Global Mapping of Hfq-dependent RNA-RNA interactions in Caulobacter crescentus

由小的调节RNA（sRNA）进行的转录后控制是细菌中基因表达调节的主要层。高通量测序技术的出现已经揭示了不同细菌物种中的数百种sRNA候选物，然而，它们的功能表征仍然缺乏。大多数sRNA通过与反式编码mRNA的分子间碱基配对起作用，导致这些转录物的稳定性、加工和/或翻译的变化。在革兰氏阴性细菌中，这些RNA之间的短的、通常不完美的相互作用通常由高度保守的RNA伴侣Hfq介导。该项目提案旨在发现模式α-变形杆菌Caulobacter crescentus中Hfq依赖的RNA-RNA相互作用。我们的初步数据显示，在C.然而，这些是如何增加这种生物的生命周期和生理学的，目前尚不清楚。在这里，我们建议采用RIL-seq（RNA相互作用的连接和测序）映射景观Hfq介导的RNA双链体形成在C。在全球范围内渐强。与其他方法相比，RIL-seq能够揭示sRNA的非常规相互作用伴侣，包括海绵RNA。RIL-seq在C. crescentus不仅有望扩大对不同sRNAs相互作用伙伴的了解，而且还将揭示这种生物体中基于RNA的调控的新机制概念。

Post-transcriptional control by small, regulatory RNAs (sRNAs) is a major layer of gene expression regulation in bacteria. The advent of high-throughput sequencing technologies has revealed hundreds of sRNA candidates in different bacterial species, however, their functional characterization is lacking behind. Most sRNAs act through inter-molecular base-pairings with trans-encoded mRNAs, leading to changes in stability, processing and/or translation of these transcripts. In Gram-negative bacteria, these short, often imperfect interactions between RNAs are typically mediated by the highly conserved RNA chaperone, Hfq. This project proposal aims at the discovery of Hfq-dependent RNA-RNA interactions in the model alpha-proteobacterium, Caulobacter crescentus. Our preliminary data revealed dozens of Hfq-binding sRNAs in C. crescentus, however, how these add to the lifecycle and physiology of this organism is currently unknown. Here, we propose to employ RIL-seq (RNA interaction by ligation and sequencing) to map the landscape Hfq-mediated RNA duplex formation in C. crescentus at a global scale. In contrast to other methods, RIL-seq is able to reveal unconventional interaction partners of sRNAs, including sponge RNAs. Application of RIL-seq to C. crescentus is expected to not only expand the knowledge on the interaction partners of distinct sRNAs, but also to uncover novel mechanistic concepts of RNA-based regulation in this organism.