Two evolutionary developmental strategies for miRNA gene regulation in animal embryogenesis [DM_miRNA-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 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.