Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A role for the elongator complex in zygotic paternal genome demethylation

This article has been updated


The life cycle of mammals begins when a sperm enters an egg. Immediately after fertilization, both the maternal and paternal genomes undergo dramatic reprogramming to prepare for the transition from germ cell to somatic cell transcription programs1. One of the molecular events that takes place during this transition is the demethylation of the paternal genome2,3. Despite extensive efforts, the factors responsible for paternal DNA demethylation have not been identified4. To search for such factors, we developed a live cell imaging system that allows us to monitor the paternal DNA methylation state in zygotes. Through short-interfering-RNA-mediated knockdown in mouse zygotes, we identified Elp3 (also called KAT9), a component of the elongator complex5, to be important for paternal DNA demethylation. We demonstrate that knockdown of Elp3 impairs paternal DNA demethylation as indicated by reporter binding, immunostaining and bisulphite sequencing. Similar results were also obtained when other elongator components, Elp1 and Elp4, were knocked down. Importantly, injection of messenger RNA encoding the Elp3 radical SAM domain mutant, but not the HAT domain mutant, into MII oocytes before fertilization also impaired paternal DNA demethylation, indicating that the SAM radical domain is involved in the demethylation process. Our study not only establishes a critical role for the elongator complex in zygotic paternal genome demethylation, but also indicates that the demethylation process may be mediated through a reaction that requires an intact radical SAM domain.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Knockdown of Elp3 prevents preferential incorporation of the CxxC–EGFP reporter into the paternal pronucleus.
Figure 2: Knockdown of Elp3 impairs DNA demethylation in the paternal pronucleus.
Figure 3: Knockdown of the elongator components Elp1 and Elp4 also impairs paternal DNA demethylation in zygotes.
Figure 4: Mutation of the cysteine-rich radical SAM domain of Elp3 impairs paternal DNA demethylation.

Change history

  • 28 January 2010

    In the paragraph beginning 'To provide direct evidence...', the reference to Fig. 3c was corrected to Fig. 2c on 28 January 2010.


  1. 1

    Reik, W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007)

    ADS  CAS  Article  Google Scholar 

  2. 2

    Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation of the zygotic paternal genome. Nature 403, 501–502 (2000)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Oswald, J. et al. Active demethylation of the paternal genome in the mouse zygote. Curr. Biol. 10, 475–478 (2000)

    CAS  Article  Google Scholar 

  4. 4

    Ooi, S. K. & Bestor, T. H. The colorful history of active DNA demethylation. Cell 133, 1145–1148 (2008)

    CAS  Article  Google Scholar 

  5. 5

    Svejstrup, J. Q. Elongator complex: how many roles does it play? Curr. Opin. Cell Biol. 19, 331–336 (2007)

    CAS  Article  Google Scholar 

  6. 6

    Howell, C. Y. et al. Genomic imprinting disrupted by a maternal effect mutation in the Dnmt1 gene. Cell 104, 829–838 (2001)

    CAS  Article  Google Scholar 

  7. 7

    Hajkova, P. et al. Epigenetic reprogramming in mouse primordial germ cells. Mech. Dev. 117, 15–23 (2002)

    CAS  Article  Google Scholar 

  8. 8

    Bhattacharya, S. K., Ramchandani, S., Cervoni, N. & Szyf, M. A mammalian protein with specific demethylase activity for mCpG DNA. Nature 397, 579–583 (1999)

    ADS  CAS  Article  Google Scholar 

  9. 9

    Santos, F., Hendrich, B., Reik, W. & Dean, W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev. Biol. 241, 172–182 (2002)

    CAS  Article  Google Scholar 

  10. 10

    Choi, Y. et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis . Cell 110, 33–42 (2002)

    CAS  Article  Google Scholar 

  11. 11

    Gong, Z. et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814 (2002)

    CAS  Article  Google Scholar 

  12. 12

    Rai, K. et al. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 135, 1201–1212 (2008)

    CAS  Article  Google Scholar 

  13. 13

    Barreto, G. et al. Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 445, 671–675 (2007)

    CAS  Article  Google Scholar 

  14. 14

    Ma, D. K. et al. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323, 1074–1077 (2009)

    ADS  CAS  Article  Google Scholar 

  15. 15

    Engel, N. et al. Conserved DNA methylation in Gadd45a-/- mice. Epigenetics 4, 98–99 (2009)

    CAS  Article  Google Scholar 

  16. 16

    Jin, S. G., Guo, C. & Pfeifer, G. P. GADD45A does not promote DNA demethylation. PLoS Genet. 4, e1000013 (2008)

    Article  Google Scholar 

  17. 17

    Allen, M. D. et al. Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase. EMBO J. 25, 4503–4512 (2006)

    CAS  Article  Google Scholar 

  18. 18

    Jorgensen, H. F., Adie, K., Chaubert, P. & Bird, A. P. Engineering a high-affinity methyl-CpG-binding protein. Nucleic Acids Res. 34, e96 (2006)

    Article  Google Scholar 

  19. 19

    Yamagata, K., Suetsugu, R. & Wakayama, T. Long-term, six-dimensional live-cell imaging for the mouse preimplantation embryo that does not affect full-term development. J. Reprod. Dev. 55, 343–350 (2009)

    Article  Google Scholar 

  20. 20

    Torres-Padilla, M. E., Bannister, A. J., Hurd, P. J., Kouzarides, T. & Zernicka-Goetz, M. Dynamic distribution of the replacement histone variant H3.3 in the mouse oocyte and preimplantation embryos. Int. J. Dev. Biol. 50, 455–461 (2006)

    CAS  Article  Google Scholar 

  21. 21

    Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009)

    ADS  CAS  Article  Google Scholar 

  22. 22

    Kim, S. H. et al. Differential DNA methylation reprogramming of various repetitive sequences in mouse preimplantation embryos. Biochem. Biophys. Res. Commun. 324, 58–63 (2004)

    CAS  Article  Google Scholar 

  23. 23

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

    CAS  Article  Google Scholar 

  24. 24

    Wittschieben, B. O. et al. A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. Mol. Cell 4, 123–128 (1999)

    CAS  Article  Google Scholar 

  25. 25

    Hawkes, N. A. et al. Purification and characterization of the human elongator complex. J. Biol. Chem. 277, 3047–3052 (2002)

    CAS  Article  Google Scholar 

  26. 26

    Wang, S. C. & Frey, P. A. S-adenosylmethionine as an oxidant: the radical SAM superfamily. Trends Biochem. Sci. 32, 101–110 (2007)

    CAS  Article  Google Scholar 

  27. 27

    Paraskevopoulou, C., Fairhurst, S. A., Lowe, D. J., Brick, P. & Onesti, S. The Elongator subunit Elp3 contains a Fe4S4 cluster and binds S-adenosylmethionine. Mol. Microbiol. 59, 795–806 (2006)

    CAS  Article  Google Scholar 

  28. 28

    Tagami, H., Ray-Gallet, D., Almouzni, G. & Nakatani, Y. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116, 51–61 (2004)

    CAS  Article  Google Scholar 

  29. 29

    Opavsky, R. et al. CpG island methylation in a mouse model of lymphoma is driven by the genetic configuration of tumor cells. PLoS Genet. 3, e167 (2007)

    Article  Google Scholar 

  30. 30

    Tremblay, K. D., Duran, K. L. & Bartolomei, M. S. A 5′ 2-kilobase-pair region of the imprinted mouse H19 gene exhibits exclusive paternal methylation throughout development. Mol. Cell. Biol. 17, 4322–4329 (1997)

    CAS  Article  Google Scholar 

  31. 31

    Jackson-Grusby, L. et al. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nature Genet. 27, 31–39 (2001)

    CAS  Article  Google Scholar 

Download references


We thank H. Song for providing the Gadd45b null mice, and K. Aoki and M. Matsuda for helping with image quantification. We are grateful to S. Wu for critical reading of the manuscript. Y.Z. is an investigator of the Howard Hughes Medical Institute.

Author Contributions Y.Z. conceived the project. Y.Z. and Y.O. designed the experiments and prepared the manuscript. Y.O. performed the majority of the experiments. K.Y. and K.H. helped with some of the experiments. T.W. provided the instruments and reagent for Y.O.’s technical training.

Author information



Corresponding author

Correspondence to Yi Zhang.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S8 with Legends and Supplementary Tables S1-S3. (PDF 1753 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Okada, Y., Yamagata, K., Hong, K. et al. A role for the elongator complex in zygotic paternal genome demethylation. Nature 463, 554–558 (2010).

Download citation

Further reading


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.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing