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Sci China Life Sci. 2016 Oct;59(10):981-992. Epub 2016 Sep 20.

Identifying and annotating human bifunctional RNAs reveals their versatile functions.

Chen G1, Yang J2, Chen J2, Song Y1, Cao R2, Shi T3, Shi L4,5,6,7.

Author information

1
Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China.
2
The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
3
The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China. tieliushi01@gmail.com.
4
Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China. lemingshi@fudan.edu.cn.
5
State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 201203, China. lemingshi@fudan.edu.cn.
6
Fudan-Zhangjiang Center for Clinical Genomics, Shanghai, 201203, China. lemingshi@fudan.edu.cn.
7
Zhanjiang Center for Translational Medicine, Shanghai, 201203, China. lemingshi@fudan.edu.cn.

Abstract

Bifunctional RNAs that possess both protein-coding and noncoding functional properties were less explored and poorly understood. Here we systematically explored the characteristics and functions of such human bifunctional RNAs by integrating tandem mass spectrometry and RNA-seq data. We first constructed a pipeline to identify and annotate bifunctional RNAs, leading to the characterization of 132 high-confidence bifunctional RNAs. Our analyses indicate that bifunctional RNAs may be involved in human embryonic development and can be functional in diverse tissues. Moreover, bifunctional RNAs could interact with multiple miRNAs and RNA-binding proteins to exert their corresponding roles. Bifunctional RNAs may also function as competing endogenous RNAs to regulate the expression of many genes by competing for common targeting miRNAs. Finally, somatic mutations of diverse carcinomas may generate harmful effect on corresponding bifunctional RNAs. Collectively, our study not only provides the pipeline for identifying and annotating bifunctional RNAs but also reveals their important gene-regulatory functions.

KEYWORDS:

RNA-seq; bifunctional RNA; noncoding RNA; tandem mass spectrometry

PMID:
27650948
DOI:
10.1007/s11427-016-0054-1
[Indexed for MEDLINE]

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