DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift.
DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift.
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DOI：
10.1038/s42003-021-02116-y
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发表时间：
2021-05-19
影响因子：
5.9
通讯作者：
Wagner W
中科院分区：
文献类型：
--
作者：
Franzen J;Georgomanolis T;Selich A;Kuo CC;Stöger R;Brant L;Mulabdić MS;Fernandez-Rebollo E;Grezella C;Ostrowska A;Begemann M;Nikolić M;Rath B;Ho AD;Rothe M;Schambach A;Papantonis A;Wagner W
原代细胞的培养扩增引起高度可重复的DNA甲基化（DNAm）变化。我们已经发现在间充质干细胞（MSCs）和其他细胞类型的长期培养过程中，CG二核苷酸（CpGs）会持续高甲基化或低甲基化。亚硫酸氢盐条形码扩增子测序（BBA-seq）表明，邻近CpGs的dna模式变得更加复杂，没有连续模式发展的证据，也没有与寡克隆亚群的关联。环状染色质构象捕获（4C）揭示了细胞核组织在早期和晚期传代之间可重复的变化，而与其他基因组区域没有丰富的相互作用，这些区域也含有与培养相关的dna变化。在MSCs的长期培养过程中，CTCF的染色质免疫沉淀没有显示出显著差异，但CTCF结合位点的培养相关高甲基化富集，低甲基化的CpGs缺乏CTCF。综上所述，我们的研究结果支持这样一种观点，即DNAm在培养扩增过程中的变化不是由目标机制直接调节的，而是类似于表观遗传漂变。Julia Franzen等人研究了细胞培养扩增过程中特定遗传位点的DNA甲基化变化是否由于特定机制或表观遗传状态的逐渐解除管制。他们的研究结果表明，CpG甲基化的变化是由于间接的表观遗传漂变，而不是DNA甲基转移酶靶向的结果。
Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift. Julia Franzen et al. investigate if changes in DNA methylation at specific genetic loci during cell culture expansion are due to a specific mechanism or gradual deregulation of an epigenetic state. Their results suggest that changes in CpG methylation are due to indirect epigenetic drift, rather than a consequence of targeting by DNA methyltransferases.
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影响因子：
64.8
作者：
Dixon JR;Jung I;Selvaraj S;Shen Y;Antosiewicz-Bourget JE;Lee AY;Ye Z;Kim A;Rajagopal N;Xie W;Diao Y;Liang J;Zhao H;Lobanenkov VV;Ecker JR;Thomson JA;Ren B
通讯作者：
Ren B
影响因子：
5.9
作者：
Fernandez-Rebollo, Eduardo;Franzen, Julia;Wagner, Wolfgang
通讯作者：
Wagner, Wolfgang
影响因子：
64.5
作者：
Kim, Tae Hoon;Abdullaev, Ziedulla K.;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
64.8
作者：
Guelen, Lars;Pagie, Ludo;van Steensel, Bas
通讯作者：
van Steensel, Bas
复制性衰老与特定转录因子结合位点处的核重组和DNA甲基化有关。
影响因子：
5.7
作者：
Hänzelmann S;Beier F;Gusmao EG;Koch CM;Hummel S;Charapitsa I;Joussen S;Benes V;Brümmendorf TH;Reid G;Costa IG;Wagner W
通讯作者：
Wagner W