ArticlePLoS computational biology2011
The role of response elements organization in transcription factor selectivity: the IFN-β enhanceosome example.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 20 citations in OpenAlex.
- Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology.Cell systems · 2023Article
- Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-DependentViruses · 2020Review
- Molecular mechanisms of the protein-protein interaction-regulated binding specificity of basic-region leucine zipper transcription factors.Journal of molecular modeling · 2019Article
- Complex sex-biased antibody responses: estrogen receptors bind estrogen response elements centered within immunoglobulin heavy chain gene enhancers.International immunology · 2019Article
- Enhanceosome transcription factors preferentially dimerize with high mobility group proteins.BMC systems biology · 2016Article
- Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.PLoS computational biology · 2015Article
- Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Article
- Combinatorial control of gene expression.BioMed research international · 2013Review
- Disentangling the many layers of eukaryotic transcriptional regulation.Annual review of genetics · 2012Review
- Two polymorphic residues account for the differences in DNA binding and transcriptional activation by NF-κB proteins encoded by naturally occurring alleles in Nematostella vectensis.Journal of molecular evolution · 2011Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
What is the mechanism through which transcription factors (TFs) assemble specifically along the enhancer DNA? The IFN-β enhanceosome provides a good model system: it is small; its components' crystal structures are available; and there are biochemical and cellular data. In the IFN-β enhanceosome, there are few protein-protein interactions even though consecutive DNA response elements (REs) overlap. Our molecular dynamics (MD) simulations on different motif combinations from the enhanceosome illustrate that cooperativity is achieved via unique organization of the REs: specific binding of one TF can enhance the binding of another TF to a neighboring RE and restrict others, through overlap of REs; the order of the REs can determine which complexes will form; and the alternation of consensus and non-consensus REs can regulate binding specificity by optimizing the interactions among partners. Our observations offer an explanation of how specificity and cooperativity can be attained despite the limited interactions between neighboring TFs on the enhancer DNA. To date, when addressing selective TF binding, attention has largely focused on RE sequences. Yet, the order of the REs on the DNA and the length of the spacers between them can be a key factor in specific combinatorial assembly of the TFs on the enhancer and thus in function. Our results emphasize cooperativity via RE binding sites organization.
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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.