Structural characterization and modeling of ncRNA-protein interactions
Structural characterization and modeling of ncRNA-protein interactions
复制标题
DOI：
10.1016/j.biosystems.2010.02.005
复制
发表时间：
2010-07-01
期刊：
影响因子：
1.6
通讯作者：
Araki, N.
中科院分区：
文献类型：
--
作者：
Nacher, J. C.;Araki, N.
最近的研究表明，非编码RNA（ncRNA）分子可能在真核细胞的调控结构中发挥重要作用。这种新的基于RNA的调节可能表明中心法则中存在隐藏层。尽管它的重要性，大规模的结构以及局部相互作用模式的ncRNA调控网络尚未调查。在这项工作中，我们收集了ncRNA分子与其调控蛋白靶点之间的调控相互作用。然后，我们构建了对应于包括智人在内的六种模式生物的ncRNA-蛋白质相互作用网络。大规模网络分析的ncRNA-蛋白质相互作用揭示了高度的相似性的程度分布的转录调控网络。此外，这些网络的局部相互作用结构的基序丰度的基础上的表征也揭示了显着的相似性ncRNA-蛋白质和TF-基因调控网络。基于所确定的基序丰度，我们提出了一个进化模型，重建度分布和预测所观察到的度指数。总之，我们的研究结果提供了对非编码RNA介导的调控的见解，并提供了有关其结构和进化机制的知识。(C)2010爱思唯尔爱尔兰有限公司版权所有。
Recent studies have suggested that noncoding RNA (ncRNA) molecules could play an important role in the regulatory architecture of eukaryotic cells. This new RNA-based regulation might indicate the existence of a hidden layer in the central dogma. In spite of its importance, the large-scale structure as well as the local interaction pattern of the ncRNA regulatory network has not been investigated. In this work, we collected regulatory interactions between ncRNA molecules and their regulated protein targets. We then constructed the ncRNA-protein interaction network corresponding to six model organisms, including Homo sapiens. The large-scale network analysis of ncRNA-protein interactions revealed a high degree of similarity for the degree distribution to that of the transcription regulatory network. Moreover, characterization of the local interaction structure of these networks based on motifs abundance also reveals significant similarities between ncRNA-protein and TFs-gene regulatory networks. Based on the identified motif abundance, we propose an evolutionary model that rebuilds the degree distribution and predicts the observed degree exponent. Taken together, our findings offer insights into the noncoding RNA-mediated regulation and provide knowledge about its structure and evolutionary mechanisms. (C) 2010 Elsevier Ireland Ltd. All rights reserved.