RNA secondary structure ensemble mapping in a living cell identifies conserved RNA regulatory switches and thermometers

RNA molecules can populate ensembles of alternative structural conformations, but comprehensively mapping RNA conformational landscapes within living cells presents significant challenges and has, as such, so far remained elusive. Here, we generated the first transcriptome-scale maps of RNA secondary structure ensembles in a living cell, using Escherichia coli as a model. Our analysis uncovered features of structurally-dynamic regions, as well as the existence of hundreds of highly-conserved bacterial RNA structural elements. Conditional structure mapping revealed extensive restructuring of RNA ensembles during cold shock, leading to the discovery of several novel RNA thermometers in the 5′ UTRs of the cspG, cspI, cpxP and lpxP mRNAs. We mechanistically characterized how these thermometers switch structure in response to cold shock and revealed the cspE chaperone-mediated regulation of lpxP. Collectively, this work reveals a previously unappreciated complexity of RNA structural dynamics in living cells, and it provides a key resource to significantly accelerate the discovery of regulatory RNA switches.