Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes
Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes
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DOI：
10.1016/j.virol.2009.07.005
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发表时间：
2009-09-30
期刊：
影响因子：
3.7
通讯作者：
Llave, Cesar
中科院分区：
文献类型：
--
作者：
Donaire, Livia;Wang, Yu;Llave, Cesar
植物病毒感染涉及病毒小RNA （vsRNAs）的产生，这些病毒小RNA （vsRNAs）可能与不同的含Argonaute （AGO）的沉默复合物结合，并介导RNA和染色质上的多种沉默作用。我们使用多路复用，高通量焦磷酸测序来分析来自不同属病毒感染的植物的vsrna群体。20 - 24个核苷酸（nts）的正义和反义vsRNAs以重叠的结构分布在整个病毒基因组中；几乎所有的基因组核苷酸位置都在数据集中表示。我们提供的证据表明，尽管病毒基因组包含作为vsRNA生产优先来源的特定区域，但每个基因组位置都可能是vsRNA形成的假定切割位点。21-、22-和24-nt的vsRNAs热点通常在相同的基因组区域重合，表明dicer样（DCL）酶之间具有相似的靶标亲和力。根据我们的研究结果，我们讨论了完美碱基配对（双链RNA）和单链RNA中不完美碱基配对结构对vsRNA形成的总体贡献。我们对vsRNA的普查扩展了目前对病毒感染植物中vsRNA的分布和组成的看法，并有助于更好地理解vsRNA的生物发生。(C) 2009爱思唯尔公司版权所有。
Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the data set. We present evidence to Suggest that every genomic position could be a putative cleavage site for vsRNA formation, although viral genomes contain specific regions that serve as preferential sources of vsRNA production. Hotspots for vsRNAs of 21-, 22-, and 24-nt usually coincide in the same genomic regions, indicating similar target affinities among Dicer-like (DCL) enzymes. In the light Of Our results, the overall contribution of perfectly base paired (double-stranded RNA and imperfectly base paired structures within single-stranded RNA to vsRNA formation is discussed. Our census of vsRNAs extends the Current view of the distribution and composition of vsRNAs in virus-infected plants, and contributes to a better understanding of vsRNA biogenesis. (C) 2009 Elsevier Inc. All rights reserved.