Fig. 3

Strategy for identifying conserved regions in mRNAs recognized by a common sRNA. As an example, the interactions between OmrA and mRNAs containing one conserved motif (gntP and malK) or two conserved motifs (xylH) are shown. a To identify conserved mRNA regions that recognize a common sRNA, we first constructed an interaction density map. The mRNA sequence segments recognized by zones or subzones of a particular sRNA were then determined based on these density maps. These short sequences were aligned and analyzed using MEME to identify conserved motifs. Significantly conserved motifs are represented by a sequence logo. b Complimentary interactions between sRNAs and mRNAs were predicted, and the conserved motifs were mapped in the mRNA. A network approach was used to graphically represent the presence of conserved motifs in the mRNAs that interacted with the sRNA zone and subzones (nodes and edges in blue). mRNAs with conserved motifs complementary to the A1 subzone, the A2 subzone, or both are shown as red, cyan, and green nodes, respectively