寻找第五种碱基：全基因组胞嘧啶甲基化测序
Finding the fifth base: genome-wide sequencing of cytosine methylation.
作者信息
Lister Ryan, Ecker Joseph R
机构信息
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.
出版信息
Genome Res. 2009 Jun;19(6):959-66. doi: 10.1101/gr.083451.108. Epub 2009 Mar 9.
Abstract
Complete sequences of myriad eukaryotic genomes, including several human genomes, are now available, and recent dramatic developments in DNA sequencing technology are opening the floodgates to vast volumes of sequence data. Yet, despite knowing for several decades that a significant proportion of cytosines in the genomes of plants and animals are present in the form of methylcytosine, until very recently the precise locations of these modified bases have never been accurately mapped throughout a eukaryotic genome. Advanced "next-generation" DNA sequencing technologies are now enabling the global mapping of this epigenetic modification at single-base resolution, providing new insights into the regulation and dynamics of DNA methylation in genomes.
摘要
现在已经有了包括几个人类基因组在内的无数真核生物基因组的完整序列，而且DNA测序技术最近的重大进展正在为大量的序列数据打开闸门。然而，尽管几十年来人们都知道植物和动物基因组中相当一部分胞嘧啶以甲基胞嘧啶的形式存在，但直到最近，这些修饰碱基的精确位置在整个真核生物基因组中从未被准确绘制出来。先进的“下一代”DNA测序技术现在能够以单碱基分辨率对这种表观遗传修饰进行全基因组图谱绘制，为基因组中DNA甲基化的调控和动态变化提供了新的见解。
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本文引用的文献
1
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Nat Biotechnol. 2009 Apr;27(4):353-60. doi: 10.1038/nbt.1530. Epub 2009 Mar 29.
2
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.靶向和全基因组规模策略揭示人类细胞中的基因体甲基化特征。
Nat Biotechnol. 2009 Apr;27(4):361-8. doi: 10.1038/nbt.1533. Epub 2009 Mar 29.
3
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.不同的DNA甲基化模式是分化的人类胚胎干细胞和发育中的人类胎儿肝脏的特征。
Genome Res. 2009 Jun;19(6):1044-56. doi: 10.1101/gr.088773.108. Epub 2009 Mar 9.
4
RNA-directed DNA methylation induces transcriptional activation in plants.RNA介导的DNA甲基化在植物中诱导转录激活。
Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1660-5. doi: 10.1073/pnas.0809294106. Epub 2009 Jan 21.
5
Next-generation DNA sequencing.下一代DNA测序
Nat Biotechnol. 2008 Oct;26(10):1135-45. doi: 10.1038/nbt1486.
6
The sequencing shakeup.测序领域的变革
Nat Biotechnol. 2008 Oct;26(10):1109-12. doi: 10.1038/nbt1008-1109.
7
Fixing the front end.修复前端。
Nat Biotechnol. 2008 Oct;26(10):1101-4. doi: 10.1038/nbt1008-1101.
8
ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis.ROS3是拟南芥中DNA去甲基化所需的一种RNA结合蛋白。
Nature. 2008 Oct 30;455(7217):1259-62. doi: 10.1038/nature07305. Epub 2008 Sep 24.
9
Reduced-representation methylation mapping.简化代表性甲基化图谱分析
Genome Biol. 2008;9(8):231. doi: 10.1186/gb-2008-9-8-231. Epub 2008 Sep 1.
10
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