An estimation method of the kinetic rates of transcription initiation by Eσ70 and Eσ38 from measurements of individual RNA productions

One of the global regulators of transcription dynamics in Escherichia coli is the intracellular population of σ factors, due to their role in gene selection for transcription. It is unknown to which degree σ factors affect the dynamics of transcription initiation, following the binding between the RNAP holoenzyme (Eσ) and the promoter, and the closed complex formation. Proposed here is a new method to study the kinetics of the underlying steps in transcription initiation from time-lapse imaging of transcription events at the single RNA level in live cells. Namely, assuming a promoter that can be transcribed by Eσ70 or Eσ38, the researchers make use of in silico data from a stochastic model of transcription dynamics of that promoter, to show that the method estimates consistently and effectively the kinetics rates of closed and open complex formation by Eσ70 and Eσ38. In the end, the necessary measurement procedures for acquiring the data needed to apply this new methodology are described.