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

Abstract

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 recentlymore » 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.« less

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [2]
  1. Univ. of Chicago, Chicago, IL (United States)
  2. Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
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
OSTI Identifier:
1557992
Alternate Identifier(s):
OSTI ID: 1524467
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 150; Journal Issue: 21; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Lequieu, Joshua, Córdoba, Andrés, Moller, Joshua, and de Pablo, Juan J. 1CPN: A coarse-grained multi-scale model of chromatin. United States: N. p., 2019. Web. doi:10.1063/1.5092976.
Lequieu, Joshua, Córdoba, Andrés, Moller, Joshua, & de Pablo, Juan J. 1CPN: A coarse-grained multi-scale model of chromatin. United States. doi:10.1063/1.5092976.
Lequieu, Joshua, Córdoba, Andrés, Moller, Joshua, and de Pablo, Juan J. Tue . "1CPN: A coarse-grained multi-scale model of chromatin". United States. doi:10.1063/1.5092976.
@article{osti_1557992,
title = {1CPN: A coarse-grained multi-scale model of chromatin},
author = {Lequieu, Joshua and Córdoba, Andrés and Moller, Joshua and de Pablo, Juan J.},
abstractNote = {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.},
doi = {10.1063/1.5092976},
journal = {Journal of Chemical Physics},
number = 21,
volume = 150,
place = {United States},
year = {2019},
month = {6}
}

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