Identifying and annotating human bifunctional RNAs reveals their versatile functions

作     者：Geng Chen Juan Yang Jiwei Chen Yunjie Song Ruifang Cao Tieliu Shi Leming Shi 

作者机构：Center for PharmacogenomicsSchool of Pharmacy and School of Life SciencesFudan UniversityShanghai 201203China The Center for Bioinformatics and Computational BiologyShanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary AnthropologySchool of Life SciencesFudan UniversityShanghai 201203China Fudan-Zhangjiang Center for Clinical GenomicsShanghai 201203China Zhanjiang Center for Translational MedicineShanghai 201203China 

出 版 物：《Science China(Life Sciences)》 (中国科学（生命科学英文版）)

年 卷 期：2016年第59卷第10期

页      面：981-992页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 071007[理学-遗传学] 

基　　金：supported in part by the National High Technology Research and Development Program of China(2015AA020104,2015AA020108) the China Human Proteomics Project(2014DF30030) the National Science Foundation of China(31471239) 

主　　题：bifunctional RNA noncoding RNA RNA-seq tandem mass spectrometry 

摘      要：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.