The human transcriptome contains thousands of long non-coding RNAs (lncRNAs). Characterizing their function is a current challenge. An emerging concept is that lncRNAs serve as protein scaffolds, forming ribonucleoproteins and bringing proteins in proximity. However, only few scaffolding lncRNAs have been characterized and the prevalence of this function is unknown. Here, we propose the first computational approach aimed at predicting scaffolding lncRNAs at large scale. We predicted the largest human lncRNA-protein interaction network to date using the catRAPID omics algorithm. In combination with tissue expression and statistical approaches, we identified 847 lncRNAs (∼5% of the long non-coding transcriptome) predicted to scaffold half of the known protein complexes and network modules. Lastly, we show that the association of certain lncRNAs to disease may involve their scaffolding ability. Overall, our results suggest for the first time that RNA-mediated scaffolding of protein complexes and modules may be a common mechanism in human cells.

Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs / Ribeiro, Diogo M; Zanzoni, Andreas; Cipriano, Andrea; Delli Ponti, Riccardo; Spinelli, Lionel; Ballarino, Monica; Bozzoni, Irene; Tartaglia, GIAN GAETANO; Brun, Christine. - In: NUCLEIC ACIDS RESEARCH. - ISSN 0305-1048. - STAMPA. - 46:2(2018), pp. 917-928. [10.1093/nar/gkx1169]

Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs

Cipriano, Andrea;Ballarino, Monica;Bozzoni, Irene;TARTAGLIA, GIAN GAETANO;
2018

Abstract

The human transcriptome contains thousands of long non-coding RNAs (lncRNAs). Characterizing their function is a current challenge. An emerging concept is that lncRNAs serve as protein scaffolds, forming ribonucleoproteins and bringing proteins in proximity. However, only few scaffolding lncRNAs have been characterized and the prevalence of this function is unknown. Here, we propose the first computational approach aimed at predicting scaffolding lncRNAs at large scale. We predicted the largest human lncRNA-protein interaction network to date using the catRAPID omics algorithm. In combination with tissue expression and statistical approaches, we identified 847 lncRNAs (∼5% of the long non-coding transcriptome) predicted to scaffold half of the known protein complexes and network modules. Lastly, we show that the association of certain lncRNAs to disease may involve their scaffolding ability. Overall, our results suggest for the first time that RNA-mediated scaffolding of protein complexes and modules may be a common mechanism in human cells.
2018
lncRNA; protein scaffolding; cancer tissues
01 Pubblicazione su rivista::01a Articolo in rivista
Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs / Ribeiro, Diogo M; Zanzoni, Andreas; Cipriano, Andrea; Delli Ponti, Riccardo; Spinelli, Lionel; Ballarino, Monica; Bozzoni, Irene; Tartaglia, GIAN GAETANO; Brun, Christine. - In: NUCLEIC ACIDS RESEARCH. - ISSN 0305-1048. - STAMPA. - 46:2(2018), pp. 917-928. [10.1093/nar/gkx1169]
File allegati a questo prodotto
File Dimensione Formato  
Ribeiro_Protein_2018.pdf

accesso aperto

Tipologia: Versione editoriale (versione pubblicata con il layout dell'editore)
Licenza: Creative commons
Dimensione 2.19 MB
Formato Adobe PDF
2.19 MB Adobe PDF Visualizza/Apri PDF

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1042134
Citazioni
  • ???jsp.display-item.citation.pmc??? 39
  • Scopus 55
  • ???jsp.display-item.citation.isi??? 55
social impact