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Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures

BACKGROUND: H2A.B, the most divergent histone variant of H2A, can significantly modulate nucleosome and chromatin structures. However, the related structural details and the underlying mechanism remain elusive to date. In this work, we built atomic models of the H2A.B-containing nucleosome core part...

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Autores principales: Peng, Junhui, Yuan, Chuang, Hua, Xinfan, Zhang, Zhiyong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362417/
https://www.ncbi.nlm.nih.gov/pubmed/32664941
http://dx.doi.org/10.1186/s13072-020-00351-x
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author Peng, Junhui
Yuan, Chuang
Hua, Xinfan
Zhang, Zhiyong
author_facet Peng, Junhui
Yuan, Chuang
Hua, Xinfan
Zhang, Zhiyong
author_sort Peng, Junhui
collection PubMed
description BACKGROUND: H2A.B, the most divergent histone variant of H2A, can significantly modulate nucleosome and chromatin structures. However, the related structural details and the underlying mechanism remain elusive to date. In this work, we built atomic models of the H2A.B-containing nucleosome core particle (NCP), chromatosome, and chromatin fiber. Multiscale modeling including all-atom molecular dynamics and coarse-grained simulations were then carried out for these systems. RESULTS: It is found that sequence differences at the C-terminal tail, the docking domain, and the L2 loop, between H2A.B and H2A are directly responsible for the DNA unwrapping in the H2A.B NCP, whereas the N-terminus of H2A.B may somewhat compensate for the aforementioned unwrapping effect. The assembly of the H2A.B NCP is more difficult than that of the H2A NCP. H2A.B may also modulate the interactions of H1 with both the NCP and the linker DNA and could further affect the higher-order structure of the chromatin fiber. CONCLUSIONS: The results agree with the experimental results and may shed new light on the biological function of H2A.B. Multiscale modeling may be a valuable tool for investigating structure and dynamics of the nucleosome and the chromatin induced by various histone variants.
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spelling pubmed-73624172020-07-17 Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures Peng, Junhui Yuan, Chuang Hua, Xinfan Zhang, Zhiyong Epigenetics Chromatin Research BACKGROUND: H2A.B, the most divergent histone variant of H2A, can significantly modulate nucleosome and chromatin structures. However, the related structural details and the underlying mechanism remain elusive to date. In this work, we built atomic models of the H2A.B-containing nucleosome core particle (NCP), chromatosome, and chromatin fiber. Multiscale modeling including all-atom molecular dynamics and coarse-grained simulations were then carried out for these systems. RESULTS: It is found that sequence differences at the C-terminal tail, the docking domain, and the L2 loop, between H2A.B and H2A are directly responsible for the DNA unwrapping in the H2A.B NCP, whereas the N-terminus of H2A.B may somewhat compensate for the aforementioned unwrapping effect. The assembly of the H2A.B NCP is more difficult than that of the H2A NCP. H2A.B may also modulate the interactions of H1 with both the NCP and the linker DNA and could further affect the higher-order structure of the chromatin fiber. CONCLUSIONS: The results agree with the experimental results and may shed new light on the biological function of H2A.B. Multiscale modeling may be a valuable tool for investigating structure and dynamics of the nucleosome and the chromatin induced by various histone variants. BioMed Central 2020-07-14 /pmc/articles/PMC7362417/ /pubmed/32664941 http://dx.doi.org/10.1186/s13072-020-00351-x Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Peng, Junhui
Yuan, Chuang
Hua, Xinfan
Zhang, Zhiyong
Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures
title Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures
title_full Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures
title_fullStr Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures
title_full_unstemmed Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures
title_short Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures
title_sort molecular mechanism of histone variant h2a.b on stability and assembly of nucleosome and chromatin structures
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362417/
https://www.ncbi.nlm.nih.gov/pubmed/32664941
http://dx.doi.org/10.1186/s13072-020-00351-x
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