Two evolutionary developmental strategies for miRNA gene regulation in animal embryogenesis [DM_miRNA-seq]. Drosophila melanogaster

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 miRNA expression in D. melanogaster embryonic development Please note that the data for the DM_mRNA-seq was already published (Levin et al., 2016, PMID 26886793) and the corresponding samples of the DM_miRNA are represented in the current study.

微小RNA（microRNA，简称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，其发挥调控作用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研究方法，通过检测秀丽隐杆线虫（Caenorhabditis elegans）与黑腹果蝇（Drosophila melanogaster）全胚胎发生过程中的miRNA表达情况，探究其功能。研究发现，在这两个物种中，转录组的miRNA组成在先前已确定的发育中期转变过程中呈现出间断式变化，形成两种主导性的miRNA表达模式：早期表达谱与晚期表达谱。令人瞩目的是，系统发育保守的miRNA多呈晚期表达，而早期表达的miRNA则与其靶基因呈反向表达模式，提示存在强烈的靶基因抑制作用。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发挥生理调控功能，而早期表达的miRNA则承担抑制性功能。综上，对两个物种全胚胎发生过程中miRNA表达的分析表明，其在胚胎发育晚期参与细胞类型的发育渠化稳定过程，并通过抑制靶基因以阻断异常表达。实验设计：针对黑腹果蝇胚胎发育过程中的miRNA表达进行时序检测。请注意，本研究中DM_mRNA-seq的相关数据已发表（Levin等，2016，PMID 26886793），且DM_miRNA对应的样本也纳入了本研究。