Activity of Small RNAs on the Stability of Targeted mRNAs In Vivo

Northern blots are extremely useful to monitor the steady state level of small regulatory RNAs (sRNAs) as well as their target mRNAs. In combination with the drug rifampicin, which blocks cellular transcription, Northern blots can be used to determine the stability of sRNAs and mRNAs. Here we describe a protocol to assess the activity of the sRNA RyhB on the stability of targeted mRNAs sodB , fumA , and iscRSUA . We also describe how to identify a sRNA-induced initial cleavage site on a target mRNA. This protocol can be used for any sRNAs and their target mRNAs.