Tension-dependent free energies of nucleosome unwrapping

Lequieu, Joshua; Cordoba, Andres; Schwartz, David C.; de Pablo, Juan J.

doi:10.1021/acscentsci.6b00201

Title: Tension-dependent free energies of nucleosome unwrapping

Journal Article · Tue Aug 23 00:00:00 EDT 2016 · ACS Central Science

DOI:https://doi.org/10.1021/acscentsci.6b00201· OSTI ID:1332925

Lequieu, Joshua ^[1]; Cordoba, Andres ^[1]; Schwartz, David C. ^[2]; de Pablo, Juan J. ^[3]

Univ. of Chicago, Chicago, IL (United States)
Univ. of Wisconsin-Madison, Madison, WI (United States)
Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)

Here, nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails contribute asymmetrically to the stability of the outer and inner turn of nucleosomal DNA and that depending on which histone tails are modified, the tension-dependent response is modulated differently.

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

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences and Engineering Division; US Department of Commerce; National Institute of Standards and Technology (NIST); National Institutes of Health (NIH) - National Human Genome Research Institute (NHGRI)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1332925

Journal Information:: ACS Central Science, Vol. 2, Issue 9; ISSN 2374-7943

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 46 works

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Title: Tension-dependent free energies of nucleosome unwrapping

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