Department of Biology, University of Virginia, Charlottesville, USA.
Genomics. 2011 Jul;98(1):40-6. doi: 10.1016/j.ygeno.2011.03.011. Epub 2011 Apr 4.
MicroRNAs (miRNAs) regulate gene expression at the post-transcriptional level in eukaryotes. Exclusive focus on mature miRNA in most expression profiling efforts has prevented effective measurement of the expression of individual miRNA (MIR) genes. Using three sequenced small RNA libraries, we adapted miRDeep, which employs a probabilistic model of miRNA biogenesis, to analyze the miRNA transcriptome in Arabidopsis. We determined that less than 40% annotated MIR genes are expressed in shoot, root or inflorescence. We found that within paralogous families the expression pattern of individual genes correlates with the phylogenetic distance. Combining novel candidates identified in this study, we deduced the maximal number of expressed MIR genes. We further estimated the sequencing depth necessary to reach a near-saturated detection rate by curve fitting simulation. These results demonstrate that signature distribution of small RNA reads along the miRNA precursor is an effective model to profile MIR gene expression in Arabidopsis.
MicroRNAs (miRNAs) 在真核生物中通过转录后水平调控基因表达。在大多数表达谱分析工作中，对成熟 miRNA 的独家关注阻止了对个别 miRNA (MIR) 基因表达的有效测量。我们使用三个已测序的小 RNA 文库，对拟南芥中的 miRNA 转录组进行了分析，该方法采用 miRNA 生物发生的概率模型对 miRDeep 进行了改编。我们确定，在芽、根或花序中表达的注释 MIR 基因不到 40%。我们发现，在直系同源家族中，个别基因的表达模式与系统发育距离相关。结合本研究中确定的新候选基因，我们推断出表达 MIR 基因的最大数量。我们还通过曲线拟合模拟估计了达到近乎饱和检测率所需的测序深度。这些结果表明，小 RNA 读段沿 miRNA 前体的特征分布是在拟南芥中对 MIR 基因表达进行分析的有效模型。
