A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
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DOI：
10.1101/gr.075572.107
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发表时间：
2008-09-01
期刊：
影响因子：
7
通讯作者：
Helliwell, Chris
中科院分区：
文献类型：
--
作者：
Zhu, Qian-Hao;Spriggs, Andrew;Helliwell, Chris
内源小RNA，包括microRNAs和siRNAs，在植物中作为转录后或转录调控因子发挥作用。MiRNA功能是植物正常发育所必需的，因此可能在水稻籽粒的生长发育中起重要作用。为了研究miRNAs在水稻籽粒发育中的作用，我们对两个发育阶段的水稻籽粒小RNA群体进行了深度测序。在一个类似于550万个序列的数据集中，我们发现了所有20个保守的植物miRNA家族的代表。我们使用一种基于miRNA和miRNA*序列存在的方法来鉴定39个在谷物中表达的新的、非保守的水稻miRNA家族。一些新的miRNAs证实了预测的靶向mRNAs的切割。我们发现了一个可能的Mirtron，表明植物也可能使用剪接内含子作为miRNAs的来源。我们还发现了一个类似miRNA的长发夹，它产生阶段性的21个核苷酸的小RNA，在发育中的颗粒中强烈表达，并表明这些小RNA起反式作用，切割目标RNA。将谷物中的miRNAs和类似miRNA的siRNAs的数量与水稻植株其他部分的siRNAs进行比较，发现许多siRNAs是以器官特有的方式表达的。
Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as post-transcriptional or transcriptional regulators in plants. miRNA function is essential for normal plant development and therefore is likely to be important in the growth of the rice grain. To investigate the roles of miRNAs in rice grain development, we carried out deep sequencing of the small RNA populations of rice grains at two developmental stages. In a data set of similar to 5.5 million sequences, we found representatives of all 20 conserved plant miRNA families. We used an approach based on the presence of miRNA and miRNA* sequences to identify 39 novel, nonconserved rice miRNA families expressed in grains. Cleavage of predicted target mRNAs was confirmed for a number of the new miRNAs. We identified a putative mirtron, indicating that plants may also use spliced introns as a source of miRNAs. We also identified a miRNA-like long hairpin that generates phased 21 nt small RNAs, strongly expressed in developing grains, and show that these small RNAs act in trans to cleave target mRNAs. Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner.