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Title: In silico evidence for sequence-dependent nucleosome sliding

Abstract

Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. Furthermore, these processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nudeosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nudeosome repositioning. The mechanism of nudeosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.

Authors:
ORCiD logo [1];  [2];  [3]
+ Show Author Affiliations
  1. Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637,
  2. Laboratory for Molecular and Computational Genomics, Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706,, Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI 53706,, UW-Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706,
  3. Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637,, Materials Science Division, Argonne National Laboratory, Argonne, IL 60439
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; US Department of Commerce; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division; Midwest Integrated Center for Computational Materials (MICCoM); National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI); National Institute of Standards and Technology (NIST), Center for Hierarchical Materials Design (CHiMaD)
OSTI Identifier:
1400015
Alternate Identifier(s):
OSTI ID: 1419955
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 114 Journal Issue: 44; Journal ID: ISSN 0027-8424
Publisher:
Proceedings of the National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; advanced sampling techniques; chromatin dynamics; molecular simulation; nudeosome repositioning

Citation Formats

Lequieu, Joshua, Schwartz, David C., and de Pablo, Juan J.. In silico evidence for sequence-dependent nucleosome sliding. United States: N. p., 2017. Web. doi:10.1073/pnas.1705685114.
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Lequieu, Joshua, Schwartz, David C., & de Pablo, Juan J.. In silico evidence for sequence-dependent nucleosome sliding. United States. https://doi.org/10.1073/pnas.1705685114
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Lequieu, Joshua, Schwartz, David C., and de Pablo, Juan J.. Wed . "In silico evidence for sequence-dependent nucleosome sliding". United States. https://doi.org/10.1073/pnas.1705685114.
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@article{osti_1400015,
title = {In silico evidence for sequence-dependent nucleosome sliding},
author = {Lequieu, Joshua and Schwartz, David C. and de Pablo, Juan J.},
abstractNote = {Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. Furthermore, these processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nudeosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nudeosome repositioning. The mechanism of nudeosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.},
doi = {10.1073/pnas.1705685114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 44,
volume = 114,
place = {United States},
year = {2017},
month = {10}
}
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https://doi.org/10.1073/pnas.1705685114
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