Epigenetic factor competition reshapes the EMT landscape

TL;DR

This paper introduces a mathematical model that captures the global competition among epigenetic factors and transcription factors, explaining complex phenotype transitions like EMT and making verifiable predictions.

Contribution

It presents a novel framework integrating local and global epigenetic competition effects into gene regulatory network models, advancing understanding of phenotype plasticity.

Findings

Explains experimental data on EMT transitions.

Predicts new regulatory interactions.

Highlights importance of global epigenetic competition.

Abstract

The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as Gene Regulatory Networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators in addition to local transcription factors, and show the counter-intuitive consequences of such interactions. We apply our approach to recent experimental findings on the Epithelial-Mesenchymal Transition (EMT). We show that it can explain the puzzling experimental data as well provide new verifiable predictions.