Abstract
A stochastic model of nuclear receptor-mediated transcription was developed based on activation of the aryl hydrocarbon receptor (AHR) by 2,3,7,8-tetrachlorodibenzodioxin (TCDD) and subsequent binding the activated AHR to xenobiotic response elements (XREs) on DNA. The model was based on effects observed in cells lines commonly used as in vitro experimental systems. Following ligand binding, the AHR moves into the cell nucleus and forms a heterodimer with the aryl hydrocarbon nuclear translocator (ARNT). In the model, a requirement for binding to DNA is that a generic coregulatory protein is subsequently bound to the AHR-ARNT dimer. Varying the amount of coregulator available within the nucleus altered both the potency and efficacy of TCDD for inducing for transcription of CYP1A1 mRNA, a commonly used marker for activation of the AHR. Lowering the amount of available cofactor slightly increased the EC50 for the transcriptional response without changing the efficacy or maximal response. Further reduction in the amount of cofactor reduced the efficacy and produced non-monotonic dose-response curves (NMDRCs) at higher ligand concentrations. The shapes of these NMDRCs were reminiscent of the phenomenon of squelching. Resource limitations for transcriptional machinery are becoming apparent in eukaryotic cells. Within single cells, nuclear receptor-mediated gene expression appears to be a stochastic process; however, intercellular communication and other aspects of tissue coordination may represent a compensatory process to maintain an organism’s ability to respond on a phenotypic level to various stimuli within an inconstant environment.
Highlights
As science begins to comprehend the workings of transcription through new techniques such as microarrays, chromatin immuno-precipitation (ChIP), and fluorescence visualizationPLOS ONE | DOI:10.1371/journal.pone.0127952 June 3, 2015Competition for Cofactors Alters Potency and Efficacy these authors are articulated in the author contributions section
We considered inclusion of negative feedback by the aryl hydrocarbon receptor repressor (AHRR) in the model.[72]
The model faithfully reproduces the transcriptional dose-response for cytochrome p450 1A1 (CYP1A1) mRNA at 6 hours from Powis et al (2011)[64] when 1500 molecules of cofactor, 1535 molecules of competing non-AHR binding proteins (Other) and 4000 molecules of RNA polymerase are present in the nucleus (Fig 1)
Summary
As science begins to comprehend the workings of transcription through new techniques such as microarrays, chromatin immuno-precipitation (ChIP), and fluorescence visualization. [17, 18] Recently, the idea of “transcription factories” has been advanced; these transcription factories are assemblies of nuclear receptors, cofactors, RNA polymerases, and other co-regulatory proteins.[19,20,21,22,23] This organization would maximize the shared utility of transcriptional resources Despite these mechanisms for resource allocation, competition for transcriptional resources among independent pathways of gene expression has been observed for a number of years.[24,25,26,27,28] In the case of ligand-activated nuclear receptors such as the aryl hydrocarbon receptor (AHR), a plethora of molecular interactions occur in moving the ligand-bound receptor to the nucleus where it can dimerize with the aryl hydrocarbon nuclear translocator (ARNT) and the liganded dimer functions as a transcription factor.[29,30,31,32,33]. This phenomenon, known as “squelching” has been observed for a number of transcriptional responses.[59,60,61,62,63] Squelching is repression of transcription at high concentrations of ligand by sequestering limiting components (e.g. coactivators) required for transcriptional activation away from the promoter in the affected gene.[63]
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