体内 RNA 相互作用组谱分析揭示了靶向中央调控枢纽的 3'UTR 加工小 RNA。
In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub.
机构信息
Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
出版信息
Nat Commun. 2023 Dec 7;14(1):8106. doi: 10.1038/s41467-023-43632-1.
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.
小非编码 RNA（sRNAs）是细菌中基因表达的重要调控因子。sRNAs 与 Hfq 或 ProQ 等主要 RNA 伴侣协同作用，与多个靶 mRNA 碱基配对，并形成大型 RNA-RNA 相互作用网络。为了系统地研究活细胞中的 RNA-RNA 相互作用组，我们开发了一种简化的体内 iRIL-seq（细胞内 RIL-seq）方法。这种通用方法非常稳健，说明了沙门氏菌中 sRNA 相互作用组在多个生长阶段的动态变化。我们已经确定了 OmpD 孔蛋白 mRNA 作为一个中央调控枢纽，它被十几个 sRNAs 靶向，包括从 fadBA mRNA 保守 3'UTR 上切割下来的 FadZ。ompD 和 FadZ 都被 CRP 激活，在脂肪酸代谢途径中构成了一种 I 型非相干前馈环。总之，我们已经建立了一种在活细胞中分析 RNA-RNA 相互作用组的方法，突出了 RNA 调控枢纽和 RNA 网络的复杂性。
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