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Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails

Yunhui Peng, Shuxiang Li, Alexey Onufriev, David Landsman, Anna R. Panchenko
doi: https://doi.org/10.1101/2020.10.30.360990
Yunhui Peng
1National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
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Shuxiang Li
2Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, ON, Canada
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Alexey Onufriev
3Physics Department, Virginia Tech, VA, USA
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David Landsman
1National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
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Anna R. Panchenko
2Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, ON, Canada
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  • For correspondence: anna.panchenko@queensu.ca
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Abstract

Despite histone tails’ critical roles in epigenetic regulation, little is known about mechanisms of how histone tails modulate the nucleosomal DNA solvent accessibility and recognition of nucleosomes by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full human nucleosome, totaling 26 microseconds of molecular dynamics simulations. We explore the histone tail binding with the nucleosomal and linker DNA and observe rapid conformational transitions between bound and unbound states allowing us to estimate kinetic and thermodynamic properties of the histone tail-DNA interactions. Different histone types exhibit distinct, although conformationally heterogeneous, binding modes and each histone type occludes specific DNA regions from the solvent. Using a comprehensive set of experimental data on nucleosome structural complexes, we find that majority of the studied nucleosome-binding proteins and histone tails target mutually exclusive regions on nucleosomal or linker DNA around the super-helical locations ±1, ±2, and ±7. This finding is explained within the generalized competitive binding and tail displacement models of partners recruitment to nucleosomes. Finally, we demonstrate the crosstalk between different histone post-translational modifications, where charge-altering modifications and mutations typically suppress tail-DNA interactions and enhance histone tail dynamics.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 30, 2020.
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Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails
Yunhui Peng, Shuxiang Li, Alexey Onufriev, David Landsman, Anna R. Panchenko
bioRxiv 2020.10.30.360990; doi: https://doi.org/10.1101/2020.10.30.360990
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Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails
Yunhui Peng, Shuxiang Li, Alexey Onufriev, David Landsman, Anna R. Panchenko
bioRxiv 2020.10.30.360990; doi: https://doi.org/10.1101/2020.10.30.360990

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