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PXD040766-1

PXD040766 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDiversity in pervasive translation. A new translational landscape of yeast.
DescriptionPervasive translation is a widespread phenomenon that plays an important role in de novo gene birth; however, its underlying mechanisms remain unclear. Based on multiple Ribosome Profiling datasets, we investigated the translational landscape of coding and noncoding regions of yeast. Therefore, we developed a new representation framework which allows the visual and comprehensive representation of the diversity of translation behaviors in yeast coding and noncoding regions. We show that if coding regions are restricted to specific regions of the translation landscape, noncoding regions are associated with a wide diversity of translation behaviors and, in contrast, populate the entire yeast translational landscape. In particular, we reveal that noncoding regions are associated with canonical translation signals but also with novel categories of translation events absent from coding regions, and which seem to be a hallmark of pervasive translation. Notably, we report thousands of translated noncoding ORFs among which, 256 led to detectable products with Mass Spectrometry while being characterized by canonical but also non-canonical translation signals. Finally, we show that the translation behavior of noncoding ORFs is not explained by features related to the emergence of function, but is rather determined by the translation start codon and the codon distribution in the three competing RNA frames. Overall, our results enable us to propose a topology of the pervasive translation landscape of a species, and open the way to future comparative analyses of this translation landscape under different conditions.
HostingRepositoryPRIDE
AnnounceDate2024-09-04
AnnouncementXMLSubmission_2024-09-04_02:43:20.689.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD040766
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterDavid Cornu
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumenttimsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-03-10 04:53:29ID requested
12024-09-04 02:43:21announced
Publication List
10.6019/PXD040766;
Keyword List
submitter keyword: genome evolution, mass spectrometry, non-canonical translation signals, de novo coding products, noncoding genome,Pervasive translation
Contact List
David Cornu
contact affiliationUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
contact emaildavid.cornu@i2bc.paris-saclay.fr
lab head
David Cornu
contact affiliationSICaPS, Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette Cedex, France
contact emaildavid.cornu@i2bc.paris-saclay.fr
dataset submitter
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Dataset FTP location
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