Endonuclease that cooperates with the MRX complex in processing meiotic and mitotic double-strand breaks by allowing the endonucleolytic removal of SPO11 from the break sites and ensuring both resection and intrachromosomal association of the broken ends. Required for proper recovery from checkpoint-mediated cell cycle arrest after DNA damage. MRX complex and SAE2 remove a small oligonucleotide(s) from the DNA ends to form an early intermediate which is rapidly processed by EXO1 and/or SGS1 to generate extensive tracts of single-stranded DNA that serve as substrate for RAD51. Plays a transitional role in the dissociation of MRE11 from, and the recruitment of RAD52 to, repair foci. Ensures that both ends of a DSB participate in a recombination event and impairs the formation of palindromic structures in the genome. With TEL1, promotes microhomology-mediated end joining (MMEJ) but inhibits non-homologous end joining (NHEJ), likely by regulating MRE11-dependent ssDNA accumulation at DNA break. SAE2 and MRX are particularly important for removal of hairpins, bulky adducts and other irregular end structures. Facilitates telomere length reequilibration and subsequent checkpoint switch off. Involved in homing efficiency of VMA1 intein VDE and in repair of transposon excision sites. Dimer or multimer. Interacts with MRE11. Accumulates in foci at the precise time when MRE11 foci disassemble and RAD52 foci assemble (PubMed:18670132). Remains associated with DSBs along with MRE11 in nuclease-deficient cells (PubMed:18670132). Phosphorylated forms accumulate periodically during the unperturbed cell cycle and in response to DNA damage in G2. Phosphorylated by MEC1 and TEL1. Mutagenesis experiments showed that several of the 5 residues located in canonical (S/T)Q motifs, which are favored for phosphorylation by ATM/ATR kinases (Ser-73, Thr-90, Ser-249, Thr-279 and Ser-289) may be phosphorylated. Phosphorylated at Ser-267 by CDC28 which is required to initiate meiotic DSB resection by allowing SPO11 removal from DSB ends. Present with 1030 molecules/cell in log phase SD medium. Belongs to the COM1/SAE2/CtIP family.