Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts.
Max Planck institute for the Physics of Complex Systems, Dresden, Germany.
Biophys J. 2020 Apr 7;118(7):1769-1781. doi: 10.1016/j.bpj.2020.02.002. Epub 2020 Feb 12.
The process of transcription initiation and elongation are primary points of control in the regulation of gene expression. Although biochemical studies have uncovered the mechanisms involved in controlling transcription at each step, how these mechanisms manifest in vivo at the level of individual genes is still unclear. Recent experimental advances have enabled single-cell measurements of RNA polymerase (RNAP) molecules engaged in the process of transcribing a gene of interest. In this article, we use Gillespie simulations to show that measurements of cell-to-cell variability of RNAP numbers and interpolymerase distances can reveal the prevailing mode of regulation of a given gene. Mechanisms of regulation at each step, from initiation to elongation dynamics, produce qualitatively distinct signatures, which can further be used to discern between them. Most intriguingly, depending on the initiation kinetics, stochastic elongation can either enhance or suppress cell-to-cell variability at the RNAP level. To demonstrate the value of this framework, we analyze RNAP number distribution data for ribosomal genes in Saccharomyces cerevisiae from three previously published studies and show that this approach provides crucial mechanistic insights into the transcriptional regulation of these genes.
转录起始和延伸过程是基因表达调控的主要控制点。尽管生化研究已经揭示了控制每个步骤转录的机制，但这些机制如何在单个基因水平上在体内表现仍然不清楚。最近的实验进展使得能够对参与感兴趣基因转录的 RNA 聚合酶 (RNAP) 分子进行单细胞测量。在本文中，我们使用 Gillespie 模拟来表明，测量 RNAP 数量和聚合酶间距离的细胞间变异性可以揭示给定基因的主要调控模式。从起始到延伸动力学的每个步骤的调控机制产生定性不同的特征，可进一步用于区分它们。最有趣的是，根据起始动力学，随机延伸可以增强或抑制 RNAP 水平的细胞间变异性。为了证明该框架的价值，我们分析了来自三个先前发表的研究中酿酒酵母核糖体基因的 RNAP 数量分布数据，并表明该方法为这些基因的转录调控提供了关键的机制见解。
