Question

How to tell if mrna levels on treatment are due to increased transcription or decresed dgradation

Answer 1

am studying a gene that's expression is increased over the course of days, presumably induced by oxidative stress. However, when I infect the cells, the mRNA levels remain constant as compared to baseline over the same period of time. I assume this is due to either inhibited transcription or increased mRNA degradation. My hunch is the virus is targeting the mRNA for degradation. I planned to treat with transcription inhibitors like actinomycin D, and then collect RNA on a timecourse assay between control and infected, and measure my mRNA-of-interest via qPCR or Northerns (although I would like to avoid using radiolabled probes). Is this acceptable method to look at mRNA decay rates? How could I go about testing if this is due to inhibited transcription?