Figure 2

Identification of novel intergenic sRNAs with sigma 70 promoters using northern blot analysis. The expression of ten transcripts from intergenic regions is shown (these candidates were selected from classes A and B; Figure 1B). The genomic locations of the sRNA regions (black boxed arrows) and the adjacent genes (white boxed arrows) are shown below each panel (black arrow, known promoter; grey arrow, predicted sigma 70 promoter for each sRNA). RNA samples were isolated from E. coli cells grown to exponential (E) or stationary (S) phase in M63 minimal medium. Total, total RNA (20 μg per lane); LM, low-molecular-weight RNA (2 μg per lane). Black triangles indicate that the band size was approximately the same as the predicted length of the sRNA based on the deep sequencing analysis. White triangles indicate bands that may represent new TSSs for downstream genes. 5S rRNA expression is shown as the loading control.