RT Journal Article
SR Electronic
T1 One-shot analysis of translated mammalian lncRNAs with AHARIBO
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.04.20.050062
DO 10.1101/2020.04.20.050062
A1 Luca Minati
A1 Claudia Firrito
A1 Alessia Del Piano
A1 Alberto Peretti
A1 Simone Sidoli
A1 Daniele Peroni
A1 Romina Belli
A1 Francesco Gandolfi
A1 Alessandro Romanel
A1 Paola Bernabò
A1 Jacopo Zasso
A1 Alessandro Quattrone
A1 Graziano Guella
A1 Fabio Lauria
A1 Gabriella Viero
A1 Massimiliano Clamer
YR 2020
UL http://biorxiv.org/content/early/2020/04/20/2020.04.20.050062.abstract
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.