Using a combination of high-throughput chemical probing and computational deconvolution, researchers have generated transcriptome-wide maps of RNA secondary structure ensembles in both E. coli and human cells.
The framework, dubbed DeConStruct, enables researchers to resolve ensembles of co-existing RNA conformations from chemical probing data. When applied to bacterial transcripts, it uncovered hundreds of candidate RNA switches, including several novel RNA thermometers. Among the newly identified thermometers are those controlling cspG, cspI, cpxP, and lpxP.
These findings expand our understanding of cold shock adaptation beyond the traditional view of passive RNA unfolding or increased rigidity at low temperatures. Instead, the data point to a more intricate picture, one where structural ensembles are actively remodeled, likely with the help of cellular chaperones, to fine-tune transcriptional and translational responses.
The team also introduced 5′UTR-MaP, a method tailored to map 5′ UTR structures in eukaryotic transcripts. Using this, they identified RNA structural switches in human CKS2 and TXNL4A mRNAs that regulate usage of upstream open reading frames (uORFs), highlighting a potential mechanism for post-transcriptional regulation in human cells that has been difficult to access at scale.
Importantly, this work challenges the notion of RNA structure as static and instead frames it as a dynamic regulatory layer shaped not only by sequence and thermodynamics, but also by cellular context. Many of the structural transitions observed in the study involve high energy barriers and likely require protein chaperones for interconversion.