College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Hangzhou, People's Republic of China.
Funct Integr Genomics. 2012 Nov;12(4):649-58. doi: 10.1007/s10142-012-0282-3. Epub 2012 May 15.
In a species, the miRNA repertoire comprises many lineage- or species-specific miRNAs. Using deep sequencing, the whole transcriptome of seedling roots was studied and a total of 18 novel miRNAs in indica rice Minghui 86 were identified. Among these novel miRNAs six were up-regulated and two were down-regulated under arsenite stress. Quantitative real-time RT-PCR analysis revealed that miR6254 was predominantly expressed in roots relative to other tissues, whereas miR6250 and miR169i-3p were constitutively expressed in all tissues examined, with high abundance in roots (miR6250) or leaves (miR169i-3p). The miR6250 and miR169i-3p miRNAs also exhibited distinct expression patterns in rice cultivars Minghui 86 and Nipponbare at different time points after arsenite treatment. The predicted targets for these miRNAs included some protein kinases, DNA, or ATP-binding proteins. Besides arsenite, the expression of targets of miR6250 and miR6254 was also up- or down-regulated in response to abiotic environmental stresses, indicative of their involvement in regulation of plant adaptation. Three types of cis-elements involved in hormone, light, and stress response were found to occur frequently in the promoter regions. Interestingly, miR6254 was originally characterized to be an exonic miRNA located in the exon of AK101391, supporting the notion that miRNAs may also originate from some exons in plants.
在一个物种中，miRNA 谱包含许多谱系或物种特异性的 miRNAs。通过深度测序，研究了幼苗根的整个转录组，共鉴定出籼稻明辉 86 中的 18 个新 miRNA。在这些新的 miRNA 中，有 6 个在亚砷酸盐胁迫下上调，有 2 个下调。定量实时 RT-PCR 分析显示，miR6254 在根中相对其他组织表达量较高，而 miR6250 和 miR169i-3p 在所有检测的组织中均持续表达，在根（miR6250）或叶（miR169i-3p）中丰度较高。miR6250 和 miR169i-3p 也在砷酸盐处理后不同时间点的明辉 86 和日本晴水稻品种中表现出不同的表达模式。这些 miRNA 的预测靶标包括一些蛋白激酶、DNA 或 ATP 结合蛋白。除了亚砷酸盐外，miR6250 和 miR6254 的靶基因的表达也在非生物环境胁迫下上调或下调，表明它们参与了植物适应的调控。在启动子区域中发现了三种与激素、光和应激反应相关的顺式元件频繁发生。有趣的是，miR6254 最初被描述为位于 AK101391 外显子中的一个外显子 miRNA，这支持了 miRNA 也可能来源于植物的某些外显子的观点。
