DSBs are potentially lethal lesions that can occur spontaneously during normal cell metabolism or by treatment of cells with DNA-damaging agents. DSBs are however normal intermediates in meiotic recombination and in programmed genome rearrangements, such as mating-type switching in budding yeast and V(D)J recombination in lymphocytes. If unrepaired or repaired inappropriately, DSBs can lead to mutagenic events such as chromosome loss, deletions, duplications or translocations. Several highly conserved proteins are recruited to DSBs for checkpoint activation and subsequent repair by non-homologous end joining (NHEJ) or homologous recombination (HR). NHEJ involves the religation of the two ends of the broken chromosome and can occur with high fidelity, or be accompanied by gain or loss of nucleotides at the junction [1
]. HR relies on the presence of a homologous duplex to template repair of the broken chromosome. Several sub-pathways of HR have been defined; these include DSBR, SDSA and SSA (). At the molecular level, all three mechanisms are initiated by 5′ to 3′ degradation of the broken DNA ends to create 3′ single-stranded DNA (ssDNA) tails. For repair by DSBR or SDSA, Rad51 binds to the resulting ssDNA tails to initiate pairing and strand invasion with homologous duplex DNA. The 3′ end from the broken chromosome is used to prime leading strand DNA synthesis templated by the donor duplex. According to the canonical DSBR model, the other end of the break interacts with the displaced strand from the donor duplex (D-loop) to prime DNA synthesis from the other end of the break [2
]. During SDSA, the invading strand that has been extended by DNA synthesis is displaced and anneals to complementary sequences exposed by 5′-3′ resection of the other side of the break [3
]. The remaining gaps can be filled by DNA synthesis and the nicks ligated. Under some circumstances a broken chromosome may present only one end for repair, for example, when a telomere becomes uncapped and is degraded. The chromosome end can then invade homologous sequences and initiate DNA synthesis from the site of strand invasion to the telomere, a process known as break-induced replication [5
]. Single-strand annealing (SSA) is restricted to DSBs that occur within a repeat or between direct repeats. Rad52 anneals complementary single-strand regions revealed by extensive resection of the DNA ends. The 3′ single-strand tails are removed by the Rad1/10 nuclease, together with Slx4 and Saw1, and the resulting gaps/nicks filled by DNA repair synthesis and ligation [6
]. This process is accompanied by deletion of one of the repeats and the intervening DNA is therefore considered to be mutagenic.
Models for DSB repair by homologous recombination
A key step in HR is the generation of ssDNA, the substrate for Rad51 binding to initiate homologous pairing and strand exchange, and for Rad52-mediated annealing [7
]. Mounting evidence indicates that ssDNA is also an important stimulus for activating the DNA damage response (DDR) and arresting the cell cycle in response to DNA damage [8
]. In a reciprocal manner, checkpoint proteins not only recognize ssDNA but affect the rate at which ssDNA arises, suggesting that the DDR regulates accumulation of ssDNA and it does so by regulating the activity of various nucleases [9
]. This review will focus on nucleases that participate in processing of DNA ends at DSBs to generate recombinogenic 3′-ssDNA tails in the model organism Saccharomyces cerevisiae
, with reference to other organisms where applicable.