Figure 5. Transcriptional start site (TSS)-mapping reveals a consistent spatial relationship between MamA sites and TSSs of methylation-affected genes.

TSSs in strain H37Rv were mapped by the strategy outlined in (A). mRNA was circularized before random-primed synthesis of cDNA. Dashes indicate the variable 3′ end of an mRNA. Gene-specific primers were then used to amplify and sequence 5′-3′ junctions. Junctions appear as transitions from clean to messy sequence due to the variable 3′ ends. (B) TSS-mapping sequence traces are shown for the four genes whose expression is reproducibly affected by MamA. MamA sites, putative sigma factor −10 binding sites, TSSs and ORFs are shown as indicated in the key.