NusG-dependent transcription pausing in Bacillus subtilis

Bacterial transcription is punctuated by RNA polymerase (RNAP) pausing that can provide time for regulatory events to occur. However, the genome-wide role of transcription elongation factors on pausing had not been examined in vivo. We determined the genome-wide effect of Bacillus subtilis NusG on RNAP pausing using RNET-seq, a nascent RNA sequencing protocol. NusG shifts RNAP to the post-translocation register, and induces pausing at ~1600 sites containing a conserved TTNTTT motif in the non-template DNA strand within the paused transcription bubble. NusG-dependent pausing was confirmed for all pause sites tested in vitro. NusG-dependent pausing in the ribD riboswitch provides time for cotranscriptional FMN binding, which decreases the concentration of FMN required for termination.