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Fig. 2 | BMC Genomics

Fig. 2

From: Codon usage and modular interactions between messenger RNA coding regions and small RNAs in Escherichia coli

Fig. 2

Modular structure of sRNAs with multiple targets. a The numbers of interactions for Spot42 (top panel) and OmrA (bottom panel) were plotted as a function of the position of each nucleotide in the primary sequence of the sRNA, allowing for construction of a density map that was then used to identify the zones (top line) and subzones (brackets) that interact with mRNAs. b Interaction zones and subzones were located in the predicted secondary structures of the sRNAs. The probability of forming a base pair is indicated using a color scale ranging from 0 (green) to 1 (red). c A network of the interactions between the mRNA and the sRNA interaction zones was then developed (Panel c). Blue circles connected by blue lines represent the sRNA structure. Boxes represent the mRNA, and edges represent interactions with the corresponding sRNA zone. Repression (red lines), empirical (solid line), and predicted (dotted line) interactions are indicated. The CAI values for each target are indicated using a color scale ranging from green (low CAI values) to red (high CAI values)

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