The development and homeostasis of multicellular organisms relies on gene regulation
within individual constituent cells. Gene regulatory circuits that increase the robustness of
gene expression frequently incorporate microRNAs as post-transcriptional regulators.
Computational approaches, synthetic gene circuits and observations in model organisms
predict that the co-regulation of microRNAs and their target mRNAs can reduce cell-to-cell
variability in the expression of target genes. However, whether microRNAs directly regulate
variability of endogenous gene expression remains to be tested in mammalian cells. Here
we use quantitative flow cytometry to show that microRNAs impact on cell-to-cell variability
of protein expression in developing mouse thymocytes. We find two distinct mechanisms
that control variation in the activation-induced expression of the microRNA target CD69.
First, the expression of miR-17 and miR-20a, two members of the miR-17-92 cluster, is coregulated
with the target mRNA Cd69 to form an activation-induced incoherent feed-forward
loop. Another microRNA, miR-181a, acts at least in part upstream of the target mRNA Cd69
to modulate cellular responses to activation. The ability of microRNAs to render gene expression
more uniform across mammalian cell populations may be important for normal development
and for disease.