Melamed Sahar, Peer Asaf, Faigenbaum-Romm Raya, Gatt Yair E, Reiss Niv, Bar Amir, Altuvia Yael, Argaman Liron, Margalit Hanah
Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
Mol Cell. 2016 Sep 1;63(5):884-97. doi: 10.1016/j.molcel.2016.07.026.
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.
与RNA伴侣蛋白Hfq相关的小RNA（sRNA）是细菌基因表达的关键转录后调节因子。解析sRNA-靶标相互作用组是理解sRNA在细胞网络中作用的重要一步。我们开发了一种广泛适用的方法，称为RIL-seq（通过连接和测序进行RNA相互作用），该方法整合了实验和计算工具，用于在全转录组范围内体内鉴定涉及Hfq相关sRNA的相互作用。通过将这种方法应用于大肠杆菌，我们发现了一个广泛的相互作用网络，其中涉及显示序列互补性的RNA对。我们扩展了已知sRNA的靶标集合，发现了在各种基因组区域编码的额外Hfq结合sRNA及其反式编码靶标，并深入了解了RNA在Hfq上的结合和可能的循环。对不同条件下sRNA相互作用组的比较揭示了sRNA库的变化以及不同条件下网络的大量重新连接。
