One-shot analysis of translated mammalian lncRNAs with AHARIBO.
LncRNA
RIBO-seq
cell biology
human
mouse
proteogenomics
proteomics
ribosome
translation
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
17 02 2021
17 02 2021
Historique:
received:
25
05
2020
accepted:
16
02
2021
pubmed:
18
2
2021
medline:
29
1
2022
entrez:
17
2
2021
Statut:
epublish
Résumé
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 peptides, 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 and peptide-producing lncRNAs. Here, we present AHA-mediated RIBOsome isolation (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 peptides. 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 of lncRNAs.
Identifiants
pubmed: 33594971
doi: 10.7554/eLife.59303
pii: 59303
pmc: PMC7932693
doi:
pii:
Substances chimiques
Peptides
0
RNA, Long Noncoding
0
Banques de données
GEO
['GSE167865']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2021, Minati et al.
Déclaration de conflit d'intérêts
LM L.M. is an employee of IMMAGINA BioTechnology S.r.l. CF C.F. is an employee of IMMAGINA BioTechnology S.r.l. AD A.D.P. is an employee of IMMAGINA BioTechnology S.r.l. AP A.P. is an employee of IMMAGINA BioTechnology S.r.l. SS, DP, RB, FG, AR, JZ, FL No competing interests declared, PB P.B. is an employee of IMMAGINA BioTechnology S.r.l. AQ A.Q. is a shareholder of IMMAGINA BioTechnology S.r.l, GG G.G. is shareholders of IMMAGINA BioTechnology S.r.l, GV G.V. is a scientific advisor of IMMAGINA BioTechnology S.r.l. MC M.C. is the founder of, director of, and a shareholder in IMMAGINA BioTechnology S.r.l., a company engaged in the development of new technologies for gene expression analysis at the ribosomal level.
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