Chen Geng, Yang Juan, Chen Jiwei, Song Yunjie, Cao Ruifang, Shi Tieliu, Shi Leming
Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China.
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.
Sci China Life Sci. 2016 Oct;59(10):981-992. doi: 10.1007/s11427-016-0054-1. Epub 2016 Sep 20.
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.
具有蛋白质编码和非编码功能特性的双功能RNA较少被研究且了解不足。在此，我们通过整合串联质谱和RNA测序数据，系统地探索了此类人类双功能RNA的特征和功能。我们首先构建了一个用于识别和注释双功能RNA的流程，从而鉴定出132个高可信度的双功能RNA。我们的分析表明，双功能RNA可能参与人类胚胎发育，并且在多种组织中发挥作用。此外，双功能RNA可与多种微小RNA（miRNA）和RNA结合蛋白相互作用以发挥相应作用。双功能RNA还可能作为竞争性内源性RNA，通过竞争共同的靶向miRNA来调控许多基因的表达。最后，多种癌症的体细胞突变可能对相应的双功能RNA产生有害影响。总体而言，我们的研究不仅提供了识别和注释双功能RNA的流程，还揭示了它们重要的基因调控功能。
