One-shot analysis of translated mammalian lncRNAs with AHARIBO

Abstract

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 between lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.

Competing Interest Statement

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. 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.