Partially Assembled Nucleosome Structures at Atomic Detail. Rychkov, G., Ilatovskiy, A., Nazarov, I., Shvetsov, A., Lebedev, D., Konev, A., Isaev-Ivanov, V., & Onufriev, A. Biophysical Journal, 112(3):460-472, 2017. cited By 15![Partially Assembled Nucleosome Structures at Atomic Detail [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo. © 2017 Biophysical Society
@ARTICLE{Rychkov2017460,
author={Rychkov, G.N. and Ilatovskiy, A.V. and Nazarov, I.B. and Shvetsov, A.V. and Lebedev, D.V. and Konev, A.Y. and Isaev-Ivanov, V.V. and Onufriev, A.V.},
title={Partially Assembled Nucleosome Structures at Atomic Detail},
journal={Biophysical Journal},
year={2017},
volume={112},
number={3},
pages={460-472},
doi={10.1016/j.bpj.2016.10.041},
note={cited By 15},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009290748&doi=10.1016%2fj.bpj.2016.10.041&partnerID=40&md5=11a123be201359b0889bc6505c1b6dc0},
affiliation={Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center “Kurchatov Institute” Orlova Roscha, Gatchina, Russian Federation; Institute of Physics, Nanotechnology and Telecommunications, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, United States; Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation; Institute of Applied Mathematics and Mechanics, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation; Departments of Computer Science and Physics Virginia Tech, Blacksburg, Virginia, United States},
abstract={The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo. © 2017 Biophysical Society},
funding_details={Российский Фонд Фундаментальных Исследований (РФФИ)obr-i 14-24-01103},
funding_details={Ministry of Education and Science of the Russian Federation8482 07.09.2012},
funding_details={Russian Science Foundation14-50-00068},
funding_details={National Institutes of HealthR01 GM099450, GM076121},
}
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Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. 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