核小体定位与基因调控：基因组学的进展
Nucleosome positioning and gene regulation: advances through genomics.
作者信息
Jiang Cizhong, Pugh B Franklin
机构信息
Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
出版信息
Nat Rev Genet. 2009 Mar;10(3):161-72. doi: 10.1038/nrg2522.
Abstract
Knowing the precise locations of nucleosomes in a genome is key to understanding how genes are regulated. Recent 'next generation' ChIP-chip and ChIP-Seq technologies have accelerated our understanding of the basic principles of chromatin organization. Here we discuss what high-resolution genome-wide maps of nucleosome positions have taught us about how nucleosome positioning demarcates promoter regions and transcriptional start sites, and how the composition and structure of promoter nucleosomes facilitate or inhibit transcription. A detailed picture is starting to emerge of how diverse factors, including underlying DNA sequences and chromatin remodelling complexes, influence nucleosome positioning.
摘要
了解核小体在基因组中的精确位置是理解基因如何被调控的关键。最近的“新一代”芯片染色质免疫沉淀技术（ChIP-chip）和测序染色质免疫沉淀技术（ChIP-Seq）加速了我们对染色质组织基本原理的理解。在这里，我们讨论核小体位置的高分辨率全基因组图谱让我们了解到核小体定位如何划分启动子区域和转录起始位点，以及启动子核小体的组成和结构如何促进或抑制转录。关于包括潜在DNA序列和染色质重塑复合物在内的多种因素如何影响核小体定位，一幅详细的图景正开始浮现。
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1
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Genome Res. 2009 Mar;19(3):360-71. doi: 10.1101/gr.084970.108. Epub 2009 Jan 5.
2
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.通过核小体定位信号编码的染色质的不同调控模式。
PLoS Comput Biol. 2008 Nov;4(11):e1000216. doi: 10.1371/journal.pcbi.1000216. Epub 2008 Nov 7.
3
The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis.组蛋白变体HTZ-1在秀丽隐杆线虫胚胎发育过程中的基因组分布及功能
PLoS Genet. 2008 Sep 12;4(9):e1000187. doi: 10.1371/journal.pgen.1000187.
4
Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.酿酒酵母中优先量化的连接子DNA长度
PLoS Comput Biol. 2008 Sep 12;4(9):e1000175. doi: 10.1371/journal.pcbi.1000175.
5
Predicting human nucleosome occupancy from primary sequence.从一级序列预测人类核小体占据情况。
PLoS Comput Biol. 2008 Aug 22;4(8):e1000134. doi: 10.1371/journal.pcbi.1000134.
6
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7
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Genome Res. 2008 Jul;18(7):1073-83. doi: 10.1101/gr.078261.108. Epub 2008 Jun 12.
8
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Genome Res. 2008 Jul;18(7):1051-63. doi: 10.1101/gr.076463.108. Epub 2008 May 13.
10
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