Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags
Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags
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陆地棉表达序列标签中 microRNA 及其靶标的计算鉴定。
DOI：
10.1016/j.gene.2007.01.034
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发表时间：
2007-06-15
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：
Qiu, Cheng Xiang;Xie, Fu Liang;Yang, Zhi Min
NlicroRNA (miRNA) 是一类调节动植物基因转录后表达的非编码 RNA。比较基因组计算方法已被开发用于预测蠕虫、人类和拟南芥中的新 miRNA。在这里，我们提出了一种基于 EST（表达序列标签）和 GSS（基因组调查序列）的组合方法，用于检测陆地棉中的新型 miRNA。这是通过使用先前已知的来自拟南芥、水稻和其他植物物种的 miRNA 序列以及一种名为 miRNAassist 的算法来爆破陆地棉 EST 和 GSS 的数据库而启动的。根据一系列过滤标准，总共检测到 37 种潜在 miRNA。利用这些潜在的 miRNA 序列，我们进一步对公开的 mRNA 数据库进行了分析，并在陆地棉中检测到了 96 个潜在靶标。根据美国国家生物技术信息中心（NCBI）（http://www.ncbi.nlm.nih.gov/）提供的mRNA信息，预测大多数miRNA靶向基因编码调节细胞生长发育、信号传导和代谢的转录因子。迄今为止，关于陆地棉物种中 miRNA 的实验或计算鉴定知之甚少。这些新的 miRNA 及其在陆地棉中的靶标已通过 miRNAassist 运行，产生的数据可能有助于我们更好地了解 miRNA 在调节陆地棉生长和发育中的可能作用。 (C) 2007 Elsevier B.V. 保留所有权利。
NlicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene post-transcriptional expression in animals and plants. Comparatively genomic computational methods have been developed to predict new miRNAs in worms, humans, and Arabidopsis. Here we present an EST (Expressed Sequence Tags) - and GSS (Genomic Survey Sequences)-based combined approach for the detection of novel miRNAs in Gossypium hirsutum. This was initiated by using previously known miRNA sequences from Arabidopsis, rice and other plant species and an algorithm called miRNAassist to blast the databases of G. hirsutum EST and GSS. A total of 37 potential miRNAs were detected following a range of filtering criteria. Using these potential miRNAs sequences, we further blasted the publicly available mRNA database and detected 96 potential targets in G. hirsutum. According to the mRNA information provided by the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/), most of the miRNA targeted genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism. So far, little is known about experimental or computational identification of miRNA in G. hirsutum species. These new miRNAs and their targets in G. hirsutum have been run through miRNAassist to yield data that may help us better understanding of the possible role of miRNAs in regulating the growth and development of G. hirsutum. (C) 2007 Elsevier B.V. All rights reserved.