ArticleNucleic acids research2016
Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 90 citations in OpenAlex.
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Article
- Short tandem repeat variants are possibly associated with RNA secondary structure and gene expression.PloS one · 2025Article
- Navigating the landscape of epitranscriptomics and host immunity.Genome research · 2024Review
- 2'-OH as a universal handle for studying intracellular RNAs.Cell chemical biology · 2024Review
- Regulation of bacterial gene expression by non-coding RNA: It is all about time!Cell chemical biology · 2024Review
- Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.PLoS computational biology · 2023Article
- Nucleic acid strand displacement - from DNA nanotechnology to translational regulation.RNA biology · 2023Article
- Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P.Nature communications · 2022Article
- Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes.Genome biology · 2021Article
- In vivo structure of the Ty1 retrotransposon RNA genome.Nucleic acids research · 2021Article
- Ribozyme-Mediated Downregulation Uncovers DNA Integrity Scanning Protein A (DisA) as a Solventogenesis Determinant inFrontiers in bioengineering and biotechnology · 2021Article
- Structured RNA Contaminants in Bacterial Ribo-Seq.mSphere · 2020Article
- Design of a small molecule that stimulates vascular endothelial growth factor A enabled by screening RNA fold-small molecule interactions.Nature chemistry · 2020Article
- An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano.RNA (New York, N.Y.) · 2020Article
- Optimization and characterization of position-selective labelling of RNA (PLOR) for diverse RNA and DNA sequences.RNA biology · 2020Article
- The how and why of lncRNA function: An innate immune perspective.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- The chemistry and applications of RNA 2'-OH acylation.Nature reviews. Chemistry · 2020Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell.
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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.