Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
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DOI：
10.1093/nar/gkg365
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发表时间：
2003-06-01
影响因子：
14.9
通讯作者：
Schlick, T
中科院分区：
文献类型：
--
作者：
Gan, HH;Pasquali, S;Schlick, T
了解RNA的结构库对于RNA基因组学研究至关重要。然而，目前发现新RNA的方法仅限于小的或已知的RNA家族。为了扩展已知的RNA结构基序，我们开发了一种二维图形表示方法，用于描述和估计RNA二级结构库的大小，包括天然存在的和其他可能的RNA基序。我们采用树图来描述RNA树图案和更一般的（双）图来描述RNA树和伪结图案。我们对RNA结构空间的估计远远小于核苷酸序列空间，这表明了寻找新RNA的新途径。具体来说，我们的调查表明，已知的RNA树和伪结只代表一个小的子集的所有可能的图案，这意味着一些'失踪'的图案可能代表新的RNA。为了帮助确定RNA样基序，我们表明，现有的功能RNA的基序聚集在一个狭窄的范围内的拓扑特征。我们还说明了我们的方法的应用程序的设计新的RNA和RNA结构的自动化比较，我们报告了几个发生在较大的RNA的RNA基序。因此，我们的图论方法的RNA结构的影响，RNA基因组学，结构分析和设计。
Understanding the structural repertoire of RNA is crucial for RNA genomics research. Yet current methods for finding novel RNAs are limited to small or known RNA families. To expand known RNA structural motifs, we develop a two-dimensional graphical representation approach for describing and estimating the size of RNA's secondary structural repertoire, including naturally occurring and other possible RNA motifs. We employ tree graphs to describe RNA tree motifs and more general (dual) graphs to describe both RNA tree and pseudoknot motifs. Our estimates of RNA's structural space are vastly smaller than the nucleotide sequence space, suggesting a new avenue for finding novel RNAs. Specifically our survey shows that known RNA trees and pseudoknots represent only a small subset of all possible motifs, implying that some of the 'missing' motifs may represent novel RNAs. To help pinpoint RNA-like motifs, we show that the motifs of existing functional RNAs are clustered in a narrow range of topological characteristics. We also illustrate the applications of our approach to the design of novel RNAs and automated comparison of RNA structures; we report several occurrences of RNA motifs within larger RNAs. Thus, our graph theory approach to RNA structures has implications for RNA genomics, structure analysis and design.