Extended Data Figure 5. Visualization of transcription profiles for ΦNM1γ6 and the ΦNM1 prophage.

Graphical presentation is the same as in Fig. S3. a, ΦNM1γ6 transcription profiles 6 and 15 min post infection (MOI 20). Comparison with ΦNM1 samples at equivalent time points (Fig. S3) reveals a marked decrease in leftward transcription to the left of the central promoter region. We calculated the fold-change in RPM between ΦNM1 and ΦNM1γ6 samples 15 min post infection. Leftward expression within the region bounded by the start of the genome and the central promoter was reduced 32-fold, while only a 4-fold reduction in leftward expression was observed overall. Meanwhile, rightward expression was reduced 4-fold both overall and in this region. This suggests an ~8-fold net reduction in leftward transcription originating from the central promoter. b, ΦNM1 prophage transcription profiles. Strong leftward transcription originates from the central promoter and a few upstream regions which are presumed to be important for lysogenic maintenance. Rightward transcription was weaker than leftward transcription as expected, but not absent. Given the strength of rightward transcription observed during the lytic cycle (Fig. S3), however, this transcription may originate from a subpopulation of cells undergoing prophage induction, rather than the stable lysogen majority.