Uncovering DCL1-dependent small RNA loci on plant genomes: a structure-based approach.
Uncovering DCL1-dependent small RNA loci on plant genomes: a structure-based approach.
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DOI：
10.1093/jxb/ert409
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发表时间：
2014-02
影响因子：
6.9
通讯作者：
Y. Meng;C. Shao;Huizhong Wang;Ming Chen
中科院分区：
文献类型：
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作者：
Y. Meng;C. Shao;Huizhong Wang;Ming Chen
在植物中，DICER-Like 1(DCL1)介导的两步切割对于microRNA(MiRNA)基因产物的加工是必不可少的。有趣的是，DCL1参与了许多小RNA(SRNAs)的产生，这些小RNA不能被归类为典型的miRNAs。然而，关于非miRNA、DCL1依赖的sRNAs的基因组和功能信息仍然有限。在这里，我们提出了一种基于二级结构的方法来识别包含新的依赖于DCL1的SRNA基因座的前体。为了证明该工作流程的有效性：首先，从水稻DCL1 RNA干扰转基因系制备的SRNA高通量测序数据集中鉴定了5898个依赖于DCL1的20-24个核苷酸的sRNA。那些与水稻前miRNAs(前体microRNAs)完美定位的基因被移除。然后将剩余的5795个sRNA定位到水稻基因组上，获得了30902个完全匹配的座位，属于2310个sRNA。利用RNA折叠技术对4631个SRNA基因座进行了二级结构预测。人工比较最小自由能(MFE)和质心两种算法的预测结果，以识别包含DCL1依赖的sRNA基因座的保守长茎结构。为了进行案例研究，对部分预测结果进行了人工筛选。结果表明，60个簇具有形成DCL1依赖的sRNAs的特征长茎结构的巨大潜力。综上所述，结果表明所提出的工作流程适用于在植物基因组上识别新的依赖于DCL1的SRNA基因座。
In plants, Dicer-like 1 (DCL1)-mediated two-step cleavages are essential for the processing of microRNA (miRNA) gene products. Interestingly, DCL1 has been indicated to be involved in the production of many small RNAs (sRNAs) that cannot be classified as canonical miRNAs. However, genomic and functional information on the non-miRNA, DCL1-dependent sRNAs is still limited. Here, we propose a secondary structure-based approach for identification of the precursors containing novel DCL1-dependent sRNA loci. To demonstrate the utility of the workflow: first, 5898 DCL1-dependent sRNAs of 20-24 nucleotides were identified from the sRNA high-throughput sequencing data sets prepared from rice DCL1 RNA interference transgenic lines. Those perfectly mapped to the rice pre-miRNAs (precursor microRNAs) were removed. The remaining 5795 sRNAs were then mapped onto the rice genome, obtaining 30 902 perfectly matched loci belonging to 2310 sRNAs. A total of 4631 clusters of sRNA loci were defined for secondary structure prediction by using RNAfold. The prediction results generated by two algorithms, namely MFE (minimum free energy) and centroid, were manually compared to identify the conserved long-stem structures containing DCL1-dependent sRNA loci. For the purpose of a case study, a portion of the prediction results was screened manually. As a result, 60 clusters displayed great potential for forming featured long-stem structures for the generation of DCL1-dependent sRNAs. Together, the results indicate that the proposed workflow is applicable for the identification of novel DCL1-dependent sRNA loci on plant genomes.