcribed strand than at a nick on the nontranscribed strand. The other pathway, which we refer to as alternative HDR, is a HDR at nicks can proceed by a pathway dependent upon canonical unique pathway quite distinct from canonical HDR. Alternative HDR factors RAD51 and BRCA2; or by an efficient alternative HDR is inhibited by RAD51 and BRCA2 and is stimulated by pathway that uses either ssDNA or nicked dsDNA donors and that is transient knockdown of these factors or by expression of the strongly inhibited by RAD51 and BRCA2. Nicks generated by either K133R D10A RAD51 dominant negative mutant, RAD51 . Alternative I-AniI or the CRISPR/Cas9 nickase are repaired by the alternative HDR preferentially uses ssDNA or nicked dsDNA donors rather HDR pathway with little accompanying mutagenic end-joining, so than intact dsDNAs. This newly identified alternative HDR path- this pathway may be usefully applied to genome engineering. way can efficiently process nicks targeted by the CRISPR/Cas9D10A These results suggest that alternative HDR at nicks may be stimu- nickase, with little accompanying mutEJ, so it is of potential prac- lated in physiological contexts in which canonical RAD51/BRCA2- tical utility for genome engineering by targeted gene correction. dependent HDR is compromised or down-regulated, which occurs In physiological contexts, alternative HDR at nicks may be frequently in tumors. stimulated under conditions in which canonical HDR is com- loss of heterozygosity | targeted gene correction | recombination | promised by mutation of key factors, or down-regulated in re- cancer | gene conversion sponse to environmental conditions or drugs. Our evidence that a nicked dsDNA donor can promote alternative HDR at a nicked dsDNA target also raises the possibility that alternative HDR at NA nicks (single-strand breaks) are the most common form nicks may contribute to loss of heterozygosity, a form of genomic Dof DNA damage. Every day tens of thousands of DNA nicks instability frequently observed in tumors. occur and are repaired in each cell (1). Nicks can be caused by oxidative stress or ionizing radiation, which generates 30 nicks Results for every double-strand break (DSB). Reactive oxygen species HDR with a Duplex Donor Is More Efficient at a Nick on the Transcribed (ROS), such as superoxide, hydrogen peroxide, and hydroxyl Strand. To study nick-initiated and DSB-initiated HDR, we used radicals, can damage a deoxyribose moiety to nick DNA directly, two versions of the I-AniI homing endonuclease. One generates or modify DNA precursors (e.g., by converting guanine to 8-oxo- DSBs, and the other, a “nickase” derivative, is disabled at one of guanine) and thereby overload downstream repair to create a burden of nicked DNA (1–4). Nicks are also intermediates in Significance essential DNA metabolism and repair pathways, including base excision repair, nucleotide excision repair, mismatch repair, ribonucleoside monophosphate removal, and regulation of Nicks are a very common form of DNA damage, but their threat superhelicity by topoisomerases. to genomic integrity has been neglected because it is assumed Nicks are efficiently repaired by the single-strand break repair that all nicks are repaired by simple religation. Here we chal- (SSBR) pathway, which assembles a repair complex at a nick in lenge that assumption. We identify a robust pathway for ho- which X-ray repair cross-complementing protein 1 (XRCC1) is mology-directed repair (HDR) that is active at DNA nicks. This a critical but noncatalytic member (5–8). XRCC1 interacts with alternative HDR pathway is stimulated upon down-regulation factors that clean up modified DNA ends to create a gap that is of key factors in canonical HDR at double-strand breaks. Al- filled by polymerase POL β, or the replicative polymerases POL δ ternative HDR at targeted nicks has immediate practical appli- cations to genome engineering. Alternative HDR can promote and e. LIG3 or other ligases then reseal the DNA backbone (5–7). repair of a nicked target by a nicked donor and may thereby Nicks can also initiate homology-directed repair (HDR) (9–12). contribute to loss of heterozygosity, a common form of ge- This has drawn considerable interest as a strategy for gene therapy nomic instability in tumors. by targeted gene correction, because nicks cause less mutagenic end-joining (mutEJ) than do DSBs (13, 14). However, the mecha- Author contributions: L.D. and N.M. designed research; L.D. performed research; L.D. nism of HDR at nicks has not been defined, either in mammalian contributed new reagents/analytic tools; L.D. and N.M. analyzed data; and L.D. and cells or in model organisms such as Saccharomyces cerevisiae.In N.M. wrote the paper. particular, it is not known whether HDR at nicks proceeds via The authors declare no conflict of interest. the canonical HDR pathway that has been characterized in This article is a PNAS Direct Submission. detail at DNA DSBs, in which free single-stranded 3′ ends are 1To whom correspondence should be addressed. E-mail: [email protected]. exposed, allowing BRCA2 to load RAD51, thus promoting This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. strand invasion (15). 1073/pnas.1400236111/-/DCSupplemental. E924–E932 | PNAS | Published online February 20, 2014 www.pnas.org/cgi/doi/10.1073/pnas.1400236111 Downloaded by guest on September 28, 2021 its two active sites so it cleaves only one DNA strand to generate and TLNT populations were transiently cotransfected with two PNAS PLUS a nick rather than a DSB (12). To compare frequencies of HDR at constructs. One transfected construct, plasmid pCS14GFP, nicks and DSBs, we used a Traffic Light (TL) reporter carrying an provided the dsDNA repair donor, which is homologous with the I-AniI site as the target for HDR (16). In cells bearing these TLTS and TLNT reporters over a region extending 2.47 kb up- reporters stably integrated in the genome, HDR by a homologous stream and 0.56 kb downstream of the I-AniI site (Fig. S1). The donor that replaces the I-AniI site and proximal stop codon will other transfected construct coexpressed wild-type I-AniI (DSB), yield GFP+ cells, whereas mutEJ events that cause a +2 frame- or its nickase (Nick) or catalytically inactive (Dead) derivatives, shift yield mCherry+ cells (Fig. 1A). To enable comparison of the along with the blue fluorescent protein mTagBFP (BFP) to en- outcomes of nicking either DNA strand, the I-AniI site was able transfectants to be identified by FACS as BFP+ cells. GFP+ inserted in both forward and reverse orientations, to create the cells among I-AniI–expressing (BFP+) cells were quantified at 3 d TLTS and TLNT reporters, which support nicking on the tran- after transfection. Control experiments showed that no GFP+ scribed or nontranscribed strand, respectively (Fig. S1). cells were generated after expression of catalytically inactive Transcription-coupled nucleotide excision repair preferen- I-AniI in the presence of donor (“Dead”; Fig. 1B, Left, and Fig. tially detects and repairs damage on the transcribed DNA strand S2A). Additional controls verified that generation of GFP+ cells (17), and a nick on the transcribed strand can arrest transcrip- depends upon HDR, by showing that no GFP+ cells were gen- tional elongation in human cell extracts (18). To determine whether erated upon transfection of constructs that expressed active I-AniI a similar strand bias characterizes nick-initiated HDR, popu- nickase or wild-type enzyme in the absence of a DNA repair donor lations of 293T cells bearing either the TLTS or TLNT reporter (Fig. S2B and Dataset S1). were established using retroviral vectors, which integrate at Comparison of HDR frequencies in 293T TLTS or 293 TLNT heterogeneous integration sites, to minimize effects of chromo- reporter populations after cotransfection with the I-AniI nickase somal position. 293T cells are a commonly used cellular model expression construct and the dsDNA repair donor showed that for repair. These highly transformed cells derive from human a nick on the transcribed strand initiated HDR with nearly embryonic kidney tissue, express SV40 large T antigen, and are eightfold greater frequency than a nick on the nontranscribed p53 deficient and exhibit a complex karyotype. The 293T TLTS strand (Fig. 1B, Center). Frequencies of mutEJ at nicks were Fig.