Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding

Abstract

mRNA translation is a key step in decoding genetic information. Genetic decoding is surprisingly heterogeneous because multiple distinct polypeptides can be synthesized from a single mRNA sequence. To study translational heterogeneity, we developed the MoonTag, a fluorescence labeling system to visualize translation of single mRNAs. When combined with the orthogonal SunTag system, the MoonTag enables dual readouts of translation, greatly expanding the possibilities to interrogate complex translational heterogeneity. By placing MoonTag and SunTag sequences in different translation reading frames, each driven by distinct translation start sites, start site selection of individual ribosomes can be visualized in real time. We find that start site selection is largely stochastic but that the probability of using a particular start site differs among mRNA molecules and can be dynamically regulated over time. This study provides key insights into translation start site selection heterogeneity and provides a powerful toolbox to visualize complex translation dynamics. The MoonTag system is a fluorescence labeling system for visualizing translation of single mRNA molecules in live cells. Combining the MoonTag system with the orthogonal SunTag system enables simultaneous measurements of translation of two open reading frames in an mRNA and reveals that ribosomes differentially decode individual mRNA molecules.