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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis
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Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis

机译：拟南芥中microRNA定向串联反式siRNA级联的生物信息学预测和实验验证

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摘要

Small RNAs play pivotal roles in regulating gene expression in higher eukaryotes. Among them, trans-acting siRNAs (ta-siRNAs) are a class of small RNAs that regulate plant development. The biogenesis of ta-siRNA depends on microRNA-targeted cleavage followed by the DCL4-mediated production of small RNAs phased in 21-nt increments relative to the cleavage site on both strands. To find TAS genes, we have used these characteristics to develop the first computational algorithm that allows for a comprehensive search and statistical evaluation of putative TAS genes from any given small RNA database. A search in Arabidopsis small RNA massively parallel signature sequencing (MPSS) databases with this algorithm revealed both known and previously unknown ta-siRNA-producing loci. We experimentally validated the biogenesis of ta-siRNAs from two PPR genes and the trans-acting activity of one of the ta-siRNAs. The production of ta-siRNAs from the identified PPR genes was directed by the cleavage of a TAS2-derived ta-siRNA instead of by microRNAs as was reported previously for TAS1a, -b. -c, TAS2, and TAS3 genes. Our results indicate the existence of a small RNA regulatory cascade initiated by miR173-directed cleavage and followed by the consecutive production of ta-siRNAs from two TAS genes.
机译：小RNA在调节高等真核生物的基因表达中起关键作用。其中，反式作用siRNA（ta-siRNA）是一类调节植物发育的小RNA。 ta-siRNA的生物发生取决于靶向microRNA的切割，然后由DCL4介导的小RNA产生，相对于两条链上的切割位点，以21 nt增量递增。为了找到TAS基因，我们利用这些特征来开发了第一个计算算法，该算法可从任何给定的小型RNA数据库中全面搜索和统计评估推定的TAS基因。使用该算法在拟南芥小RNA大规模平行签名测序（MPSS）数据库中进行搜索，发现了已知和先前未知的产生ta-siRNA的基因座。我们通过实验验证了来自两个PPR基因的ta-siRNA的生物发生以及一个ta-siRNA的反式活性。由鉴定的PPR基因产生ta-siRNA的过程是由TAS2衍生的ta-siRNA的切割而不是如先前针对TAS1a，-b报道的microRNA进行的。 -c，TAS2和TAS3基因。我们的结果表明，存在由miR173定向切割引发的小RNA调控级联反应，随后由两个TAS基因连续产生ta-siRNA。

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