ArticleNature structural & molecular biology2008
A quantitative model of transcription factor-activated gene expression.
Article in Nature structural & molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
90 citing papers in PubMed, 153 citations in OpenAlex.
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- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
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- A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression.Scientific reports · 2024Article
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- Single-molecule chromatin configurations link transcription factor binding to expression in human cells.bioRxiv : the preprint server for biology · 2024Article
- PGEProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient.Cell systems · 2023Article
- Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models.mSystems · 2022Article
- A Toolkit for Precise, Multigene Control inACS synthetic biology · 2022Article
- Effects of size, cooperativity, and competitive binding on protein positioning on DNA.Biophysical journal · 2021Article
- TATA and paused promoters active in differentiated tissues have distinct expression characteristics.Molecular systems biology · 2021Article
- Exploring the effect of network topology, mRNA and protein dynamics on gene regulatory network stability.Nature communications · 2021Article
- Precise determination of input-output mapping for multimodal gene circuits using data from transient transfection.PLoS computational biology · 2020Article
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- Kinetic control of stationary flux ratios for a wide range of biochemical processes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A challenge facing biology is to develop quantitative, predictive models of gene regulation. Eukaryotic promoters contain transcription factor binding sites of differing affinity and accessibility, but we understand little about how these variables combine to generate a fine-tuned, quantitative transcriptional response. Here we used the PHO5 promoter in budding yeast to quantify the relationship between transcription factor input and gene expression output, termed the gene-regulation function (GRF). A model that captures variable interactions between transcription factors, nucleosomes and the promoter faithfully reproduced the observed quantitative changes in the GRF that occur upon altering the affinity of transcription factor binding sites, and implicates nucleosome-modulated accessibility of transcription factor binding sites in increasing the diversity of gene expression profiles. This work establishes a quantitative framework that can be applied to predict GRFs of other eukaryotic genes.
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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.