ArticleCell reports2012
Operator sequence alters gene expression independently of transcription factor occupancy in bacteria.
Article in Cell reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators.Nucleic acids research · 2025Article
- Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.ACS synthetic biology · 2025Review
- Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns.PLoS computational biology · 2024Article
- Delaying production with prokaryotic inducible expression systems.Microbial cell factories · 2024Review
- Deciphering regulatory architectures from synthetic single-cell expression patterns.bioRxiv : the preprint server for biology · 2024Article
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- Regulatory properties of transcription factors with diverse mechanistic function.PLoS computational biology · 2024Article
- Cell factory engineering: Challenges and opportunities for synthetic biology applications.Biotechnology and bioengineering · 2023Review
- TReSR: A PCR-compatible DNA sequence design method for engineering proteins containing tandem repeats.PloS one · 2023Article
- Article
- Concentration-dependent transcriptional switching through a collective action of cis-elements.Science advances · 2022Article
- Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli.Molecular systems biology · 2022Article
- Quantifying the regulatory role of individual transcription factors in Escherichia coli.Cell reports · 2021Article
- Allostery through DNA drives phenotype switching.Nature communications · 2021Article
- Review
- Nonequilibrium models of optimal enhancer function.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Insights into Transcriptional Repression of the Homologous Toxin-Antitoxin CassettesInternational journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
A canonical quantitative view of transcriptional regulation holds that the only role of operator sequence is to set the probability of transcription factor binding, with operator occupancy determining the level of gene expression. In this work, we test this idea by characterizing repression in vivo and the binding of RNA polymerase in vitro in experiments where operators of various sequences were placed either upstream or downstream from the promoter in Escherichia coli. Surprisingly, we find that operators with a weaker binding affinity can yield higher repression levels than stronger operators. Repressor bound to upstream operators modulates promoter escape, and the magnitude of this modulation is not correlated with the repressor-operator binding affinity. This suggests that operator sequences may modulate transcription by altering the nature of the interaction of the bound transcription factor with the transcriptional machinery, implying a new layer of sequence dependence that must be confronted in the quantitative understanding of gene expression.
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