Figure 2.

Measuring the Effect of the sRNA on Target mRNA Levels

(A) Only a subset of the targets shows an expression change following sRNA overexpression. Shown are Volcano plots of RNA-seq results of gene expression change following sRNA overexpression. Gene expression change is represented by the log₂ fold change in expression levels, as obtained from DESeq2 analysis (Love et al., 2014) (x axis). The statistical significance of the change is represented as −log₁₀p (y axis). p is the p value corrected for multiple hypothesis testing (padj from DESeq2). For clarity, only genes with −log₁₀p ≤ 20 are presented. Green dots represent the sRNA targets that were detected by RIL-seq applied to E. coli grown to a certain growth phase or condition (GcvB to exponential phase; MicA, ArcZ, and CyaR to stationary phase; and RyhB to exponential phase under iron limitation). Black dots represent the rest of the E. coli genes. The dashed line represents the statistical significance threshold (p ≤ 0.1).

(B) sRNA targets detected by RIL-seq were enriched among genes showing a statistically significant change in expression level following overexpression of the sRNA (statistical significance of the enrichment was computed by hypergeometric test). Black numbers represent non-target genes showing a statistically significant change in expression (both up- and downregulated). Blue/green numbers represent RIL-seq targets that showed/did not show a statistically significant change in expression.

See also Figures S1, S3, and S4, and Tables S1, S2, S3, and S4.