Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex

Abstract

AbstractBackgroundmicroRNAs are a class of small RNAs that induce transcriptional inhibition via binding to the 3’-untranslated region (3’UTR) of their target mRNAs. In addition to other developmental processes, miRNAs are particularly important during brain development. However, the composition and temporal dynamics of miRNA regulatory networks are not yet sufficiently characterized.ResultsWe performed small RNA sequencing of mouse embryonic cortical samples at E14, E17, and P0 as well as in neural progenitor cells (NPCs) differentiatedin vitrointo neurons. Using co-expression network analysis, we detected clusters of miRNAs that were co-regulated at distinct developmental stages with miRNAs such as miR-92a/b acting as hubs during early and miR-124 and miR-137 during late neurogenesis. Notably, the validated targets of hub miRNAs up-regulated at P0 were significantly enriched for genes down-regulated at this time point. These targets included important mediators of alternative splicing which is a crucial process during neuronal differentiation. In a co-targeting network of miRNAs sharing more targets than expected by chance, we observed that more abundant miRNAs were significantly associated with more co-targeting associations. Using luciferase reporter assays, we demonstrated that simultaneous binding of miRNA pairs to neurodevelopmentally relevant genes exerted an enhanced gene silencing effect compared to single miRNAs.ConclusionsOur study provides a comprehensive resource of longitudinal changes in the expression patterns of miRNAs during corticogenesis. Furthermore, we highlight several potential mechanisms through which miRNA regulatory networks can act as modulators of embryonic brain development.