核小体在单分子分辨率下的结构动力学。
Structural dynamics of nucleosomes at single-molecule resolution.
机构信息
Department of Physics, Bio-X Program, Stanford University, Stanford, CA 94305, USA.
出版信息
Trends Biochem Sci. 2012 Oct;37(10):425-35. doi: 10.1016/j.tibs.2012.06.006. Epub 2012 Jul 23.
Abstract
The detailed mechanisms of how DNA that is assembled around a histone core can be accessed by DNA-binding proteins for transcription, replication, or repair, remain elusive nearly 40 years after Kornberg's nucleosome model was proposed. Uncovering the structural dynamics of nucleosomes is a crucial step in elucidating the mechanisms regulating genome accessibility. This requires the deconvolution of multiple structural states within an ensemble. Recent advances in single-molecule methods enable unprecedented efficiency in examining subpopulation dynamics. In this review, we summarize studies of nucleosome structure and dynamics from single-molecule approaches and how they advance our understanding of the mechanisms that govern DNA transactions.
摘要
近 40 年前，科恩伯格（Kornberg）提出核小体模型以来，关于组装在组蛋白核心周围的 DNA 如何被 DNA 结合蛋白用于转录、复制或修复的详细机制仍然难以捉摸。阐明调控基因组可及性的机制的关键步骤是揭示核小体的结构动力学。这需要对整体中的多个结构状态进行分解。单分子方法的最新进展使检查亚群动力学的效率前所未有。在这篇综述中，我们总结了单分子方法研究核小体结构和动力学的进展，以及它们如何推进我们对控制 DNA 交易的机制的理解。
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本文引用的文献
1
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Cold Spring Harb Protoc. 2012 Jan 1;2012(1):34-49. doi: 10.1101/pdb.top067488.
2
Effects of DNA methylation on the structure of nucleosomes.DNA 甲基化对核小体结构的影响。
J Am Chem Soc. 2012 Jan 11;134(1):173-5. doi: 10.1021/ja210273w. Epub 2011 Dec 15.
3
The dynamics of the nucleosome: thermal effects, external forces and ATP.核小体的动力学：热效应、外力和 ATP。
FEBS J. 2011 Oct;278(19):3619-32. doi: 10.1111/j.1742-4658.2011.08283.x. Epub 2011 Sep 2.
4
Histone fold modifications control nucleosome unwrapping and disassembly.组蛋白折叠修饰控制核小体的展开和拆卸。
Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12711-6. doi: 10.1073/pnas.1106264108. Epub 2011 Jul 18.
5
A quantitative model of nucleosome dynamics.核小体动力学的定量模型。
Nucleic Acids Res. 2011 Oct;39(19):8306-13. doi: 10.1093/nar/gkr422. Epub 2011 Jul 14.
6
Dynamics of nucleosome invasion by DNA binding proteins.DNA 结合蛋白对核小体的入侵动力学。
J Mol Biol. 2011 Aug 12;411(2):430-48. doi: 10.1016/j.jmb.2011.05.044. Epub 2011 Jun 6.
7
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