PXD040766-1

PXD040766 is an original dataset announced via ProteomeXchange.

Title	Diversity in pervasive translation. A new translational landscape of yeast.
Description	Pervasive 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.
HostingRepository	PRIDE
AnnounceDate	2024-09-04
AnnouncementXML	Submission_2024-09-04_02:43:20.689.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD040766
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	David Cornu
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-10 04:53:29	ID requested
⏵ 1	2024-09-04 02:43:21	announced

10.6019/PXD040766;

submitter keyword: genome evolution, mass spectrometry, non-canonical translation signals, de novo coding products, noncoding genome,Pervasive translation

David Cornu
contact affiliation	Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
contact email	david.cornu@i2bc.paris-saclay.fr
lab head
David Cornu
contact affiliation	SICaPS, Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette Cedex, France
contact email	david.cornu@i2bc.paris-saclay.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040766
     1. Label: PRIDE project
     2. Name: Diversity in pervasive translation. A new translational landscape of yeast.