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PXD037085-1

PXD037085 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleThe natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids
DescriptionAneuploidy, an imbalance in chromosome copy numbers, causes genetic disorders, and drives cancer progression, drug tolerance, and antimicrobial resistance. While aneuploidy can confer stress resistance, it is not well understood how cells overcome the fitness burden caused by aberrant chromosomal copy numbers. Studies using both systematically generated and natural aneuploid yeasts triggered an intense debate about the role of dosage compensation, concluding that aneuploidy is transmitted to the transcriptome and proteome without significant buffering at the chromosome-wide level, and is, at least in lab strains, associated with significant fitness costs. Conversely, systematic sequencing and phenotyping of large collections of natural isolates revealed that aneuploidy is frequent and has few, if any, fitness costs in nature. To address these discrepant findings, we developed a platform that yields highly precise proteomic measurements across large numbers of genetically diverse samples and applied it to natural isolates collected as part of the 1011 genomes project (Peter, J. et al, 2018). For 613 of the isolates, we were able to match the proteomes to their corresponding transcriptomes and genomes, subsequently quantifying the effect of aneuploidy on gene expression by comparing 95 aneuploid with 518 euploid strains. We find, as in previous studies, that aneuploid gene dosage is not buffered chromosome-wide at the transcriptome level. Importantly, in the proteome, we detect an attenuation of aneuploidy by about 25% below the aneuploid gene dosage in natural yeast isolates. Furthermore, this chromosome-wide dosage compensation is associated with the ubiquitin-proteasome system (UPS), which is expressed at higher levels and has increased activity across natural aneuploid strains. Thus, through systematic exploration of the species-wide diversity of the yeast proteome, we shed light on a long-standing debate about the biology of aneuploids, revealing that aneuploidy tolerance is mediated through chromosome-wide dosage compensation at the proteome level.
HostingRepositoryMassIVE
AnnounceDate2024-03-11
AnnouncementXMLSubmission_2024-03-11_22:08:28.993.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChristoph Messner
SpeciesList scientific name: Yeast;
ModificationListNo PTMs are included in the dataset
InstrumentTripleTOF 6600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-09-30 01:44:43ID requested
12024-03-11 22:08:29announced
Publication List
no publication
Keyword List
submitter keyword: Yeast, large-scale, high-throughput, diversity, aneuploidy, proteomics, wild isolates
Contact List
Prof. Dr. Markus Ralser
contact affiliationCharite Universitatsmedizin Berlin
contact emailmarkus.ralser@charite.de
lab head
Christoph Messner
contact affiliationUniversity of Z�rich
contact emailmessner.ch@gmail.com
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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