哺乳动物受精后由一个受精卵发育成一个完整的个体，DNA甲基化则是指导受精卵发育成早期胚胎、进而发育成完整个体的重要表观遗传调控方式之一。中科院北京基因组所刘江团队2013年揭示模式生物斑马鱼继承父代精子的甲基化图谱，但哺乳动物子代如何继承表观遗传信息仍知之甚少。

刘江团队与南京大学黄行许团队的近期合作研究结果，揭示了哺乳动物中子代如何继承亲代DNA甲基化图谱的规律，更新了关于受精之后DNA甲基化图谱重新编程的传统认识，相关论文于2014年5月8日再次发表在国际学术期刊《细胞》上。

哺乳动物中，DNA甲基化在早期胚胎发育和原始生殖细胞形成过程中的重编程和遗传规律

在中科院北京基因组所核酸测序和高性能计算平台的有力支撑下，刘江研究团队在表观信息遗传规律方面取得了系列性成果。2013年他们以斑马鱼为研究模型，发现精子的DNA甲基化图谱和卵子的甲基化图谱有巨大的差别，子代中父源DNA稳定保持精子的甲基化图谱、而母源DNA却抛弃卵子的甲基化图谱并完全转变成精子的甲基化图谱，最终父源和母源DNA都具有与精子一致的甲基化图谱。哺乳动物受精后也需要使父源DNA和母源DNA具有一样的DNA甲基化图谱，但哺乳动物使用了与斑马鱼完全不同的机制。

过去的研究发现父源和母源DNA都经历全基因组水平的去甲基化过程，但认为父源DNA上的甲基化是通过生物酶的催化反应而去的甲基化，而母源DNA上的甲基化是通过DNA复制而被动的稀释导致DNA的去甲基化;除此之外，过去的研究认为只有父源的DNA甲基化可以被氧化，而母源的DNA甲基化不会被氧化。刘江和黄行许团队的研究发现，无论是父本还是母本来源的DNA都应该是通过生物酶的催化反应而去甲基化，并且发现了父源和母源的DNA都被氧化的重要过程。

通过对哺乳动物和鱼类的进化比较，刘江等进而推测提出哺乳动物全基因组特异的去甲基化过程导致了印记基因的产生，从而使胎盘类生殖方式的哺乳动物得以进化出来。换言之，表观遗传重新编程方式的进化，可能是产生胎盘生殖方式的哺乳动物的重要一环。

这些重要发现和理论突破，不仅改写了该领域长久以来的传统理论，而且将对生殖健康、进化生物学和发育生物学的研究具有重要意义。

此工作获得了973、中国科学院先导专项和自然基金委的资助。

原文摘要：

Programming and Inheritance of Parental DNA Methylomes in Mammals

Lu Wang, Jun Zhang, Jialei Duan, Xinxing Gao, Wei Zhu, Xingyu Lu, Lu Yang, Jing Zhang, Guoqiang Li, Weimin Ci, Wei Li, Qi Zhou,Neel Aluru, Fuchou Tang, Chuan He, Xingxu Huang, Jiang Liu

The reprogramming of parental methylomes is essential for embryonic development. In mammals, paternal 5-methylcytosines (5mCs) have been proposed to be actively converted to oxidized bases. These paternal oxidized bases and maternal 5mCs are believed to be passively diluted by cell divisions. By generating single-base resolution, allele-specific DNA methylomes from mouse gametes, early embryos, and primordial germ cell (PGC), as well as single-base-resolution maps of oxidized cytosine bases for early embryos, we report the existence of 5hmC and 5fC in both maternal and paternal genomes and find that 5mC or its oxidized derivatives, at the majority of demethylated CpGs, are converted to unmodified cytosines independent of passive dilution from gametes to four-cell embryos. Therefore, we conclude that paternal methylome and at least a significant proportion of maternal methylome go through active demethylation during embryonic development. Additionally, all the known imprinting control regions (ICRs) were classified into germ-line or somatic ICRs.

MethylC-Seq Library Generation
DNA was extracted using QIAamp DNA Mini Kit (QIAGEN). Purified DNA spiked in with 0.1% unmethylated cl857 Sam7 lambda DNA
(Promega) was sonicated using the microtube protocol-300 of Covaris S2 (Applied Biosystems). End-repair, dA-tailing and ligation
were performed using the NEBNext End Repair Module, dA-Tailing Module and NEB T4 ligase. The adaptor-ligated DNA with insert
size larger than 200 bp was selected by gel electrophoresis. Bisulfite conversion was performed using the EZ DNA methylation-Gold
Kit (Zymo Research) according to the manufacturer’s instructions. The time of 64
C incubation was 2 hr for some libraries. Bisulfitetreated
DNA was amplified using ZymoTaq DNA Polymerase or KAPA HiFi HotStart Uracil+ ReadyMixwith 14-15 cycles.