Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

J Biol Chem. 2016 May 6;291(19):10293-306. doi: 10.1074/jbc.M115.691154. Epub 2016 Feb 24.

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.

Keywords: DNA-binding protein; computational biology; cooperativity; heterodimer-DNA interactions; specificity models; transcription; transcription regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • DNA / chemistry
  • DNA / metabolism*
  • Humans
  • Models, Molecular*
  • PPAR gamma / chemistry
  • PPAR gamma / metabolism*
  • Protein Multimerization
  • Retinoid X Receptor alpha / chemistry
  • Retinoid X Receptor alpha / metabolism*

Substances

  • PPAR gamma
  • Retinoid X Receptor alpha
  • DNA