NSF/BSF: Post-Transcriptional Regulation of Gene Expression: From Molecular Interactions to the Network Level

转录是蛋白质合成的第一步，包括将DNA序列复制到RNA序列中。除了对基因表达的转录调节外，还有一个调节层，称为转录后调节。在真核生物中，microRNAs(MiRNAs)是这一调控网络的关键介体。转录后调控仍然知之甚少，许多基本问题仍然悬而未决。基于miRNA的调控机制的一些特征使其不同于其他基因调控机制：它是化学计量的，因此出现竞争效应，它发生在细胞质中，它涉及调控因子和靶标的运输。这个项目的目标是了解从单个分子的运动和相互作用到网络水平的转录后调控产生的跨时空尺度的细胞属性。该项目将支持科罗拉多州柯林斯堡韦伯中学的外展项目。学生的研究经验将与学校教师协调发展，并整合到其中一个既定的特殊计划中，即韦伯航空航天教育风险投资(WAVE)，该计划为学生提供引人入胜、具有挑战性和严谨的体验，模拟如何组织和进行行星外探索，目的是鼓励学生从事空间科学研究和未来的行业职业生涯。与学校教师的合作将使WAVE课程实现有价值的创新。主要活动将集中在使用RNA和DNA的生物标记物检测生命的存在，参加单分子RNA跟踪的演示，以及评估活细胞中的运动RNA。这个项目的目标是(I)剖析复杂的细胞环境对转录后调控的影响，以及(Ii)阐明转录后网络的串扰效应。PI将使用光学成像来跟踪活细胞中单分子水平的miRNAs和mRNAs的路径。实验轨迹将使用理论和计算方法进行分析，其中包括首次穿越过程和用于计算动力学速率系数的反常扩散理论。这些系数将用于数学模型。对多条路径的分析将确定局部化模式，并破译是否应将网络划分为一组弱耦合的子网络。有人认为，理解转录后调控的一个关键因素在于它与转录调控网络的耦合。将建立一个数据驱动的数学模型，将转录和转录后调控结合为定向(转录)和双向(转录后)链接的混合网络。该项目由物理部的生命系统物理学项目和分子和细胞生物科学部的系统和合成生物学及遗传机制群共同支持。该奖项反映了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。

Transcription is the first step on the path of protein synthesis and consists of copying a DNA sequence into an RNA sequence. In addition to the transcriptional regulation of gene expression, a regulatory layer exists, known as post-transcriptional regulation. In eukaryotes, micro RNAs (miRNAs) are key mediators of this regulatory network. Post-transcriptional regulation is still poorly understood and many fundamental questions remain open. Some features of miRNA-based regulation make it different from other mechanisms of gene regulation: it is stoichiometric and, thus, competition effects emerge, it occurs in the cytoplasm, and it involves transport of both the regulator and targets. The goal of this project is to understand cellular properties that arise from post-transcriptional regulation across spatiotemporal scales, from the motion and interactions of individual molecules to the network level. This project will support an outreach program at Webber Middle School in Fort Collins, CO. Research experiences for students will be developed in coordination with school teachers and integrated within an established exceptional program therein, namely the Webber’s Aerospace Ventures in Education (WAVE), which offers students an engaging, challenging, and rigorous experience simulating how to organize and conduct extra-planetary exploration with the goal of encouraging students to pursue space science research and future careers within the industry. The collaboration with school teachers will enable valuable innovations to the WAVE curriculum. The main activities will focus on testing for the presence of life using biomarkers of RNA and DNA, attending demonstrations of single-molecule RNA tracking, and evaluating the motion RNA in live cells. The objectives of this project are (i) to dissect the effects of the complex cell environment on post-transcriptional regulation and (ii) to elucidate the crosstalk effects of the post-transcriptional network. The PIs will use optical imaging to track the paths of miRNAs and mRNAs at the single-molecule level in living cells. Experimental trajectories will be analyzed using theoretical and computational approaches that include first passage processes and anomalous diffusion theory for the calculation of kinetic rates coefficients. These coefficients will be employed in mathematical models. The analysis of multiple paths will determine localization patterns and decipher whether the network should be divided into a set of weakly coupled subnetworks. It is posited that a key factor in understanding post-transcriptional regulation lies in its coupling to the transcriptional regulation network. A data-driven mathematical model that combines transcriptional and post-transcriptional regulations as a mixed network of directed (transcription) and bidirectional (post-transcription) links will be built. This project is being jointly supported by the Physics of Living Systems program in the Division of Physics and the Systems and Synthetic Biology and Genetic Mechanisms Clusters in the Division of Molecular and Cellular Biosciences.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.