The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.

The organization of nucleosomes along the Eukaryotic genome is maintained over time despite disruptive events such as replication. During this complex process, histones and DNA can form a variety of non-canonical nucleosome conformations, but their precise molecular details and roles during nucleoso...

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Autores principales:	Giovanni B Brandani, Cheng Tan, Shoji Takada
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/8940b376cee94063a189044cf8c96314
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id	oai:doaj.org-article:8940b376cee94063a189044cf8c96314
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spelling	oai:doaj.org-article:8940b376cee94063a189044cf8c963142021-12-02T19:57:22ZThe kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.1553-734X1553-735810.1371/journal.pcbi.1009253https://doaj.org/article/8940b376cee94063a189044cf8c963142021-07-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009253https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The organization of nucleosomes along the Eukaryotic genome is maintained over time despite disruptive events such as replication. During this complex process, histones and DNA can form a variety of non-canonical nucleosome conformations, but their precise molecular details and roles during nucleosome assembly remain unclear. In this study, employing coarse-grained molecular dynamics simulations and Markov state modeling, we characterized the complete kinetics of nucleosome assembly. On the nucleosome-positioning 601 DNA sequence, we observe a rich transition network among various canonical and non-canonical tetrasome, hexasome, and nucleosome conformations. A low salt environment makes nucleosomes stable, but the kinetic landscape becomes more rugged, so that the system is more likely to be trapped in off-pathway partially assembled intermediates. Finally, we find that the co-operativity between DNA bending and histone association enables positioning sequence motifs to direct the assembly process, with potential implications for the dynamic organization of nucleosomes on real genomic sequences.Giovanni B BrandaniCheng TanShoji TakadaPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 7, p e1009253 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Giovanni B Brandani Cheng Tan Shoji Takada The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
description	The organization of nucleosomes along the Eukaryotic genome is maintained over time despite disruptive events such as replication. During this complex process, histones and DNA can form a variety of non-canonical nucleosome conformations, but their precise molecular details and roles during nucleosome assembly remain unclear. In this study, employing coarse-grained molecular dynamics simulations and Markov state modeling, we characterized the complete kinetics of nucleosome assembly. On the nucleosome-positioning 601 DNA sequence, we observe a rich transition network among various canonical and non-canonical tetrasome, hexasome, and nucleosome conformations. A low salt environment makes nucleosomes stable, but the kinetic landscape becomes more rugged, so that the system is more likely to be trapped in off-pathway partially assembled intermediates. Finally, we find that the co-operativity between DNA bending and histone association enables positioning sequence motifs to direct the assembly process, with potential implications for the dynamic organization of nucleosomes on real genomic sequences.
format	article
author	Giovanni B Brandani Cheng Tan Shoji Takada
author_facet	Giovanni B Brandani Cheng Tan Shoji Takada
author_sort	Giovanni B Brandani
title	The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
title_short	The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
title_full	The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
title_fullStr	The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
title_full_unstemmed	The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
title_sort	kinetic landscape of nucleosome assembly: a coarse-grained molecular dynamics study.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/8940b376cee94063a189044cf8c96314
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The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.

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