Epigenetic Control and Reprogramming-Induced Potential Landscapes of Gene Regulatory Networks: A Quantitative Theoretical Approach

Abstract: We develop an extended Dynamical Mean Field Theory framework to analyze gene regulatory networks (GRNs) incorporating epigenetic modifications. Building on the Hopfield network model analogy to spin glass systems, our approach introduces dynamic terms representing DNA methylation and histone modification to capture their regulatory influence on gene expression. The resulting formulation reduces high-dimensional GRN dynamics to effective stochastic equations, enabling the characterization of both stable and oscillatory states in epigenetically regulated systems. This framework provides a tractable and quantitative method for linking gene regulatory dynamics with epigenetic control, offering new theoretical insights into developmental processes and cell fate decisions.