{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T22:11:43Z","timestamp":1791151903377,"version":"4.1.0"},"reference-count":71,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2011,5,26]],"date-time":"2011-05-26T00:00:00Z","timestamp":1306368000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1002089","type":"journal-article","created":{"date-parts":[[2011,5,26]],"date-time":"2011-05-26T21:06:34Z","timestamp":1306443994000},"page":"e1002089","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":70,"title":["A Genetic and Structural Study of Genome Rearrangements Mediated by High Copy Repeat Ty1 Elements"],"prefix":"10.1371","volume":"7","author":[{"given":"Jason E.","family":"Chan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard D.","family":"Kolodner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2011,5,26]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1126\/science.1058040","article-title":"The sequence of the human genome.","volume":"291","author":"JC Venter","year":"2001","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome.","volume":"409","author":"ES Lander","year":"2001","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"e254","DOI":"10.1371\/journal.pbio.0050254","article-title":"The diploid genome sequence of an individual human.","volume":"5","author":"S Levy","year":"2007","journal-title":"PLoS Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1086\/378594","article-title":"An Alu transposition model for the origin and expansion of human segmental duplications.","volume":"73","author":"JA Bailey","year":"2003","journal-title":"Am J Hum Genet"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1006\/mgme.1999.2864","article-title":"Alu repeats and human disease.","volume":"67","author":"PL Deininger","year":"1999","journal-title":"Mol Genet Metab"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/j.cell.2009.07.042","article-title":"Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes.","volume":"138","author":"J Lange","year":"2009","journal-title":"Cell"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1038\/25292","article-title":"Genetic instabilities in human cancers.","volume":"396","author":"C Lengauer","year":"1998","journal-title":"Nature"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/35082608","article-title":"Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae.","volume":"411","author":"K Myung","year":"2001","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/12687","article-title":"Gross chromosomal rearrangements in Saccharomyces cerevisiae replication and recombination defective mutants.","volume":"23","author":"C Chen","year":"1999","journal-title":"Nat Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1016\/j.molcel.2005.02.008","article-title":"A biological network in Saccharomyces cerevisiae prevents the deleterious effects of endogenous oxidative DNA damage.","volume":"17","author":"ME Huang","year":"2005","journal-title":"Mol Cell"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1038\/nature08217","article-title":"Specific pathways prevent duplication-mediated genome rearrangements.","volume":"460","author":"CD Putnam","year":"2009","journal-title":"Nature"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1101\/gr.8.5.464","article-title":"Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence.","volume":"8","author":"JM Kim","year":"1998","journal-title":"Genome Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/0092-8674(80)90131-2","article-title":"DNA rearrangements associated with a transposable element in yeast.","volume":"21","author":"GS Roeder","year":"1980","journal-title":"Cell"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/0092-8674(80)90130-0","article-title":"Genetic events associated with an insertion mutation in yeast.","volume":"21","author":"DT Chaleff","year":"1980","journal-title":"Cell"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"5621","DOI":"10.1073\/pnas.79.18.5621","article-title":"Movement of yeast transposable elements by gene conversion.","volume":"79","author":"GS Roeder","year":"1982","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"16144","DOI":"10.1073\/pnas.242624799","article-title":"Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.","volume":"99","author":"MJ Dunham","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/genetics\/160.1.97","article-title":"Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae: retrotransposon Ty1 plays a crucial role in chromosomal rearrangements.","volume":"160","author":"K Umezu","year":"2002","journal-title":"Genetics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1093\/genetics\/110.3.397","article-title":"Resolution of dicentric chromosomes by Ty-mediated recombination in yeast.","volume":"110","author":"RT Surosky","year":"1985","journal-title":"Genetics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2942","DOI":"10.1128\/MCB.8.7.2942","article-title":"Meiotic recombination between repeated transposable elements in Saccharomyces cerevisiae.","volume":"8","author":"M Kupiec","year":"1988","journal-title":"Mol Cell Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1093\/genetics\/119.3.549","article-title":"Allelic and ectopic recombination between Ty elements in yeast.","volume":"119","author":"M Kupiec","year":"1988","journal-title":"Genetics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1093\/genetics\/122.4.759","article-title":"Mitotic and meiotic gene conversion of Ty elements and other insertions in Saccharomyces cerevisiae.","volume":"122","author":"A Vincent","year":"1989","journal-title":"Genetics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"11845","DOI":"10.1073\/pnas.0804529105","article-title":"Double-strand breaks associated with repetitive DNA can reshape the genome.","volume":"105","author":"JL Argueso","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e1001228","DOI":"10.1371\/journal.pgen.1001228","article-title":"Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination.","volume":"6","author":"ML Hoang","year":"2010","journal-title":"PLoS Genet"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/j.cell.2004.12.039","article-title":"Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites.","volume":"120","author":"FJ Lemoine","year":"2005","journal-title":"Cell"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"e6389","DOI":"10.1371\/journal.pone.0006389","article-title":"Stabilization of dicentric translocations through secondary rearrangements mediated by multiple mechanisms in S. cerevisiae.","volume":"4","author":"V Pennaneach","year":"2009","journal-title":"PLoS ONE"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1016\/j.cell.2006.04.042","article-title":"The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks.","volume":"125","author":"V Narayanan","year":"2006","journal-title":"Cell"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.mrfmmm.2008.07.013","article-title":"Large inverted repeats in the vicinity of a single double-strand break strongly affect repair in yeast diploids lacking Rad51.","volume":"645","author":"B Downing","year":"2008","journal-title":"Mutat Res"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2601","DOI":"10.1128\/MCB.01740-06","article-title":"Inverted DNA repeats channel repair of distant double-strand breaks into chromatid fusions and chromosomal rearrangements.","volume":"27","author":"K VanHulle","year":"2007","journal-title":"Mol Cell Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1534\/genetics.108.087940","article-title":"Defective break-induced replication leads to half-crossovers in Saccharomyces cerevisiae.","volume":"179","author":"A Deem","year":"2008","journal-title":"Genetics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1534\/genetics.109.106385","article-title":"Chromosome aberrations resulting from double-strand DNA breaks at a naturally occurring yeast fragile site composed of inverted ty elements are independent of Mre11p and Sae2p.","volume":"183","author":"AM Casper","year":"2009","journal-title":"Genetics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1126\/science.1075277","article-title":"Maintenance of genome stability in Saccharomyces cerevisiae.","volume":"297","author":"RD Kolodner","year":"2002","journal-title":"Science"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/BF00269415","article-title":"Selection of spontaneous mutants by inositol starvation in yeast.","volume":"143","author":"SA Henry","year":"1975","journal-title":"Mol Gen Genet"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e1000933","DOI":"10.1371\/journal.pgen.1000933","article-title":"Post-replication repair suppresses duplication-mediated genome instability.","volume":"6","author":"CD Putnam","year":"2010","journal-title":"PLoS Genet"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1093\/genetics\/159.4.1449","article-title":"Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance.","volume":"159","author":"DT Scholes","year":"2001","journal-title":"Genetics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.dnarep.2006.02.005","article-title":"Esc4\/Rtt107 and the control of recombination during replication.","volume":"5","author":"JK Chin","year":"2006","journal-title":"DNA Repair (Amst)"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1126\/science.1133234","article-title":"Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication.","volume":"315","author":"J Han","year":"2007","journal-title":"Science"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1091\/mbc.E07-09-0961","article-title":"Regulation of rtt107 recruitment to stalled DNA replication forks by the cullin rtt101 and the rtt109 acetyltransferase.","volume":"19","author":"TM Roberts","year":"2008","journal-title":"Mol Biol Cell"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1093\/genetics\/107.2.179","article-title":"Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae.","volume":"107","author":"F Winston","year":"1984","journal-title":"Genetics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1093\/genetics\/115.4.649","article-title":"Three genes are required for trans-activation of Ty transcription in yeast.","volume":"115","author":"F Winston","year":"1987","journal-title":"Genetics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1534\/genetics.102.012708","article-title":"Increase in Ty1 cDNA recombination in yeast sir4 mutant strains at high temperature.","volume":"168","author":"SJ Radford","year":"2004","journal-title":"Genetics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/S1097-2765(02)00495-1","article-title":"Inhibition of reverse transcription in vivo by elevated manganese ion concentration.","volume":"9","author":"EC Bolton","year":"2002","journal-title":"Mol Cell"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1093\/genetics\/118.2.203","article-title":"Isolation and analysis of a novel class of suppressor of Ty insertion mutations in Saccharomyces cerevisiae.","volume":"118","author":"JS Fassler","year":"1988","journal-title":"Genetics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1146\/annurev.genet.38.072902.091500","article-title":"Recombination proteins in yeast.","volume":"38","author":"BO Krogh","year":"2004","journal-title":"Annu Rev Genet"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1093\/genetics\/140.4.1199","article-title":"The role of DNA repair genes in recombination between repeated sequences in yeast.","volume":"140","author":"B Liefshitz","year":"1995","journal-title":"Genetics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1093\/genetics\/138.3.587","article-title":"Use of a chromosomal inverted repeat to demonstrate that the RAD51 and RAD52 genes of Saccharomyces cerevisiae have different roles in mitotic recombination.","volume":"138","author":"AJ Rattray","year":"1994","journal-title":"Genetics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1101\/gad.10.16.2025","article-title":"A Rad52 homolog is required for RAD51-independent mitotic recombination in Saccharomyces cerevisiae.","volume":"10","author":"Y Bai","year":"1996","journal-title":"Genes Dev"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"2048","DOI":"10.1128\/MCB.21.6.2048-2056.2001","article-title":"Genetic requirements for RAD51- and RAD54-independent break-induced replication repair of a chromosomal double-strand break.","volume":"21","author":"L Signon","year":"2001","journal-title":"Mol Cell Biol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1128\/MCB.21.5.1819-1827.2001","article-title":"Two survivor pathways that allow growth in the absence of telomerase are generated by distinct telomere recombination events.","volume":"21","author":"Q Chen","year":"2001","journal-title":"Mol Cell Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"13262","DOI":"10.1073\/pnas.0405443101","article-title":"Chromosome healing through terminal deletions generated by de novo telomere additions in Saccharomyces cerevisiae.","volume":"101","author":"CD Putnam","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"2344","DOI":"10.1128\/MCB.24.6.2344-2351.2004","article-title":"RAD51-dependent break-induced replication in yeast.","volume":"24","author":"AP Davis","year":"2004","journal-title":"Mol Cell Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1093\/genetics\/126.4.851","article-title":"Gene conversion tracts stimulated by HOT1-promoted transcription are long and continuous.","volume":"126","author":"K Voelkel-Meiman","year":"1990","journal-title":"Genetics"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/genetics\/147.2.371","article-title":"\u201cBreak copy\u201d duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae.","volume":"147","author":"DM Morrow","year":"1997","journal-title":"Genetics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1093\/genetics\/150.3.1037","article-title":"Chromosome break-induced DNA replication leads to nonreciprocal translocations and telomere capture.","volume":"150","author":"G Bosco","year":"1998","journal-title":"Genetics"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"7131","DOI":"10.1073\/pnas.93.14.7131","article-title":"Double-strand break repair in the absence of RAD51 in yeast: a possible role for break-induced DNA replication.","volume":"93","author":"A Malkova","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1128\/MCB.01469-08","article-title":"Aberrant double-strand break repair resulting in half crossovers in mutants defective for Rad51 or the DNA polymerase delta complex.","volume":"29","author":"CE Smith","year":"2009","journal-title":"Mol Cell Biol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"5359","DOI":"10.1128\/MCB.02084-07","article-title":"Reduced levels of DNA polymerase delta induce chromosome fragile site instability in yeast.","volume":"28","author":"FJ Lemoine","year":"2008","journal-title":"Mol Cell Biol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/genetics\/111.1.7","article-title":"Rad52-independent mitotic gene conversion in Saccharomyces cerevisiae frequently results in chromosomal loss.","volume":"111","author":"JE Haber","year":"1985","journal-title":"Genetics"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nature05723","article-title":"Template switching during break-induced replication.","volume":"447","author":"CE Smith","year":"2007","journal-title":"Nature"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"5406","DOI":"10.1128\/MCB.00161-06","article-title":"Control of translocations between highly diverged genes by Sgs1, the Saccharomyces cerevisiae homolog of the Bloom&apos;s syndrome protein.","volume":"26","author":"KH Schmidt","year":"2006","journal-title":"Mol Cell Biol"},{"key":"ref60","doi-asserted-by":"crossref","DOI":"10.1101\/pdb.prot4149","article-title":"Isolation of Yeast Genomic DNA for Southern Blot Analysis.","volume":"2006","author":"DC Amberg","year":"2006","journal-title":"Cold Spring Harbor Protocols"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/0378-1119(85)90120-9","article-title":"Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors.","volume":"33","author":"C Yanisch-Perron","year":"1985","journal-title":"Gene"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1126\/science.285.5429.901","article-title":"Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.","volume":"285","author":"EA Winzeler","year":"1999","journal-title":"Science"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1093\/genetics\/122.1.19","article-title":"A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.","volume":"122","author":"RS Sikorski","year":"1989","journal-title":"Genetics"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1093\/genetics\/28.6.491","article-title":"Mutations of Bacteria from Virus Sensitivity to Virus Resistance.","volume":"28","author":"SE Luria","year":"1943","journal-title":"Genetics"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1007\/BF02986080","article-title":"The distribution of the numbers of mutants in bacterial populations.","volume":"49","author":"DE Lea","year":"1949","journal-title":"Journal of Genetics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1186\/1471-2105-8-221","article-title":"Ringo\u2013an R\/Bioconductor package for analyzing ChIP-chip readouts.","volume":"8","author":"J Toedling","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics.","volume":"5","author":"RC Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"18196","DOI":"10.1073\/pnas.0608566103","article-title":"Suppression of spontaneous genome rearrangements in yeast DNA helicase mutants.","volume":"103","author":"KH Schmidt","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/S0092-8674(01)00227-6","article-title":"Suppression of spontaneous chromosomal rearrangements by S phase checkpoint functions in Saccharomyces cerevisiae.","volume":"104","author":"K Myung","year":"2001","journal-title":"Cell"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"5226","DOI":"10.1128\/MCB.00894-09","article-title":"The Saccharomyces cerevisiae Rad6 postreplication repair and Siz1\/Srs2 homologous recombination-inhibiting pathways process DNA damage that arises in asf1 mutants.","volume":"29","author":"ES Kats","year":"2009","journal-title":"Mol Cell Biol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1073\/pnas.1232239100","article-title":"Saccharomyces cerevisiae chromatin-assembly factors that act during DNA replication function in the maintenance of genome stability.","volume":"100","author":"K Myung","year":"2003","journal-title":"Proc Natl Acad Sci U S A"}],"container-title":["PLoS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1002089","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,24]],"date-time":"2021-11-24T07:07:48Z","timestamp":1637737668000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1002089"}},"subtitle":[],"editor":[{"given":"James E.","family":"Haber","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2011,5,26]]},"references-count":71,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2011,5,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1002089","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,5,26]]}}}