ArticleNucleic acids research2012
Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- The role ofEpigenetics · 2026Review
- Protein-inducible ribosomal frameshifting enables programmable translational control for genetic circuit design in Escherichia coli.Journal of biological engineering · 2026Article
- START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Advances in engineered trans-acting regulatory RNAs and their application in bacterial genome engineering.Journal of industrial microbiology & biotechnology · 2019Review
- Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry.ACS synthetic biology · 2019Article
- RNA-based dynamic genetic controllers: development strategies and applications.Current opinion in biotechnology · 2018Review
- Binary addition in a living cell based on riboregulation.PLoS genetics · 2018Article
- Model-based design of RNA hybridization networks implemented in living cells.Nucleic acids research · 2017Article
- RNAblueprint: flexible multiple target nucleic acid sequence design.Bioinformatics (Oxford, England) · 2017Article
- Design of Artificial Riboswitches as Biosensors.Sensors (Basel, Switzerland) · 2017Review
- Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator.Nucleic acids research · 2017Article
- Opportunities in the design and application of RNA for gene expression control.Nucleic acids research · 2016Review
- Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.Nucleic acids research · 2016Article
- Natural antisense RNAs as mRNA regulatory elements in bacteria: a review on function and applications.Cellular & molecular biology letters · 2016Review
- RNA folding with hard and soft constraints.Algorithms for molecular biology : AMB · 2016Article
- Designer cell signal processing circuits for biotechnology.New biotechnology · 2015Review
- A cis-encoded sRNA, Hfq and mRNA secondary structure act independently to suppress IS200 transposition.Nucleic acids research · 2015Article
- Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression.Nucleic acids research · 2015Article
- Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems.ACS synthetic biology · 2015Article
- Creating small transcription activating RNAs.Nature chemical biology · 2015Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-coding RNAs (ncRNAs) are versatile regulators in cellular networks. While most trans-acting ncRNAs possess well-defined mechanisms that can regulate transcription or translation, they generally lack the ability to directly sense cellular signals. In this work, we describe a set of design principles for fusing ncRNAs to RNA aptamers to engineer allosteric RNA fusion molecules that modulate the activity of ncRNAs in a ligand-inducible way in Escherichia coli. We apply these principles to ncRNA regulators that can regulate translation (IS10 ncRNA) and transcription (pT181 ncRNA), and demonstrate that our design strategy exhibits high modularity between the aptamer ligand-sensing motif and the ncRNA target-recognition motif, which allows us to reconfigure these two motifs to engineer orthogonally acting fusion molecules that respond to different ligands and regulate different targets in the same cell. Finally, we show that the same ncRNA fused with different sensing domains results in a sensory-level NOR gate that integrates multiple input signals to perform genetic logic. These ligand-sensing ncRNA regulators provide useful tools to modulate the activity of structurally related families of ncRNAs, and building upon the growing body of RNA synthetic biology, our ability to design aptamer-ncRNA fusion molecules offers new ways to engineer ligand-sensing regulatory circuits.
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