miR-124 function during Ciona intestinalis neuronal development includes extensive interaction with the Notch signaling pathway

Abstract

The nervous system-enriched microRNA miR-124 is necessary for proper nervous system development, although the mechanismremains poorly understood. Here, through a comprehensive analysis of miR-124 and its gene targets, we demonstrate that, in thechordate ascidian Ciona intestinalis, miR-124 plays an extensive role in promoting nervous system development. We discoveredthat feedback interaction between miR-124 and Notch signaling regulates the epidermal-peripheral nervous system (PNS) fatechoice in tail midline cells. Notch signaling silences miR-124 in epidermal midline cells, whereas in PNS midline cells miR-124silences Notch, Neuralized and all three Ciona Hairy/Enhancer-of-Split genes. Furthermore, ectopic expression of miR-124 issufficient to convert epidermal midline cells into PNS neurons, consistent with a role in modulating Notch signaling. Morebroadly, genome-wide target extraction with validation using an in vivo tissue-specific sensor assay indicates that miR-124 shapesneuronal progenitor fields by downregulating non-neural genes, notably the muscle specifier Macho-1 and 50 Brachyuryregulatednotochord genes, as well as several anti-neural factors including SCP1 and PTBP1. 3_UTR conservation analysis revealsthat miR-124 targeting of SCP1 is likely to have arisen as a shared, derived trait in the vertebrate/tunicate ancestor and targetingof PTBP1 is conserved among bilaterians except for ecdysozoans, while extensive Notch pathway targeting appears to be Cionaspecific. Altogether, our results provide a comprehensive insight into the specific mechanisms by which miR-124 promotesneuronal development. © 2011.