Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome

Bioinformatics
Lixin Cheng, Kwong-Sak Leung

Abstract

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. 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 i...Continue Reading

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Citations

Jul 3, 2020·Clinical and Translational Medicine·Xueyan LiuLixin Cheng
May 30, 2020·Bioinformatics·Tianyi ZhaoLiang Cheng
Oct 30, 2020·Frontiers in Cell and Developmental Biology·Chuan-Chuan NanLixin Cheng
Apr 18, 2021·BMC Genomics·Xubin ZhengLixin Cheng
May 18, 2021·Frontiers in Cell and Developmental Biology·Xubin ZhengLixin Cheng
Apr 29, 2020·Biomacromolecules·Miao LiuJiang Xia
Jun 9, 2020·Analytical Chemistry·Linting LiRuibing Wang

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