论文标题

表观遗传因素竞争重塑EMT景观

Epigenetic factor competition reshapes the EMT landscape

论文作者

Al-Radhawi, M. Ali, Tripathi, Shubham, Zhang, Yun, Sontag, Eduardo D., Levine, Herbert

论文摘要

等生细胞中不同表型之间的出现和过渡可以归因于表观遗传标记,外部信号和基因调节元件的复杂相互作用。这些元素包括染色质重塑剂,组蛋白修饰剂,转录因子和调节性RNA。称为基因调节网络(GRN)的数学模型是揭示此类复杂网络工作的越来越重要的工具。在此类模型中,通常提出表观遗传因素对直接参与相关基因表达的染色质区域作用。但是,这些因素在全球范围内运作,并互相竞争为全基因组范围的竞争。因此,调节剂活性的扰动可以重新分布整个基因组的表观遗传标记,并调节竞争调节剂的水平。在本文中,我们提出了一个概念和数学建模框架,该框架除了局部转录因子外,还结合了拮抗表观遗传调节器之间的局部和全球竞争效应,并显示了这种相互作用的反直觉后果。我们将我们的方法应用于上皮 - 间质转变(EMT)的最新实验发现。我们表明,它可以解释令人困惑的实验数据,并提供新的可验证预测。

The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as Gene Regulatory Networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators in addition to local transcription factors, and show the counter-intuitive consequences of such interactions. We apply our approach to recent experimental findings on the Epithelial-Mesenchymal Transition (EMT). We show that it can explain the puzzling experimental data as well provide new verifiable predictions.

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