PT  - JOURNAL ARTICLE
AU  - Luca Minati
AU  - Claudia Firrito
AU  - Alessia Del Piano
AU  - Alberto Peretti
AU  - Simone Sidoli
AU  - Daniele Peroni
AU  - Romina Belli
AU  - Francesco Gandolfi
AU  - Alessandro Romanel
AU  - Paola Bernabò
AU  - Jacopo Zasso
AU  - Alessandro Quattrone
AU  - Graziano Guella
AU  - Fabio Lauria
AU  - Gabriella Viero
AU  - Massimiliano Clamer
TI  - One-shot analysis of translated mammalian lncRNAs with AHARIBO
AID  - 10.1101/2020.04.20.050062
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.04.20.050062
4099  - http://biorxiv.org/content/early/2020/04/20/2020.04.20.050062.short
4100  - http://biorxiv.org/content/early/2020/04/20/2020.04.20.050062.full
AB  - 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.Competing Interest StatementM.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. L.M, A.P, C.F., A.D.P., P.B are employees of IMMAGINA BioTechnology S.r.l. A.Q and G.G. are shareholders of IMMAGINA BioTechnology S.r.l. G.V is a scientific advisor of IMMAGINA BioTechnology S.r.l. All of the other authors declare no competing interests.