BIOPHYSICS SEMINAR Featuring Jingyi Fei “RNA-Based Gene Expression and Regulation at Single-Molecule and Single-Cell Levels”

Abstract

The efficiency, accuracy, and regulation of gene expression are of fundamental importance to living systems. Single-molecule and single-cell imaging approaches have provided powerful means for studying these aspects of gene expression, allowing us to characterize the in vitro and in vivo dynamics of the gene expression machinery at unprecedented precision and depth. Here, I will present applications of such imaging approaches to study two classes of RNA molecules that perform diverse catalytic and regulatory functions during gene expression. First, I will discuss the use of single-molecule fluorescence resonance energy transfer to characterize the conformational dynamics of the ribosome as it translates an mRNA into the encoded protein product and the role that these conformational dynamics play in driving and regulating protein synthesis. Second, I will discuss the use of a new imaging and analysis platform based on super resolution fluorescence microscopy, which enabled the first in vivo determination of base pairing-mediated target search kinetics. Specifically, this platform was used to investigate the target search kinetics of a stress-induced bacterial small RNA (sRNA) that induces the degradation of target mRNAs. The data reveal that the sRNA binds to a primary target mRNA in a reversible and dynamic fashion, and that formation of the sRNA-mRNA complexes is rate-limiting, dictating the overall efficiency of regulation in vivo. Examination of a secondary target indicated that differences in the target search kinetics contribute to setting the regulation priority among different target mRNAs. This super-resolution imaging and analysis approach provides a conceptual framework that can be generalized to other sRNA systems and other target search processes.