PXD022679

PXD022679 is an original dataset announced via ProteomeXchange.

Title	One-shot analysis of translated mammalian lncRNAs with AHARIBO
Description	A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_13:37:02.085.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD022679
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Romina Belli
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	6x(13)C; 6x(13)C; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-23 09:36:12	ID requested
⏵ 1	2024-10-07 13:37:02	announced

10.7554/elife.59303;

10.6019/PXD022679;

Minati L, Firrito C, Del Piano A, Peretti A, Sidoli S, Peroni D, Belli R, Gandolfi F, Romanel A, Bernabo P, Zasso J, Quattrone A, Guella G, Lauria F, Viero G, Clamer M, One-shot analysis of translated mammalian lncRNAs with AHARIBO. Elife, 10():(2021) [pubmed]

submitter keyword: Ribosome, proteogenomics, proteomics, RIBO-seq,LncRNA, RNA, translatome, translation

Massimiliano Clamer
contact affiliation	IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo (Italy)
contact email	mclamer@immaginabiotech.com
lab head
Romina Belli
contact affiliation	University of Trento
contact email	romina.belli@unitn.it
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/2021/09/PXD022679

PRIDE project URI

• PRIDE
  1. PXD022679
     1. Label: PRIDE project
     2. Name: One-shot analysis of translated mammalian lncRNAs with AHARIBO