Ion counting demonstrates a high electrostatic field generated by the nucleosome

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Abstract

The first step towards the eukaryotic nuclear DNA compaction process is the formation of a nucleosome, which comprises of the negatively charged DNA wrapped around a positively charged histone protein octamer. Often, it is assumed that the complexation of the DNA into the nucleosome completely attenuates the DNA charge and hence the electrostatic field generated by the molecule. In contrast, theoretical and computational studies suggest that the nucleosome retains a strong, negative electrostatic field. Despite their fundamental implications for chromatin organization and function, these opposing views of nucleosome electrostatics have not been experimentally tested. Herein, we directly measure nucleosome electrostatics and find that while nucleosome formation reduces the complex charge by half, the nucleosome nevertheless maintains a strong negative electrostatic field. Our studies highlight the importance of considering the polyelectrolyte nature of the nucleosome and its impact on processes ranging from factor binding to DNA compaction.

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All data generated or analyzed during this study are included in the manuscript and supporting files. Source data and source code files have been provided for Figures 3 and 4.

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Magdalena Gebala

Department of Biochemistry, Stanford University, Stanford, United States

For correspondence
mgebala@stanford.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-1086-5548
Stephanie L Johnson

Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.
Geeta J Narlikar

Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States

Competing interests
Geeta J Narlikar, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0002-1920-0147
Daniel Herschlag

Department of Biochemistry, Stanford University, Stanford, United States

For correspondence
herschla@stanford.edu

Competing interests
No competing interests declared.

Funding

National Institutes of Health (P01GM066275)

Daniel Herschlag

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.