A framework for modeling how E-P communication regulates transcription dynamics. (A,B) Schematic for a biological model: The upstream E-P communication in the cell nucleus (A) guides the downstream transcription, which is a multistep process in which only the main steps are depicted (B). (C–E) Schematic for a physical model: A generalized Rouse model is proposed to model chromatin spatial motion including E-P communication (indicated by the red spring with coefficient kEP), where r = [r1, · · · , rN]T represents nuclesome positions in 3D (C). A link function vector λ = H(ds) bridges the temporal disconnection between the upstream and the downstream (D), where ds is the E-P spatial distance, and H is a Hill-like function vector. (E) A schematic of a transcription process, where s = [s1, · · · , sK]T is the vector of the gene's states, and λ is a vector of state switching rates. (F,G) Mathematical model: A 4D nucleome equation (F) is derived to model the spatiotemporal evolution of the entire system, and the characteristics of the three distributions of interest are schematically shown (G).
