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 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 lncRNAs.
- Luca Minati
- Claudia Firrito
- Alessia Del Piano
- Alberto Peretti
- Paola Bernabo
- Massimiliano Clamer
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Howard Y Chang, Stanford University, United States
- Received: May 25, 2020
- Accepted: February 16, 2021
- Accepted Manuscript published: February 17, 2021 (version 1)
© 2021, Minati et al.
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