TY - JOUR
T1 - Modeling the Spatial Motion of Chromatin and the Whole Process of Gene Transcription
AU - Chen , Haowen
AU - Huang , Zihang
AU - Cao , Wenjie
AU - Zhang , Jiajun
AU - Zhou , Tianshou
JO - CSIAM Transactions  on Life Sciences
VL - 2
SP - 258
EP - 279
PY - 2025
DA - 2025/06
SN - 1
DO - http://doi.org/10.4208/csiam-ls.SO-2024-0003a
UR - https://global-sci.org/intro/article_detail/csiam-ls/24162.html
KW - Gene transcription, polymer model, chromatin dynamics, E-P communication, encounter probability.
AB - <p style="text-align: justify;">Biological experiments have verified that chromatin organization has importance influence on gene expression, but the conventional models of gene expression neglect this influence, in particular the effect of enhancer-promoter (E-P) communication on gene expression. Here we first review properties of the classical Rouse
model that is a quite accurate description of chromatin as confirmed by microscopy
experiments. Second, we extend this model to the polymer models with long-range
interactions so that they include E-P communications that are typically long-range interactions. We also carry out theoretical analysis for the extended models. Third, we
establish mathematical models for the whole process of gene transcription, which consider connections between upstream chromatin dynamics and downstream promoter
kinetics. These connections consider two possible ways of regulation: The one via
E-P encounter probability and the other via E-P spatial distance, both supported by
a different experimental measurement. These models lay solid foundations not only
for the deep study of gene-expression dynamics but also for the statistical inference of
experimental data.</p>