ArticleNature biotechnology2026
Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.
Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.Nucleic acids research · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- VIRSE: a variational Bayesian framework for RNA structural ensemble inference.Briefings in bioinformatics · 2026Article
- Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell.Nature methods · 2026Article
- Localized ribosome access and distal tuning via thebioRxiv : the preprint server for biology · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning.Nature communications · 2026Article
- Alternative Splicing: Molecular Mechanisms, Biological Functions, Diseases, and Potential Therapeutic Targets.MedComm · 2025Review
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.bioRxiv : the preprint server for biology · 2025Article
- Control of gene output by intron RNA structure.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
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Abstract
RNA molecules can populate ensembles of alternative structural conformations; however, comprehensively mapping RNA conformational landscapes within living cells presents notable challenges and has, as such, so far remained elusive. Here, we generate transcriptome-scale maps of RNA secondary structure ensembles in both Escherichia coli and human cells, uncovering features of structurally heterogeneous regions. By combining ensemble deconvolution and covariation analyses, we report the discovery of several bacterial RNA thermometers in the 5' untranslated regions (UTRs) of the cspG, cspI, cpxP and lpxP mRNAs of Escherichia coli. We mechanistically characterize how these thermometers switch structure in response to cold shock and reveal the CspE chaperone-mediated regulation of lpxP. Furthermore, we introduce a method for the transcriptome-scale mapping of 5' UTR structures in eukaryotes and leverage it to uncover RNA structural switches regulating the differential usage of open reading frames in the 5' UTRs of the CKS2 and TXNL4A mRNAs in HEK293 cells. Collectively, this work reveals the complexity of RNA structural dynamics in living cells and provides a resource to accelerate the discovery of regulatory RNA switches.
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