PXD022679 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-11-23 09:36:12 | ID requested | |
⏵ 1 | 2024-10-07 13:37:02 | announced | |
Publication List
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] |
Keyword List
submitter keyword: Ribosome, proteogenomics, proteomics, RIBO-seq,LncRNA, RNA, translatome, translation |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD022679
- Label: PRIDE project
- Name: One-shot analysis of translated mammalian lncRNAs with AHARIBO