Molecular Properties of Transcription Factors that Control Cell-to-Cell Variability in Gene Expression

相同环境中的遗传相同的细胞在基因表达方面可能具有较大的细胞间差异。这些差异的一个主要原因是，转录发生在随机的“突发”活动。表达的随机爆发使发育期间的细胞类型多样化，有助于癌细胞中的化疗抗性，并阻碍重编程实验中纯细胞类型的产生。尽管爆发是发育和疾病中基因表达的一个重要特性，但细胞间表达变异的分子原因仍然知之甚少。基因的平均表达水平和细胞间变异性在发育中都很重要。一个关键的实验观察是，具有相同平均表达的基因可以具有不同的细胞间变异性。因此，分子机制必须发展到从平均表达水平解偶联细胞间变异性的调节。细胞如何控制细胞间变异而不影响平均表达尚不清楚。我们建议使用“突发模型”的表达作为一个框架，从平均表达水平分离细胞间变异的调节。突发模型表明，表达的平均值和变异性可以通过独立控制基因的“突发大小”（每次突发产生的mRNA数量）和“突发频率”（突发之间的时间）来分离。产生大但不频繁爆发的基因（发育调节因子）将具有高平均水平和高细胞间变异性，而具有较小更频繁爆发的基因（代谢酶）可以达到相同的平均水平，变异性要小得多。因此，确定分离爆发大小和频率控制的分子机制将是解释表达平均值和变异性独立控制的重要一步。我们建议，以确定是否扰动不同的转录因子（TF）的功能有可分离的影响突发的大小和频率。我们的目标的成功完成将有助于从细胞间变异性中分离出平均水平的调节。这些结果将1）告知自然选择是否可以独立于平均水平改变细胞间变异性，2）阐明在细胞命运决定期间产生高变异性的调控机制，以及3）建议在依赖于TF异位表达的应用中抑制细胞间变异性的方法。

Genetically identical cells in the same environment can have large cell-to-cell differences in gene expression. A major reason for these differences is that transcription occurs in stochastic “bursts” of activity. Stochastic bursts of expression diversify cell types during development, contribute to chemotherapeutic resistance in cancer cells, and hinder the production of pure cell types in reprogramming experiments. Although bursting is an important property of gene expression in development and disease, the molecular causes of cell to- cell variability in expression remain poorly understood. Both the mean expression levels and cell-to-cell variability of genes are important in development. A key experimental observation is that genes with the same mean expression can have different cell-to-cell variability. Therefore, molecular mechanisms must have evolved to uncouple the regulation of cell-to-cell variability from mean expression levels. How cells can control cell-to-cell variability without influencing mean expression is unknown. We propose to use the “Bursty Model” of expression as a framework for separating the regulation of cell to- cell variability from mean expression levels. The Bursty Model suggests that the mean and variability of expression can be separated through independent control of a gene’s “burst size'' (the number of mRNAs produced per burst) and “burst frequency” (the time between bursts). Genes producing large but infrequent bursts (developmental regulators) would have both high mean levels and high cell-to-cell variability, while genes with smaller more frequent bursts (metabolic enzymes) could reach the same mean levels with much less variability. Therefore, identifying the molecular mechanisms that separate the control of burst size and frequency would be an important step towards explaining the independent control of mean and variability in expression. We propose to determine whether perturbations to different transcription factor (TF) functions have separable effects on burst size and frequency. Successful completion of our aims would help uncouple the regulation of mean levels from cell-to-cell variability. The results would 1) inform whether natural selection can alter cell-to-cell variability independent of mean levels, 2) shed light on regulatory mechanisms that generate high variability during cell fate decisions, and 3) suggest ways to suppress cell-to-cell variability in applications that rely on the ectopic expression of TFs.