Genomic analysis of rice microRNA promoters and clusters
Genomic analysis of rice microRNA promoters and clusters
复制标题
水稻 microRNA 启动子和簇的基因组分析。
DOI：
10.1016/j.gene.2008.11.016
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发表时间：
2009-02-15
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：
Cui, Xiao;Xu, Si Min;Yang, Zhi Min
MicroRNAs （miRNAs）是内源性的单链非编码小rna，长度约为21 nt，对发育和应激具有负性调节作用。水稻mirna是单子叶mirna的代表，其中许多在拟南芥和其他植物物种中不保守。先前的研究表明，大多数植物mirna是通过独立的转录单位表达的，而其他一些mirna则与其宿主基因一起转录。尽管越来越多的水稻miRNA被发现，但对miRNA基因的转录调控知之甚少。在这项研究中，我们对水稻启动子/转录起始位点（TSS）和TATA-box区域周围的miRNA转录本进行了基因组分析，并对miRNA簇的组织进行了分析。通过生物信息学方法检测了212个水稻miRNA前序列的249个启动子，发现保守的水稻miRNA基因比非保守的miRNA基因拥有更大的启动子比例。我们进一步在全球范围内分析了pri-miRNA的基因组组织，发现52个水稻miRNA基因出现在18个簇中。这些集群中的miRNA序列比对显示了集群内的许多miRNA相似物。获得的数据可能有助于我们了解pre-miRNA上游的特定序列以及miRNA簇在水稻植物中的功能意义。(C) 2008 Elsevier B.V.版权所有
MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs with a length of about 21 nt, that negatively regulate development and stresses. Rice miRNAs are representative of the monocot miRNAs, and many of them are non-conserved in Arabidopsis and the other plant species. Previous studies have shown that a majority of plant miRNAs are expressed from independent transcription units, whereas some others are transcribed with their host genes. Despite of the fact that a growing number of rice miRNAs are discovered, little is known about the transcriptional regulation of miRNA genes. In this study, we performed genomic analysis of rice miRNA transcripts surrounding the regions of promoter/transcription start site (TSS) and TATA-box, and organization of miRNA clusters. We detected 249 promoters for 212 rice pre-miRNA sequences via bioinformatics approach and found that the conserved rice miRNA genes have a greater proportion of promoters than the non-conserved miRNA genes. We further globally analyzed the genomic organization of pri-miRNAs and found that 52 rice miRNA genes appear in 18 clusters. Alignment of the miRNA sequences in these clusters shows a number of miRNA paralogs within the cluster. The data obtained may aid our understanding of the specific sequences upstream of pre-miRNAs and the functional implications of miRNA clusters in rice plants. (C) 2008 Elsevier B.V. All rights reserved.