An experimental verification of the predicted effects of promoter TATA-box polymorphisms associated with human diseases on interactions between the TATA boxes and TATA-binding protein

PloS One
L K SavinkovaN A Kolchanov

Abstract

Human genome sequencing has resulted in a great body of data, including a stunningly large number of single nucleotide polymorphisms (SNPs) with unknown phenotypic manifestations. Identification and comprehensive analysis of regulatory SNPs in human gene promoters will help quantify the effects of these SNPs on human health. Based on our experimental and computer-aided study of SNPs in TATA boxes and the use of literature data, we have derived an equation for TBP/TATA equilibrium binding in three successive steps: TATA-binding protein (TBP) sliding along DNA due to their nonspecific affinity for each other ↔ recognition of the TATA box ↔ stabilization of the TBP/TATA complex. Using this equation, we have analyzed TATA boxes containing SNPs associated with human diseases and made in silico predictions of changes in TBP/TATA affinity. An electrophoretic mobility shift assay (EMSA)-based experimental study performed under the most standardized conditions demonstrates that the experimentally measured values are highly correlated with the predicted values: the coefficient of linear correlation, r, was 0.822 at a significance level of α<10⁻⁷ for equilibrium K(D) values, (-ln K(D)), and 0.785 at a significance level of α<10⁻³ for chan...Continue Reading

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Related Concepts

MBL2 protein, human
NOS2A protein, human
Xenobiotic Monooxygenases
Globin
Early Promoters, Genetic
Plasma Protein Binding Capacity
Ag-Zn Superoxide Dismutase
TATA Box
Computational Molecular Biology
Single Nucleotide Polymorphism

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