A microRNA-mRNA expression network during oral siphon regeneration in Ciona

Abstract

Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in Ciona robusta, and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed (DE), we also identified 57 novel microRNAs, several of which are among the most highly DE. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGF-β during early regrowth, and negative regulation of extracellular proteases in late stage regeneration. Consistent with the expression results we found that inhibition of TGF-β signaling blocked OS regeneration. A correlation network was subsequently inferred for all predicted microRNA-mRNA target pairs expressed during regeneration. Network based clustering associated transcripts into 22 non-overlapping groups, functional analysis of which showed enrichment of stress response, signaling pathway and extracellular protease categories could be related to specific microRNAs. Finally, predicted targets of the miR-9 cluster suggest a role in regulating differentiation and proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle.