寻找人类基因组中的远端调控元件。
Finding distal regulatory elements in the human genome.
机构信息
Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Dr., MC 0407, La Jolla, CA 92093-0407, USA.
出版信息
Curr Opin Genet Dev. 2009 Dec;19(6):541-9. doi: 10.1016/j.gde.2009.09.006. Epub 2009 Oct 23.
Abstract
Transcriptional regulation of human genes depends not only on promoters and nearby cis-regulatory elements, but also on distal regulatory elements such as enhancers, insulators, locus control regions, and silencing elements, which are often located far away from the genes they control. Our knowledge of human distal regulatory elements is very limited, but the last several years have seen rapid progress in the development of strategies to identify these long-range regulatory sequences throughout the human genome. Here, we review these advances, focusing on two important classes of distal regulatory sequences-enhancers and insulators.
摘要
人类基因的转录调控不仅依赖于启动子和附近的顺式调控元件，还依赖于远距离的调控元件，如增强子、绝缘子、基因座控制区和沉默元件，这些元件通常位于它们所调控的基因的远处。我们对人类远距离调控元件的了解非常有限，但在过去几年中，人们开发出了识别整个人类基因组中这些长距离调控序列的策略，并取得了快速进展。在这里，我们回顾这些进展，重点关注两类重要的远距离调控序列——增强子和绝缘子。
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本文引用的文献
1
Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus.黏连蛋白在发育调控的IFNG基因座处形成染色体顺式相互作用。
Nature. 2009 Jul 16;460(7253):410-3. doi: 10.1038/nature08079. Epub 2009 May 20.
2
Diversity and complexity in DNA recognition by transcription factors.转录因子对DNA识别的多样性与复杂性
Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.
3
How cohesin and CTCF cooperate in regulating gene expression.黏连蛋白和CTCF如何协同调节基因表达。
Chromosome Res. 2009;17(2):201-14. doi: 10.1007/s10577-008-9017-7. Epub 2009 Mar 24.
4
Histone modifications at human enhancers reflect global cell-type-specific gene expression.人类增强子上的组蛋白修饰反映了整体细胞类型特异性基因表达。
Nature. 2009 May 7;459(7243):108-12. doi: 10.1038/nature07829. Epub 2009 Mar 18.
5
A census of human transcription factors: function, expression and evolution.人类转录因子普查：功能、表达与进化
Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538.
6
ChIP-seq accurately predicts tissue-specific activity of enhancers.染色质免疫沉淀测序（ChIP-seq）能准确预测增强子的组织特异性活性。
Nature. 2009 Feb 12;457(7231):854-8. doi: 10.1038/nature07730.
7
CTCF-dependent enhancer-blocking by alternative chromatin loop formation.通过替代性染色质环形成实现的CTCF依赖性增强子阻断
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20398-403. doi: 10.1073/pnas.0808506106. Epub 2008 Dec 12.
8
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.对染色质屏障区域中绝缘子结合蛋白CTCF的全局分析揭示了活性结构域和抑制结构域的划分。
Genome Res. 2009 Jan;19(1):24-32. doi: 10.1101/gr.082800.108. Epub 2008 Dec 3.
9
Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules.增强核受体诱导的转录需要核马达和染色质间颗粒中依赖LSD1的基因网络。
Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19199-204. doi: 10.1073/pnas.0810634105. Epub 2008 Dec 3.
10
Long-range chromosomal interactions and gene regulation.远程染色体相互作用与基因调控。
Mol Biosyst. 2008 Nov;4(11):1046-57. doi: 10.1039/b803580f. Epub 2008 Aug 13.
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