Hfq LiRIP-seq in Salmonella

We have developed a novel approach named LiRIP-seq to profile the global RNA-RNA interactome in Salmonella enterica. By pulse expressing T4 RNA ligase from an inducible pBAD promoter, LiRIP-seq enables in vivo proximity ligation of Hfq-bound RNAs to their interaction partners. This is followed by enrichment of ligation products (RNA chimeras) using Hfq-coIP and subsequent RNA-seq analysis. Overall design: Salmonella wild type or hfq::3xFLAG tagged strains carrying the plasmid pYC582 or empty vector were grown in LB medium at 37 °C. T4 RNA ligase was induced for 30 min by addition of L-arabinose when the culture reached the indicated OD600 (0.3, 1.5, 2.0+2.5h). RNA-RNA interactomes were profiled by Hfq-coIP and subsequent RNA-seq analysis.