Quantitative models for transcriptional dynamics monitored using an MS2-GFP system

Abstract

Gene expression begins with transcription, in which the information in the DNA sequence of a gene is copied into mRNA. The process of transcription can be divided into three distinct steps: initiation, elongation, and termination. In this review, we discuss how the time rates of these three steps can be obtained by analyzing fluorescence signals from the transcription sites of mRNA labeled with the MS2-GFP system. Particularly, we focus on the analysis methods using (1) the auto-correlation of fluorescence fluctuation and (2) the fluorescence change upon inhibition of transcription initiation. These analysis methods can be also applied to the translational dynamics of a protein labeled using the SunTag system. We provide the full mathematical derivation of the models and relate the theoretical predictions to experimental data to facilitate broader applications of the analysis methods.