One-shot analysis of translated mammalian lncRNAs with AHARIBO
- IMMAGINA biotechnology, Italy
- Albert Einstein College of Medicine, United States
- University of Trento, Italy
- CNR Unit at Trento, Italy
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 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.
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided. All sequencing data are deposited in public archives and made available upon publication.
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The Translational Landscape of the Human HeartPublicly available and interactive web application for exploring the results of this paper, http://shiny.mdc-berlin.de/cardiac-translatome/.
Article and author information
Author details
Massimiliano Clamer
Funding
Autonumus Province of Trento adn Banca Intesa (LP6/99)
- 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.
Reviewing Editor
- Howard Y Chang, Stanford University, United States
Publication history
- Received: May 25, 2020
- Accepted: February 16, 2021
- Accepted Manuscript published: February 17, 2021 (version 1)
- Version of Record published: March 4, 2021 (version 2)
Copyright
© 2021, Minati et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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One-shot analysis of translated mammalian lncRNAs with AHARIBO
eLife 10:e59303.
https://doi.org/10.7554/eLife.59303
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