Small RNAs (sRNAs) associated with the RNA chaperon protein Hfq are key posttranscriptional regulators of gene expression in bacteria. Deciphering the sRNA-target interactome is an essential step toward understanding the roles of sRNAs in the cellular networks. We developed a broadly applicable methodology termed RIL-seq (RNA interaction by ligation and sequencing), which integrates experimental and computational tools for in vivo transcriptome-wide identification of interactions involving Hfq-associated sRNAs. By applying this methodology to Escherichia coli we discovered an extensive network of interactions involving RNA pairs showing sequence complementarity. We expand the ensemble of targets for known sRNAs, uncover additional Hfq-bound sRNAs encoded in various genomic regions along with their trans encoded targets, and provide insights into binding and possible cycling of RNAs on Hfq. Comparison of the sRNA interactome under various conditions has revealed changes in the sRNA repertoire as well as substantial re-wiring of the network between conditions.
Bibliographical noteFunding Information:
This study was supported by the European Research Council Advanced Grant #322920, I-CORE Programs of the Planning and Budgeting Committee and The Israel Science Foundation (grants 1796/12 and 41/1), and the Israel Science Foundation administered by the Israeli Academy for Sciences and Humanities (grant 1411/13). We thank T. Kaplan for his helpful advice, R. Rehani for her contribution to the experiments, H. Aiba for the hfq-Flag strain, O. Pines for the Saccharomyces cerevisiae strain, S. Pearl-Mizrahi, O. Shechter, and M. Nitzan for technical assistance, G. Storz for work conducted by S.M. in her lab and for very helpful advice, S. Altuvia, E. Holmqvist, I. Rosenshine, and S. Ben-Yehuda for their very useful comments, and K. McDowall and J. Wade for data sharing.
© 2016 Elsevier Inc.