A module of microRNAs cooperatively regulating neurogenesis

MicroRNAs (miRNAs) are essential regulators of all developmental processes, including neurogenesis, when the production of large numbers of neurons from a limited number of neural stem cells depends on the precise control of determination, proliferation and differentiation. However, miRNA regulation of target mRNAs is highly promiscuous, a single miRNA can target many mRNAs and vice versa, raising the question of how specificity is achieved to elicit a precise regulatory response. Here we introduce in vivo AGO-APP, a novel approach to purify Argonaute-bound miRNAs directly from living cells and tissues. Using this technology, we isolate actively inhibiting miRNAs from different neural cell populations in the larval Drosophila central nervous system. We identify a defined group of miRNAs that redundantly target all iconic genes known to control the transition from neuroblasts to neurons. In vivo functional studies demonstrate that knockdown of individual miRNAs among this group does not induce detectable cellular phenotypes. However, simultaneous knockdown of multiple miRNAs leads to precocious stem cell differentiation, demonstrating functional interdependence. Our study shows that miRNAs cooperate within a regulatory module to specify the targeted gene network. Overall design: Using the UAS-Gal4 system we generated transgenic flies conditionnally expressing a T6B-YFP fusion protein either in neuroblast (nab driver) or in the entire neuronal lineage (elav driver) or in glial cells (repo driver). After induction at the L3 larvae stage, T6B bound micro-RNAs were pulled down using an anti-GFP antibody and sequenced. Micro-RNA sequencing was performed using the Illumina protocol modified by Kim et al. (2019).