Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network

<jats:title>Abstract</jats:title><jats:p>Oscillations are crucial to the sustenance of living organisms, across a wide variety of biological processes. In eukaryotes, oscillatory dynamics are thought to arise from interactions at the protein and RNA levels; however, the role of non-coding RNA in regulating these dynamics remains understudied. In this work, using a mathematical model, we show how non-coding RNA acting as microRNA (miRNA) sponges in a conserved miRNA - transcription factor feedback motif, can give rise to oscillatory behaviour. Control of these non-coding RNA can dynamically create oscillations or stability, and we show how this behaviour predisposes to oscillations in the stochastic limit. These results, supported by emerging evidence for the role of miRNA sponges in development, point towards key roles of different species of miRNA sponges, such as circular RNA, potentially in the maintenance of yet unexplained oscillatory behaviour. These results help to provide a paradigm for understanding functional differences between the many redundant, but distinct RNA species thought to act as miRNA sponges in nature, such as long non-coding RNA, pseudogenes, competing mRNA, circular RNA, and 3’ UTRs.</jats:p><jats:sec><jats:title>Author summary</jats:title><jats:p>We analyze the effects of a newly discovered species of non-coding RNA, acting as microRNA (miRNA) sponges, on intracellular signalling dynamics. We show that oscillatory behaviour can arise in a time-varying manner in an over-represented transcriptional feedback network. These results point towards novel hypotheses for the roles of different species of miRNA sponges, such as their increasingly understood role in neural development.</jats:p></jats:sec>