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

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.