Dynamic microRNA regulatory networks in establishing the Cellular specificity of developing human brains (miRNA-seq)

MicroRNAs (miRNAs) regulate many neurodevelopmental events, including proliferation, neurogenesis, neuronal migration, and cell survival. Individual miRNAs interact with hundreds of mRNA transcripts, but the precise landscape of these interactions in the context of cell-type-specificity has not been determined. Here, we used multiple parallel approaches, including AGO2-HITS-CLIP, combined mRNA and miRNA single-cell profiling and bipartite network analysis, to reveal a non-uniformity of miRNA-mRNA interactions that supports both defined cell-type identities as well as their dynamic transitions during human brain development at stages of peak neurogenesis. miRNA-mRNA clusters dynamically exploit the redundancy of the miRNA target code to differentially cluster across transitions in brain development. Using cell-type-specific functional properties of miRNA-mRNA interactions, we identify the role of great ape-specific miR-2115 in regulating cortical progenitor cell proliferation by targeting a radial glia enriched gene, origin recognition complex subunit 4 (ORC4). Together, our study suggests that miRNAs contribute to cell identity by regulating the expression of cell-type-specific transcripts. AGO2-HITS-CLIP was performed on human prenatal brain tissue samples and miRNA and mRNA libraries were prepared separately from the band corresponding to AGO2:miRNA:mRNA complex (130 kDa). Libraries were sequenced on Ion Torrent platform.