Studies Track Protein Relevant to Stem Cells, Cancer

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' _4 z5 v- y3 _+ @" H: aScienceDaily (Mar. 30, 2011) — Last year, a research team at the University of North Carolina at Chapel Hill discovered one way the protein Tet 1 helps stem cells keep their pluripotency -- the unique ability to become any cell type in the body. In two new studies, the team takes a broad look at the protein's location in the mouse genome, revealing a surprising dual function and offering the first genome-wide location of the protein and its product, 5-hydroxymethylcytosine -- dubbed the "sixth base" of DNA.
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" Y8 g1 V; b+ R7 GUNC biochemist Yi Zhang, PhD, whose team conducted the studies, called the findings an important step in understanding the molecular mechanisms behind cell differentiation and the development of cancer. The findings appear in two recent papers, published March 30, 2011 online in Nature and in the April 1, 2011 issue of Genes & Development.
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4 c8 @# M# y$ ]; R. Y( _"There is no doubt that Tet proteins are relevant to cancer," said Zhang, Kenan distinguished professor of biochemistry and biophysics. Zhang is also an investigator of the Howard Hughes Medical Institute and a member of the UNC Lineberger Comprehensive Cancer Center. Tet proteins were initially discovered in leukemia as fusion proteins, which are commonly found in cancer cells, where they may function as oncoproteins.7 l' l, N7 K% T8 M5 \* V% S6 T, w
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In addition, Zhang said, "Tet is likely to be one of the important players for stem cell reprogramming." Learning to "reprogram" cells in the adult body to make them behave like stem cells has long been a goal for stem cell researchers; understanding how Tet proteins operate could help advance stem-cell based treatments.
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Tet proteins are known to help stem cells stay pluripotent. Zhang's team analyzed Tet1's occupancy across the entire mouse embryonic stem cell genome. They found that the protein works by using a two-pronged approach to maintain the mouse embryonic stem cell state.) d+ i7 T' O3 L* j  @" ?1 A" L8 Q
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"On one hand, it silences the genes that are important for differentiation. On the other hand, it also activates pluripotency genes," said Zhang.) H1 I$ [3 j' t: R7 [7 c! h1 m. d5 c

  ~. x3 S) n. P8 _- r) ?+ jThe team then focused its attention on the Tet1-catalyzed reaction product,5-hydroxymethylcytosine. 5-hydroxymethylcytosine is a modified version of cytosine -- the "C" in the four main DNA bases, A, T, G, and C. 5-methylcytosine and 5-hydroxymethylcytosine have been called the fifth and sixth bases of DNA, but since 5-hydroxymethylcytosine was discovered only recently, scientists know little about it.- Q, M  C. x3 ]  W- h: _& e

) Y( X. k7 I& a& Y" p"Everybody is trying to understand what 5-hydroxymethylcytosine is doing," said Zhang. "Is it an intermediate, or is it an end product? What is its biological function?" Zhang's team mapped the distribution of 5-hydroxymethylcytosine across the genome, offering new insights to its role in development and disease.
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"It's the first time we have the whole picture of where this new modification is in embryonic stem cells," said Zhang. "We found that its role in regulating transcription is complicated. It's not simply activating or repressing genes -- it depends on the context."
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Like much of science, the research answers some questions while raising others. "This study is just beginning," said Zhang. Although Tet1 is known to generate 5-hydroxymethylcytosine, there are places where one exists without the other. Further investigation could reveal more about the relationship between the two and whether other enzymes may play a role. In addition, scientists need to examine how Tet1 and 5-hydroxymethylcytosine function in animal models.
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Study collaborators include UNC postdoctoral researchers Ana D'Alessio, Shinsuke Ito, and Kai Xia, as well as Yi Sun and Hao Wu of the University of California, Los Angeles School of Medicine; Zhibin Wang of the Johns Hopkins School of Public Health; and Kairong Cui and Keji Zhao of the National Heart, Lung, and Blood Institute.
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. b" [+ ^/ ], r# ZTwo papers related to the news:
6 U4 m8 r  O2 Q1 K! L9 ~& X0 B; wMarch 30, 2011 online in Nature : F3 ~4 w& t5 Z$ X, k1 p
Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells3 J' X+ F1 f3 ^, u

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and in the April 1, 2011 issue of Genes & Development.
3 `: b; h2 k/ t7 c# i( W' RGenome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells' ^: j# |, F( T, K8 ]5 ^+ O

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jun8013

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2010年北卡罗来纳大学(UNC)的研究组发现了一种新方法，蛋白质Tet1能帮助干细胞保持其多能性。在最新的两项研究中，该研究组宏观地观察到蛋白质在小鼠基因组中的位置，揭示了其令人惊奇的双重功能，并提供了蛋白质的首个基因组内的位置及其产物-5-羟甲基胞嘧啶，被称为DNA的"第六个碱基"的基因组。
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# b( A" N2 i- }# W, CHao Wu,Ana C. D’Alessio, Shinsuke Ito, Kai Xia, Zhibin Wang, Kairong Cui, Keji Zhao,Yi Eve Sun & Yi Zhang
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Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity1. The recent demonstration that members of the Ten-eleven translocation (Tet) family of proteins can convert 5-methylcytosine to 5-hydroxymethylcytosine raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state2, 3. We have recently demonstrated that Tet1 is specifically expressed in murine embryonic stem (ES) cells and is required for ES cell maintenance2. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing, here we show in mouse ES cells that Tet1 is preferentially bound to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes. Despite an increase in levels of DNA methylation at many Tet1-binding sites, Tet1 depletion does not lead to downregulation of all the Tet1 targets. Interestingly, although Tet1-mediated promoter hypomethylation is required for maintaining the expression of a group of transcriptionally active genes, it is also involved in repression of Polycomb-targeted developmental regulators. Tet1 contributes to silencing of this group of genes by facilitating recruitment of PRC2 to CpG-rich gene promoters. Thus, our study not only establishes a role for Tet1 in modulating DNA methylation levels at CpG-rich promoters, but also reveals a dual function of Tet1 in promoting transcription of pluripotency factors as well as participating in the repression of Polycomb-targeted developmental regulators.
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0 H$ t1 n; Z* _+ c主持该项研究的UNC大学生物化学家Yi Zhang博士认为该发现是理解细胞分化及癌症发展背后的分子机制的一大重要步骤，目前已刊登在2011年3月30日的Nature杂志及2011年4月1日的Genes & Development上。
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生物化学和生物物理学家Zhang,Kenan教授认为，毫无疑问的是蛋白质Tet与癌症相关。Zhang,Kenan教授同时是霍华德休斯医学研究所的研究员以及UNC莱恩伯格综合癌症中心的成员。最初，蛋白质Tet在白血病中作为融合蛋白标记物被发现，这常见于癌症细胞中。在癌症细胞中，他们可能发挥癌蛋白质的功能。
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8 I1 Q1 m/ H1 [' k: x- m此外，Zhang认为Tet可能是干细胞重组中的一个重要成员。在成人体内学习"重组"细胞使其像干细胞那样发挥作用，一直是研究人员的目标；了解蛋白质Tet如何运作能帮助推进以干细胞为基础的疾病治疗。
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蛋白质Tet能帮助干细胞保持多能性。Zhang研究组分析了Tet1在整个小鼠胚胎干细胞基因组中的存留时间。他们发现Tet1采用双管齐下的办法维持小鼠胚胎干细胞的状态。一方面，Tet1可对分化起重要作用的基因保持"沉默"；另一方面Tet1也可激活多能性基因。
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# v8 \, ^' e% t研究组着重于研究Tet1催化反应产物-5羟甲基胞嘧啶。5羟甲基胞嘧啶是胞嘧啶的修改版-C在四个主要的DNA碱基：A、T、G、C。5羟甲基胞嘧啶和5甲基胞嘧啶分别被称为是DNA第五、第六个碱基，但是5羟甲基胞嘧啶是最近才被发现，科学家对此了解很少。& S& O% m0 Z- Z
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每个人都试图了解5羟甲基胞嘧啶是做什么的，是中间产物还是一个最终物？它的生物学功能是什么？Zhang研究组绘制了5羟甲基胞嘧啶在整个基因组的分布，对于它在生长和疾病中的地位提供了新的见解。( q0 H# N& i$ r( _9 `
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这是我们第一次了解到5羟甲基胞嘧啶在胚胎干细胞中的全貌。我们发现在它在调节转录方面的作用是复杂的，不仅仅是激活或抑制基因，这取决于环境。
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( e5 n- [& N8 w9 v: |( E4 T! x  z0 x该研究在回答了一些问题的同时也提出了其他的问题。该研究仅仅是一个开始。众所周知，Tet1产生了5羟甲基胞嘧啶，然而并不是非此即彼地存在。研究人员开展的进一步研究揭示了两者的关系，以及是否有其他的酶可能发挥作用。此外，科学家有必要了解Tet1和5羟甲基胞嘧啶是如何在动物模型中发挥作用。