PXD000872

PXD000872 is an original dataset announced via ProteomeXchange.

Title	Forty-four novel protein-coding loci discovered using a PIT approach in rat male germ cells
Description	Spermatogenesis is a complex process, dependent upon the successive activation and/or repression of thousands of gene products, and ends with the production of haploid male gametes. RNA sequencing of male germ cells in the rat identified thousands of novel testicular unannotated transcripts, named TUTs. Although such RNAs are usually annotated as long non-coding RNAs, it is possible that some of these TUTs code for protein. To test this possibility, we used a “Proteomics Informed by Transcriptomics” strategy, combining shotgun proteomics analyses and RNA sequencing data for enriched populations of rat testicular cells. Among 3559 TUTs and 506 lncRNAs found in meiotic and post-meiotic germ cells, 44 encoded at least one peptide. We show that these novel high-confidence protein-coding loci exhibit several genomic features intermediate between those of lncRNAs and mRNAs. We experimentally validated the testicular expression pattern of two of these novel protein-coding gene candidates, both highly conserved in mammals: one for a vesicle-associated membrane protein, we named VAMP-9, and the other for an enolase domain-containing protein. This study confirms the potential of PIT approaches for the discovery of protein coding transcripts initially thought to be untranslated, or unknown transcripts. Our results contribute to the understanding of spermatogenesis by characterizing two novel proteins, implicated by their strong expression in germ cells.
HostingRepository	PRIDE
AnnounceDate	2014-09-12
AnnouncementXML	Submission_2014-09-12_07:28:01.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sophie Chocu
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; phosphorylated residue
Instrument	LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2014-04-02 06:37:52	ID requested
⏵ 1	2014-09-12 07:28:02	announced

Chocu S, Evrard B, Lavigne R, Rolland AD, Aubry F, J, é, gou B, Chalmel F, Pineau C, Forty-four novel protein-coding loci discovered using a proteomics informed by transcriptomics (PIT) approach in rat male germ cells. Biol Reprod, 91(5):123(2014) [pubmed]

curator keyword: Biological

submitter keyword: Rat, testis, Spermatocytes, spermatids, LC-MS/MS.

Sophie Chocu
contact affiliation	Biogenouest Proteomics Core Facility IRSET – INSERM U1085 Rennes, France
contact email	sophie.chocu@univ-rennes1.fr
lab head
Sophie Chocu
contact affiliation	Plate-forme Protéomique Biogenouest IRSET – INSERM U1085
contact email	sophie.chocu@univ-rennes1.fr
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/2014/09/PXD000872

PRIDE project URI

• PRIDE
  1. PXD000872
     1. Label: PRIDE project
     2. Name: Forty-four novel protein-coding loci discovered using a PIT approach in rat male germ cells