TitleA microRNA-mRNA expression network during oral siphon regeneration in .
Publication TypeJournal Article
Year of Publication2017
AuthorsSpina EJ, Guzman E, Zhou H, Kosik KS, Smith WC
Date Published2017 05 15
KeywordsAnimals, Ciona intestinalis, Gene Expression Profiling, Gene Regulatory Networks, High-Throughput Nucleotide Sequencing, MicroRNAs, Mouth, Regeneration, RNA, Messenger, Wound Healing

Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in , 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 cluster suggest a role in regulating differentiation and the proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle.

Alternate JournalDevelopment
PubMed ID28432214
PubMed Central IDPMC5450834
Grant ListR01 HD038701 / HD / NICHD NIH HHS / United States