Functional characterization of plant small RNAs based on next-generation sequencing data
Functional characterization of plant small RNAs based on next-generation sequencing data
复制标题
基于下一代测序数据的植物小RNA功能表征
DOI：
10.1016/j.compbiolchem.2010.10.001
复制
发表时间：
2010-12-01
影响因子：
3.1
通讯作者：
Chen, Dijun
中科院分区：
文献类型：
--
作者：
Chen, Ming;Meng, Yijun;Chen, Dijun
The currently developed next-generation sequencing (NGS) technology has significantly enhanced our capacity of small RNA (sRNA) exploration. Several ambitious sRNA projects have been established based on the technical support of NGS. Thanks to the high-throughput feature of NGS, huge amounts of sRNA sequencing data have been generated. However, much more research efforts are needed to further exploit these valuable data. In this study, we carried out functional analyses of sRNAs from 26 angiosperms by utilizing public sRNA NGS data. We proposed that the endogenous sRNAs largely represented by the 24-nt ones had a potential role in transposable element (TE) control in both Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), based on the comparison of sRNA locus densities within the TEs to the non-TE genes. Functional analysis was performed for the predicted targets of the conserved sRNAs that were classified into eudicot-specific, monocot-specific, and angiosperm-conserved ones. Moreover, several miRNA families were found to be highly conserved, and miR396 was suggested to be the most conserved miRNA family between the eudicots and the monocots, indicating its essential role in angiosperm development. At last, we demonstrated that it was a great challenge for researchers to fully exploit these huge sRNA NGS datasets and numerous sRNA species remained to be uncovered and functionally characterized. (C) 2010 Elsevier Ltd. All rights reserved.
