ArticleMolecular cell2021
Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.
Article in Molecular cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 89 citations in OpenAlex.
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism.Nucleic acids research · 2026Article
- Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae.Journal of visualized experiments : JoVE · 2026Article
- Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch.Nature communications · 2026Article
- RNA-Micelles as Self-Assembling Structures for Efficient Co-Delivery of Synergistic siRNA and Nucleoside Analogues to Treat CRC Lung Metastasis.Advanced functional materials · 2026Article
- StraD: a coarse-grained simulation of co-transcriptional RNA folding.NAR genomics and bioinformatics · 2025Article
- CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.Molecular cell · 2025Article
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme.Nucleic acids research · 2024Article
- Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography.Nature communications · 2024Article
- Single-molecule force spectroscopy of toehold-mediated strand displacement.Nature communications · 2024Article
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- Kinetic pathway of HIV-1 TAR cotranscriptional folding.Nucleic acids research · 2024Article
- The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch.Nucleic acids research · 2024Article
- RNA-based controllers for engineering gene and cell therapies.Current opinion in biotechnology · 2024Review
- Regulation of bacterial gene expression by non-coding RNA: It is all about time!Cell chemical biology · 2024Review
- Tailor made: the art of therapeutic mRNA design.Nature reviews. Drug discovery · 2024Review
- Programmable modulation of ribosomal frameshifting by mRNA targeting CRISPR-Cas12a system.iScience · 2023Article
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
The series of RNA folding events that occur during transcription can critically influence cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a method to uncover details of cotranscriptional RNA folding. We model the folding of the Escherichia coli signal recognition particle (SRP) RNA and show that it requires specific local structural fluctuations within a key hairpin to engender efficient cotranscriptional conformational rearrangement into the functional structure. All-atom molecular dynamics simulations suggest that this rearrangement proceeds through an internal toehold-mediated strand-displacement mechanism, which can be disrupted with a point mutation that limits local structural fluctuations and rescued with compensating mutations that restore these fluctuations. Moreover, a cotranscriptional folding intermediate could be cleaved in vitro by recombinant E. coli RNase P, suggesting potential cotranscriptional processing. These results from experiment-guided multi-scale modeling demonstrate that even an RNA with a simple functional structure can undergo complex folding and processing during synthesis.
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