State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China ; Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100781, China.
Archaea. 2014 May 14;2014:671059. doi: 10.1155/2014/671059. eCollection 2014.
Growing evidence indicates that miRNA genes exist in the archaeal genome, though the functional role of such noncoding RNA remains unclear. Here, we integrated the phylogenetic information of available archaeal genomes to predict miRNA seeds (typically defined as the 2-8 nucleotides of mature miRNAs) on the genomic scale. Finally, we found 2649 candidate seeds with significant conservation signal. Eleven of 29 unique seeds from previous study support our result (P value <0.01), which demonstrates that the pipeline is suitable to predict experimentally detectable miRNA seeds. The statistical significance of the overlap between the detected archaeal seeds and known eukaryotic seeds shows that the miRNA may evolve before the divergence of these two domains of cellular life. In addition, miRNA targets are enriched for genes involved in transcriptional regulation, which is consistent with the situation in eukaryote. Our research will enhance the regulatory network analysis in Archaea.
越来越多的证据表明，miRNA 基因存在于古菌基因组中，尽管这些非编码 RNA 的功能作用尚不清楚。在这里，我们整合了现有古菌基因组的系统发育信息，在基因组范围内预测 miRNA 种子（通常定义为成熟 miRNA 的 2-8 个核苷酸）。最后，我们发现了 2649 个具有显著保守信号的候选种子。来自之前研究的 29 个独特种子中的 11 个支持我们的结果（P 值<0.01），这表明该管道适用于预测实验可检测的 miRNA 种子。检测到的古菌种子与已知真核生物种子之间的重叠的统计学意义表明，miRNA 可能在这两个细胞生命领域分化之前就已经进化了。此外，miRNA 的靶标富集了参与转录调控的基因，这与真核生物的情况一致。我们的研究将增强古菌中的调控网络分析。
