Initiation of homologous recombination at DNA nicks

Abstract

Discontinuities in only a single strand of the DNA duplex occur frequently, as a result of DNA damage or as intermediates in essential nuclear processes and DNA repair. Nicks are the simplest of these lesions: they carry clean ends bearing 3′-hydroxyl groups that can undergo ligation or prime new DNA synthesis. In contrast, single-strand breaks also interrupt only one DNA strand, but they carry damaged ends that require clean-up before subsequent steps in repair. Despite their apparent simplicity, nicks can have significant consequences for genome stability. The availability of enzymes that can introduce a nick almost anywhere in a large genome now makes it possible to systematically analyze repair of nicks. Recent experiments demonstrate that nicks can initiate recombination via pathways distinct from those active at double-strand breaks (DSBs). Recombination at targeted DNA nicks can be very efficient, and because nicks are intrinsically less mutagenic than DSBs, nick-initiated gene correction is useful for genome engineering and gene therapy. This review revisits some physiological examples of recombination at nicks, and outlines experiments that have demonstrated that nicks initiate homology-directed repair by distinctive pathways, emphasizing research that has contributed to our current mechanistic understanding of recombination at nicks in mammalian cells.

Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations

“…Nicks are therefore normally not processed by double-strand break repair machineries. However, there is some evidence supporting the hypothesis that nicks may be recombinogenic (Maizels and Davis, 2018;Strathern et al, 1991) which is in agreement with our data. For example, in S. pombe, mating type switching occurs by homologous recombination after the conversion of a nick into a DSB during replication (Arcangioli, 1998;Dalgaard and Klar, 2001).…”

Acetylation and Deacetylation of DNA Repair Proteins in Cancers

“…CtBP-interacting protein (CtIP), exonuclease 1 (EXO1), and MRN complex participate in DNA-end resection and creates stretches of ssDNA coated by replication protein A (RPA) (70). CtIP is contributed to license HR and hamper NHEJ by activating DNA end resection.…”

Development of hRad51–Cas9 nickase fusions that mediate HDR without double-stranded breaks

“…We sought to improve ratios of desired:undesired HDR products by exploring the initiation of HDR from a DNA nick rather than a DSB. In contrast to DSBs, DNA nicks generally do not induce undesired genome modification 13–15 , a principle exploited by base editors to minimize editing byproducts 3,5,16 . Mutating catalytic residues in programmable nucleases can result in programmable nickases that cleave only one of the two strands of DNA at the target locus 17–20 .…”