Computational identification of novel microRNAs and targets in Brassica napus
Computational identification of novel microRNAs and targets in Brassica napus
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DOI：
10.1016/j.febslet.2007.02.074
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发表时间：
2007-04-03
期刊：
影响因子：
3.5
通讯作者：
Yang, Zhi Min
中科院分区：
文献类型：
--
作者：
Xie, Fu Liang;Huang, Si Qi;Yang, Zhi Min
微小RNA（miRNAs）是一类新发现的非蛋白质编码小RNA，长度约为22个核苷酸。越来越多的证据表明，miRNAs在生物过程中发挥多种作用，包括发育、细胞增殖和凋亡以及应激反应。在这项研究中，我们综合了几种方法对甘蓝型油菜中潜在的miRNAs及其靶标进行计算预测。我们利用来自拟南芥、水稻和其他植物物种的已知miRNAs，针对表达序列标签（EST）和基因组勘测序列（GSS）数据库，在甘蓝型油菜中搜索潜在的miRNAs。经过一系列严格的筛选标准，共检测到21种潜在的miRNAs。利用这些潜在的miRNA序列，我们进一步对mRNA数据库进行比对，在该物种中发现了67个潜在靶标。根据美国国立医学图书馆（NCBI）提供的mRNA靶标信息（http://www.ncbi.nlm.nih.gov/），大多数靶标mRNA似乎参与植物生长、发育和应激反应。为了验证甘蓝型油菜中miRNAs的预测结果，我们进行了基于逆转录聚合酶链反应（RT - PCR）的成熟miRNA表达检测。我们鉴定出了5种对生长素、镉胁迫和磷饥饿有响应的miRNAs。到目前为止，对于甘蓝型油菜物种中miRNA的实验或计算鉴定知之甚少。为了提高比对搜索的效率，我们开发了一种工具（miRNAassist），它能够以高灵敏度和特异性识别miRNAs及其靶标的同源物。该程序可在Windows操作系统平台上运行。如有需要，miRNAassist可免费获取。（c）2007欧洲生物化学学会联合会。由爱思唯尔出版集团出版。保留所有权利。
MicroRNAs (miRNAs) are a newly discovered class of non-protein-coding small RNAs with roughly 22 nucleotidelong. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation and apoptosis and stress responses. In this research, several approaches were combined to make computational prediction of potential miRNAs and their targets in Brassica napus. We used previously known miRNAs from Arabidopsis, rice and other plant species against both expressed sequence tags (EST) and genomic survey sequence (GSS) databases to search for potential miRNAs in B. napus. A total of 21 potential miRNAs were detected following a range of strict filtering criteria. Using these potential miRNA sequences, we could further blast the mRNA database and found 67 potential targets in this species. According to the mRNA target information provided by NCBI (http://www.ncbi.nlm.nih.gov/), most of the target mRNAs appeared to be involved in plant growth, development and stress responses. To validate the prediction of miRNAs in B. napus, we performed a RT-PCR based assay of mature miRNA expression. Five miRNAs were identified in response to auxin, cadmium stress and phosphate starvation. So far, little is known about experimental or computational identification of miRNA in B. napus species. To improve efficiency for blast search, we developed an implementation (miRNAassist) that can identify homologs of miRNAs and their targets, with high sensitivity and specificity. The program is allowed to be run on Windows Operation System platform. miRNAassist is freely available if required. (c) 2007 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.