Noise and dynamics in eukaryotic gene expression

描述(申请人提供)：在这个项目中，我们建议对单细胞真核生物酿酒酵母中基因表达的随机性的起源和后果进行实验和计算相结合的调查。这项工作的目标是深入了解随机性，或噪声，在真核基因调控和表达的动态中所起的作用，以及基因表达噪声产生的机制。 我们以前已经用实验和计算相结合的方法证明，转录效率和转录控制机制直接与某些真核启动子基因表达中的噪音水平有关。我们还证明了密码子使用和基因表达噪声之间可能存在的联系，表明基因表达噪声的一个可能的决定因素可能是在基因组中编码的。此外，我们已经证明，调节蛋白中噪声的增加可以对双峰反应产生深远的影响，这对于细胞分化和在克隆细胞群体中维持表型变异是至关重要的。这些结果需要进一步研究确定基因表达中噪声水平的具体机制，以及这种噪声如何直接影响细胞表型。因此，该项目的具体目标是：(1)确定转录重新启动过程如何影响给定基因表达的异质性水平；(2)研究密码子的使用如何调节基因表达的异质性水平；(3)检测噪声对克隆细胞群体中单个启动子的分级和双峰反应的影响；以及(4)探索在一个研究得很好的细胞过程中涉及的关键调控基因表达中噪声增加的表型后果。我们将把我们的实验结果与基因表达的随机模型结合起来，以帮助确定影响噪音的转录和翻译过程中的特定机制。 通过将实验研究与计算模型相结合，我们旨在更清楚地了解基因和启动子序列等遗传变量如何调节基因表达噪声，以及这些噪声如何影响细胞表型。我们的目标是开发工具，可以用来更好地预测噪音对细胞行为的影响，从而能够更精确地控制基因表达和细胞功能。

DESCRIPTION (provided by applicant): In this project, we propose a combined experimental and computational investigation of the origins and consequences of stochasticity in gene expression in the single-cell eukaryote Saccharomyces cerevisiae. The goal of this work is to gain insight into the role that stochasticity, or noise, plays in the dynamics of eukaryotic gene regulation and expression, and the mechanisms through which gene expression noise arises. We have previously shown, using a combined experimental and computational approach that transcriptional efficiency and the mechanism of transcriptional control directly relate to the level of noise in gene expression from certain eukaryotic promoters. We have also demonstrated a plausible link between codon usage and gene expression noise, indicating that a possible determinant of gene expression noise may be encoded in the genome. Moreover, we have shown that increased noise in a regulatory protein can have profound effects on bimodal responses, which can be critical for cellular differentiation and the maintenance of phenotypic variation within a clonal population of cells. These results warrant further study of the specific mechanisms involved in determining the level of noise in gene expression, as well as how such noise can directly affect cell phenotype. Accordingly, the specific aims of this project are: (1) to determine how the process of transcriptional reinitiation affects the level of heterogeneity in the expression of a given gene; (2) to examine how codon usage can modulate the level of heterogeneity in the expression of a gene; (3) to examine the effects of noise on graded versus bimodal responses of a single promoter in a clonal population of cells; and (4) to explore the phenotypic consequences of increased noise in the expression of a key regulatory gene involved in a well-studied cellular process. We will couple our experimental findings to stochastic models of gene expression to assist in determining specific mechanisms in the processes of transcription and translation that affect noise. By combining experimental studies with computational models, we aim to more clearly understand how genetic variables, such as gene and promoter sequence can modulate gene expression noise, and how such noise can affect cell phenotype. Our goal is to develop tools, which can be used to better predict the effects of noise on cell behavior, thereby enabling more precise control of gene expression and cell function.