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, we also identified 57 novel microRNAs, several of which are among the most highly differentially expressed. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGFβ during early regrowth, and negative regulation of extracellular proteases in late stage regeneration. Consistent with the expression results, we found that inhibition of TGFβ 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, the functional analysis of which showed enrichment of stress response, signaling pathway and extracellular protease categories that could be related to specific microRNAs. Predicted targets of the miR-9 cluster suggest a role in regulating differentiation and the proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle.
The authors declare no competing or financial interests.
Conceptualization: E.J.S., W.C.S., K.S.K.; Methodology: E.J.S., E.G., H.Z., W.C.S., K.S.K.; Software: E.J.S., H.Z.; Validation: E.J.S., E.G.; Investigation: E.J.S., E.G.; Formal analysis and investigation: E.J.S.; Writing - original draft preparation: E.J.S., W.C.S.; Writing - review and editing: E.J.S., W.C.S., K.S.K.; Funding acquisition: W.C.S.; Resources: W.C.S., K.S.K.; Supervision: W.C.S., K.S.K.
This work was supported by the National Institutes of Health [HD038701 to W.C.S.]. Deposited in PMC for release after 12 months.
Raw and processed data (transcript counts) are available from the NCBI Gene Expression Omnibus repository under accession number GSE84837 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=kvwtoqcutdwfzep&acc=GSE84837).
Supplementary information available online at http://dev.biologists.org/lookup/doi/10.1242/dev.144097.supplemental
- Received August 25, 2016.
- Accepted April 10, 2017.