ArticleNature methods2018
Metagenomic mining of regulatory elements enables programmable species-selective gene expression.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 113 citations in OpenAlex.
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- High-throughput engineering of ligand-activated splicing ribozyme through domain insertion.bioRxiv : the preprint server for biology · 2026Article
- CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.Nature communications · 2026Article
- Design prokaryotic cis-regulatory elements using language model.Nucleic acids research · 2026Article
- Information storage across a microbial community using universal RNA barcoding.Nature biotechnology · 2026Article
- A unified computational framework for quantitative design and optimization of transcriptional regulation across bacterial species.Nucleic acids research · 2026Article
- Unraveling the start element and regulatory divergence of core promoters across the domain bacteria.Nucleic acids research · 2025Article
- De novo promoter design method based on deep generative and dynamic evolution algorithm.Nucleic acids research · 2025Article
- Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteria.Nature communications · 2025Article
- Biotechnological advances in plant growth-promoting rhizobacteria for sustainable agriculture.World journal of microbiology & biotechnology · 2024Review
- Synthetic promoter design iniScience · 2024Article
- Construction of Whole Cell Bacterial Biosensors as an Alternative Environmental Monitoring Technology to Detect Naphthenic Acids in Oil Sands Process-Affected Water.ACS synthetic biology · 2024Article
- Transfer learning for cross-context prediction of protein expression from 5'UTR sequence.Nucleic acids research · 2024Article
- Emerging methylation-based approaches in microbiome engineering.Biotechnology for biofuels and bioproducts · 2024Review
- Generating information-dense promoter sequences with optimal string packing.PLoS computational biology · 2024Article
- Species-specific design of artificial promoters by transfer-learning based generative deep-learning model.Nucleic acids research · 2024Article
- mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.Nature methods · 2024Article
- Toolbox of Characterized Genetic Parts forACS synthetic biology · 2024Article
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Authors and funding
10 authors at 5 institutions in 1 country.
Funding
Abstract
Robust and predictably performing synthetic circuits rely on the use of well-characterized regulatory parts across different genetic backgrounds and environmental contexts. Here we report the large-scale metagenomic mining of thousands of natural 5' regulatory sequences from diverse bacteria, and their multiplexed gene expression characterization in industrially relevant microbes. We identified sequences with broad and host-specific expression properties that are robust in various growth conditions. We also observed substantial differences between species in terms of their capacity to utilize exogenous regulatory sequences. Finally, we demonstrate programmable species-selective gene expression that produces distinct and diverse output patterns in different microbes. Together, these findings provide a rich resource of characterized natural regulatory sequences and a framework that can be used to engineer synthetic gene circuits with unique and tunable cross-species functionality and properties, and also suggest the prospect of ultimately engineering complex behaviors at the community level.
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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.