In vivo RNA interactome profiling reveals 3’UTR-processed small RNA targeting a central regulatory hub

作者：Fang Liu, Ziying Chen, Shuo Zhang, Kejing Wu, Cheng Bei, Chuan Wang, Yanjie Chao · 发表于：Nature Communications · 年份：2023 · DOI：10.1038/s41467-023-43632-1 · 被引用次数：42 · 研究领域：RNA and protein synthesis mechanisms、RNA Research and Splicing、RNA modifications and cancer

Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3'UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.