ArticleCell reports2021
Quantifying the regulatory role of individual transcription factors in Escherichia coli.
Article in Cell reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Synthetic transcriptional repression systems in plants.Plant cell reports · 2026Review
- Core elements play distinct roles in promoter birth and transcriptional regulation.Nature communications · 2026Article
- Decoupling between activation time and steady-state level in input-output responses.PLoS computational biology · 2026Article
- Universal scaling law: transcription factors homeostatically control promoter activity.Signal transduction and targeted therapy · 2026Article
- A unified computational framework for quantitative design and optimization of transcriptional regulation across bacterial species.Nucleic acids research · 2026Article
- Emergence of activation or repression in transcriptional control under a fixed molecular context.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Decoupling between activation time and steady-state level in input-output responses.bioRxiv : the preprint server for biology · 2025Article
- 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
- Article
- Regulatory properties of transcription factors with diverse mechanistic function.PLoS computational biology · 2024Article
- Article
- Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli.Molecular systems biology · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Gene regulation often results from the action of multiple transcription factors (TFs) acting at a promoter, obscuring the individual regulatory effect of each TF on RNA polymerase (RNAP). Here we measure the fundamental regulatory interactions of TFs in E. coli by designing synthetic target genes that isolate individual TFs' regulatory effects. Using a thermodynamic model, each TF's regulatory interactions are decoupled from TF occupancy and interpreted as acting through (de)stabilization of RNAP and (de)acceleration of transcription initiation. We find that the contribution of each mechanism depends on TF identity and binding location; regulation immediately downstream of the promoter is insensitive to TF identity, but the same TFs regulate by distinct mechanisms upstream of the promoter. These two mechanisms are uncoupled and can act coherently, to reinforce the observed regulatory role (activation/repression), or incoherently, wherein the TF regulates two distinct steps with opposing effects.
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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.