ArticleNature communications2014
Design of synthetic yeast promoters via tuning of nucleosome architecture.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Context-aware synthetic promoter design using neural networks enables rewiring of eukaryotic transcriptional networks.NPJ systems biology and applications · 2026Article
- Transcriptional regulation: efficient genetic engineering tools for non-conventional yeasts.FEMS yeast research · 2026Review
- Biological parts in yeast synthetic biology: from regulatory elements to predictive design platforms.FEMS yeast research · 2026Review
- Benchmarking the PAM compatibility of Cas12a variants for high-throughput yeast genetic variant engineering.Applied and environmental microbiology · 2025Article
- Combinatorial Alkali-Responsive Hybrid Promoters as Tools for Heterologous Protein Expression in Saccharomyces cerevisiae.Microbial biotechnology · 2025Article
- Basal association of a transcription factor favors early gene expression.PLoS genetics · 2025Article
- Artificial Intelligence in Advancing Algal Bioactive Ingredients: Production, Characterization, and Application.Foods (Basel, Switzerland) · 2025Review
- Advancing cellulose utilization and engineering consolidated bioprocessing yeasts: current state and perspectives.Applied microbiology and biotechnology · 2025Review
- Engineering artificial cross-species promoters with different transcriptional strengths.Synthetic and systems biotechnology · 2025Article
- Advances and perspectives in genetic expression and operation for the oleaginous yeastSynthetic and systems biotechnology · 2024Review
- AI-Assisted Rational Design and Activity Prediction of Biological Elements for Optimizing Transcription-Factor-Based Biosensors.Molecules (Basel, Switzerland) · 2024Review
- Increased CONature communications · 2024Article
- Systematic sequence engineering enhances the induction strength of the glucose-regulated GTH1 promoter of Komagataella phaffii.Nucleic acids research · 2023Article
- Stepwise genetic modification for efficient expression of heterologous proteins in Aspergillus nidulans.Applied microbiology and biotechnology · 2023Article
- The current situations and limitations of genetic engineering in cyanobacteria: a mini review.Molecular biology reports · 2023Review
- Optimization of Constitutive Promoters Using a Promoter-Trapping Vector inInternational journal of molecular sciences · 2023Article
- Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis.ACS synthetic biology · 2023Article
- Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae.Journal of industrial microbiology & biotechnology · 2023Review
- Perspective: Multiomics and Machine Learning Help Unleash the Alternative Food Potential of Microalgae.Advances in nutrition (Bethesda, Md.) · 2023Article
- Controlling gene expression with deep generative design of regulatory DNA.Nature communications · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Model-based design of biological parts is a critical goal of synthetic biology, especially for eukaryotes. Here we demonstrate that nucleosome architecture can have a role in defining yeast promoter activity and utilize a computationally-guided approach that can enable both the redesign of endogenous promoter sequences and the de novo design of synthetic promoters. Initially, we use our approach to reprogram native promoters for increased expression and evaluate their performance in various genetic contexts. Increases in expression ranging from 1.5- to nearly 6-fold in a plasmid-based system and up to 16-fold in a genomic context were obtained. Next, we demonstrate that, in a single design cycle, it is possible to create functional, purely synthetic yeast promoters that achieve substantial expression levels (within the top sixth percentile among native yeast promoters). In doing so, this work establishes a unique DNA-level specification of promoter activity and demonstrates predictive design of synthetic parts.
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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.