RNA-Seq samples of E. coli K12 MG1655, deletion of ryhB sRNA gene, 2,2'-Dipyridy

Bacteria adapt to environmental changes by remodeling their gene expression programs. The change in expression of specific genes is due to the combined effects of various regulators, among them small RNAs (sRNAs). Here we present a straightforward RNA-seq-based approach to infer the contribution of a sRNA to the total change in gene expression levels of specific genes in response to shifts in environmental conditions, demonstrated here for the sRNA RyhB in cells growing under iron limitation stress. We show that the contribution of RyhB to changes in expression levels of specific genes upon iron limitation varies between the genes, from relatively mild contribution to the expression change of some genes to ~100% effect on the expression change of other genes. Interestingly, the contribution of RyhB is high for genes undergoing in total mild expression changes and relatively low for genes undergoing in total high expression changes, implying that for almost all affected genes RyhB renders small changes in expression upon iron limitation. Determining the contribution of a sRNA to the total changes in expression levels of genes in response to an environmental change is important for understanding the integration of regulation by sRNAs in the cellular networks regulating cellular physiology.