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A unique regulatory phase of DNA methylation in the early mammalian embryo

Nature volume 484, pages 339–344 (2012)Cite this article

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Abstract

DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of 5-methylcytosine at fertilization, followed by passive loss that reaches a minimum at the blastocyst stage. However, this model is based on limited data, and so far no base-resolution maps exist to support and refine it. Here we generate genome-scale DNA methylation maps in mouse gametes and from the zygote through post-implantation. We find that the oocyte already exhibits global hypomethylation, particularly at specific families of long interspersed element 1 and long terminal repeat retroelements, which are disparately methylated between gametes and have lower methylation values in the zygote than in sperm. Surprisingly, the oocyte contributes a unique set of differentially methylated regions (DMRs)—including many CpG island promoters—that are maintained in the early embryo but are lost upon specification and absent from somatic cells. In contrast, sperm-contributed DMRs are largely intergenic and become hypermethylated after the blastocyst stage. Our data provide a genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic, before returning to the canonical somatic pattern.

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Figure 1: Global CpG methylation dynamics across early murine embryogenesis.
Figure 2: Major transitions in DNA methylation levels during early development.
Figure 3: Specific families of LINE and LTR retroelements exhibit the most dramatic methylation changes in the sperm to zygote transition.
Figure 4: Differentially methylated regions represent discrete gamete-specific feature classes.
Figure 5: DMRs resolve after cleavage to univalent hyper- or hypomethylated values in a gamete-of-origin-specific fashion.

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Gene Expression Omnibus

Data deposits

RRBS data is deposited at the Gene Expression Omnibus under accession number GSE34864.

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Acknowledgements

We would like to thank all members of the Meissner and Regev laboratories. M. Garber, N. Yosef, J. Ye, R. Koche, C. Bock, R. Maehr and D. Egli for technical advice and discussion. We thank all members of the Broad Sequencing Platform, in particular F. Kelly and J. Meldrim, T. Fennel, K. Tibbetts and J. Fostel. We also thank S. Levine, M. Gravina and K. Thai from the MIT BioMicro Center. A.R. is an investigator of the Merkin Foundation for Stem Cell Research at the Broad Institute. This work was supported by the NIH Pioneer Award (5DP1OD003958), the Burroughs Wellcome Career Award at the Scientific Interface and HHMI (to A.R.), the Harvard Stem Cell Institute (to T.S.M.) and the NIH (5RC1AA019317, U01ES017155 and P01GM099117), the Massachusetts Life Science Center and the Pew Charitable Trusts (to A.M.) and a Center for Excellence in Genome Science from the NHGRI (1P50HG006193-01, to A.R. and A.M.).

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Author notes

  1. Zachary D. Smith and Michelle M. Chan: These authors contributed equally to this work.

Authors and Affiliations

  1. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA ,

    Zachary D. Smith, Michelle M. Chan, Tarjei S. Mikkelsen, Hongcang Gu, Andreas Gnirke, Aviv Regev & Alexander Meissner

  2. Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA ,

    Zachary D. Smith, Tarjei S. Mikkelsen & Alexander Meissner

  3. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA,

    Zachary D. Smith & Alexander Meissner

  4. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA ,

    Michelle M. Chan

  5. Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA,

    Aviv Regev

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Contributions

Z.D.S. and A.M. conceived the study and Z.D.S., M.M.C. and A.M. facilitated its design. Z.D.S. collected samples and performed methylation profiling, M.M.C. performed all analysis with assistance from T.S.M. and Z.D.S. H.G. and A.G. provided critical technical assistance and expertise. Z.D.S., M.M.C., T.S.M., A.R. and A.M. interpreted the data. Z.D.S., M.M.C. and A.M. wrote the paper with the assistance of the other authors.

Corresponding author

Correspondence to Alexander Meissner.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-11 and full legends for Supplementary Tables 1- 4 and Supplementary Movie 1. (PDF 1636 kb)

Supplementary Table 1

This file contains promoter methylation levels at fertilization and across early embryonic development - see legend in Supplementary Information file. (XLS 3760 kb)

Supplementary Table 2

This file contains Long Interspersed Element (LINE) retrotransposon feature methylation across early embryonic development - see legend in Supplementary Information file. (XLS 28 kb)

Supplementary Table 3

This file contains Long Terminal Repeat (LTR) retrotransposon feature methylation across early embryonic development - see legend in Supplementary Information file. (XLS 42 kb)

Supplementary Table 4

This file contains feature designation and methylation status for identified oocyte-contributed Differentially Methylated Regions (DMRs) across early embryonic development - see legend in Supplementary Information file. (XLS 149 kb)

Supplementary Movie 1

This file contains a movie of a representative polar body biopsy for zygotes and cleavage stage embryos collected in this study - see legend in Supplementary Information file. (MOV 7166 kb)

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Smith, Z., Chan, M., Mikkelsen, T. et al. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 484, 339–344 (2012). https://doi.org/10.1038/nature10960

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