title: Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models.
abstract: Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its impact on heterodimer DNA binding specificity models is still lacking. Here, we used a novel integrative approach, combining microfluidics-steered measurements of dimer-DNA assembly with mechanistic modeling of the implicated protein-protein-DNA interactions to quantitatively interrogate the cooperative DNA binding behavior of the adipogenic peroxisome proliferator-activated receptor γ (PPARγ):retinoid X receptor α (RXRα) heterodimer. Using the high throughput MITOMI (mechanically induced trapping of molecular interactions) platform, we derived equilibrium DNA binding data for PPARγ, RXRα, as well as the PPARγ:RXRα heterodimer to more than 300 target DNA sites and variants thereof. We then quantified cooperativity underlying heterodimer-DNA binding and derived an integrative heterodimer DNA binding constant. Using this cooperativity-inclusive constant, we were able to build a heterodimer-DNA binding specificity model that has superior predictive power than the one based on a regular one-site equilibrium. Our data further revealed that individual nucleotide substitutions within the target site affect the extent of cooperativity in PPARγ:RXRα-DNA binding. Our study therefore emphasizes the importance of assessing cooperativity when generating DNA binding specificity models for heterodimers.
authors.affiliation: From the Institute of Bioengineering, Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
authors.forename: Alina
authors.initials: A
authors.lastname: Isakova
authors.affiliation: From the Institute of Bioengineering, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
authors.forename: Yves
authors.initials: Y
authors.lastname: Berset
authors.affiliation: Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland vassily.hatzimanikatis@epfl.ch.
authors.forename: Vassily
authors.initials: V
authors.lastname: Hatzimanikatis
authors.affiliation: From the Institute of Bioengineering, Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland bart.deplancke@epfl.ch.
authors.forename: Bart
authors.initials: B
authors.lastname: Deplancke
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D047495:PPAR gamma / Q000737:chemistry / Q000378:metabolism*; D055503:Protein Multimerization; D047490:Retinoid X Receptor alpha / Q000737:chemistry / Q000378:metabolism*
chemical_list: D047495:PPAR gamma; D047490:Retinoid X Receptor alpha; D004247:DNA
keywords: DNA-binding protein; computational biology; cooperativity; heterodimer-DNA interactions; specificity models; transcription; transcription regulation