Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
Plant J. 2010 Jun 1;62(5):742-59. doi: 10.1111/j.1365-313X.2010.04187.x. Epub 2010 Feb 26.
MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. Currently, miRBase (version 13) lists 142 and 353 miRNAs from Arabidopsis and rice (Oryza sativa), respectively. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. In contrast with the well-characterized miRNA targets that are cleaved in Arabidopsis, only a few such targets have been confirmed in rice. To identify small RNA targets in rice, we applied the 'degradome sequencing' approach, which globally identifies the remnants of small RNA-directed target cleavage by sequencing the 5' ends of uncapped RNAs. One hundred and sixty targets of 53 miRNA families (24 conserved and 29 rice-specific) and five targets of TAS3-small interfering RNAs (siRNAs) were identified. Surprisingly, an additional conserved target for miR398, which has not been reported so far, has been validated. Besides conserved homologous transcripts, 23 non-conserved genes for nine conserved miRNAs and 56 genes for 29 rice-specific miRNAs were also identified as targets. Besides miRNA targets, the rice degradome contained fragments derived from MIRNA precursors. A closer inspection of these fragments revealed a unique pattern distinct from siRNA-producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants.
微小 RNA (miRNA)-引导的靶 RNA 表达对真核生物的各种生物过程至关重要。目前，miRBase（版本 13）分别列出了拟南芥和水稻（Oryza sativa）中的 142 种和 353 种 miRNA。miRNA 在不同的生物网络中的整合依赖于其 RNA 靶标的确认。与在拟南芥中被切割的特征明确的 miRNA 靶标相比，在水稻中只确认了少数这样的靶标。为了鉴定水稻中的小 RNA 靶标，我们应用了“降解组测序”方法，通过测序未加帽 RNA 的 5' 端，全局鉴定小 RNA 指导的靶标切割的残基。鉴定了 53 个 miRNA 家族（24 个保守和 29 个水稻特异性）的 160 个靶标和 5 个 TAS3-小干扰 RNA (siRNA) 的靶标。令人惊讶的是，验证了一个额外的保守 miR398 靶标，迄今为止尚未报道过。除了保守同源转录本外，还鉴定了 9 个保守 miRNA 的 23 个非保守基因和 29 个水稻特异性 miRNA 的 56 个基因作为靶标。除了 miRNA 靶标，水稻降解组还包含 MIRNA 前体的片段。对这些片段的仔细检查揭示了一种与 siRNA 产生基因座明显不同的独特模式。这一特性可以作为植物中 miRNA 与 siRNA 分离的辅助标准之一。
