RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells

Abstract

BackgroundDistinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other’s expression levels. Theoretical predictions suggest that not only the mean expression levels of targets but also the fluctuations around the means are coupled through miRNAs. This may result in striking effects on a broad range of cellular processes, such as cell differentiation and proliferation. Although several studies have reported the functional relevance of this mechanism of interaction, detailed experiments are lacking that study this phenomenon in controlled conditions by mimicking a physiological range.ResultsWe used an experimental design based on two bidirectional plasmids and flow cytometry measurements of cotransfected mammalian cells. We validated a stochastic gene interaction model that describes how mRNAs can influence each other’s fluctuations in a miRNA-dependent manner in single cells. We show that miRNA–target correlations eventually lead to either bimodal cell population distributions with high and low target expression states, or correlated fluctuations across targets when the pool of unbound targets and miRNAs are in near-equimolar concentration. We found that there is an optimal range of conditions for the onset of cross-regulation, which is compatible with 10–1000 copies of targets per cell.ConclusionsOur results are summarized in a phase diagram for miRNA-mediated cross-regulation that links experimentally measured quantities and effective model parameters. This phase diagram can be applied to in vivo studies of RNAs that are in competition for miRNA binding.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1162-x) contains supplementary material, which is available to authorized users.

Single cell transcriptomes reveal characteristics of miRNA in gene expression noise reduction

“…Previous studies were mainly focused on the role of miRNAs but neglected the miRNA-mediated cross-talk among competing targets. Recent works have found that the cross-talk among competing targets could enhance the stability of gene expression [13,14,45]. Here, we observed a positive correlation between the abundance of targets pool and noise reduction ( Fig.…”

Quantitative understanding of molecular competition as a hidden layer of gene regulatory network

“…The introduction of R (miRNA) as repressor can decrease the noise of lowly expressed genes, meanwhile generate a noise peak in the "R near-equimolar" regime for highly expressed genes ( Fig. 5A), consistent with previous studies (41,42).…”

Kinetic Modelling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs

“…We also recalled that the system Eq (2) possesses a unique, asymptotically stable steady state [64]. However, both theoretical and experimental studies have shown that miRNAs, in peculiar conditions of stoichiometry, induce bimodal distributions in the expression level of their targets [45,60,78]. As reviewed in [79] and shown in [80], some biological systems may present bimodality just as a consequence of stochasticity and despite being monostable at the deterministic level.…”