Identification of novel Oryza sativa miRNAs in deep sequencing-based small RNA libraries of rice infected with Rice stripe virus.
Identification of novel Oryza sativa miRNAs in deep sequencing-based small RNA libraries of rice infected with Rice stripe virus.
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DOI：
10.1371/journal.pone.0046443
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Chen J
中科院分区：
文献类型：
--
作者：
Guo W;Wu G;Yan F;Lu Y;Zheng H;Lin L;Chen H;Chen J
microRNAs（miRNAs）在真核生物的发育过程中起着重要的调控作用。基于深度测序的方法为鉴定新型miRNA提供了强大的高通量策略，并且先前已用于鉴定来自水稻的100多种新型miRNA。这些报道大多与水稻发育、组织分化或非生物胁迫相关，但与病毒感染相关的新的水稻miRNAs很少被发现。在前期的工作中，我们构建了水稻条纹病毒（Rice stripe virus，RSV）侵染水稻的小RNA（small RNA，sRNA）文库，并对其进行了测序，描述了RSV RNA基因组中小干扰RNA（small interfering RNA，siRNA）的特征。我们现在报告从RSV感染水稻的sRNA文库中丰富的sRNA（至少有100个测序读数）中鉴定出新的miRNA。通过北方杂交和RT-PCR检测，鉴定出7个前体序列未知的新的miRNAs（pn-miRNAs），并将其确认为新的miRNAs（n-miRNAs）。进一步分析表明，在感染RSV的水稻中，7个n-miRNAs中有5个表达上调，另外2个表达下调。此外，还鉴定了从19种已知的miRNA前体中新产生的23种pn-miRNA。这是首次报道由RSV感染相关的新前体产生的新型水稻miRNAs。
MicroRNAs (miRNAs) play essential regulatory roles in the development of eukaryotes. Methods based on deep-sequencing have provided a powerful high-throughput strategy for identifying novel miRNAs and have previously been used to identify over 100 novel miRNAs from rice. Most of these reports are related to studies of rice development, tissue differentiation, or abiotic stress, but novel rice miRNAs related to viral infection have rarely been identified. In previous work, we constructed and pyrosequenced the small RNA (sRNA) libraries of rice infected with Rice stripe virus and described the character of the small interfering RNAs (siRNA) derived from the RSV RNA genome. We now report the identification of novel miRNAs from the abundant sRNAs (with a minimum of 100 sequencing reads) in the sRNA library of RSV-infected rice. 7 putative novel miRNAs (pn-miRNAs) whose precursor sequences have not previously been described were identified and could be detected by Northern blot or RT-PCR, and were recognized as novel miRNAs (n-miRNAs). Further analysis showed that 5 of the 7 n-miRNAs were up-expressed while the other 2 n-miRNAs were down-expressed in RSV-infected rice. In addition, 23 pn-miRNAs that were newly produced from 19 known miRNA precursors were also identified. This is first report of novel rice miRNAs produced from new precursors related to RSV infection.
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