One-shot analysis of translated mammalian lncRNAs with AHARIBO

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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.

The following previously published data sets were used

(2011) Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
GEO, GSE30839.

https://www.cell.com/fulltext/S0092-8674%2811%2901192-5#secd1715918e1381
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https://www.cell.com/cell/fulltext/S0092-8674(19)30508-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867419305082%3Fshowall%3Dtrue

Article and author information

Author details

Luca Minati

Ribosome engineering, IMMAGINA biotechnology, Trento, Italy

Competing interests
Luca Minati, L.M is an employee of IMMAGINA BioTechnology S.r.l..
Claudia Firrito

Ribosome engineering, IMMAGINA biotechnology, Trento, Italy

Competing interests
Claudia Firrito, C.F. is an employee of IMMAGINA BioTechnology S.r.l..
Alessia Del Piano

Ribosome engeneering, IMMAGINA biotechnology, Trento, Italy

Competing interests
Alessia Del Piano, A.D.P is an employee of IMMAGINA BioTechnology S.r.l..
Alberto Peretti

Ribosome engineering, IMMAGINA biotechnology, Trento, Italy

Competing interests
Alberto Peretti, A.P. is an employee of IMMAGINA BioTechnology S.r.l..
Simone Sidoli

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States

Competing interests
No competing interests declared.
Daniele Peroni

Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-0862-266X
Romina Belli

Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-5690-2797
Francesco Gandolfi

Laboratory of Bioinformatics and Computational Genomics, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

Competing interests
No competing interests declared.
Alessandro Romanel

Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

Competing interests
No competing interests declared.
Paola Bernabo

Ribosome engineering, IMMAGINA biotechnology, Trento, Italy

Competing interests
Paola Bernabo, P.B is an employee of IMMAGINA BioTechnology S.r.l..
Jacopo Zasso

Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-3151-6443
Alessandro Quattrone

Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

Competing interests
Alessandro Quattrone, A.Q is a shareholder of IMMAGINA BioTechnology S.r.l.
Graziano Guella

Department of Physics, University of Trento, Trento, Italy

Competing interests
Graziano Guella, G.G. is shareholders of IMMAGINA BioTechnology S.r.l.
Fabio Lauria

Institute of Biophysics, CNR Unit at Trento, Trento, Italy

Competing interests
No competing interests declared.
Gabriella Viero

Institute of Biophysics, CNR Unit at Trento, Trento, Italy

Competing interests
Gabriella Viero, G.V is a scientific advisor of IMMAGINA BioTechnology S.r.l..

"This ORCID iD identifies the author of this article:" 0000-0002-6755-285X
Massimiliano Clamer

Ribosome engineering, IMMAGINA biotechnology, Trento, Italy

For correspondence
mclamer@immaginabiotech.com

Competing interests
Massimiliano Clamer, 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..

"This ORCID iD identifies the author of this article:" 0000-0001-8185-059X

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.

Copyright

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.