ReviewRNA (New York, N.Y.)2013
On the importance of cotranscriptional RNA structure formation.
Review in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
93 citing papers in PubMed.
- InteRRact: a web server for the interactive exploration and comparison of transcriptome-wide RNA-RNA interactions.NAR genomics and bioinformatics · 2026Article
- Elucidating structure-function relationships in the mammalian nucleolus.Nature reviews. Molecular cell biology · 2026Review
- RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.NAR genomics and bioinformatics · 2026Article
- Cellular-state control using ribozyme-scaffolded miRNA-sensing and CRISPR-mediated actuation.Cell reports methods · 2026Article
- StraD: a coarse-grained simulation of co-transcriptional RNA folding.NAR genomics and bioinformatics · 2025Article
- Switchable RNA motifs for dynamic transcriptional control of RNA condensates.Nucleic acids research · 2025Article
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display.Nature communications · 2025Article
- Tissue-specific modulation of CRISPR activity by miRNA-sensing guide RNAs.Nucleic acids research · 2025Article
- Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography.Nature communications · 2024Article
- Modular RNA motifs for orthogonal phase separated compartments.Nature communications · 2024Article
- A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration.Nature communications · 2024Article
- RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations.Nucleic acids research · 2024Article
- Regulation of bacterial gene expression by non-coding RNA: It is all about time!Cell chemical biology · 2024Review
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.Nucleic acids research · 2023Article
- Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly.Biomolecules · 2023Review
- Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution.Nature communications · 2023Article
- Article
- Temperature Matters: Bacterial Response to Temperature Change.Journal of microbiology (Seoul, Korea) · 2023Review
33 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.