Transcriptomic profiles and RNA half-life of M. acetivorans growing in acetate, methanol, and trimethylamine

The goal of this work was to measure the half-lives of RNA transcripts and identify which genes in Methanosarcina acetivorans C2A were differentially expressed between methylotrophic and acetitrophic growth substrates. We used this data to predict metabolic phenotype under different growth condition and hypothesize whether key metabolic genes were transcriptionally or degradationally regulated. Overall design: The mRNA from Methanosarcina acetivorans C2A grown on acetate, methanol and trimethylamine was harvested, sequenced and mapped to the M. acetivorans genome. For each condition, mRNA was harvested at 6 or 7 timepoints after halting transcription with actinomycin D. Degradation rates were computed genome-wide for the three growth substrates. Genes differentially expressed genes between each condition were identified.