ArticleNature genetics2013
Mapping the fine structure of a eukaryotic promoter input-output function.
Article in Nature genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
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- Perfect adaptation achieved by transport limitations governs the inorganic phosphate response inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance.Nature communications · 2022Article
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- How affinity of the ELT-2 GATA factor binding toDevelopment (Cambridge, England) · 2020Article
- Recent insights into the genotype-phenotype relationship from massively parallel genetic assays.Evolutionary applications · 2019Review
- Cell-free gene-regulatory network engineering with synthetic transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif.Nucleic acids research · 2018Article
- Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions.Scientific reports · 2018Article
- Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Digital logic circuits in yeast with CRISPR-dCas9 NOR gates.Nature communications · 2017Article
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- Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators.Genome research · 2017Article
- Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations.Cancer discovery · 2016Review
- SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics.Scientific reports · 2016Article
- How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories.Microbiology and molecular biology reviews : MMBR · 2016Review
- Integrative Comparison of the Role of the PHOSPHATE RESPONSE1 Subfamily in Phosphate Signaling and Homeostasis in Rice.Plant physiology · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The precise tuning of gene expression levels is essential for the optimal performance of transcriptional regulatory networks. We created 209 variants of the Saccharomyces cerevisiae PHO5 promoter to quantify how different binding sites for the transcription factor Pho4 affect its output. We found that transcription-factor binding affinities determined in vitro could quantitatively predict the output of a complex yeast promoter. Promoter output was precisely tunable by subtle changes in binding-site affinity of less than 3 kcal mol(-1), which are accessible by modifying 1-2 bases. Our results provide insights into how transcription-factor binding sites regulate gene expression, their possible evolution and how they can be used to precisely tune gene expression. More generally, we show that in vitro binding-energy landscapes of transcription factors can precisely predict the output of a native yeast promoter, indicating that quantitative models of transcriptional regulatory networks are feasible.
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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.