TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.
TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.
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DOI：
10.1038/s41588-017-0002-y
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发表时间：
2018-01
期刊：
影响因子：
30.8
通讯作者：
Huangfu D
中科院分区：
文献类型：
--
作者：
Verma N;Pan H;Doré LC;Shukla A;Li QV;Pelham-Webb B;Teijeiro V;González F;Krivtsov A;Chang CJ;Papapetrou EP;He C;Elemento O;Huangfu D
TET酶将5-甲基胞嘧啶氧化为5-羟甲基胞嘧啶，从而导致DNA去甲基化。然而，tet介导的DNA去甲基化和转录输出之间的直接联系很难建立，因为很难区分全局效应和位点特异性效应。在这里，我们发现TET1/2/3三敲除（TKO）的人胚胎干细胞（hESCs）在未分化状态下表现出显著的二价启动子超甲基化，而没有整体相应的基因表达减少。关注二价PAX6位点，我们发现DNMT3B结合增加与启动子超甲基化有关，这导致分化过程中神经分化缺陷和PAX6诱导失败。在TKO hESCs中，dcas9介导的位点特异性去甲基化和DNMT3B的整体失活部分逆转了PAX6启动子的高甲基化，并促进了向神经外胚层的分化。结合进一步的全基因组甲基化以及TET1和DNMT3B ChIP-Seq分析，我们得出结论，TET蛋白保护二价启动子免于从头甲基化，以确保分化时强大的谱系特异性转录。
The TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish due to challenges of distinguishing global versus locus-specific effects. Here we show that TET1/2/3 triple knockout (TKO) human embryonic stem cells (hESCs) exhibit prominent bivalent promoter hypermethylation without an overall corresponding gene expression decrease in the undifferentiated state. Focusing on the bivalent PAX6 locus, we find increased DNMT3B binding is associated with promoter hypermethylation, which precipitates a neural differentiation defect and failure of PAX6 induction during differentiation. dCas9-mediated locus-specific demethylation and global inactivation of DNMT3B in TKO hESCs partially reverses the hypermethylation at the PAX6 promoter and improves differentiation to neuroectoderm. Taken together with further genome-wide methylation and TET1 and DNMT3B ChIP-Seq analysis, we conclude that the TET proteins safeguard bivalent promoters from de novo methylation to ensure robust lineage-specific transcription upon differentiation.
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一个 iCRISPR 平台，用于在人类多能干细胞中进行快速、可多重、可诱导的基因组编辑。
影响因子：
23.9
作者：
Gonzalez, Federico;Zhu, Zengrong;Shi, Zhong-Dong;Lelli, Katherine;Verma, Nipun;Li, Qing V.;Huangfu, Danwei
通讯作者：
Huangfu, Danwei
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
5.3
作者：
Liang, GG;Chan, MF;Jones, PA
通讯作者：
Jones, PA
影响因子：
23.9
作者：
Fouse, Shaun D.;Shen, Yin;Fan, Guoping
通讯作者：
Fan, Guoping