ArticleBMC molecular biology2004
Co-transcriptional folding is encoded within RNA genes.
Article in BMC molecular biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
- Hierarchical analysis of RNA secondary structures with pseudoknots based on sections.PLoS computational biology · 2026Article
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo.Nucleic acids research · 2021Article
- A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control.Nature chemical biology · 2019Article
- LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.Bioinformatics (Oxford, England) · 2019Article
- Self-powered RNA nanomachine driven by metastable structure.Nucleic acids research · 2019Article
- Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization.eLife · 2016Article
- Design, synthesis, and application of Spinach molecular beacons triggered by strand displacement.Methods in enzymology · 2015Article
- Single-molecule studies of riboswitch folding.Biochimica et biophysica acta · 2014Review
- Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers.Nucleic acids research · 2014Article
- On the importance of cotranscriptional RNA structure formation.RNA (New York, N.Y.) · 2013Review
- COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.Nucleic acids research · 2013Article
- Efficient procedures for the numerical simulation of mid-size RNA kinetics.Algorithms for molecular biology : AMB · 2012Article
- The shape-shifting quasispecies of RNA: one sequence, many functional folds.Physical chemistry chemical physics : PCCP · 2011Article
- TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.PLoS computational biology · 2010Article
- Faster computation of exact RNA shape probabilities.Bioinformatics (Oxford, England) · 2010Article
- You're one in a googol: optimizing genes for protein expression.Journal of the Royal Society, Interface · 2009Review
- Dynamics of co-transcriptional pre-mRNA folding influences the induction of dystrophin exon skipping by antisense oligonucleotides.PloS one · 2008Article
- Computational methods in noncoding RNA research.Journal of mathematical biology · 2008Review
- Theoretical analysis of noncanonical base pairing interactions in RNA molecules.Journal of biosciences · 2007Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundMost of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription.
methodsThe main aim of this work is to study if and how co-transcriptional folding is encoded within the primary and secondary structure of RNA genes. In order to achieve this, we study the known primary and secondary structures of a comprehensive data set of 361 RNA genes as well as a set of 48 RNA sequences that are known to differ from the originally transcribed sequence units. We detect co-transcriptional folding by defining two measures of directedness which quantify the extend of asymmetry between alternative helices that lie 5' and those that lie 3' of the known helices with which they compete.
resultsWe show with statistical significance that co-transcriptional folding strongly influences RNA sequences in two ways: (1) alternative helices that would compete with the formation of the functional structure during co-transcriptional folding are suppressed and (2) the formation of transient structures which may serve as guidelines for the co-transcriptional folding pathway is encouraged.
conclusionsThese findings have a number of implications for RNA secondary structure prediction methods and the detection of RNA genes.
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