ArticleMolecular systems biology2012
A model of spatially restricted transcription in opposing gradients of activators and repressors.
Article in Molecular systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- Two coacting shadow enhancers regulate twin of eyeless expression during early Drosophila development.Genetics · 2025Article
- Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns.PLoS computational biology · 2024Article
- Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants.iScience · 2024Article
- Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm.Mathematical biosciences · 2021Article
- Article
- Article
- Genomic architecture of Shh-dependent cochlear morphogenesis.Development (Cambridge, England) · 2019Article
- The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages.PloS one · 2019Article
- Analysis of the transcriptional logic governing differential spatial expression in Hh target genes.PloS one · 2019Article
- An information theoretic treatment of sequence-to-expression modeling.PLoS computational biology · 2018Article
- Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis.Scientific reports · 2016Article
- An ancient yet flexible cis-regulatory architecture allows localized Hedgehog tuning by patched/Ptch1.eLife · 2016Article
- A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.Cell systems · 2015Article
- Signal integration by the CYP1A1 promoter--a quantitative study.Nucleic acids research · 2015Article
- A theoretical framework for the regulation of Shh morphogen-controlled gene expression.Development (Cambridge, England) · 2014Article
- Bipartite recognition of DNA by TCF/Pangolin is remarkably flexible and contributes to transcriptional responsiveness and tissue specificity of wingless signaling.PLoS genetics · 2014Article
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
- Transcriptional regulation of graded Hedgehog signaling.Seminars in cell & developmental biology · 2014Review
- Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.Genome research · 2014Article
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4 authors.
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Abstract
Morphogens control patterns of transcription in development, often by establishing concentration gradients of a single transcriptional activator. However, many morphogens, including Hedgehog, create opposing activator and repressor gradients (OARGs). In contrast to single activator gradients, it is not well understood how OARGs control transcriptional patterns. We present a general thermodynamic model that explains how spatial patterns of gene expression are established within OARGs. The model predicts that differences in enhancer binding site affinities for morphogen-responsive transcription factors (TFs) produce discrete transcriptional boundaries, but only when either activators or repressors bind cooperatively. This model quantitatively predicts the boundaries of gene expression within OARGs. When trained on experimental data, our model accounts for the counterintuitive observation that increasing the affinity of binding sites in enhancers of Hedgehog target genes produces more restricted transcription within Hedgehog gradients in Drosophila. Because our model is general, it may explain the role of low-affinity binding sites in many contexts, including mammalian Hedgehog gradients.
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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.