Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

To understand the contribution of mRNA synthesis and degradation rates towards setting protein concentrations, we performed RNA-sequencing based measurements of mRNA abundance and degradation to facilitate comparisons with recently collected proteomic datasets (Mori 2021) in the same E. coli strain. For mRNA abundance determination, we grew E. coli exponentially in several different growth media and extracted total RNA. To determine mRNA degradation rates, Rifampicin was added to inhibit transcription initiation in exponentially growing E. coli and RNA was extracted from different samples over the next 11 minutes for sequencing.