A new model for gene regulation

The development of any organism is controlled by networks of genes working together. These genes are themselves tightly regulated at multiple levels as part of the many cell-differentiation programs of higher eukaryotes. This tight regulation is predominantly imposed at the level of gene transcription that, in turn, is initiated by a set of regulatory proteins called transcription factors (TFs). Certain TFs have the ability to cooperate on DNA elements as heterodimers, providing an alternative mode of gene regulation. Publishing in the Journal of Biological Chemistry, EPFL scientists have now built a computer model of DNA binding specificity for these heterodimers that provides superior predictive power over existing models.

The labs of Bart Deplancke and Vassily Hatzimanikatis used a novel approach that combines microfluidics and mechanistic modeling. The researchers used a high-throughput microfluidic platform to monitor dimer-DNA assembly and to measure the strength of underlying molecular interactions.

The team studied the DNA binding of two TFs, PPARγ, RXRα, as well as the heterodimer they form, PPARγ:RXRα. The heterodimer regulates the expression of a large number of genes, including some involved in the development of adipose tissue. The scientists were able to measure cooperative heterodimer binding to more than 300 target DNA sites and variants thereof.

In order to understand the nature of these cooperative interactions and to characterize the “strength” of cooperative heterodimer-DNA binding with respect to the composition of the DNA target site, the researchers, led by Alina Isakova and Yves Berset, built a mechanistic model that accounts for all possible intermediate and final complexes that can occur between two TFs and DNA.

Using the model, the team was able to derive a novel and comprehensive cooperativity constant for heterodimer-DNA binding, which they further used to construct the position weight matrix for PPARγ:RXRα binding to multiple DNA sites. The DNA binding specificity model they obtained shows superior predictive power than regular models based on a one-site equilibrium. Importantly, the data also shows for the first time that individual nucleotide substitutions within the DNA target site can alter the degree of cooperativity in heterodimer-DNA binding.

The authors state that the study “emphasizes the importance of assessing cooperativity when generating DNA binding specificity models for heterodimers.”

This work represents a collaboration between EPFL’s Institute of Bioengineering and Institute of Chemical Sciences and Engineering. It was funded by the Swiss National Science Foundation, EPFL and SystemsX.ch, and the Swiss Initiative in Systems Biology.

Reference

Isakova A, Berset Y, Hatzimanikatis V, Deplancke B. Quantification of cooperativity in heterodimer-DNA binding improves the accuracy of binding specificity models. Journal of Biological Chemistry 24 February 2016. DOI: 10.1074/jbc.M115.691154