Engineering gene expression noise to modulate the collective inflammatory response

这个项目的意义在于展示如何通过人工设计基因表达在细胞间分布的适度变化来改变关键的生物功能，有时被称为“噪音”。虽然合成基因工程方法经常被用来改变平均基因表达，但调节噪音的研究还不够深入。此外，这项研究旨在提高学生在科学和工程领域追求更高职业的坚持性。计算和分子生物学的暑期研究实习将提供给当地社区大学。这项研究将通过开发合成方法来精确调节基因表达噪音，从而广泛影响系统和合成生物学领域。这项研究的总体目标是系统地改变炎症信号激活后的基因表达噪音，并展示它如何影响先天免疫细胞中炎症反应的集体细胞激活。需要检验的中心假设是，启动子上的染色质环境和RNA聚合酶II的调节是基因表达噪声的主要决定因素。这些过程可以被综合地定位，以合理地改变转录过程中细胞间的可变性，从而改变细胞群体的反应。这一假说得到了初步数据的支持，这些数据表明启动子对转录的允许性会影响转录噪音。为了实现这项研究的目标，CRISPR-Cas9技术将被用来招募表观遗传调节因子，以靶向启动子来改变基因表达噪音。还将开发一个数学模型来预测转录中特定的分子步骤如何调节噪音。最后，为了探索调节噪音的生物学意义，这些工具将被用来预测和测试改变转录分布如何改变细胞群体中的炎症反应。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The significance of this project is to show how critical biological functions can be modified by synthetically engineering modest changes in the distribution of gene expression across cells, sometimes referred to as “noise”. While synthetic genetic engineering approaches are often used to change average gene expression, modulating noise is under-explored. In addition, this research seeks to improve the persistence of students in pursuing more advanced careers in science and engineering. Summer research internships in computational and molecular biology will be provided to local community college. This research will broadly impact the field of systems and synthetic biology by developing synthetic approaches to precisely modulate gene expression noise. The overall objective of this research is to systematically alter gene expression noise following activation of inflammatory signaling and demonstrate how it impacts collective cell activation of the inflammatory response in innate immune cells. The central hypothesis to be tested is that the chromatin environment at the promoter and RNA polymerase II regulation are major determinants of gene expression noise. These processes can be synthetically targeted to rationally alter cell-to-cell variability during transcription to change cell-population responses. This hypothesis is supported by preliminary data demonstrating that a promoter’s permissiveness for transcription affects transcriptional noise. To achieve the objectives of this research, CRISPR-Cas9 technology will be used to recruit epigenetic regulators to target promoters to alter gene expression noise. A mathematical model will also be developed to predict how specific molecular steps in transcription modulate noise. Finally, to explore the biological significance of modulating noise, these tools will be used to predict and test how altering transcript distributions changes the inflammatory response in a cell population.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.