Homeorhesis in Waddington's Landscape by Epigenetic Feedback Regulation

TL;DR

This paper presents a theoretical model combining gene expression and epigenetic feedback to explain the robustness and hierarchical landscape changes during cell differentiation, providing insights into developmental homeorhesis.

Contribution

It introduces a novel dynamical-system model that incorporates epigenetic feedback to elucidate the origin of landscape changes and valley branching in cell differentiation.

Findings

Hierarchical fixed-point attractors shape the epigenetic landscape.

Epigenetic feedback induces landscape robustness and valley branching.

The model explains homeorhesis as slow feedback reinforcement in development.

Abstract

In multicellular organisms, cells differentiate into several distinct types during early development. Determination of each cellular state, along with the ratio of each cell type, as well as the developmental course during cell differentiation are highly regulated processes that are robust to noise and environmental perturbations throughout development. Waddington metaphorically depicted this robustness as the epigenetic landscape in which the robustness of each cellular state is represented by each valley in the landscape. This robustness is now conceptualized as an approach toward an attractor in a gene-expression dynamical system. However, there is still an incomplete understanding of the origin of landscape change, which is accompanied by branching of valleys that corresponds to the differentiation process. Recent progress in developmental biology has unveiled the molecular processes involved in epigenetic modification, which will be a key to understanding the nature of slow landscape change. Nevertheless, the contribution of the interplay between gene expression and epigenetic modification to robust landscape changes, known as homeorhesis, remains elusive. Here, we introduce a theoretical model that combines epigenetic modification with gene expression dynamics driven by a regulatory network. In this model, epigenetic modification changes the feasibility of expression, i.e., the threshold for expression dynamics, and a slow positive-feedback process from expression to the threshold level is introduced. Under such epigenetic feedback, several fixed-point attractors with distinct expression patterns are generated hierarchically shaping the epigenetic landscape with successive branching of valleys. This theory provides a quantitative framework for explaining homeorhesis in development as postulated by Waddington, based on dynamical-system theory with slow feedback reinforcement.