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Nonhomologous repair mechanisms have been relatively less well studied, despite their potential importance in generating chromosomal rearrangements. We have developed a Saccharomyces cerevisiae-based assay to identify and characterize homology-independent chromosomal rearrangements associated with repair of a unique DSB generated within an engineered URA3 gene. Approximately 1% of successfully repaired cells have accompanying chromosomal rearrangements consisting of large insertions, deletions, aberrant gene conversions, or other more complex changes. We have analyzed rearrangements in isogenic wild-type, rad52, yku80, and rad52 yku80 strains, to determine the types of events that occur in the presence or absence of these key repair proteins. Deletions were found in all strain backgrounds, but insertions were dependent upon the presence of Yku80p. A rare RAD52- and YKU80-independent form of deletion was present in all strains. These events were characterized by long one-sided deletions (up to 13 kb) and extensive imperfect overlapping sequences (7-22 bp) at the junctions. Our results demonstrate that the frequency and types of repair events depend on the specific genetic context. This approach can be applied to a number of problems associated with chromosome stability.<\/jats:p>","DOI":"10.1093\/genetics\/163.3.843","type":"journal-article","created":{"date-parts":[[2021,4,23]],"date-time":"2021-04-23T05:34:34Z","timestamp":1619156074000},"page":"843-856","source":"Crossref","is-referenced-by-count":77,"title":["Ku-Dependent and Ku-Independent End-Joining Pathways Lead to Chromosomal Rearrangements During Double-Strand Break Repair in <i>Saccharomyces cerevisiae<\/i>"],"prefix":"10.1093","volume":"163","author":[{"given":"Xin","family":"Yu","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abram","family":"Gabriel","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2003,3,1]]},"reference":[{"key":"2022010519191796700_R1","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1093\/genetics\/116.4.541","article-title":"A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains","volume":"116","author":"Alani","year":"1987","journal-title":"Genetics"},{"key":"2022010519191796700_R2","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1093\/genetics\/126.3.535","article-title":"A defect in mismatch repair in Saccharomyces cerevisiae stimulates ectopic recombination between homeologous genes by an excision repair dependent process","volume":"126","author":"Bailis","year":"1990","journal-title":"Genetics"},{"key":"2022010519191796700_R3","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/0921-8777(94)90065-5","article-title":"One-sided invasion events in homologous recombination at double-strand breaks","volume":"314","author":"Belmaaza","year":"1994","journal-title":"Mutat. 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