1CPN: A coarse-grained multi-scale model of chromatin

Lequieu, Joshua; Córdoba, Andrés; Moller, Joshua; de Pablo, Juan J.

doi:10.1063/1.5092976

Title: 1CPN: A coarse-grained multi-scale model of chromatin

Journal Article · Tue Jun 04 00:00:00 EDT 2019 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.5092976· OSTI ID:1557992

^[1];

^[1]; Moller, Joshua ^[1];

^[2]

Univ. of Chicago, Chicago, IL (United States)
Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)

A central question in epigenetics is how histone modifications influence the 3D structure of eukaryotic genomes and, ultimately, how this 3D structure is manifested in gene expression. The wide range of length scales that influence the 3D genome structure presents important challenges; epigenetic modifications to histones occur on scales of angstroms, yet the resulting effects of these modifications on genome structure can span micrometers. There is a scarcity of computational tools capable of providing a mechanistic picture of how molecular information from individual histones is propagated up to large regions of the genome. In this work, a new molecular model of chromatin is presented that provides such a picture. This new model, referred to as 1CPN, is structured around a rigorous multiscale approach, whereby free energies from an established and extensively validated model of the nucleosome are mapped onto a reduced coarse-grained topology. As such, 1CPN incorporates detailed physics from the nucleosome, such as histone modifications and DNA sequence, while maintaining the computational efficiency that is required to permit kilobase-scale simulations of genomic DNA. The 1CPN model reproduces the free energies and dynamics of both single nucleosomes and short chromatin fibers, and it is shown to be compatible with recently developed models of the linker histone. It is applied here to examine the effects of the linker DNA on the free energies of chromatin assembly and to demonstrate that these free energies are strongly dependent on the linker DNA length, pitch, and even DNA sequence. In conclusion, the 1CPN model is implemented in the LAMMPS simulation package and is distributed freely for public use.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Science Foundation (NSF); Chilean Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT); Fondo Nacional de Desarrollo Científico y Tecnologico (FONDECYT); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division - Midwest Integrated Center for Computational Materials (MICCoM); USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1557992

Alternate ID(s):: OSTI ID: 1524467

Journal Information:: Journal of Chemical Physics, Vol. 150, Issue 21; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 18 works

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Dynamic condensation of linker histone C-terminal domain regulates chromatin structure. Luque, Antoni; Collepardo-Guevara, Rosana; Grigoryev, Sergei Oxford University Press (OUP) https://doi.org/10.17863/cam.66338	journalarticle	January 2014
Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria Chen, Chongyi; Wang, Wenqin; Li, Gene-Wei Biophysical Journal, Vol. 102, Issue 3 https://doi.org/10.1016/j.bpj.2011.11.2628	journal	January 2012
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping Rao, Suhas S. P.; Huntley, Miriam H.; Durand, Neva C. Cell, Vol. 162, Issue 3 https://doi.org/10.1016/j.cell.2015.07.024	journal	July 2015
Spatial Organization of Chromatin Domains and Compartments in Single Chromosomes Wang, Siyuan; Su, Jun-Han; Beliveau, Brian J. Biophysical Journal, Vol. 112, Issue 3 https://doi.org/10.1016/j.bpj.2016.11.1199	journal	February 2017
Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS Brackley, C. A.; Morozov, A. N.; Marenduzzo, D. arXiv https://doi.org/10.48550/arxiv.1404.1704	text	January 2014
Coarse-grained Modeling of DNA Curvature Freeman, Gordon S.; Hinckley, Daniel M.; Lequieu, Joshua P. arXiv https://doi.org/10.48550/arxiv.1404.7726	text	January 2014
Tension-dependent Free Energies of Nucleosome Unwrapping Lequieu, Joshua; Cordoba, Andres; Schwartz, David C. arXiv https://doi.org/10.48550/arxiv.1607.05742	text	January 2016

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Polymer physics across scales: Modeling the multiscale behavior of functional soft materials and biological systems Spakowitz, Andrew J. The Journal of Chemical Physics, Vol. 151, Issue 23 https://doi.org/10.1063/1.5126852	journal	December 2019

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