ArticlePLoS computational biology2007
Enhancer responses to similarly distributed antagonistic gradients in development.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases.Human molecular genetics · 2024Article
- DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.Nature genetics · 2022Article
- Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks.Nucleic acids research · 2021Article
- Article
- Bayesian model selection for the Drosophila gap gene network.BMC bioinformatics · 2019Article
- Article
- Quantitative modeling of gene expression using DNA shape features of binding sites.Nucleic acids research · 2016Article
- A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.Cell systems · 2015Article
- NetExplore: a web server for modeling small network motifs.Bioinformatics (Oxford, England) · 2015Article
- Incorporating chromatin accessibility data into sequence-to-expression modeling.Biophysical journal · 2015Article
- Design principles of stripe-forming motifs: the role of positive feedback.Scientific reports · 2014Article
- Analytic approaches to stochastic gene expression in multicellular systems.Biophysical journal · 2013Review
- Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic.PLoS genetics · 2013Article
- Mutual repression enhances the steepness and precision of gene expression boundaries.PLoS computational biology · 2012Article
- Article
- Gene length may contribute to graded transcriptional responses in the Drosophila embryo.Developmental biology · 2011Article
- Article
- The gap gene network.Cellular and molecular life sciences : CMLS · 2011Review
- Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression.PLoS computational biology · 2010Article
- A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.PloS one · 2009Article
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Authors and funding
2 authors.
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Abstract
Formation of spatial gene expression patterns in development depends on transcriptional responses mediated by gene control regions, enhancers. Here, we explore possible responses of enhancers to overlapping gradients of antagonistic transcriptional regulators in the Drosophila embryo. Using quantitative models based on enhancer structure, we demonstrate how a pair of antagonistic transcription factor gradients with similar or even identical spatial distributions can lead to the formation of distinct gene expression domains along the embryo axes. The described mechanisms are sufficient to explain the formation of the anterior and the posterior knirps expression, the posterior hunchback expression domain, and the lateral stripes of rhomboid expression and of other ventral neurogenic ectodermal genes. The considered principles of interaction between antagonistic gradients at the enhancer level can also be applied to diverse developmental processes, such as domain specification in imaginal discs, or even eyespot pattern formation in the butterfly wing.
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