High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells.
High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells.
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DOI：
10.1016/j.celrep.2013.01.001
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发表时间：
2013-02-21
期刊：
影响因子：
8.8
通讯作者：
Zheng Y
中科院分区：
文献类型：
--
作者：
Sun Z;Terragni J;Borgaro JG;Liu Y;Yu L;Guan S;Wang H;Sun D;Cheng X;Zhu Z;Pradhan S;Zheng Y
我们描述了使用独特的dna修饰依赖性限制性内切酶AbaSI结合测序（Aba-seq）来绘制小鼠E14胚胎干细胞的高分辨率羟甲基组。AbaSI的特异性能够在低占用区域灵敏地检测5-羟甲基胞嘧啶（5hmC）。生物信息学分析表明，基因区域的5hmc与5mC的分布密切相关。5hmC通常在CpG岛被耗尽，只在一小部分重复元素中被富集。在CTCF的结合位点上观察到规律间隔和振荡的5hmC模式。5hmC在单甲基化组蛋白H3赖氨酸4 （H3K4me1）标记的平衡增强子上富集，而在乙酰化组蛋白H3赖氨酸27 （H3K27Ac）标记的活性增强子上不富集。非cg羟甲基化似乎普遍存在于线粒体基因组中。我们提出，一些数量的瞬时稳定的5hmc可能表明一种平衡的表观遗传状态或去甲基化中间产物，而其他的可能表明TET酶装置在局部可达的染色体环境。
We describe the use of a unique DNA-modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq) to map high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The specificity of AbaSI enables sensitive detection of 5-hydroxymethylcytosine (5hmC) at low-occupancy regions. Bioinformatic analysis suggests 5hmCs in genic regions closely follow the 5mC distribution. 5hmC is generally depleted in CpG islands and only enriched in a small set of repetitive elements. A regularly spaced and oscillating 5hmC pattern was observed at the binding sites of CTCF. 5hmC is enriched at the poised enhancers with the monomethylated histone H3 lysine 4 (H3K4me1) marks, but not at the active enhancers with the acetylated histone H3 lysine 27 (H3K27Ac) marks. Non-CG hydroxymethylation appears to be prevalent in the mitochondrial genome. We propose that some amounts of transiently stable 5hmCs may indicate a poised epigenetic state or demethylation intermediate, whereas others may suggest a locally accessible chromosomal environment for the TET enzymatic apparatus.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
DOI：
10.1073/pnas.1012311108
发表时间：
2011-03-01
影响因子：
11.1
作者：
Shock, Lisa S.;Thakkar, Prashant V.;Taylor, Shirley M.
通讯作者：
Taylor, Shirley M.
影响因子：
14.9
作者：
Jin SG;Kadam S;Pfeifer GP
通讯作者：
Pfeifer GP
影响因子：
11.4
作者：
Martens, JHA;O'Sullivan, RJ;Jenuwein, T
通讯作者：
Jenuwein, T
影响因子：
7
作者：
Cuddapah, Suresh;Jothi, Raja;Zhao, Keji
通讯作者：
Zhao, Keji