DNA methylation is a crucial element in the epigenetic regulation of mammalian embryonic development1,2,3,4,5. However, its dynamic patterns have not been analysed at the genome scale in human pre-implantation embryos due to technical difficulties and the scarcity of required materials. Here we systematically profile the methylome of human early embryos from the zygotic stage through to post-implantation by reduced representation bisulphite sequencing and whole-genome bisulphite sequencing. We show that the major wave of genome-wide demethylation is complete at the 2-cell stage, contrary to previous observations in mice. Moreover, the demethylation of the paternal genome is much faster than that of the maternal genome, and by the end of the zygotic stage the genome-wide methylation level in male pronuclei is already lower than that in female pronuclei. The inverse correlation between promoter methylation and gene expression gradually strengthens during early embryonic development, reaching its peak at the post-implantation stage. Furthermore, we show that active genes, with the trimethylation of histone H3 at lysine 4 (H3K4me3) mark at the promoter regions in pluripotent human embryonic stem cells, are essentially devoid of DNA methylation in both mature gametes and throughout pre-implantation development. Finally, we also show that long interspersed nuclear elements or short interspersed nuclear elements that are evolutionarily young are demethylated to a milder extent compared to older elements in the same family and have higher abundance of transcripts, indicating that early embryos tend to retain higher residual methylation at the evolutionarily younger and more active transposable elements. Our work provides insights into the critical features of the methylome of human early embryos, as well as its functional relation to the regulation of gene expression and the repression of transposable elements.

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Primary accessions

Gene Expression Omnibus

Data deposits

All sequencing data were deposited at the NCBI Gene Expression Omnibus (GEO) under accession number GSE49828.


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F.T. and J.Q. were supported by grants from the National Basic Research Program of China (2012CB966704, 2011CB944504 and 2011CB966303) and from the National Natural Science of China (31322037, 31230047, 31271543 and 81170538). J.Q. and F.T. were supported by a grant from the Beijing Municipal Science and Technology Commission (Z131100005213006). L.Y. was supported by grants from the National Natural Science Foundation of China (81000275) and National Basic Research Program of China (2011CB944503). R.L. was supported by a grant from National Key Technologies Research and Development Program (2012BAI32B01).

Author information

Author notes

    • Hongshan Guo
    • , Ping Zhu
    • , Liying Yan
    •  & Rong Li

    These authors contributed equally to this work.


  1. Biodynamic Optical Imaging Center & Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China

    • Hongshan Guo
    • , Ping Zhu
    • , Liying Yan
    • , Rong Li
    • , Boqiang Hu
    • , Ying Lian
    • , Jie Yan
    • , Xiulian Ren
    • , Shengli Lin
    • , Junsheng Li
    • , Xiaohu Jin
    • , Xiaodan Shi
    • , Ping Liu
    • , Xianlong Li
    • , Fan Guo
    • , Xinglong Wu
    • , Xiaoying Fan
    • , Jun Yong
    • , Lu Wen
    • , Sunney X. Xie
    • , Fuchou Tang
    •  & Jie Qiao
  2. Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China

    • Ping Zhu
  3. Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China

    • Liying Yan
    • , Rong Li
    • , Ying Lian
    • , Jie Yan
    • , Xiulian Ren
    • , Shengli Lin
    • , Junsheng Li
    • , Xiaohu Jin
    • , Xiaodan Shi
    • , Ping Liu
    •  & Jie Qiao
  4. Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China

    • Xiaoye Wang
    • , Wei Wang
    •  & Yuan Wei
  5. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA

    • Jun Yong
    •  & Sunney X. Xie
  6. Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China

    • Fuchou Tang


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F.T. and J.Q. conceived the experiments and supervised the project. H.G., L.Y., R.L., Y.L. J.Y., X.R., S.L., J.L., X.J., X.S., P.L., X.W., W.W., Y.W., X.L., F.G., X.W., X.F., J.Y. and L.W. performed the experiments. P.Z and B.H. did all of the bioinformatic analyses. S.X.X., J.Q. and F.T. wrote the manuscript with help from all of the authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Fuchou Tang or Jie Qiao.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    Summary of the numbers of embryos or cells of each biological replicate used for the RRBS analysis in this study.

  2. 2.

    Supplementary Table 2

    Summary of the sequencing qualities, reads mapping, and the covered CpG sites and their mean coverage depths at 1, 5, and 10 in each stage of the RRBS dataset. The right-hand column shows the average bisulfite conversion rate of each stage.

  3. 3.

    Supplementary Table 3

    Summary of the sequencing qualities, reads mapping, and the covered CpG sites and their mean coverage depths at 1, 5, and 10 of each single cell RRBS and WGBS samples. The right-hand column shows the average bisulfite conversion rate of each stage.

  4. 4.

    Supplementary Table 4

    The list of the filtered ASM regions covered in our WGBS of post-implanted liver tissue, including the chromosome positions, called SNPs positions, SNP genotypes, and the chromosome locations of the allele specific methylation regions.

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