biostudies-literatureMinati LAutonomous Province of Trentoe59303https://www.ebi.ac.uk/biostudies/studies/S-EPMC7932693biostudies-literatureUnknown10A 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 syeLifeOne-shot analysis of translated mammalian lncRNAs with AHARIBO.PMC7932693LP6/99Belli RBernabo PLauria FClamer MPeretti ADel Piano ASidoli SZasso JFirrito CPeroni DMinati LGuella GQuattrone ARomanel AGandolfi FViero GfalseOne-shot analysis of translated mammalian lncRNAs with AHARIBO.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 sy2021-01-01T00:00:00Z2021 Feb2026-05-08T14:14:48.656Z2021-03-12T08:16:49ZS-EPMC79326933359497110.7554/eLife.59303