Conifers have a unique small RNA silencing signature
Conifers have a unique small RNA silencing signature
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DOI：
10.1261/rna.1052008
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发表时间：
2008-08-01
期刊：
影响因子：
4.5
通讯作者：
Unrau, Peter J.
中科院分区：
文献类型：
--
作者：
Dolgosheina, Elena V.;Morin, Ryan D.;Unrau, Peter J.
植物产生小RNA以在称为RNA沉默的过程中在转录或转录后水平负调节基因、病毒核酸和重复元件。虽然RNA沉默已经在动物界的不同门中进行了广泛的研究（例如，例如，在一个实施例中，小鼠、苍蝇、蠕虫），植物界的类似研究主要集中在被子植物上，因此限制了植物中RNA沉默的进化研究。在这里，我们报告了一个意想不到的系统发育差异之间的维管植物的小RNA的大小分布。通过从新鲜生长的茎组织中提取总RNA，我们对24种维管植物中的小RNA进行了调查。我们发现，针叶树，从其他种子轴承植物辐射; 2.6亿年前，未能产生大量的24-核苷酸（nt）RNA，已知引导DNA甲基化和异染色质形成的被子植物。相反，它们合成了一群不同的小RNA，长度正好是21个核苷酸。这一发现得到了证实的高通量测序的小RNA序列从针叶树，扭叶松。针叶树EST搜索揭示了一个新的Dicer样（DCL）家族的存在，这可能是负责观察到的小RNA表达的变化。DCL 3是一种在被子植物中使24-nt RNA成熟的酶，但没有证据表明这一点。我们推测，在针叶树中发现的21-nt RNA的多样性可能有助于维持其异常大的基因组的组织。
Plants produce small RNAs to negatively regulate genes, viral nucleic acids, and repetitive elements at either the transcriptional or post-transcriptional level in a process that is referred to as RNA silencing. While RNA silencing has been extensively studied across the different phyla of the animal kingdom (e. g., mouse, fly, worm), similar studies in the plant kingdom have focused primarily on angiosperms, thus limiting evolutionary studies of RNA silencing in plants. Here we report on an unexpected phylogenetic difference in the size distribution of small RNAs among the vascular plants. By extracting total RNA from freshly growing shoot tissue, we conducted a survey of small RNAs in 24 vascular plant species. We find that conifers, which radiated from the other seed-bearing plants; 260 million years ago, fail to produce significant amounts of 24-nucleotide (nt) RNAs that are known to guide DNA methylation and heterochromatin formation in angiosperms. Instead, they synthesize a diverse population of small RNAs that are exactly 21-nt long. This finding was confirmed by high-throughput sequencing of the small RNA sequences from a conifer, Pinus contorta. A conifer EST search revealed the presence of a novel Dicer-like (DCL) family, which may be responsible for the observed change in small RNA expression. No evidence for DCL3, an enzyme that matures 24-nt RNAs in angiosperms, was found. We hypothesize that the diverse class of 21-nt RNAs found in conifers may help to maintain organization of their unusually large genomes.