Fig. 4. iRIL-seq determines mRNA regulatory hubs.

a Circos plot showing the mRNA regulatory hubs that interact with at least four sRNA candidates. The hub mRNAs were depicted on the left hemisphere, with their interacting sRNAs on the right. sRNAs interacting with ompD are in bold. b Genome browser screenshots showing chimeric reads mapped to the 5’ region of ompD. The location of Shine-Dalgarno sequence was indicated as an orange box. c Verification of OmpD regulation by different sRNAs. The Salmonella WT strain containing an empty vector or sRNA overexpression plasmids was grown overnight in LB. Total proteins were analyzed by 12% SDS-PAGE. The gel was stained with Coomassie brilliant blue, or subjected to Western blotting using a polyclonal anti-OMP antiserum. ΔompD served as a OmpD-null control. The OmpD bands are indicated by asterisks. The levels of OmpD from three replicates are quantified. Blot shown is representative of n = 3 biological replicates. Graph bar represents mean relative protein abundance. Error bars indicate standard deviations from n = 3 biological replicates. Source data are provided as a Source Data file.