Gardner Paul P, Eldai Hisham
School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
Nucleic Acids Res. 2015 Jan;43(2):691-8. doi: 10.1093/nar/gku1327. Epub 2014 Dec 17.
RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam.
RNA在所有细胞生命中发挥着各种各样重要的功能。这些功能包括在翻译、构建翻译机制和信使RNA成熟过程中发挥重要作用。最近的发现包括调控基因表达的微小RNA（miRNA）和细菌小RNA（sRNA）、帮助原核生物感知环境的热传感器、核糖开关及其他顺式调控元件，以及抑制转座的真核生物piRNA。然而，从最初发现一种RNA到确定其功能之间可能会有很长一段时间。我们提出了一种生物信息学方法来表征RNA基序，这些基序是许多RNA结构-功能关系的关键组成部分。在某些情况下，这些基序可以为研究人员提供关于未表征RNA的功能假设。此外，我们引入了一个基于轮廓的新RNA基序数据库——RMfam，并举例说明了一些用于研究RNA进化和功能表征的应用。与这项工作相关的所有数据和脚本可从以下网址获取：https://github.com/ppgardne/RMfam 。
