Two evolutionary developmental strategies for miRNA gene regulation in animal embryogenesis [CE_RNA-seq]

miRNAs play essential roles in the mechanics of gene regulation, however, on an organismal-scale, the processes in they are deployed are not well understood. Here, we adopt an evolutionary developmental approach to study miRNA function by examining their expression throughout embryogenesis in both C. elegans and D. melanogaster. We find that, in both species, the miRNA complement of the transcriptome shifts in a punctuated fashion during the previously identified mid-developmental transition specifying two dominant modes of miRNA expression: an early and a late profile. Strikingly, we find that phylogenetically conserved miRNAs are expressed late, while early expressed miRNAs are inversely expressed with their targets suggesting strong target-inhibition. Our work exposes two distinct strategies of miRNA function comprising late-expressed physiological roles and early expressed repressive roles. In summary, the expression of miRNAs throughout embryogenesis in two species implicates their role in the canalization of cell-types during late phases of embryogenesis and repressing targets to lock-down misexpression. Overall design: A timecourse of mRNA expression in C. elegans embryonic developmet微小RNA（microRNA，miRNA）在基因调控机制中发挥着至关重要的作用，但在生物体尺度上，其发挥调控功能的具体过程仍未得到充分阐释。 本研究采用进化发育生物学方法，通过探究秀丽隐杆线虫（Caenorhabditis elegans，C. elegans）与黑腹果蝇（Drosophila melanogaster，D. melanogaster）全胚胎发育过程中的miRNA表达情况，对miRNA的功能展开研究。 研究发现，在两个物种中，转录组的miRNA组成均在此前已被证实的发育中期转变阶段呈现出间断性变化，形成两种主导性的miRNA表达模式：早期表达谱与晚期表达谱。值得注意的是，系统发育保守的miRNA均呈现晚期表达特征，而早期表达的miRNA则与其靶基因呈反向表达模式，这提示二者之间存在强烈的靶标抑制作用。 本研究揭示了miRNA功能的两种截然不同的策略：晚期表达的miRNA承担生理调控功能，而早期表达的miRNA则发挥靶基因抑制作用。综上，通过对两个物种全胚胎发育过程中miRNA表达情况的分析，我们发现miRNA在胚胎发育后期参与细胞类型的渠化调控，并通过抑制靶基因来阻断异常表达。 整体实验设计：秀丽隐杆线虫胚胎发育过程中的信使RNA（messenger RNA，mRNA）表达时序分析。