ArticleNucleic acids research2014
Physical constraints determine the logic of bacterial promoter architectures.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- CDBProm: the Comprehensive Directory of Bacterial Promoters.NAR genomics and bioinformatics · 2024Article
- Identifying the Gene Regulatory Network of the Starvation-Induced Transcriptional Activator Nla28.Journal of bacteriology · 2022Article
- Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance.Nature communications · 2022Article
- Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.Nucleic acids research · 2019Article
- Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors.Genome biology · 2018Article
- Transcription factor target site search and gene regulation in a background of unspecific binding sites.Journal of theoretical biology · 2018Article
- In silico design of context-responsive mammalian promoters with user-defined functionality.Nucleic acids research · 2017Article
- The G-Box Transcriptional Regulatory Code in Arabidopsis.Plant physiology · 2017Article
- Nuclear morphologies: their diversity and functional relevance.Chromosoma · 2017Review
- Assembly PCR synthesis of optimally designed, compact, multi-responsive promoters suited to gene therapy application.Scientific reports · 2016Article
- How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- Reliable scaling of position weight matrices for binding strength comparisons between transcription factors.BMC bioinformatics · 2015Article
- Hybrid incompatibility arises in a sequence-based bioenergetic model of transcription factor binding.Genetics · 2014Article
- Facilitated diffusion buffers noise in gene expression.Physical review. E, Statistical, nonlinear, and soft matter physics · 2014Article
- Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression.Computational and structural biotechnology journal · 2014Review
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Authors and funding
3 authors.
Funding
Abstract
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA) when searching for their target sites. Using computer simulations of this search process, we show that the organization of the binding sites, in conjunction with TF copy number and binding site affinity, plays an important role in determining not only the steady state of promoter occupancy, but also the order at which TFs bind. These effects can be captured by facilitated diffusion-based models, but not by standard thermodynamics. We show that the spacing of binding sites encodes complex logic, which can be derived from combinations of three basic building blocks: switches, barriers and clusters, whose response alone and in higher orders of organization we characterize in detail. Effective promoter organizations are commonly found in the E. coli genome and are highly conserved between strains. This will allow studies of gene regulation at a previously unprecedented level of detail, where our framework can create testable hypothesis of promoter logic.
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