Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa).
Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa).
复制标题
水稻根部小RNA介导的基因调控网络的构建（Oryza sativa）
DOI：
10.1186/1471-2164-14-510
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发表时间：
2013-07-27
期刊：
影响因子：
4.4
通讯作者：
Meng Y
中科院分区：
文献类型：
--
作者：
Ma X;Shao C;Wang H;Jin Y;Meng Y
研究背景根系在植物对土壤的固着、对矿产资源和水资源的开发利用等方面起着重要作用。根发育的分子机制已被广泛研究，以改善根系构型，特别是对作物。一些microRNA（miRNA）家族已被证明参与植物根的发育。然而，是否其他小RNA（sRNA）的物种，占据了植物内源sRNA人口的主要部分，具有潜在的作用，在根的发育仍不清楚。ResultsIn这项研究中，通过使用sRNA高通量测序数据，我们做了比较的sRNA积累水平之间的水稻根尖和整个根。分别提取了在根尖和全根中高度积累的sRNA。在Argonaute 1（AGO1）富集分析之后，包括具有执行靶切割的巨大潜力的sRNA用于靶预测和基于降解产物组测序数据的验证。结果，获得了根尖和整个根的由富含AGO1的sRNA调节的靶标的列表。从靶基因的微阵列数据中发现了进一步的证据，以支持一些sRNA-靶相互作用。具体而言，某些靶基因在根尖和整个根中的表达模式与调控sRNA的表达模式相反。此外，几个目标被认为在根发育中发挥重要作用的基础上，文献mining.ConclusionsTogether，调控网络的sRNAs高度积累在根尖或在整个根可以推进我们目前的理解的sRNAs参与的分子机制，水稻根发育。而且，sRNA靶点列表可以作为进一步功能研究的基础。
BackgroundThe root systems play essential roles for plants to anchorage to the soil, and to exploit the mineral and water resources. The molecular mechanisms underlying root development have been extensively studied to improve root system architecture, especially for the crops. Several microRNA (miRNA) families have been demonstrated to be involved in plant root development. However, whether the other small RNA (sRNA) species, which occupy a dominant portion of the plant endogenous sRNA population, possess potential roles in root development remains unclear.ResultsIn this study, by using sRNA high-throughput sequencing data, we made a comparison of the sRNA accumulation levels between the rice root tips and the whole roots. The sRNAs highly accumulated in the root tips and in the whole roots were extracted respectively. After Argonaute 1 (AGO1) enrichment analysis, the sRNAs with great potential of performing target cleavages were included for target prediction and degradome sequencing data-based validation. As a result, lists of the targets regulated by the AGO1-enriched sRNAs were obtained for both the root tips and the whole roots. Further evidences were identified from microarray data of the target genes to support some of the sRNA—target interactions. Specifically, the expression patterns of certain target genes in the root tips and the whole roots were contrary to those of the regulating sRNAs. Besides, several targets were indicated to play important roles in root development based on literature mining.ConclusionsTaken together, the regulatory networks mediated by the sRNAs highly accumulated in the root tips or in the whole roots could advance our current understanding of the sRNA-involved molecular mechanisms underlying rice root development. And, the sRNA—target lists could serve as the basis for further functional investigations.
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