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ファイル | 記述 | サイズ | フォーマット | |
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journal.pcbi.1009253.pdf | 2.2 MB | Adobe PDF | 見る/開く |
タイトル: | The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study |
著者: | Brandani, Giovanni B. Tan, Cheng Takada, Shoji |
著者名の別形: | 譚, 丞 高田, 彰二 |
キーワード: | Nucleosomes Histones Biochemical simulations Metastasis Genomics Chromatin Molecular dynamics Nucleosome mapping |
発行日: | Jul-2021 |
出版者: | Public Library of Science (PLoS) |
誌名: | PLoS Computational Biology |
巻: | 17 |
号: | 7 |
論文番号: | e1009253 |
抄録: | 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. |
著作権等: | © 2021 Brandani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
URI: | http://hdl.handle.net/2433/276672 |
DOI(出版社版): | 10.1371/journal.pcbi.1009253 |
PubMed ID: | 34314440 |
出現コレクション: | 学術雑誌掲載論文等 |
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