Methods for Modeling and Measuring Steady-State Transcription Rates


During my PhD in the lab of Eric Galburt, I became interested in how one could use kinetics to make predictions regarding transcriptional activity. To phrase it differently, how does DNA sequence (which encodes for the basal transcription kinetics) lead to gene regulation?  Using a simplified mathematical model (https://doi.org/10.1073/pnas.1809454115) I illustrated how individual DNA sequence motifs can affect the steady-state rate of RNA production via changes in the initiation kinetics and drew caution in using an isolated sequence motif or rate constant when trying to predict transcriptional activity. To ultimately test these predictions, I described methods for a fluorescent-based readout of steady-state transcription. This facile method can be used for any DNA-dependent RNA polymerase and can be scaled up to make high-throughput, genome-wide kinetic measurements.        

Publications


High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase


Drake Jensen, Ana Ruiz Manzano, Maxwell Rector, Eric J Tomko, M. Thomas Record, Eric A. Galburt

Nucleic Acids Research, vol. 51(19), 2023


The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation


Drake Jensen, Eric A. Galburt

Journal of Bacteriology, vol. 203(8), 2021


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