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Significance Cells adapt to their environment by modulating the amount of RNA transcripts produced in a gene-specific manner. While some transcription factors are recruited via DNA sequence motifs, other factors bind directly to RNA polymerase to modulate the rate constants underlying the initiation process. Here, I describe a freely available web-based tool to quantitatively evaluate how factor-induced changes in the rate constants connecting initiation intermediates combine to regulate the amount of RNA produced per time. I use these calculations to show that multifaceted kinetic mechanisms may lead to differential and promoter-specific regulation. Finally, I explore the mechanisms of two factors essential for the response of bacteria to stress. The insights provided help to understand the logic of bacterial gene regulation.

The calculation of transcript flux ratios reveals single regulatory mechanisms capable of activation and repression