Gérard Claude, Novák Béla
Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
PLoS One. 2013 Dec 23;8(12):e83372. doi: 10.1371/journal.pone.0083372. eCollection 2013.
microRNAs (miRNAs) are small noncoding RNAs that are important post-transcriptional regulators of gene expression. miRNAs can induce thresholds in protein synthesis. Such thresholds in protein output can be also achieved by oligomerization of transcription factors (TF) for the control of gene expression. First, we propose a minimal model for protein expression regulated by miRNA and by oligomerization of TF. We show that miRNA and oligomerization of TF generate a buffer, which increases the robustness of protein output towards molecular noise as well as towards random variation of kinetics parameters. Next, we extend the model by considering that the same miRNA can bind to multiple messenger RNAs, which accounts for the dynamics of a minimal competing endogenous RNAs (ceRNAs) network. The model shows that, through common miRNA regulation, TF can control the expression of all proteins formed by the ceRNA network, even if it drives the expression of only one gene in the network. The model further suggests that the threshold in protein synthesis mediated by the oligomerization of TF can be propagated to the other genes, which can increase the robustness of the expression of all genes in such ceRNA network. Furthermore, we show that a miRNA could increase the time delay of a "Goodwin-like" oscillator model, which may favor the occurrence of oscillations of large amplitude. This result predicts important roles of miRNAs in the control of the molecular mechanisms leading to the emergence of biological rhythms. Moreover, a model for the latter oscillator embedded in a ceRNA network indicates that the oscillatory behavior can be propagated, via the shared miRNA, to all proteins formed by such ceRNA network. Thus, by means of computational models, we show that miRNAs could act as vectors allowing the propagation of robustness in protein synthesis as well as oscillatory behaviors within ceRNA networks.
微小RNA(miRNA)是一类小的非编码RNA,是基因表达重要的转录后调节因子。miRNA可诱导蛋白质合成的阈值。蛋白质输出中的此类阈值也可通过转录因子(TF)的寡聚作用来实现,以控制基因表达。首先,我们提出了一个由miRNA和TF寡聚作用调节蛋白质表达的最小模型。我们表明,miRNA和TF寡聚作用产生了一个缓冲器,它增加了蛋白质输出对分子噪声以及动力学参数随机变化的稳健性。接下来,我们通过考虑同一miRNA可与多个信使RNA结合来扩展该模型,这解释了最小竞争性内源RNA(ceRNA)网络的动力学。该模型表明,通过共同的miRNA调节,TF可以控制ceRNA网络形成的所有蛋白质的表达,即使它只驱动网络中一个基因的表达。该模型进一步表明,由TF寡聚作用介导的蛋白质合成阈值可以传播到其他基因,这可以增加此类ceRNA网络中所有基因表达的稳健性。此外,我们表明,miRNA可以增加“古德温样”振荡器模型的时间延迟,这可能有利于大振幅振荡的发生。这一结果预测了miRNA在控制导致生物节律出现的分子机制中的重要作用。此外,嵌入ceRNA网络中的后一种振荡器模型表明,振荡行为可以通过共享的miRNA传播到由该ceRNA网络形成的所有蛋白质。因此,通过计算模型,我们表明miRNA可以作为载体,在ceRNA网络内传播蛋白质合成的稳健性以及振荡行为。