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. 2023 Dec 7;14:8106. doi: 10.1038/s41467-023-43632-1

Fig. 2. Global profiling of RNA-RNA interactome by iRIL-seq across growth stages.

Fig. 2

a Western blot confirmed the pulldown of Hfq at three growth stages. Salmonella WT and Hfq::FLAG strains carrying pYC582 were grown in LB. T4 RNA ligase was induced with L-arabinose for 30 min, before reaching the indicated growth stages (EP: Exponential Phase at OD 0.5, ESP: Early Stationary Phase at OD 2.0, SP: Stationary Phase at OD 2.0 + 3 h). Cells were collected and subjected to iRIL-seq. Input, total proteins from bacterial lysates. IP, proteins after immunoprecipitation using an anti-FLAG antibody. Blot shown is representative of n = 2 biological replicates. b Relative fraction of individual sRNAs as singleton and S-chimeric fragments in iRIL samples. Percentage represents the reads of a given sRNA compared to all reads from top 100 sRNAs in a library. c Venn diagram analysis of RNA–RNA interactions at three growth stages. d–f Circos plots represent RNA interaction networks at three growth stages. RNA-RNA interactions from three growth stages were represented on the Salmonella chromosome. Circumference: Interacting sRNAs in order of genomic context. Labeled sRNAs interact with at least five putative targets, and their interactions are shown in color. Other interactions are black. Source data are provided as a Source Data file.