ArticlePLoS computational biology2019
Mapping DNA sequence to transcription factor binding energy in vivo.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 66 citations in OpenAlex.
- Motif-Cluster: Motif driven prioritization of transcription factor binding clusters.PLoS computational biology · 2026Article
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- Core elements play distinct roles in promoter birth and transcriptional regulation.Nature communications · 2026Article
- De novo promoters emerge more readily from random DNA than from genomic DNA.Science advances · 2026Article
- Informational blueprints reveal condition-dependent gene regulatory architectures.bioRxiv : the preprint server for biology · 2026Article
- Predictive modeling of gene expression and localization of DNA binding site using deep convolutional neural networks.PLoS computational biology · 2026Article
- The latent cis-regulatory potential of mobile DNA in Escherichia coli.Nature communications · 2025Article
- The Environment-Dependent Regulatory Landscape of thebioRxiv : the preprint server for biology · 2025Article
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- Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.Nature communications · 2025Article
- Abundant clock proteins point to missing molecular regulation in the plant circadian clock.Molecular systems biology · 2025Article
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- The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR.Nature communications · 2024Article
- 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
- Article
- Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors.Cell systems · 2024Article
- Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants.iScience · 2024Article
- Transcription factor interactions explain the context-dependent activity of CRX binding sites.PLoS computational biology · 2024Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Despite the central importance of transcriptional regulation in biology, it has proven difficult to determine the regulatory mechanisms of individual genes, let alone entire gene networks. It is particularly difficult to decipher the biophysical mechanisms of transcriptional regulation in living cells and determine the energetic properties of binding sites for transcription factors and RNA polymerase. In this work, we present a strategy for dissecting transcriptional regulatory sequences using in vivo methods (massively parallel reporter assays) to formulate quantitative models that map a transcription factor binding site's DNA sequence to transcription factor-DNA binding energy. We use these models to predict the binding energies of transcription factor binding sites to within 1 kBT of their measured values. We further explore how such a sequence-energy mapping relates to the mechanisms of trancriptional regulation in various promoter contexts. Specifically, we show that our models can be used to design specific induction responses, analyze the effects of amino acid mutations on DNA sequence preference, and determine how regulatory context affects a transcription factor's sequence specificity.
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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.