RAG1 and RAG2 cleave DNA to generate blunt signal ends and hairpin coding ends at antigen receptor loci in lymphoid cells. During V(D)J recombination, repair of these RAG-generated double-strand breaks (DSBs) by the nonhomologous end-joining (NHEJ) pathway contributes substantially to the antigen receptor diversity necessary for immune system function, although recent evidence also supports the ability of RAG-generated breaks to undergo homology-directed repair (HDR). We have determined that RAG-generated chromosomal breaks can be repaired by pathways other than NHEJ in mouse embryonic stem (ES) cells, although repair by these pathways occurs at a significantly lower frequency than NHEJ. HDR frequency was estimated to be >40-fold lower than NHEJ frequency for both coding end and signal end reporters. Repair by single-strand annealing was estimated to occur at a comparable or lower frequency than HDR. As expected, V(D)J recombination was substantially impaired in cells deficient for the NHEJ components Ku70, XRCC4, and DNA-PKcs. Concomitant with decreased NHEJ, RAG-induced HDR was increased in each of the mutants, including cells lacking DNA-PKcs, which has been implicated in hairpin opening. HDR was increased to the largest extent in Ku70 ؊/؊ cells, implicating the Ku70/80 DNA end-binding protein in regulating pathway choice. Thus, RAGgenerated DSBs are typically repaired by the NHEJ pathway in ES cells, but in the absence of NHEJ components, a substantial fraction of breaks can be efficiently channeled into alternative pathways in these cells.Nonhomologous end-joining (NHEJ) of DNA doublestrand breaks (DSBs) created by the RAG recombinase during V(D)J recombination generates a substantial portion of the diversity found in antigen receptors (6, 11). The RAG recombinase, composed of the RAG1 and RAG2 proteins, initiates recombination by introducing nicks at recombination signal sequences (RSS elements), each composed of conserved heptamer and nonamer sequences separated by a nonconserved spacer of either 12 bp or 23 bp. Through a transesterification reaction the nicks become converted to DSBs, resulting in two hairpin coding ends and two blunt signal ends. The signal ends undergo precise joining, whereas the hairpin coding ends undergo further processing prior to joining, resulting in a diverse set of junctions. In addition to the cleavage reaction, the RAG proteins participate in end processing and joining, possibly by maintaining the ends in a postcleavage complex, which serves as a scaffold to facilitate repair (1,14,38,48,52).The proteins involved in NHEJ of RAG-induced DSBs during V(D)J recombination include the DNA end-binding protein Ku70/80, the Ser/Thr kinase DNA-PKcs, the XRCC4/ ligase IV complex, and the Artemis protein, which has endonuclease activity (6, 24). Mutant cell lines for each of these NHEJ proteins have severely impaired formation of coding joints during V(D)J recombination, whereas only Ku70/80-and XRCC4/ligase IV-deficient cells are markedly impaired for signal joint formation (2,8,12,23,...