Modulation of RNA Polymerase Assembly Dynamics in Transcriptional Regulation

Gorski, Stanislaw A.; Snyder, Sara K.; John, Sam; Grummt, Ingrid; Misteli, Tom

doi:10.1016/j.molcel.2008.04.021

Cited by 80 publications

(89 citation statements)

References 46 publications

(91 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…An FHDC implies that changes in factor concentration act like a rheostat to give a continuum of responses (2,4,36,37), which suggests that gene expression by steroid receptors during development, differentiation, and homeostasis employs differential control, as seen with other transcription factors and morphogens (38)(39)(40)(41). This rheostat model is fully compatible with the many observations that the binding of steroid receptors and transcription factors is rapid and readily reversible (12,13,42). Indeed, the rapid binding of steroid receptors is a consequence of FHDC and a prediction of our theoretical framework.…”

Section: Discussionsupporting

confidence: 64%

A theoretical framework for gene induction and experimental comparisons

Ong

Blackford

Kagan

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

113

View full text Add to dashboard Cite

Ligand-mediated gene induction by steroid receptors is a multistep process characterized by a dose-response curve for gene product that follows a first-order Hill equation. This behavior has classically been explained by steroid binding to receptor being the rate-limiting step. However, this predicts a constant potency of gene induction (EC 50 ) for a given receptor-steroid complex, which is challenged by the findings that various cofactors/reagents can alter this parameter in a gene-specific manner. These properties put strong constraints on the mechanisms of gene induction and raise two questions: How can a first-order Hill dose-response curve (FHDC) arise from a multistep reaction sequence, and how do cofactors modify potency? Here we introduce a theoretical framework in which a sequence of steps yields an FHDC for the final product as a function of the initial agonist concentration. An exact determination of all constants is not required to describe the final FHDC. The theory predicts mechanisms for cofactor/reagent effects on gene-induction potency and maximal activity and it assigns a relative order to cofactors in the sequence of steps. The theory is supported by several observations from glucocorticoid receptor-mediated gene induction. It identifies the mechanism and matches the measured dose-response curves for different concentrations of the combination of cofactor Ubc9 and receptor. It also predicts that an FHDC cannot involve the DNA binding of preformed receptor dimers, which is validated experimentally. The theory is general and can be applied to any biochemical reaction that shows an FHDC.dose-response | Michaelis-Menten | gene expression | steroid receptors | glucocorticoids | pharmacology I n ligand-mediated gene induction, the amount of gene expressed depends on the amount of ligand present. Thus, the specific shape and properties of the dose-response curve of gene induction, which is of crucial importance for development, differentiation, and homeostasis in many biological systems, provide a quantitative means for probing the gene-induction process. In many cases, the dose-response curve in gene induction obeys a sigmoidal curve, but not all sigmoidal curves have the same shape. For example, a dose-response curve obeying a first-order Hill equation or function (Hill coefficient equal to 1) goes from 10 to 90% of maximum activity over an 81-fold change in ligand concentration, whereas only a 9-fold change is required in a secondorder Hill function, which thus has a different shape (Fig. S1). (A first-order Hill function is sometimes called a Michaelis-Menten function.) Depending upon the shape of the dose-response curve, the responsiveness of gene induction to the same variation in ligand concentration will differ greatly. In addition to the shape, the position or potency [i.e., concentration required for 50% of maximal response (EC 50 )] and maximum activity (A max ) of the dose-response curve are required to specify the amount of gene expressed for a given amount of ligand. Despite the vital...

show abstract

Section: Discussionsupporting

confidence: 64%

A theoretical framework for gene induction and experimental comparisons

Ong

Blackford

Kagan

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

113

View full text Add to dashboard Cite

show abstract

“…Previous FRAP experiments have shown that the Pol I machinery dynamically assembles at the rDNA promoter, individual Pol I subunits, or subcomplexes interacting with rDNA in a stochastic manner (10,13). If Ser170/172 phosphorylation promotes dissociation of TIF-IA from Pol I, the nucleolar residence time of GFPtagged TIF-IA should be lower than that of TIF-IAS170/172A and TIF-IA/RPA43.…”

Section: Resultsmentioning

confidence: 99%

Phosphorylation by Casein Kinase 2 Facilitates rRNA Gene Transcription by Promoting Dissociation of TIF-IA from Elongating RNA Polymerase I

Bierhoff

Dundr

Michels

et al. 2008

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

The protein kinase casein kinase 2 (CK2) phosphorylates different components of the RNA polymerase I (Pol I) transcription machinery and exerts a positive effect on rRNA gene (rDNA) transcription. Here we show that CK2 phosphorylates the transcription initiation factor TIF-IA at serines 170 and 172 (Ser170/172), and this phosphorylation triggers the release of TIF-IA from Pol I after transcription initiation. Inhibition of Ser170/172 phosphorylation or covalent tethering of TIF-IA to the RPA43 subunit of Pol I inhibits rDNA transcription, leading to perturbation of nucleolar structure and cell cycle arrest. Fluorescence recovery after photobleaching and chromatin immunoprecipitation experiments demonstrate that dissociation of TIF-IA from Pol I is a prerequisite for proper transcription elongation. In support of phosphorylation of TIF-IA switching from the initiation into the elongation phase, dephosphorylation of Ser170/172 by FCP1 facilitates the reassociation of TIF-IA with Pol I, allowing a new round of rDNA transcription. The results reveal a mechanism by which the functional interplay between CK2 and FCP1 sustains multiple rounds of Pol I transcription.

show abstract

“…Stochastic assembly of transcription factors at their target sites has been described in several systems (14). For HMGB1 and GR, Agresti et al argue that in living cells the stochastic assembly of rapidly moving chromatin binding protein at specific binding sites mutually reinforces their chromatin interactions (1).…”

Section: Discussionmentioning

confidence: 99%

The Nucleosome Binding Protein HMGN3 Modulates the Transcription Profile of Pancreatic β Cells and Affects Insulin Secretion

Ueda¹,

Furusawa²,

Kurahashi³

et al. 2009

Molecular and Cellular Biology

View full text Add to dashboard Cite

Improper glucose-stimulated insulin secretion from pancreatic ␤ cells is a major factor in the onset of type 2 diabetes. We now report that HMGN3, a nuclear protein that binds to nucleosomes and affects chromatin function, is highly expressed in ␤ cells and that in mice, loss of HMGN3 impairs glucose-stimulated insulin secretion and leads to a diabetic phenotype. In pancreatic ␤ cells, loss of HMGN3 affects the transcription of several genes involved in glucose-stimulated insulin secretion, including that of the Glut2 glucose transporter. Chromatin immunoprecipitation reveals that HMGN3 and the transcription factor PDX1 mutually reinforce their specific binding to the chromatin in the promoter of the Glut2 gene, thereby regulating GLUT2 protein levels in pancreatic islets and in ␤ cells. Our results identify a new regulator of glucose homeostasis and demonstrate a link between the activity of a nucleosome binding structural protein and the regulation of insulin secretion.

show abstract

Modulation of RNA Polymerase Assembly Dynamics in Transcriptional Regulation

Cited by 80 publications

References 46 publications

A theoretical framework for gene induction and experimental comparisons

A theoretical framework for gene induction and experimental comparisons

Phosphorylation by Casein Kinase 2 Facilitates rRNA Gene Transcription by Promoting Dissociation of TIF-IA from Elongating RNA Polymerase I

The Nucleosome Binding Protein HMGN3 Modulates the Transcription Profile of Pancreatic β Cells and Affects Insulin Secretion

Contact Info

Product

Resources

About