Three mammalian genes encoding DNA ligases have been identified. However, the role of each of these enzymes in mammalian DNA metabolism has not been established. In this study, we show that two forms of mammalian DNA ligase III, ␣ and , are produced by a conserved tissue-specific alternative splicing mechanism involving exons encoding the C termini of the polypeptides. DNA ligase III-␣ cDNA, which encodes a 103-kDa polypeptide, is expressed in all tissues and cells, whereas DNA ligase III- cDNA, which encodes a 96-kDa polypeptide, is expressed only in the testis. During male germ cell differentiation, elevated expression of DNA ligase III- mRNA is restricted, beginning only in the latter stages of meiotic prophase and ending in the round spermatid stage. The joining of DNA single-strand breaks is an essential step in the completion of lagging-strand DNA synthesis and DNA excision repair pathways. Additionally, exchanges between homologous DNA duplexes, which are completed by the cleavage of Holliday junctions, require DNA joining events to generate intact recombinant molecules.Three human genes encoding DNA ligases have been identified (4, 10, 45). Genetic and biochemical studies on the product of the LIG1 gene indicate that this enzyme functions to join Okazaki fragments during DNA replication (4,5,30,36,42,46). The sensitivity of the DNA ligase I-mutant cell line 46BR to DNA damage by alkylating agents and the abnormal repair of uracil-containing DNA substrates by 46BR cell extracts implicate DNA ligase I in DNA base excision repair (5,20,24,30,38). The recent characterization of an interaction between DNA polymerase , which is essential for base excision repair of alkylation damage in mammalian cells (35), and DNA ligase I within a multiprotein complex that catalyzes the repair of a uracil-containing DNA substrate provides evidence at the molecular level that DNA ligase I is involved in DNA base excision repair (29).The LIG3 and LIG4 genes encode polypeptides that have similar electrophoretic mobilities in denaturing polyacrylamide gels (45). These gene products, with molecular masses of about 100 kDa, can be distinguished by the ability of DNA ligase III to form a stable complex with the product of the human XRCC1 gene (8,9,45). Human XRCC1 was cloned by its ability to complement the hypersensitivity of the Chinese hamster ovary cell line EM9 to DNA-alkylating agents (39, 40). Because the EM9 cell line is defective in the joining of DNA single-strand breaks and contains reduced levels of DNA ligase III activity, it appears that DNA ligase III functions in the repair of DNA single-strand breaks that arise either by the direct action of a DNA-damaging agent, such as ionizing radiation, or as a consequence of DNA repair enzymes excising lesions (8,9,25,39,40). At present, very little is known about the cellular role of DNA ligase IV.Analysis of the steady-state levels of DNA ligases I and III mRNAs in different human tissues and cells revealed that both of these genes are highly expressed in the testis. In ...