Multiscale modeling of genome organization with maximum entropy optimization
Name
5.0044150.pdf
Description
Published version
Size
17.85 MB
Format
Adobe PDF
Checksum (MD5)
27a5831e6dd5999013899d8cf932ad70
Author(s)
Lin, Xingcheng
Qi, Yifeng
Latham, Andrew P
Zhang, Bin
Date Issued
July 7, 2021
Journal
The Journal of Chemical Physics
Publisher
AIP Publishing
Citation
Lin, Xingcheng, Qi, Yifeng, Latham, Andrew P and Zhang, Bin. 2021. "Multiscale modeling of genome organization with maximum entropy optimization." The Journal of Chemical Physics, 155 (1).
Version
Final published version
Abstract
Three-dimensional (3D) organization of the human genome plays an essential role in all DNA-templated processes, including gene transcription, gene regulation, and DNA replication. Computational modeling can be an effective way of building high-resolution genome structures and improving our understanding of these molecular processes. However, it faces significant challenges as the human genome consists of over 6 × 109 base pairs, a system size that exceeds the capacity of traditional modeling approaches. In this perspective, we review the progress that has been made in modeling the human genome. Coarse-grained models parameterized to reproduce experimental data via the maximum entropy optimization algorithm serve as effective means to study genome organization at various length scales. They have provided insight into the principles of whole-genome organization and enabled de novo predictions of chromosome structures from epigenetic modifications. Applications of these models at a near-atomistic resolution further revealed physicochemical interactions that drive the phase separation of disordered proteins and dictate chromatin stability in situ. We conclude with an outlook on the opportunities and challenges in studying chromosome dynamics.
MIT Department
Massachusetts Institute of Technology. Department of Chemistry
Terms of Use
Creative Commons Attribution 4.0 International license
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1063/5.0044150
