title: Identifying and annotating human bifunctional RNAs reveals their versatile functions.
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.
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China.
authors.forename: Geng
authors.initials: G
authors.lastname: Chen
authors.affiliation: 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.
authors.forename: Juan
authors.initials: J
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Jiwei
authors.initials: J
authors.lastname: Chen
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China.
authors.forename: Yunjie
authors.initials: Y
authors.lastname: Song
authors.affiliation: 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.
authors.forename: Ruifang
authors.initials: R
authors.lastname: Cao
authors.affiliation: 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.
authors.forename: Tieliu
authors.initials: T
authors.lastname: Shi
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China. lemingshi@fudan.edu.cn.|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.|Fudan-Zhangjiang Center for Clinical Genomics, Shanghai, 201203, China. lemingshi@fudan.edu.cn.|Zhanjiang Center for Translational Medicine, Shanghai, 201203, China. lemingshi@fudan.edu.cn.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
mesh_terms: D000595:Amino Acid Sequence; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D047108:Embryonic Development / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation / Q000379:methods*; D009154:Mutation; D011485:Protein Binding; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D016601:RNA-Binding Proteins; D012313:RNA
keywords: RNA-seq; bifunctional RNA; noncoding RNA; tandem mass spectrometry