ArticleNature communications2020
Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
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Who cites it
39 citing papers in PubMed.
- Living circuit boards built by printing bacterial transistors.Nature chemical biology · 2026Article
- Leaky recombinant expression reveals design constraints of bicistronic synthetic operons in Escherichia coli.Scientific reports · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Quantitative Coarse-Grained Modeling of Microbial Metabolism: Uncovering Growth Laws, Environmental Responses, and Host-Circuit Coupling.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Design of CRISPRi-Based Synthetic Gene Circuits in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Broad-Host-Range Synthetic Biology: Rethinking Microbial Chassis as a Design Variable.ACS synthetic biology · 2025Review
- Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control.Nucleic acids research · 2025Article
- Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity.RNA (New York, N.Y.) · 2025Article
- Engineering intercellular communication using M13 phagemid and CRISPR-based gene regulation for multicellular computing in Escherichia coli.Nature communications · 2025Article
- Corrosion-resistant single-atom catalysts for direct seawater electrolysis.National science review · 2025Review
- The switch-liker's guide to plant synthetic gene circuits.The Plant journal : for cell and molecular biology · 2025Review
- Biosensor characterization: formal methods from the perspective of proteome fractions.Synthetic biology (Oxford, England) · 2025Article
- Emerging trends in genome integration tools for precision engineering of diverse bacterial species.Synthetic biology (Oxford, England) · 2025Review
- A long-context language model for deciphering and generating bacteriophage genomes.Nature communications · 2024Article
- Probing the orthogonality and robustness of the mammalian RNA-binding protein Musashi-1 in Escherichia coli.Journal of biological engineering · 2024Article
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.bioRxiv : the preprint server for biology · 2024Article
- Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq.Nature communications · 2024Article
- Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology.Nature communications · 2024Article
- Biophysical characterization of synthetic adhesins for predicting and tuning engineered living material properties.Matter · 2024Article
- Synthetic microbiology in sustainability applications.Nature reviews. Microbiology · 2024Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To perform their computational function, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to characterize parts in the context of the circuit and identify the origins of failures. Here, we take snapshots of a large genetic circuit in different states: RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts (promoters, ribozymes, RBSs, terminators) are parameterized and used to inform a mathematical model that can predict circuit performance, dynamics, and robustness. The circuit behaves as designed; however, it is riddled with genetic errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons, and a failed gate. While not impacting the expected Boolean logic, they reduce the prediction accuracy and could lead to failures when the parts are used in other designs. Finally, the cellular power (RNAP and ribosome usage) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host.
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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.