Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development.
Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development.
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DOI：
10.1038/s41467-021-21532-6
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发表时间：
2021-02-24
影响因子：
16.6
通讯作者：
van Oudenaarden A
中科院分区：
文献类型：
--
作者：
Sen M;Mooijman D;Chialastri A;Boisset JC;Popovic M;Heindryckx B;Chuva de Sousa Lopes SM;Dey SS;van Oudenaarden A
DNA 甲基化 (5mC) 对于细胞身份至关重要。在植入前哺乳动物发育过程中，5mC 从亲本基因组中整体擦除对于将配子甲基化组重置为囊胚中的细胞至关重要。虽然主动和被动去甲基化模式均被认为在此过程中发挥作用，但这两种机制对 5mC 擦除的相对贡献仍不清楚。在这里，我们报告了一种单细胞方法 (scMspJI-seq)，该方法能够对 5mC 进行链特异性定量，使我们能够系统地探讨全局去甲基化的动态。当应用于小鼠胚胎干细胞时，我们发现了显着的细胞间链特异性 5mC 异质性，一小群细胞在染色体的两条 DNA 链之间显示出不对称水平的 5mCpG，表明维持甲基化的丧失。接下来，在植入前小鼠胚胎中，我们发现甲基化维持一直活跃到 16 细胞阶段，随后在 32 细胞发育阶段的早期囊胚内的一小部分细胞中被动去甲基化。最后，人类植入前胚胎定性地显示出与小鼠胚胎相似的暂时延迟的去甲基化动态。总的来说，这些结果表明 scMspJI-seq 是一种灵敏且经济高效的方法，可绘制单细胞中 5mC 链特异性全基因组模式。从亲本基因组中删除 DNA 甲基化对于将分化配子的甲基化重置为囊胚中的多能细胞至关重要。在这里，作者提出了一种高通量单细胞方法，能够对 DNA 甲基化进行链特异性定量，并识别早期哺乳动物发育过程中 DNA 去甲基化动态的不同模式。
DNA methylation (5mC) is central to cellular identity. The global erasure of 5mC from the parental genomes during preimplantation mammalian development is critical to reset the methylome of gametes to the cells in the blastocyst. While active and passive modes of demethylation have both been suggested to play a role in this process, the relative contribution of these two mechanisms to 5mC erasure remains unclear. Here, we report a single-cell method (scMspJI-seq) that enables strand-specific quantification of 5mC, allowing us to systematically probe the dynamics of global demethylation. When applied to mouse embryonic stem cells, we identified substantial cell-to-cell strand-specific 5mC heterogeneity, with a small group of cells displaying asymmetric levels of 5mCpG between the two DNA strands of a chromosome suggesting loss of maintenance methylation. Next, in preimplantation mouse embryos, we discovered that methylation maintenance is active till the 16-cell stage followed by passive demethylation in a fraction of cells within the early blastocyst at the 32-cell stage of development. Finally, human preimplantation embryos qualitatively show temporally delayed yet similar demethylation dynamics as mouse embryos. Collectively, these results demonstrate that scMspJI-seq is a sensitive and cost-effective method to map the strand-specific genome-wide patterns of 5mC in single cells. Erasure of DNA methylation from the parental genomes is critical to reset the methylome of differentiated gametes to pluripotent cells in the blastocyst. Here, the authors present a high-throughput single-cell method that enables strand-specific quantification of DNA methylation and identify distinct modes of DNA demethylation dynamics during early mammalian development.
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影响因子：
4.6
作者：
Okamoto Y;Yoshida N;Suzuki T;Shimozawa N;Asami M;Matsuda T;Kojima N;Perry AC;Takada T
通讯作者：
Takada T
影响因子：
10.5
作者：
CARLSON, LL;PAGE, AW;BESTOR, TH
通讯作者：
BESTOR, TH
早期人类发育过程中DNA甲基化动力学的全基因组分析。
影响因子：
4.5
作者：
Okae H;Chiba H;Hiura H;Hamada H;Sato A;Utsunomiya T;Kikuchi H;Yoshida H;Tanaka A;Suyama M;Arima T
通讯作者：
Arima T
影响因子：
4
作者：
Petrussa, Laetitia;Van de Velde, Hilde;De Rycke, Martine
通讯作者：
De Rycke, Martine
影响因子：
3.7
作者：
Huang Y;Pastor WA;Shen Y;Tahiliani M;Liu DR;Rao A
通讯作者：
Rao A