Letter | Published:

DNA methylation dynamics of the human preimplantation embryo

Nature volume 511, pages 611615 (31 July 2014) | Download Citation

Abstract

In mammals, cytosine methylation is predominantly restricted to CpG dinucleotides and stably distributed across the genome, with local, cell-type-specific regulation directed by DNA binding factors1,2,3. This comparatively static landscape is in marked contrast with the events of fertilization, during which the paternal genome is globally reprogrammed. Paternal genome demethylation includes the majority of CpGs, although methylation remains detectable at several notable features4,5,6,7. These dynamics have been extensively characterized in the mouse, with only limited observations available in other mammals, and direct measurements are required to understand the extent to which early embryonic landscapes are conserved8,9,10. We present genome-scale DNA methylation maps of human preimplantation development and embryonic stem cell derivation, confirming a transient state of global hypomethylation that includes most CpGs, while sites of residual maintenance are primarily restricted to gene bodies. Although most features share similar dynamics to those in mouse, maternally contributed methylation is divergently targeted to species-specific sets of CpG island promoters that extend beyond known imprint control regions. Retrotransposon regulation is also highly diverse, and transitions from maternally to embryonically expressed elements. Together, our data confirm that paternal genome demethylation is a general attribute of early mammalian development that is characterized by distinct modes of epigenetic regulation.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

Data deposits

RRBS data is deposited at the Gene Expression Omnibus under accession number GSE51239.

References

  1. 1.

    & DNA methylation landscapes: provocative insights from epigenomics. Nature Rev. Genet. 9, 465–476 (2008)

  2. 2.

    et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011)

  3. 3.

    et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477–481 (2013)

  4. 4.

    et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 35, 88–93 (2003)

  5. 5.

    et al. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nature Genet. 43, 811–814 (2011)

  6. 6.

    et al. Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet. 8, e1002440 (2012)

  7. 7.

    et al. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 484, 339–344 (2012)

  8. 8.

    , , & DNA methylation pattern in human zygotes and developing embryos. Reproduction 128, 703–708 (2004)

  9. 9.

    et al. Evaluation of epigenetic marks in human embryos derived from IVF and ICSI. Hum. Reprod. 25, 2387–2395 (2010)

  10. 10.

    et al. Evidence for conserved DNA and histone H3 methylation reprogramming in mouse, bovine and rabbit zygotes. Epigenetics Chromatin 1, 8 (2008)

  11. 11.

    et al. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146, 1029–1041 (2011)

  12. 12.

    et al. Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development. Genes Dev. 22, 1607–1616 (2008)

  13. 13.

    et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nature Struct. Mol. Biol. 20, 1131–1139 (2013)

  14. 14.

    et al. Establishment of totipotency does not depend on Oct4A. Nature Cell Biol. 15, 1089–1097 (2013)

  15. 15.

    & DNA methylation dynamics during the mammalian life cycle. Phil. Trans. R. Soc. Lond. B 368, 20110328 (2013)

  16. 16.

    et al. Targets and dynamics of promoter DNA methylation during early mouse development. Nature Genet. 42, 1093–1100 (2010)

  17. 17.

    et al. Sex-specific exons control DNA methyltransferase in mammalian germ cells. Development 125, 889–897 (1998)

  18. 18.

    et al. Conservation of the H19 noncoding RNA and H19IGF2 imprinting mechanism in therians. Nature Genet. 40, 971–976 (2008)

  19. 19.

    & Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol. 13, R107 (2012)

  20. 20.

    et al. Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells. Retrovirology 10, 115 (2013)

  21. 21.

    et al. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nature Struct. Mol. Biol. 21, 423–425 (2014)

  22. 22.

    , & Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 16, 78–87 (2006)

  23. 23.

    , & Selection against deleterious LINE-1-containing loci in the human lineage. Mol. Biol. Evol. 18, 926–935 (2001)

  24. 24.

    & New insights into establishment and maintenance of DNA methylation imprints in mammals. Phil. Trans. R. Soc. Lond. B 368, 20110336 (2013)

  25. 25.

    & Active human retrotransposons: variation and disease. Curr. Opin. Genet. Dev. 22, 191–203 (2012)

  26. 26.

    et al. Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines. Cell Stem Cell 4, 103–106 (2009)

  27. 27.

    & Isolation and maintenance of mouse epiblast stem cells. Methods Mol. Biol. 636, 25–44 (2010)

  28. 28.

    et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454 766–770 10.1038/nature07107 (2008)

  29. 29.

    et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010)

  30. 30.

    , & Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue. Epigenet. Chromatin 4, 1 (2011)

  31. 31.

    & Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 9440–9445 (2003)

Download references

Acknowledgements

We would like to thank all members of the Meissner, Regev and Eggan laboratories, in particular M. Ziller for critical reading of the text and K. Koszka for supervising human embryo thawing. We also thank D. Sakkas and R. Holmes of Boston IVF for clinical assessment of embryo morphology and viability, as well as S. Levine, M. Gravina and K. Thai from the MIT BioMicro Center. Finally, we thank T. S. Mikkelsen, H. Gu, and A. Gnirke from the Broad Institute for their guidance and expertise. A.R. is an investigator of the Merkin Foundation for Stem Cell Research at the Broad Institute. This work was supported by the Harvard Stem Cell Institute (K.E.), and NIH Pioneer Award (5DP1OD003958), the Burroughs Wellcome Career Award at the Scientific Interface and HHMI (to A.R. and K.E.), P01GM099117 (to A.M. and K. E.) and a Center for Excellence in Genome Science from the NHGRI (1P50HG006193-01, to A.R. and A.M.). A.M. is a New York Stem Cell Foundation Robertson Investigator. This research was supported by The New York Stem Cell Foundation.

Author information

Author notes

    • Zachary D. Smith
    • , Michelle M. Chan
    •  & Kathryn C. Humm

    These authors contributed equally to this work.

Affiliations

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

    • Zachary D. Smith
    • , Michelle M. Chan
    • , Rahul Karnik
    • , Aviv Regev
    • , Kevin Eggan
    •  & Alexander Meissner
  2. Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA

    • Zachary D. Smith
    • , Rahul Karnik
    • , Kevin Eggan
    •  & Alexander Meissner
  3. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA

    • Zachary D. Smith
    • , Kathryn C. Humm
    • , Rahul Karnik
    • , Shila Mekhoubad
    • , Kevin Eggan
    •  & Alexander Meissner
  4. Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA

    • Zachary D. Smith
    • , Shila Mekhoubad
    •  & Kevin Eggan
  5. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA

    • Michelle M. Chan
  6. Division of Reproductive Endocrinology & Infertility, Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA

    • Kathryn C. Humm
  7. Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts 02215, USA

    • Kathryn C. Humm
  8. Boston IVF, Waltham, Massachusetts 02451, USA

    • Kathryn C. Humm
  9. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA

    • Kathryn C. Humm
    •  & Aviv Regev
  10. Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA

    • Aviv Regev
  11. Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA

    • Kevin Eggan

Authors

  1. Search for Zachary D. Smith in:

  2. Search for Michelle M. Chan in:

  3. Search for Kathryn C. Humm in:

  4. Search for Rahul Karnik in:

  5. Search for Shila Mekhoubad in:

  6. Search for Aviv Regev in:

  7. Search for Kevin Eggan in:

  8. Search for Alexander Meissner in:

Contributions

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

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Kevin Eggan or Alexander Meissner.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    Promoter methylation and gene expression values over human preimplantation development and ESC derivation: Methylation of promoters and corresponding gene expression dynamics across human early development and during ESC derivation. Expression is calculated as the fragments per kb per million (FPKM).

  2. 2.

    Supplementary Table 2

    Methylation dynamics of orthologous human and mouse CpG islands: Methylation values in human CGI promoters over preimplantation development. Nearest gene refers to the TSS that is most proximal to the CGI. Human CGIs that aligned to mouse but did not maintain CGI status are indicated under the mouse proximal gene annotation and methylation over the orthologous region is reported when captured (Methods).

  3. 3.

    Supplementary Table 3

    Mean LTR subfamily methylation and expression dynamics over human preimplantation development: Family and subfamily designations, genomic representation as indicated by repeat masker, and the number of members captured by RRBS are included. Mean methylation is reported for subfamilies over the human preimplantation and ESC derivation timeline. Expression is calculated as the fragments per kb per million (FPKM), which accounts for differences in genomic representation. Total expression refers to the fragments per million (FPM) and indicates the total contribution of a given family to the transcriptome (Methods).

  4. 4.

    Supplementary Table 4

    Mean LINE subfamily methylation and expression dynamics over human preimplantation development: Subfamily level mean methylation and expression, including both mean and total, dynamics for LINEs over human preimplantation and ESC derivation, organized as in Supplementary Table 3.

  5. 5.

    Supplementary Table 5

    Mean SINE subfamily methylation and expression dynamics over human preimplantation development: Subfamily level mean methylation and expression, including both mean and total, dynamics for SINEs over human preimplantation and ESC derivation, organized as in Supplementary Table 3.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature13581

Further reading Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.