Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems.
Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems.
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DOI：
10.1186/s13059-014-0576-y
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发表时间：
2015-02-04
期刊：
影响因子：
12.3
通讯作者：
Meehan RR
中科院分区：
文献类型：
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作者：
Nestor CE;Ottaviano R;Reinhardt D;Cruickshanks HA;Mjoseng HK;McPherson RC;Lentini A;Thomson JP;Dunican DS;Pennings S;Anderton SM;Benson M;Meehan RR
哺乳动物细胞系的DNA甲基化谱与它们所来源的原代组织的DNA甲基化谱不同，随着培养时间的延长，表现出与体内甲基化谱的越来越大的差异。很少有研究直接研究了原代哺乳动物细胞适应培养的初始表观遗传和转录后果，并且这种表观遗传失调发生的潜在机制尚不清楚。我们证明，小鼠胚胎成纤维细胞的适应细胞培养的结果在表观遗传和转录状态的快速重编程。我们观察到全球5-羟甲基胞嘧啶（5hmC）擦除三天内的文化开始。基因型5hmC的丢失与总体5-甲基胞嘧啶（5mC）水平无关，并且可以通过添加维生素C部分挽救。值得注意的是，5hmC的丢失与转录的伴随变化无关。在培养开始的7天内也观察到5mC的离散启动子特异性增益。在全球5hmC丢失的背景下，我们确定了少数发育重要的基因，这些基因在培养物中保持了它们的5hmC谱，包括印迹基因座Gnas和H19。在CD4 + T细胞对培养物的适应中鉴定了类似的结果。我们报告了一个戏剧性的和新的后果，适应哺乳动物细胞培养中发生的5hmC的全球损失，这表明快速伴随的甲基胞嘧啶双加氧酶活性的损失。所观察到的表观遗传和转录重编程发生得比以前假设的要早得多，并且对于使用细胞系作为体内表观遗传和生理过程的忠实模拟物具有重要意义。本文的在线版本（doi：10.1186/s13059 - 014 - 0576-y）包含补充材料，可供授权用户使用。
The DNA methylation profiles of mammalian cell lines differ from those of the primary tissues from which they were derived, exhibiting increasing divergence from the in vivo methylation profile with extended time in culture. Few studies have directly examined the initial epigenetic and transcriptional consequences of adaptation of primary mammalian cells to culture, and the potential mechanisms through which this epigenetic dysregulation occurs is unknown. We demonstrate that adaptation of mouse embryonic fibroblasts to cell culture results in a rapid reprogramming of epigenetic and transcriptional states. We observed global 5-hydroxymethylcytosine (5hmC) erasure within three days of culture initiation. Loss of genic 5hmC was independent of global 5-methylcytosine (5mC) levels and could be partially rescued by addition of vitamin C. Significantly, 5hmC loss was not linked to concomitant changes in transcription. Discrete promoter-specific gains of 5mC were also observed within seven days of culture initiation. Against this background of global 5hmC loss we identified a handful of developmentally important genes that maintained their 5hmC profile in culture, including the imprinted loci Gnas and H19. Similar outcomes were identified in the adaption of CD4+ T cells to culture. We report a dramatic and novel consequence of adaptation of mammalian cells to culture in which global loss of 5hmC occurs, suggesting rapid concomitant loss of methylcytosine dioxygenase activity. The observed epigenetic and transcriptional re-programming occurs much earlier than previously assumed, and has significant implications for the use of cell lines as faithful mimics of in vivo epigenetic and physiological processes. The online version of this article (doi:10.1186/s13059-014-0576-y) contains supplementary material, which is available to authorized users.
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影响因子：
16.8
作者：
Leitch, Harry G.;McEwen, Kirsten R.;Turp, Aleksandra;Encheva, Vesela;Carroll, Tom;Grabole, Nils;Mansfield, William;Nashun, Buhe;Knezovich, Jaysen G.;Smith, Austin;Surani, M. Azim;Hajkova, Petra
通讯作者：
Hajkova, Petra
影响因子：
3.7
作者：
Globisch D;Münzel M;Müller M;Michalakis S;Wagner M;Koch S;Brückl T;Biel M;Carell T
通讯作者：
Carell T
影响因子：
14.9
作者：
EHRLICH, M;GAMASOSA, MA;GEHRKE, C
通讯作者：
GEHRKE, C
影响因子：
56.9
作者：
Hellman, Asaf;Chess, Andrew
通讯作者：
Chess, Andrew
影响因子：
14.8
作者：
通讯作者：
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