Li Qilin, Ahsan Md Asif, Chen Hongjun, Xue Jitong, Chen Ming
Department of Bioinformatics, College of Life Sciences, Zhejiang University , Hangzhou 310058, China.
James D. Watson Institute of Genome Sciences, Zhejiang University , Hangzhou 310058, China.
ACS Synth Biol. 2018 Feb 16;7(2):655-663. doi: 10.1021/acssynbio.7b00386. Epub 2018 Feb 5.
Most noncoding RNAs are considered by their expression at low levels and as having a limited phylogenetic distribution in the cytoplasm, indicating that they may be only involved in specific biological processes. However, recent studies showed the protein-coding potential of ncRNAs, indicating that they might be a source of some special proteins. Although there are increasing noncoding RNAs identified to be able to code proteins, it is challenging to distinguish coding RNAs from previously annotated ncRNAs, and to detect the proteins from their translation. In this article, we designed a pipeline to identify these noncoding RNAs in Arabidopsis thaliana from three NCBI GEO data sets with coding potential and predict their translation products. 31 311 noncoding RNAs were predicted to be translated into peptides, and they showed lower conservation rate than common proteins. In addition, we built an interaction network between these peptides and annotated Arabidopsis proteins using BIPS, which included 69 peptides from noncoding RNAs. Peptides in the interaction network showed different characteristics from other noncoding RNA-derived peptides, and they participated in several crucial biological processes, such as photorespiration and stress-responses. All the information of putative ncPEPs and their interaction with proteins predicted above are finally integrated in a database, PncPEPDB ( http://bis.zju.edu.cn/PncPEPDB ). These results showed that peptides derived from noncoding RNAs may play important roles in noncoding RNA regulation, which provided another hypothesis that noncoding RNA may regulate the metabolism via their translation products.
大多数非编码RNA被认为表达水平较低，且在细胞质中的系统发育分布有限，这表明它们可能仅参与特定的生物学过程。然而，最近的研究表明非编码RNA具有蛋白质编码潜力，这表明它们可能是某些特殊蛋白质的来源。尽管越来越多的非编码RNA被鉴定出能够编码蛋白质，但区分编码RNA和先前注释的非编码RNA，以及检测它们翻译产生的蛋白质仍然具有挑战性。在本文中，我们设计了一个流程，从三个具有编码潜力的NCBI GEO数据集中鉴定拟南芥中的这些非编码RNA，并预测它们的翻译产物。预计有31311个非编码RNA会被翻译成肽段，并且它们的保守率低于普通蛋白质。此外，我们使用BIPS构建了这些肽段与注释的拟南芥蛋白质之间的相互作用网络，其中包括来自非编码RNA的69个肽段。相互作用网络中的肽段表现出与其他非编码RNA衍生肽段不同的特征，并且它们参与了几个关键的生物学过程，如光呼吸和应激反应。上述预测的假定非编码RNA衍生肽段及其与蛋白质相互作用的所有信息最终整合到一个数据库PncPEPDB（http://bis.zju.edu.cn/PncPEPDB）中。这些结果表明，非编码RNA衍生的肽段可能在非编码RNA调控中发挥重要作用，这提供了另一种假说，即非编码RNA可能通过其翻译产物调节代谢。
