ArticleNature communications2021
Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 52 citations in OpenAlex.
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- Core elements play distinct roles in promoter birth and transcriptional regulation.Nature communications · 2026Article
- PromoterAtlas: decoding regulatory sequences across Gammaproteobacteria using a transformer model.Nature communications · 2026Article
- Coordination chemistry-enabled drug delivery systems: metal-ligand platforms for controlled release and targeted therapeutics.Journal of nanobiotechnology · 2026Review
- Design of the biosensor-dependent coupling system stabilizes the high-synthesis phenotype of cell factory.Nature communications · 2026Article
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- A novel approach to enhance resistance to vascular disease by expressing cell-death-inducing fungal elicitors in the xylem tissue.Plant biotechnology journal · 2025Article
- Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteria.Nature communications · 2025Article
- Modeling and designing enhancers by introducing and harnessing transcription factor binding units.Nature communications · 2025Article
- Targeted mutagenesis of specific genomic DNA sequences in animals for thebioRxiv : the preprint server for biology · 2024Article
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- Sequence modeling and design from molecular to genome scale with Evo.Science (New York, N.Y.) · 2024Article
- Flexibility and sensitivity in gene regulation out of equilibrium.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Delaying production with prokaryotic inducible expression systems.Microbial cell factories · 2024Review
- Generating information-dense promoter sequences with optimal string packing.PLoS computational biology · 2024Article
- Scalable design of orthogonal DNA barcode libraries.Nature computational science · 2024Article
- Regulatory properties of transcription factors with diverse mechanistic function.PLoS computational biology · 2024Article
- Synthetic Homoserine Lactone Sensors for Gram-PositiveACS synthetic biology · 2024Article
- Fine-Tuning Gene Expression in Bacteria by Synthetic Promoters.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.
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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.