Double strand breaks (DSBs) can be repaired by homology independent nonhomologous end joining (NHEJ) pathways involving proteins such as Ku70/80, DNAPKcs, Xrcc4/Ligase 4, and the Mre11/Rad50/Nbs1 (MRN) complex. DSBs can also be repaired by homology-dependent pathways (HDR), in which the MRN and CtIP nucleases produce single strand ends that engage homologous sequences either by strand invasion or strand annealing. The entry of ends into HDR pathways underlies protocols for genomic manipulation that combine site-specific DSBs with appropriate informational donors. Most strategies utilize long duplex donors that participate by strand invasion. Work in yeast indicates that single strand oligonucleotide (SSO) donors are also active, over considerable distance, via a single strand annealing pathway. We examined the activity of SSO donors in mammalian cells at DSBs induced either by a restriction nuclease or by a targeted interstrand cross-link. SSO donors were effective immediately adjacent to the break, but activity declined sharply beyond ϳ100 nucleotides. Overexpression of the resection nuclease CtIP increased the frequency of SSO-mediated sequence modulation distal to the break site, but had no effect on the activity of an SSO donor adjacent to the break. Genetic and in vivo competition experiments showed that sequence conversion by SSOs in the immediate vicinity of the break was not by strand invasion or strand annealing pathways. Instead these donors competed for ends that would have otherwise entered NHEJ pathways.
Non-homologous end joining (NHEJ)3 repair is un-templated, as there is no requirement, or even apparent use, for an informational reference sequence acting in trans. NHEJ might be regarded as a collection of operations (end processing by nucleases, limited single strand exposure of the ends, fill in by polymerases, ligation), without requirement for a specific order of events (1). In mammalian cells the best characterized version of NHEJ, often termed "classical" (C-NHEJ) (2, 3), utilizes several factors, including Ku70/80, Artemis, XLF, DNAPKcs, Xrcc4/DNA ligase 4, pol, pol, and XLF/Cernunnos (4 -8).Although precise joining of restriction enzyme cleaved ends can occur, the pathway is frequently mutagenic, resulting in the introduction of short deletions at the break site (9 -11).Deletions at the DSB are sometimes bounded by short homology elements located on either side of the break. These have been described as the product of a microhomology mediated end joining (MMEJ) pathway (5, 12). Deletions without microhomologies are also recovered and recent work suggests that the MRN complex plays an important role in both versions of deletional NHEJ (2, 13-15). A backup pathway involving poly(ADP-ribose) polymerase 1 and ligase III has been described as well (16,17). It should be noted that whether end joining in the absence of one of the canonical factors is evidence of different discrete pathways, or simply a variation on a fundamental scheme, is a matter for discussion (7). Nonetheless, NHEJ is the dom...