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一种在酵母中以碱基对分辨率绘制核小体图谱的化学方法。

A chemical approach to mapping nucleosomes at base pair resolution in yeast.

作者信息

Brogaard Kristin R, Xi Liqun, Wang Ji-Ping, Widom Jonathan

机构信息

Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.

出版信息

Methods Enzymol. 2012;513:315-34. doi: 10.1016/B978-0-12-391938-0.00014-8.

DOI:10.1016/B978-0-12-391938-0.00014-8
PMID:22929776
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5101424/
Abstract

Most eukaryotic DNA exists in DNA-protein complexes known as nucleosomes. The exact locations of nucleosomes along the genome play a critical role in chromosome functions and gene regulation. However, the current methods for nucleosome mapping do not provide the necessary accuracy to identify the precise nucleosome locations. Here we describe a new experimental approach that directly maps nucleosome center locations in vivo genome-wide at single base pair resolution.

摘要

大多数真核生物的DNA存在于被称为核小体的DNA-蛋白质复合物中。核小体在基因组上的确切位置在染色体功能和基因调控中起着关键作用。然而,目前用于核小体定位的方法无法提供确定精确核小体位置所需的精度。在此,我们描述了一种新的实验方法,该方法能在全基因组范围内以单碱基对分辨率直接在体内定位核小体中心位置。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/3af65234ba57/nihms827228f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/cec8b5000439/nihms827228f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/78e6c7d50309/nihms827228f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/19420b6792a9/nihms827228f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/c2ddb91a36b2/nihms827228f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/7b02fd8a68f7/nihms827228f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/f4ab16d6e05c/nihms827228f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/3af65234ba57/nihms827228f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/cec8b5000439/nihms827228f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/78e6c7d50309/nihms827228f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/19420b6792a9/nihms827228f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/c2ddb91a36b2/nihms827228f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/7b02fd8a68f7/nihms827228f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/f4ab16d6e05c/nihms827228f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a8b/5101424/3af65234ba57/nihms827228f7.jpg

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本文引用的文献

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2
The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere.芽殖酵母的着丝粒核小体定位完美,覆盖整个着丝粒。
Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12687-92. doi: 10.1073/pnas.1104978108. Epub 2011 Jul 18.
3
Occlusion of regulatory sequences by promoter nucleosomes in vivo.体内调控序列被启动子核小体所封闭。
转录诱导的六聚体-核小体复合物由 Chd1 和 FACT 解决。
Mol Cell. 2024 Sep 19;84(18):3423-3437.e8. doi: 10.1016/j.molcel.2024.08.022. Epub 2024 Sep 12.
4
Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.星系 Dnpatterntools 用于核小体定位序列模式的计算分析。
Int J Mol Sci. 2022 Apr 28;23(9):4869. doi: 10.3390/ijms23094869.
5
Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins.复制起始点处细胞周期依赖的染色质动力学
Genes (Basel). 2021 Dec 16;12(12):1998. doi: 10.3390/genes12121998.
6
Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos.基于化学图的核小体定位预测,使用 Bioconductor 包 nuCpos。
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7
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8
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9
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10
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PLoS One. 2017 Oct 26;12(10):e0186974. doi: 10.1371/journal.pone.0186974. eCollection 2017.
PLoS One. 2011 Mar 3;6(3):e17521. doi: 10.1371/journal.pone.0017521.
4
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5
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6
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8
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