microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes

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 co-regulated 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.

多细胞生物的发育与内稳态依赖于其各组成细胞内的基因调控。可提升基因表达鲁棒性的基因调控回路，常将微小RNA（microRNA）作为转录后调控因子纳入其中。计算方法、合成基因回路以及模式生物中的观测结果均表明，微小RNA与其靶信使RNA（mRNA）的共调控，可降低靶基因表达的细胞间异质性。不过，微小RNA是否能直接调控内源基因表达的异质性，仍有待在哺乳动物细胞中验证。本研究利用定量流式细胞术（quantitative flow cytometry）证实，微小RNA会影响发育中小鼠胸腺细胞的蛋白质表达细胞间异质性。我们发现了两种截然不同的机制，可调控微小RNA靶标CD69的激活诱导型表达差异。其一，miR-17与miR-20a（miR-17-92簇的两个成员）的表达与靶信使RNA Cd69共调控，形成激活诱导型非相干前馈环。另一项机制则是，微小RNA miR-181a至少可通过作用于靶信使RNA Cd69的上游区域，调控细胞的激活应答反应。微小RNA使哺乳动物细胞群体内基因表达更为均一的能力，可能在正常发育与疾病进程中发挥重要作用。