Figure 4
Examples of σB-dependent transcripts identified by RNA-Seq. In each panel (A, B, and C), red and blue lines representing normalized RNA-Seq coverage (i.e. the number of reads that match an annotated gene after normalization across runs) in the two 10403S replicates and green and black lines represent normalized RNA-Seq coverage in the ΔsigB strain replicates; the numbers at the top right in each panel indicates the normalized RNA-Seq coverage represented by the horizontal line shown. Panel (A) depicts LMRG_02382 and LMRG_02383 (shown as blue bars), which form an operon (indicated by a long white bar) with a defined Rho-independent terminator (purple bar) downstream of LMRG_02383; the three positive frames of translation with the coding regions in blue and stop codons shown as vertical black bars are also shown. A σB-dependent promoter (red bar) was identified upstream of the operon and the RNA-Seq coverage data clearly shows that the transcription of this operon is positively regulated by σB (i.e. almost no coverage was obtained from the ΔsigB strain). Panel (B) depicts SbrE (Rli47), a σB-dependent noncoding RNA (ncRNA) with Rho-independent terminator and a σB-dependent promoter identified; annotated features as well as positive and negative frames of translation are shown at the bottom with stop codons shown as vertical black bars. Panel (C) shows the 5' end of LMRG_01602 illustrating the position of a σB-dependent promoter in relation to the start codon of the gene and the transcriptional start site determined by RNA-Seq. The black triangle indicates the transcriptional start site determined by RACE-PCR as previously described by Kazmierczak et al. [23].