In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases.
In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases.
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DNA 甲基转移酶对 CpG 和非 CpG DNA 甲基化的体内控制。
DOI：
10.1371/journal.pgen.1002750
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发表时间：
2012-06
期刊：
影响因子：
4.5
通讯作者：
Walter J
中科院分区：
文献类型：
--
作者：
Arand J;Spieler D;Karius T;Branco MR;Meilinger D;Meissner A;Jenuwein T;Xu G;Leonhardt H;Wolf V;Walter J
在特定的基因组背景下，酶对对称和非对称DNA甲基化模式的设置和维持的控制尚不清楚。在这里，我们描述了通过对选定的单拷贝基因和重复元件（LINE1, B1， iap - ltr -反转录转座子和主要卫星）的亚硫酸亚铁发夹扩增子的高分辨率测序产生的DNA甲基化模式的综合分析。该分析明确地确定了大量的区域不完全甲基化维持，即半甲基化的CpG位置，在不同的细胞类型中程度不同。此外，非cpg胞嘧啶甲基化仅限于ESCs，并仅由Dnmt3a和Dnmt3b催化。这种序列位置、细胞类型和区域依赖的非CpG甲基化与邻近的CpG甲基化密切相关，并且需要Dnmt3L的存在。生成的146,000个CpG双体的综合数据集用于应用和开发参数估计的隐马尔可夫模型（HMM），以计算DNA甲基转移酶（Dnmts）对新生和维持DNA甲基化的相对贡献。比较模型包括野生型ESCs和Dnmt1、Dnmt3a、Dnmt3b或Dnmt3a/3b缺失的突变型ESCs。HMM分析发现Dnmt1在某些重复元件和单拷贝序列上具有相当大的从头甲基化活性。Dnmt3a和Dnmt3b具有从头开始的功能。然而，这两种酶对于维持ESCs中不同重复和单拷贝序列的对称CpG甲基化也是必不可少的。DNA甲基化是一种稳定的共价表观遗传修饰，主要局限于哺乳动物的cpg -二核苷酸。一般来说，它与基因组DNA区域的沉默有关。三种具有催化活性的DNA甲基转移酶（Dnmts）与其他（co-）因子一起设定和维持CpG甲基化。在DNA复制之后，Dnmts对维持CpG和非CpG甲基化的体内贡献尚不清楚，特别是因为体内DNA甲基化模式可能是高度动态的。在我们的工作中，我们使用超深度测序来确定分别缺失Dnmts 1、3a、3b和3L的ESCs中两条DNA链的甲基化状态。使用隐马尔可夫模型，我们使用参数估计拟合计算每种酶对维持DNA甲基化模式的相对贡献。虽然一般来说，该模型支持将dnmt分类为维持功能和新生功能，但它反对严格的酶特定功能分类。我们观察到Dnmts在不同类型的重复元件和选定的单拷贝基因上设置和维持CpG和非CpG甲基化的环境依赖贡献的证据。我们进一步明确了Dnmt3a/3b和3L依赖于特定序列位置的非cpg甲基化，并且仅限于ESCs。
The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements (LINE1, B1, IAP-LTR-retrotransposons, and major satellites). The analysis unambiguously identifies a substantial amount of regional incomplete methylation maintenance, i.e. hemimethylated CpG positions, with variant degrees among cell types. Moreover, non-CpG cytosine methylation is confined to ESCs and exclusively catalysed by Dnmt3a and Dnmt3b. This sequence position–, cell type–, and region-dependent non-CpG methylation is strongly linked to neighboring CpG methylation and requires the presence of Dnmt3L. The generation of a comprehensive data set of 146,000 CpG dyads was used to apply and develop parameter estimated hidden Markov models (HMM) to calculate the relative contribution of DNA methyltransferases (Dnmts) for de novo and maintenance DNA methylation. The comparative modelling included wild-type ESCs and mutant ESCs deficient for Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3a/3b, respectively. The HMM analysis identifies a considerable de novo methylation activity for Dnmt1 at certain repetitive elements and single copy sequences. Dnmt3a and Dnmt3b contribute de novo function. However, both enzymes are also essential to maintain symmetrical CpG methylation at distinct repetitive and single copy sequences in ESCs. DNA methylation is a stable covalent epigenetic modification of cytosines mostly confined to CpG-dinucleotides in mammals. In general, it is associated with silencing of genomic DNA regions. Three catalytically active DNA methyltransferases (Dnmts) set and maintain CpG methylation in cooperation with other (co-)factors. The in vivo contribution of the Dnmts to maintain CpG and non-CpG methylation following rounds of DNA replication are not well understood, particularly since in vivo DNA methylation patterns can be highly dynamic. In our work, we use ultradeep sequencing to determine the methylation status of both DNA strands in ESCs depleted for Dnmts 1, 3a, 3b, and 3L, respectively. Using hidden Markov models, we calculate the relative contribution of each of the enzymes for the maintenance of DNA methylation patterns using parameter estimated fitting. While in general the modelling supports a classification of Dnmts into maintenance and de novo functions, it argues against a strict enzyme specific functional categorisation. We observe evidence for a context-dependent contribution of Dnmts to set and maintain CpG and non-CpG methylation at distinct classes of repetitive elements and selected single copy genes. We furthermore unambiguously identify Dnmt3a/3b and 3L dependent non-CpG methylation at specific sequence positions and confined to ESCs.
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影响因子：
23.9
作者：
Dawlaty, Meelad M.;Ganz, Kibibi;Powell, Benjamin E.;Hu, Yueh-Chiang;Markoulaki, Styliani;Cheng, Albert W.;Gao, Qing;Kim, Jongpil;Choi, Sang-Woon;Page, David C.;Jaenisch, Rudolf
通讯作者：
Jaenisch, Rudolf
根据双链甲基化模式对人类 DNA 甲基转移酶的体内特性进行统计推断。
影响因子：
3.7
作者：
Fu AQ;Genereux DP;Stöger R;Burden AF;Laird CD;Stephens M
通讯作者：
Stephens M
影响因子：
4.8
作者：
Gowher, H;Jeltsch, A
通讯作者：
Jeltsch, A
影响因子：
4.8
作者：
Gowher, H;Liebert, K;Jeltsch, A
通讯作者：
Jeltsch, A
影响因子：
3.5
作者：
Kato, Yuzuru;Kaneda, Masahiro;Sasaki, Hiroyuki
通讯作者：
Sasaki, Hiroyuki