PXD044523

PXD044523 is an original dataset announced via ProteomeXchange.

Title	Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
Description	Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. Regulation of transcript and protein abundances can affect the final phenotypes and has been related to many human diseases. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level (r = 0.165). While the protein co-expression network recapitulates the major biological functions, differential expression patterns reveal proteomic signatures related to specific populations, mainly domesticated. Most importantly, comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3.6%), with mostly common local QTL. Our results demonstrate that transcriptome and proteome are clearly two distinct layers of regulation, governed by distinct genetic bases in natural populations, and therefore highlight the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship. This submission contains the raw files for the wild isolates collection, the library used for the analysis and the corresponding DIA-NN report and associated files.
HostingRepository	PRIDE
AnnounceDate	2024-04-30
AnnouncementXML	Submission_2024-04-30_14:56:51.891.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anja Freiwald
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-12 03:45:51	ID requested
⏵ 1	2024-04-30 14:56:52	announced

Dataset with its publication pending

submitter keyword: gene regulation, protein and RNA correlation, yeast, quantitative proteomics, genetic control, pQTL

Markus Ralser
contact affiliation	Charité Universitätsmedizin, Department of Biochemistry, 10117 Berlin, Germany The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK Max Planck Institute for Molecular Genetics, Berlin, Germany
contact email	Markus.ralser@charite.de
lab head
Anja Freiwald
contact affiliation	Charité
contact email	anja.freiwald@charite.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/04/PXD044523

PRIDE project URI

• PRIDE
  1. PXD044523
     1. Label: PRIDE project
     2. Name: Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast