维系的纽带：绘制动态增强子-启动子相互作用组图谱
The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome.
作者信息
Spurrell Cailyn H, Dickel Diane E, Visel Axel
机构信息
MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA.
出版信息
Cell. 2016 Nov 17;167(5):1163-1166. doi: 10.1016/j.cell.2016.10.054.
Abstract
Coupling chromosome conformation capture to molecular enrichment for promoter-containing DNA fragments enables the systematic mapping of interactions between individual distal regulatory sequences and their target genes. In this Minireview, we describe recent progress in the application of this technique and related complementary approaches to gain insight into the lineage- and cell-type-specific dynamics of interactions between regulators and gene promoters.
摘要
将染色体构象捕获与含启动子DNA片段的分子富集相结合，能够系统地绘制单个远端调控序列与其靶基因之间的相互作用图谱。在这篇小型综述中，我们描述了该技术及相关补充方法在应用方面的最新进展，以深入了解调控因子与基因启动子之间相互作用的谱系和细胞类型特异性动态变化。
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本文引用的文献
1
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Cell Rep. 2016 Nov 15;17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059.
2
Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.对正常人类乳腺表观基因组的分析揭示了细胞特异性活性增强子状态及相关转录因子网络。
Cell Rep. 2016 Nov 15;17(8):2060-2074. doi: 10.1016/j.celrep.2016.10.058.
3
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.《染色质接触图谱汇编揭示人类基因组中的空间活跃区域》
Cell Rep. 2016 Nov 15;17(8):2042-2059. doi: 10.1016/j.celrep.2016.10.061.
4
Chromosome conformation elucidates regulatory relationships in developing human brain.染色体构象揭示了发育中的人类大脑中的调控关系。
Nature. 2016 Oct 27;538(7626):523-527. doi: 10.1038/nature19847. Epub 2016 Oct 19.
5
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Nat Commun. 2016 Oct 5;7:12923. doi: 10.1038/ncomms12923.
6
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Nat Commun. 2015 Nov 30;6:10069. doi: 10.1038/ncomms10069.
7
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Genome Res. 2015 Apr;25(4):582-97. doi: 10.1101/gr.185272.114. Epub 2015 Mar 9.
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9
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Nat Commun. 2015 Feb 18;6:6351. doi: 10.1038/ncomms7351.
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