Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
Genomics Proteomics Bioinformatics. 2013 Feb;11(1):56-60. doi: 10.1016/j.gpb.2012.12.004. Epub 2013 Jan 11.
Endogenously-encoded microRNAs (miRNAs) are a class of small regulatory RNAs that modulate gene expression at the post-transcriptional level. In plants, miRNAs have increasingly been identified by experiments based on next-generation sequencing (NGS). However, promoter organization is currently unknown for most plant miRNAs, which are transcribed by RNA polymerase II. This deficiency prevents a comprehensive understanding of miRNA-mediated gene networks. In this study, by analyzing full-length cDNA sequences related to miRNAs, we mapped transcription start sites (TSSs) for 62 and 55 miRNAs in Arabidopsis and rice, respectively. The average free energy (AFE) profiles in the vicinity of TSSs were studied for both species. By employing position weight matrices (PWM) for 99 plant cis-elements, we discovered that three cis-elements were over-represented in the miRNA promoters of both species, while four and ten cis-elements were over-represented in Arabidopsis only and in rice only. Thus, comparison of miRNA promoters between Arabidopsis and rice provides a new perspective for studying miRNA regulation in plants.
内源性编码的 microRNAs（miRNAs）是一类小的调节 RNA，可在转录后水平调节基因表达。在植物中，基于下一代测序（NGS）的实验已经越来越多地鉴定出 miRNAs。然而，大多数由 RNA 聚合酶 II 转录的植物 miRNAs 的启动子组织目前尚不清楚。这一缺陷妨碍了对 miRNA 介导的基因网络的全面理解。在这项研究中，通过分析与 miRNAs 相关的全长 cDNA 序列，我们分别在拟南芥和水稻中绘制了 62 个和 55 个 miRNAs 的转录起始位点（TSS）。对两个物种的 TSS 附近的平均自由能（AFE）图谱进行了研究。通过使用 99 个植物顺式元件的位置权重矩阵（PWM），我们发现三个顺式元件在两个物种的 miRNA 启动子中过度表达，而四个和十个顺式元件仅在拟南芥和水稻中过度表达。因此，拟南芥和水稻之间的 miRNA 启动子比较为研究植物中的 miRNA 调控提供了新的视角。
