Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.
Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.
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DOI：
10.1186/gb-2012-13-10-r99
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发表时间：
2012-10-17
期刊：
影响因子：
12.3
通讯作者：
Landweber LF
中科院分区：
文献类型：
--
作者：
Bracht JR;Perlman DH;Landweber LF
DNA的胞嘧啶甲基化在真核生物中是保守的，并且在动物、植物和真菌的分化和发育过程中调节基因表达起着重要的功能作用。羟甲基化是最近发现的另一种表观遗传修饰，标志着胚胎干细胞多能性的重要基因。在这里，我们描述从头胞嘧啶甲基化和羟甲基化的纤毛虫Oxytrichatrifallax。这些DNA修饰仅发生在核发育和程序性基因组重排期间。我们检测甲基胞嘧啶和羟甲基胞嘧啶直接通过高分辨率的纳米流UPLC质谱，并间接通过免疫荧光，甲基DNA免疫沉淀和亚硫酸氢盐测序。我们描述了这些修改在三类消除的DNA：生殖系限制的转座子和卫星重复，异常的DNA重排，和DNA从父母的基因组进行降解。甲基化和羟甲基化通常发生在相同的序列元件上，在所有序列背景下修饰胞嘧啶。我们发现，DNA甲基转移酶抑制药物阿扎胞苷和地西他滨诱导基因组重排过程中的体细胞和种系序列元件的去甲基化，从而提高水平的种系限制性重复元件exconjugant细胞。这些数据强烈支持胞嘧啶DNA甲基化/羟甲基化和DNA消除之间的功能联系。我们确定了一个基序强烈丰富的甲基化/羟甲基化的地区，我们建议，这个基序招募DNA修饰机器特定的染色体在父母的大核。在O. trifallax，提高了它可能采用一种新的胞嘧啶甲基化机制来标记DNA序列，以便在基因组重排过程中消除。
Cytosine methylation of DNA is conserved across eukaryotes and plays important functional roles regulating gene expression during differentiation and development in animals, plants and fungi. Hydroxymethylation was recently identified as another epigenetic modification marking genes important for pluripotency in embryonic stem cells. Here we describe de novo cytosine methylation and hydroxymethylation in the ciliate Oxytricha trifallax. These DNA modifications occur only during nuclear development and programmed genome rearrangement. We detect methylcytosine and hydroxymethylcytosine directly by high-resolution nano-flow UPLC mass spectrometry, and indirectly by immunofluorescence, methyl-DNA immunoprecipitation and bisulfite sequencing. We describe these modifications in three classes of eliminated DNA: germline-limited transposons and satellite repeats, aberrant DNA rearrangements, and DNA from the parental genome undergoing degradation. Methylation and hydroxymethylation generally occur on the same sequence elements, modifying cytosines in all sequence contexts. We show that the DNA methyltransferase-inhibiting drugs azacitidine and decitabine induce demethylation of both somatic and germline sequence elements during genome rearrangements, with consequent elevated levels of germline-limited repetitive elements in exconjugant cells. These data strongly support a functional link between cytosine DNA methylation/hydroxymethylation and DNA elimination. We identify a motif strongly enriched in methylated/hydroxymethylated regions, and we propose that this motif recruits DNA modification machinery to specific chromosomes in the parental macronucleus. No recognizable methyltransferase enzyme has yet been described in O. trifallax, raising the possibility that it might employ a novel cytosine methylation machinery to mark DNA sequences for elimination during genome rearrangements.
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影响因子：
64.5
作者：
Bhutani N;Burns DM;Blau HM
通讯作者：
Blau HM
影响因子：
6.4
作者：
Daskalos, Alexandros;Nikolaidis, Georgios;Liloglou, Triantafillos
通讯作者：
Liloglou, Triantafillos
影响因子：
--
作者：
Chung, Pei-Han;Yao, Meng-Chao
通讯作者：
Yao, Meng-Chao
影响因子：
56.9
作者：
Gaudet, F;Hodgson, JG;Jaenisch, R
通讯作者：
Jaenisch, R
影响因子：
64.5
作者：
HERRICK, G;CARTINHOUR, S;WILLIAMS, K
通讯作者：
WILLIAMS, K