Sgs1 is a RecQ family DNA helicase required for genome stability in Saccharomyces cerevisiae whose human homologs BLM, WRN, and RECQL4 are mutated in Bloom's, Werner, and Rothmund Thomson syndromes, respectively. Sgs1 and mismatch repair (MMR) are inhibitors of recombination between similar but divergent (homeologous) DNA sequences. Here we show that SGS1, but not MMR, is critical for suppressing spontaneous, recurring translocations between diverged genes in cells with mutations in the genes encoding the checkpoint proteins Mec3, Rad24, Rad9, or Rfc5, the chromatin assembly factors Cac1 or Asf1, and the DNA helicase Rrm3. The S-phase checkpoint kinase and telomere maintenance factor Tel1, a homolog of the human ataxia telangiectasia (ATM) protein, prevents these translocations, whereas the checkpoint kinase Mec1, a homolog of the human ATM-related protein, and the Rad53 checkpoint kinase are not required. The translocation structures observed suggest involvement of a dicentric intermediate and break-induced replication with multiple cycles of DNA template switching.RecQ-like DNA helicases play important roles in the maintenance of genome stability from bacteria to humans. The only member of the RecQ family of 3Ј to 5Ј DNA helicases in the yeast Saccharomyces cerevisiae is Sgs1. Sgs1 has been implicated in the coordination between DNA replication and recombination, in the regulation of homologous recombination (HR) and the suppression of crossover products during HR, and in S-phase checkpoint activation as well as in transcription (16,26,38,49,61,96). As a consequence, cells that lack Sgs1 display a hyperrecombination phenotype, accumulate extrachromosomal ribosomal DNA (rDNA) circles, frequently missegregate chromosomes during mitosis and meiosis, have modestly increased rates of accumulating gross chromosomal rearrangements (GCRs), are sensitive to agents such as hydroxyurea and methyl-methanesulfonate, and show signs of premature aging (29,58,61,86,100,101,104).To date, five human genes encoding RecQ-like (RECQL) proteins have been identified. Mutations in RECQL2 (WRN) (105), RECQL3 (BLM) (23), and RECQL4 (41, 42) cause three rare, cancer-prone disorders, Werner syndrome (WS), Bloom's syndrome (BS), and a subset of Rothmund Thomson syndrome (Type II RTS) (97), respectively, while defects in RECQL1 (73, 74) and RECQL5 (41) have not been linked to a disease. Besides short stature, early onset of diabetes mellitus, and immunodeficiency, BS is characterized by extreme cancer risk, which has been estimated to be 150 to 300 times higher than the risk of malignancy in the unaffected population; in 168 BS patients, 100 cancers of many types had arisen at a mean age of 24.7 years, with many of the patients suffering from multiple primary cancers (31). Although WS patients share some of these symptoms, including early onset of diabetes mellitus and increased cancer susceptibility, they also show numerous other signs of accelerated aging not typical for BS. RTS patients also show a high prevalence of cancers, especially...