Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome
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AbstractMotivation:
Moonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding RNAs (lncRNAs) has never been undertaken. Here, we introduce a novel methodology, MoonFinder, for the identification of moonlighting lncRNAs. MoonFinder is a statistical algorithm identifying moonlighting lncRNAs without a priori knowledge through the integration of protein interactome, RNA–protein interactions and functional annotation of proteins.

Results:
We identify 155 moonlighting lncRNA candidates and uncover that they are a distinct class of lncRNAs characterized by specific sequence and cellular localization features. The non-coding genes that transcript moonlighting lncRNAs tend to have shorter but more exons and the moonlighting lncRNAs have a variable localization pattern with a high chance of residing in the cytoplasmic compartment in comparison to the other lncRNAs. Moreover, moonlighting lncRNAs and moonlighting proteins are rather mutually exclusive in terms of both their direct interactions and interacting partners. Our results also shed light on how the moonlighting candidates and their interacting proteins implicated in the formation and development of cancers and other diseases.

Availability and implementation:
The code implementing MoonFinder is supplied as an R package in the supplementary material.

Supplementary information:
Supplementary data are available at Bioinformatics online.
All Author(s) ListLixin Cheng, Kwong Sak Leung
Journal nameBioinformatics
Year2018
Month10
Day15
Volume Number34
Issue Number20
Pages3519 - 3528
ISSN1367-4803
eISSN1460-2059
LanguagesEnglish-United Kingdom

Last updated on 2020-31-05 at 02:06