Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure–function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA–RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA–RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell.
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机译:转换术语± Sup> [n i Sub>] f(+/-) min sup>的条件最小化结构的逻辑动态过程的方法Sub> AND ± Sup> [m i Sub>] f(+/-) min Sub>在功能添加结构中± Sup> f < Sub> 1 Sub>(Σ RU Sub>) min Sub>,不带纹波f 1 Sub>(± Sup>←←)和循环ΔtΣ Sub>→5∙f(&)-和5个条件逻辑函数f(&)-,并通过三元数系统的算术公理同时转换术语参数的过程f RU Sub>(+ 1,0,-1)及其实现其的功能结构(俄罗斯逻辑版本)