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序列对染色质的“编程”——核小体密码中除了GC含量还有更多内容吗?

Chromatin 'programming' by sequence--is there more to the nucleosome code than %GC?

作者信息

Hughes Amanda, Rando Oliver J

机构信息

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street No, 903, Worcester, MA 01605, USA.

出版信息

J Biol. 2009;8(11):96. doi: 10.1186/jbiol207. Epub 2009 Dec 23.

DOI:10.1186/jbiol207
PMID:20067596
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2804288/
Abstract

The role of genomic sequence in directing the packaging of eukaryotic genomes into chromatin has been the subject of considerable recent debate. A new paper from Tillo and Hughes shows that the intrinsic thermodynamic preference of a given sequence in the yeast genome for the histone octamer can largely be captured with a simple model, and in fact is mostly explained by %GC. Thus, the rules for predicting nucleosome occupancy from genomic sequence are much less complicated than has been claimed. See research article http://www.biomedcentral.com/1471-2105/10/442.

摘要

基因组序列在指导真核生物基因组包装成染色质过程中的作用,一直是近期相当多争论的主题。蒂洛和休斯的一篇新论文表明,酵母基因组中给定序列对组蛋白八聚体的内在热力学偏好,在很大程度上可以用一个简单模型来捕捉,实际上主要由%GC来解释。因此,从基因组序列预测核小体占据率的规则比声称的要简单得多。见研究文章http://www.biomedcentral.com/1471-2105/10/442 。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e15a/2804288/3dbc69e95bbc/jbiol207-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e15a/2804288/3dbc69e95bbc/jbiol207-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e15a/2804288/3dbc69e95bbc/jbiol207-1.jpg

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本文引用的文献

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Nucleic Acids Res. 2010 Jan;38(3):709-19. doi: 10.1093/nar/gkp1043. Epub 2009 Nov 24.
3
High-resolution nucleosome mapping reveals transcription-dependent promoter packaging.高分辨率核小体作图揭示了转录依赖性启动子包装。
ISRN Mol Biol. 2012 Oct 15;2012:245706. doi: 10.5402/2012/245706. eCollection 2012.
4
Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species.一组近交青鳉物种中核小体相位、序列不对称性与组织特异性表达之间的关联。
BMC Genomics. 2015 Nov 19;16:978. doi: 10.1186/s12864-015-2198-5.
5
Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection.针对单纯疱疹病毒1型(HSV-1)的全基因组核小体图谱显示,在裂解感染期间,核小体沉积于偏好位置。
PLoS One. 2015 Feb 24;10(2):e0117471. doi: 10.1371/journal.pone.0117471. eCollection 2015.
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