{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T04:16:04Z","timestamp":1790914564570,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pgen.1011454","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T00:00:00Z","timestamp":1730851200000}}],"reference-count":96,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2024,10,25]],"date-time":"2024-10-25T00:00:00Z","timestamp":1729814400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R01CA229532"],"award-info":[{"award-number":["R01CA229532"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM148975"],"award-info":[{"award-number":["R01GM148975"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["T32GM007133"],"award-info":[{"award-number":["T32GM007133"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["T32HG002760"],"award-info":[{"award-number":["T32HG002760"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    Aneuploidy produces myriad consequences in health and disease, yet models of the deleterious effects of chromosome amplification are still widely debated. To distinguish the molecular determinants of aneuploidy stress, we measured the effects of duplicating individual genes in cells with different chromosome duplications, in wild-type cells (\n                    <jats:italic>SSD1<\/jats:italic>\n                    +) and cells sensitized to aneuploidy by deletion of RNA-binding protein Ssd1 (\n                    <jats:italic>ssd1\u0394<\/jats:italic>\n                    ). We identified gene duplications that are nearly neutral in wild-type euploid cells but significantly deleterious in euploids lacking\n                    <jats:italic>SSD1<\/jats:italic>\n                    or in\n                    <jats:italic>SSD1+<\/jats:italic>\n                    aneuploid cells with different chromosome duplications. Several of the most deleterious genes are linked to translation. In contrast, duplication of other genes benefits multiple\n                    <jats:italic>ssd1\u0394<\/jats:italic>\n                    aneuploids over controls, and this group is enriched for translational effectors. Furthermore, both wild-type and especially\n                    <jats:italic>ssd1\u0394<\/jats:italic>\n                    aneuploids with different chromosome amplifications show increased sensitivity to translational inhibitor nourseothricin. We used comparative modeling of aneuploid growth defects, based on the cumulative fitness costs measured for single-gene duplication. Our results present a model in which the deleterious effects of aneuploidy emerge from an interaction between the cumulative burden of many amplified genes on a chromosome and a subset of duplicated genes that become toxic in that context. These findings provide a perspective on the dual impact of individual genes and overall genomic burden, offering new avenues for understanding aneuploidy and its cellular consequences.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1011454","type":"journal-article","created":{"date-parts":[[2024,10,25]],"date-time":"2024-10-25T13:39:08Z","timestamp":1729863548000},"page":"e1011454","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["The response to single-gene duplication implicates translation as a key vulnerability in aneuploid yeast"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2013-4391","authenticated-orcid":true,"given":"H. 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P.","family":"Gasch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,10,25]]},"reference":[{"key":"pgen.1011454.ref001","first-page":"54","article-title":"The diverse consequences of aneuploidy","volume":"21","author":"NK Chunduri","year":"2019","journal-title":"Nat Cell Biol 2019 211."},{"key":"pgen.1011454.ref002","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1016\/j.ceb.2010.06.003","article-title":"Hyde: Role of Aneuploidy in Cellular Adaptation and Cancer","volume":"22","author":"N Pavelka","year":"2010","journal-title":"Curr Opin Cell Biol"},{"key":"pgen.1011454.ref003","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1083\/jcb.201301061","article-title":"Aneuploidy in health, disease, and aging","volume":"201","author":"RM Ricke","year":"2013","journal-title":"J Cell 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Biotechnol"},{"key":"pgen.1011454.ref041","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1016\/j.cell.2009.04.029","article-title":"Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity","volume":"138","author":"T Vavouri","year":"2009","journal-title":"Cell"},{"key":"pgen.1011454.ref042","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1073\/pnas.80.1.228","article-title":"Instability of dicentric plasmids in yeast","volume":"80","author":"C Mann","year":"1983","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pgen.1011454.ref043","first-page":"2397","article-title":"Genetic manipulation of centromere function","volume":"7","author":"A Hill","year":"1987","journal-title":"Mol Cell Biol"},{"key":"pgen.1011454.ref044","first-page":"541","article-title":"Genome-wide genetic analysis of polyploidy in yeast","volume":"443","author":"Z Storchov\u00e1","year":"2006","journal-title":"Nat 2006 4437111."},{"key":"pgen.1011454.ref045","doi-asserted-by":"crossref","first-page":"2259","DOI":"10.1101\/gad.287474.116","article-title":"The pleiotropic deubiquitinase Ubp3 confers aneuploidy tolerance","volume":"30","author":"SE Dodgson","year":"2016","journal-title":"Genes Dev"},{"key":"pgen.1011454.ref046","doi-asserted-by":"crossref","first-page":"E1344","DOI":"10.1073\/pnas.1400129111","article-title":"Protein phosphatase PP1\/GLC7 interaction domain in yeast eIF2\u03b3 bypasses targeting subunit requirement for eIF2\u03b1 dephosphorylation","volume":"111","author":"M Rojas","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pgen.1011454.ref047","doi-asserted-by":"crossref","first-page":"4857","DOI":"10.1038\/sj.emboj.7600473","article-title":"Polyamines regulate their synthesis by inducing expression and blocking degradation of ODC antizyme","volume":"23","author":"R Palanimurugan","year":"2004","journal-title":"EMBO 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Saccharomyces cerevisiae.","author":"K Halwas","year":"2022","journal-title":"Int J Mol Sci."},{"key":"pgen.1011454.ref052","doi-asserted-by":"crossref","first-page":"7733","DOI":"10.1074\/jbc.M611105200","article-title":"Polyamine Uptake by DUR3 and SAM3 in Saccharomyces cerevisiae","volume":"282","author":"T Uemura","year":"2007","journal-title":"J Biol Chem"},{"key":"pgen.1011454.ref053","doi-asserted-by":"crossref","first-page":"2562","DOI":"10.1074\/jbc.M507651200","article-title":"The yeast translation release factors Mrf1p and Sup45p (eRF1) are methylated, respectively, by the methyltransferases Mtq1p and Mtq2p.","volume":"281","author":"B Polevoda","year":"2006","journal-title":"J Biol Chem"},{"key":"pgen.1011454.ref054","doi-asserted-by":"crossref","first-page":"4671","DOI":"10.1128\/MCB.00430-10","article-title":"The RNA Recognition Motif of Eukaryotic Translation Initiation Factor 3g (eIF3g) Is Required for Resumption of Scanning of Posttermination Ribosomes for Reinitiation 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Haupt","year":"1978","journal-title":"J Antibiot (Tokyo)."},{"key":"pgen.1011454.ref058","article-title":"Premature aging in aneuploid yeast is caused in part by aneuploidy-induced defects in Ribosome Quality Control","author":"LE Escalante","year":"2024","journal-title":"bioRxiv"},{"key":"pgen.1011454.ref059","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1534\/genetics.115.185660","article-title":"Chromosome-specific and global effects of aneuploidy in Saccharomyces cerevisiae","volume":"202","author":"SE Dodgson","year":"2016","journal-title":"Genetics"},{"key":"pgen.1011454.ref060","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-018-4556-6","article-title":"The deregulated microRNAome contributes to the cellular response to aneuploidy","volume":"19","author":"M D\u00fcrrbaum","year":"2018","journal-title":"BMC 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Cai","year":"2023","journal-title":"FASEB J"},{"key":"pgen.1011454.ref065","first-page":"12","article-title":"Dyrk1a from Gene Function in Development and Physiology to Dosage Correction across Life Span in Down Syndrome.","author":"H Atas-Ozcan","year":"2021","journal-title":"Genes (Basel)."},{"key":"pgen.1011454.ref066","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.neuron.2006.05.022","article-title":"Increased App expression in a mouse model of Down\u2019s syndrome disrupts NGF transport and causes cholinergic neuron degeneration","volume":"51","author":"A Salehi","year":"2006","journal-title":"Neuron"},{"key":"pgen.1011454.ref067","doi-asserted-by":"crossref","first-page":"e1005592","DOI":"10.1371\/journal.pcbi.1005592","article-title":"Ribosome reinitiation can explain length-dependent translation of messenger RNA","volume":"13","author":"DW Rogers","year":"2017","journal-title":"PLOS Comput 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Chunduri","year":"2021","journal-title":"Nat Commun."},{"key":"pgen.1011454.ref078","first-page":"07.19.604323","article-title":"Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis.","volume":"2024","author":"HA Dutcher","year":"2024","journal-title":"bioRxiv."},{"key":"pgen.1011454.ref079","doi-asserted-by":"crossref","first-page":"1003675","DOI":"10.1371\/journal.pgen.1003675","article-title":"Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling.","volume":"9","author":"B Zinshteyn","year":"2013","journal-title":"PLoS Genet."},{"key":"pgen.1011454.ref080","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1016\/j.cell.2015.05.022","article-title":"Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity","volume":"161","author":"DD Nedialkova","year":"2015","journal-title":"Cell"},{"key":"pgen.1011454.ref081","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1016\/j.molcel.2017.11.002","article-title":"Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation","volume":"68","author":"HJ Chou","year":"2017","journal-title":"Mol Cell"},{"key":"pgen.1011454.ref082","doi-asserted-by":"crossref","first-page":"990","DOI":"10.4161\/rna.20531","article-title":"Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications","volume":"9","author":"A Patil","year":"2012","journal-title":"RNA Biol"},{"key":"pgen.1011454.ref083","first-page":"10","article-title":"Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories","author":"DE Robinson","year":"2021","journal-title":"Elife"},{"key":"pgen.1011454.ref084","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1007\/978-1-4939-2269-7_23","article-title":"Chemical genomic profiling via barcode sequencing to predict compound mode of action","volume":"1263","author":"JS Piotrowski","year":"2015","journal-title":"Methods Mol Biol"},{"key":"pgen.1011454.ref085","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"MD Robinson","year":"2010","journal-title":"Genome Biol"},{"key":"pgen.1011454.ref086","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1011454.ref087","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B."},{"key":"pgen.1011454.ref088","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome-wide expression patterns","volume":"95","author":"MB Eisen","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pgen.1011454.ref089","doi-asserted-by":"crossref","first-page":"3246","DOI":"10.1093\/bioinformatics\/bth349","article-title":"Java Treeview\u2014extensible visualization of microarray data","volume":"20","author":"AJ Saldanha","year":"2004","journal-title":"Bioinformatics"},{"key":"pgen.1011454.ref090","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/s12859-017-1571-6","article-title":"Avoiding the pitfalls of gene set enrichment analysis with SetRank","volume":"18","author":"C Simillion","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"pgen.1011454.ref091","first-page":"40","article-title":"Saccharomyces Genome Database: The genomics resource of budding yeast","author":"JM Cherry","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pgen.1011454.ref092","doi-asserted-by":"crossref","first-page":"2.4.1","DOI":"10.1002\/0471250953.bi0204s00","article-title":"Discovering Novel Sequence Motifs with MEME.","volume":"00","author":"TL Bailey","year":"2003","journal-title":"Curr Protoc Bioinforma."},{"key":"pgen.1011454.ref093","first-page":"2021.08.23.457422.","article-title":"SEA: Simple Enrichment Analysis of motifs.","author":"TL Bailey","year":"2021","journal-title":"bioRxiv."},{"key":"pgen.1011454.ref094","doi-asserted-by":"crossref","first-page":"W297","DOI":"10.1093\/nar\/gkab408","article-title":"IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation","volume":"49","author":"G Erdos","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pgen.1011454.ref095","first-page":"2012","article-title":"YeastMine\u2014an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit.","author":"R Balakrishnan","year":"2012","journal-title":"Database J Biol Databases Curation."},{"key":"pgen.1011454.ref096","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/s41586-021-04295-4","article-title":"Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis","volume":"601","author":"KC 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