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 bifuncti...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.展开更多
DREAM/calsenilin/KChIP3 is a calcium binding protein of the neuronal calcium sensor superfamily.DREAM interacts with DRE(downstream regulatory element) sites in the DNA to regulate transcription and with many proteins...DREAM/calsenilin/KChIP3 is a calcium binding protein of the neuronal calcium sensor superfamily.DREAM interacts with DRE(downstream regulatory element) sites in the DNA to regulate transcription and with many proteins to exert specialized functions in different subcellular compartments.Work from different laboratories has identified a growing list of interacting proteins that constitutes the DREAM interactome.The knowledge of these interactions has greatly contributed to the understanding of the various physiological functions of DREAM.展开更多
文摘由柑橘黄单胞柑橘亚种(Xanthomonas citri subsp.citri,Xcci)引起的柑橘溃疡病是我国柑橘生产上的一种重要病害。我们在前期研究中发现,Xcci广西菌株N8中有一个与306菌株的XAC3126同源的基因,可能参与调控病原菌的致病性。预测该基因编码一个单功能反应调控蛋白。为明确该基因的生物学功能,本研究对该基因进行缺失突变和功能互补,获得了相应的缺失突变体和互补菌株。致病性测定发现,该基因缺失导致Xcci在柑橘上的致病性显著下降,并且其胞外多糖产量、运动性,以及生物膜形成能力均显著降低,而互补菌株的这些表型恢复至野生型水平。进一步通过RT-qPCR分析该基因缺失对Xcci运动性相关基因及胞外多糖相关基因转录的影响,发现相比野生型菌株,缺失突变体在丰富培养基NB中培养时,这些基因的表达均下降,表明该基因的产物是通过调控多种致病因子的表达来影响病原菌在柑橘上的致病性。据此,我们将该基因命名为embR(Extracellular polysaccharide,motility and biofilm formation related regulator)。
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)
文摘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.
基金supported by grants from Ministerio Ciencia e Innovacion (Grant Nos.SAF2007-62449 to José R.Naranjo,SAF2005-04682 and SAF2008-03469 to Britt Mellstrom)CIBERNED to Britt Mellstrom and José R.Naranjo and from Comunidad Autonoma de Madrid,Fundación La Caixa(Grant No.BM04-167-0)the EU 6th Framework Program (NeuroNE)to José R.Naranjo
文摘DREAM/calsenilin/KChIP3 is a calcium binding protein of the neuronal calcium sensor superfamily.DREAM interacts with DRE(downstream regulatory element) sites in the DNA to regulate transcription and with many proteins to exert specialized functions in different subcellular compartments.Work from different laboratories has identified a growing list of interacting proteins that constitutes the DREAM interactome.The knowledge of these interactions has greatly contributed to the understanding of the various physiological functions of DREAM.
