Distinct RNA species may compete for binding microRNAs, a class of small non-coding transcripts involved in post-transcriptional downregulation. This competition creates an indirect interaction between microRNA targets that behave as microRNA sponges and eventually influence each other expression levels. Theoretical predictions suggest that not only the mean target expression levels but also the fluctuations around the means are coupled through microRNAs, potentially resulting in even more striking effects on a broad range of cellular processes. With 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 microRNA-dependent manner in single cells.