ReviewThe Biochemical journal2011
Gene-specific transcription activation via long-range allosteric shape-shifting.
Review in The Biochemical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs.Journal of molecular biology · 2022Review
- Allostery, and how to define and measure signal transduction.Biophysical chemistry · 2022Review
- Allosteric conformational ensembles have unlimited capacity for integrating information.eLife · 2021Article
- Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines.International journal of molecular sciences · 2020Article
- Protein ensembles link genotype to phenotype.PLoS computational biology · 2019Review
- Inducible super-enhancers are organized based on canonical signal-specific transcription factor binding elements.Nucleic acids research · 2017Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions.PLoS computational biology · 2016Article
- Molecular mechanism of the priming by jasmonic acid of specific dehydration stress response genes in Arabidopsis.Epigenetics & chromatin · 2016Article
- Conformational selection and induced fit for RNA polymerase and RNA/DNA hybrid backtracked recognition.Frontiers in molecular biosciences · 2015Article
- Principles of allosteric interactions in cell signaling.Journal of the American Chemical Society · 2014Review
- Drosophila melanogaster Hox transcription factors access the RNA polymerase II machinery through direct homeodomain binding to a conserved motif of mediator subunit Med19.PLoS genetics · 2014Article
- Multiple conformational selection and induced fit events take place in allosteric propagation.Biophysical chemistry · 2014Review
- Allosteric conformational barcodes direct signaling in the cell.Structure (London, England : 1993) · 2013Review
- The spatial structure of cell signaling systems.Physical biology · 2013Article
- DNA G-quadruplex formation in response to remote downstream transcription activity: long-range sensing and signal transducing in DNA double helix.Nucleic acids research · 2013Article
- Identification of the hypoxia-inducible factor 2α nuclear interactome in melanoma cells reveals master proteins involved in melanoma development.Molecular & cellular proteomics : MCP · 2013Article
- The underappreciated role of allostery in the cellular network.Annual review of biophysics · 2013Review
- Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription.Plant physiology · 2012Article
- Mutual remodeling and conformation grid: a mediator code?Structure (London, England : 1993) · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
How is specificity transmitted over long distances at the molecular level? REs (regulatory elements) are often far from transcription start sites. In the present review we discuss possible mechanisms to explain how information from specific REs is conveyed to the basal transcription machinery through TFs (transcription factors) and the Mediator complex. We hypothesize that this occurs through allosteric pathways: binding of a TF to a RE results in changes in the AD (activation domain) of the TF, which binds to Mediator and alters the distribution of the Mediator conformations, thereby affecting transcription initiation/activation. We argue that Mediator is formed by highly disordered proteins with large densely packed interfaces that make efficient long-range signal propagation possible. We suggest two possible general mechanisms for Mediator action: one in which Mediator influences PIC (pre-initiation complex) assembly and transcription initiation, and another in which Mediator exerts its effect on the already assembled but stalled transcription complex. We summarize (i) relevant information from the literature about Mediator composition, organization and structure; (ii) Mediator interaction partners and their effect on Mediator conformation, function and correlation to the RNA Pol II (polymerase II) CTD (C-terminal domain) phosphorylation; and (iii) propose that different allosteric signal propagation pathways in Mediator relate to PIC assembly and polymerase activation of the stalled transcription complex. The emerging picture provides for the first time a mechanistic view of allosteric signalling from the RE sequence to transcription activation, and an insight into how gene specificity and signal transmission can take place in transcription initiation.
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Registered trials
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.