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Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa

Nature Structural & Molecular Biology volume 17, pages 679–687 (2010)Cite this article

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Abstract

In higher eukaryotes, histone methylation is involved in maintaining cellular identity during somatic development. As most nucleosomes are replaced by protamines during spermatogenesis, it is unclear whether histone modifications function in paternal transmission of epigenetic information. Here we show that two modifications important for Trithorax- and Polycomb-mediated gene regulation have methylation-specific distributions at regulatory regions in human spermatozoa. Histone H3 Lys4 dimethylation (H3K4me2) marks genes that are relevant in spermatogenesis and cellular homeostasis. In contrast, histone H3 Lys27 trimethylation (H3K27me3) marks developmental regulators in sperm, as in somatic cells. However, nucleosomes are only moderately retained at regulatory regions in human sperm. Nonetheless, genes with extensive H3K27me3 coverage around transcriptional start sites in particular tend not to be expressed during male and female gametogenesis or in preimplantation embryos. Promoters of orthologous genes are similarly modified in mouse spermatozoa. These data are compatible with a role for Polycomb in repressing somatic determinants across generations, potentially in a variegating manner.

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Figure 1: Methylated histones are present in human sperm and localize to distinct promoter sets.
Figure 2: DNA methylation of CpG islands is mutually exclusive with H3K4 methylation in sperm.
Figure 3: Spermatogenic and highly expressed genes are marked by H3K4me2 in sperm.
Figure 4: H3K27me3 and H3K4me2 in sperm reflect differential history and potential for expression during development.
Figure 5: Evolutionary conservation of H3K27me3- and H3K4me2-marked promoters in mouse spermatozoa.
Figure 6: Even distribution of nucleosomes along the human sperm genome with modest enrichments around TSSs.
Figure 7: Histone modification coverage in human sperm.

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References

  1. Chong, S. & Whitelaw, E. Epigenetic germline inheritance. Curr. Opin. Genet. Dev. 14, 692–696 (2004).

    Article  CAS  PubMed  Google Scholar 

  2. Hochedlinger, K. & Jaenisch, R. Nuclear transplantation, embryonic stem cells, and the potential for cell therapy. N. Engl. J. Med. 349, 275–286 (2003).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  4. Puschendorf, M. et al. PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Nat. Genet. 40, 411–420 (2008).

    Article  CAS  PubMed  Google Scholar 

  5. Albert, M. & Peters, A.H. Genetic and epigenetic control of early mouse development. Curr. Opin. Genet. Dev. 19, 113–121 (2009).

    Article  CAS  PubMed  Google Scholar 

  6. Balhorn, R., Gledhill, B.L. & Wyrobek, A.J. Mouse sperm chromatin proteins: quantitative isolation and partial characterization. Biochemistry 16, 4074–4080 (1977).

    Article  CAS  PubMed  Google Scholar 

  7. Gatewood, J.M., Cook, G.R., Balhorn, R., Bradbury, E.M. & Schmid, C.W. Sequence-specific packaging of DNA in human sperm chromatin. Science 236, 962–964 (1987).

    Article  CAS  PubMed  Google Scholar 

  8. Gardiner-Garden, M., Ballesteros, M., Gordon, M. & Tam, P.P. Histone- and protamine-DNA association: conservation of different patterns within the β-globin domain in human sperm. Mol. Cell. Biol. 18, 3350–3356 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Wykes, S.M. & Krawetz, S.A. The structural organization of sperm chromatin. J. Biol. Chem. 278, 29471–29477 (2003).

    Article  CAS  PubMed  Google Scholar 

  10. Pittoggi, C. et al. A fraction of mouse sperm chromatin is organized in nucleosomal hypersensitive domains enriched in retroposon DNA. J. Cell Sci. 112, 3537–3548 (1999).

    CAS  PubMed  Google Scholar 

  11. Hammoud, S.S. et al. Distinctive chromatin in human sperm packages genes for embryo development. Nature 460, 473–478 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. van der Heijden, G.W. et al. Sperm-derived histones contribute to zygotic chromatin in humans. BMC Dev. Biol. 8, 34 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Sparmann, A. & van Lohuizen, M. Polycomb silencers control cell fate, development and cancer. Nat. Rev. Cancer 6, 846–856 (2006).

    Article  CAS  PubMed  Google Scholar 

  14. Hublitz, P., Albert, M. & Peters, A.H. Mechanisms of transcriptional repression by histone lysine methylation. Int. J. Dev. Biol. 53, 335–354 (2009).

    Article  CAS  PubMed  Google Scholar 

  15. Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).

    Article  CAS  PubMed  Google Scholar 

  16. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Shen, X. et al. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol. Cell 32, 491–502 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Mohn, F. et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 30, 755–766 (2008).

    Article  CAS  PubMed  Google Scholar 

  19. Ezhkova, E. et al. Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells. Cell 136, 1122–1135 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Margueron, R. et al. Role of the Polycomb protein EED in the propagation of repressive histone marks. Nature 461, 762–767 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hansen, K.H. et al. A model for transmission of the H3K27me3 epigenetic mark. Nat. Cell Biol. 10, 1291–1300 (2008).

    Article  CAS  PubMed  Google Scholar 

  22. Alsheimer, M., Fecher, E. & Benavente, R. Nuclear envelope remodelling during rat spermiogenesis: distribution and expression pattern of LAP2/thymopoietins. J. Cell Sci. 111, 2227–2234 (1998).

    CAS  PubMed  Google Scholar 

  23. Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).

    Article  CAS  PubMed  Google Scholar 

  25. Imamura, M. et al. Transcriptional repression and DNA hypermethylation of a small set of ES cell marker genes in male germline stem cells. BMC Dev. Biol. 6, 34 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Pan, G. et al. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1, 299–312 (2007).

    Article  CAS  PubMed  Google Scholar 

  27. Zhao, X.D. et al. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1, 286–298 (2007).

    Article  CAS  PubMed  Google Scholar 

  28. Bracken, A.P., Dietrich, N., Pasini, D., Hansen, K.H. & Helin, K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20, 1123–1136 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Chalmel, F. et al. The conserved transcriptome in human and rodent male gametogenesis. Proc. Natl. Acad. Sci. USA 104, 8346–8351 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Geremia, R., Boitani, C., Conti, M. & Monesi, V. RNA synthesis in spermatocytes and spermatids and preservation of meiotic RNA during spermiogenesis in the mouse. Cell Differ. 5, 343–355 (1977).

    Article  CAS  PubMed  Google Scholar 

  31. Namekawa, S.H. et al. Postmeiotic sex chromatin in the male germline of mice. Curr. Biol. 16, 660–667 (2006).

    Article  CAS  PubMed  Google Scholar 

  32. Zeng, F. & Schultz, R.M. RNA transcript profiling during zygotic gene activation in the preimplantation mouse embryo. Dev. Biol. 283, 40–57 (2005).

    Article  CAS  PubMed  Google Scholar 

  33. Ohta, H., Tohda, A. & Nishimune, Y. Proliferation and differentiation of spermatogonial stem cells in the w/wv mutant mouse testis. Biol. Reprod. 69, 1815–1821 (2003).

    Article  CAS  PubMed  Google Scholar 

  34. Anderson, E.L. et al. Stra8 and its inducer, retinoic acid, regulate meiotic initiation in both spermatogenesis and oogenesis in mice. Proc. Natl. Acad. Sci. USA 105, 14976–14980 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kaneda, M. et al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 429, 900–903 (2004).

    Article  CAS  PubMed  Google Scholar 

  36. Strumpf, D. et al. Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development 132, 2093–2102 (2005).

    Article  CAS  PubMed  Google Scholar 

  37. Ng, R.K. et al. Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5. Nat. Cell Biol. 10, 1280–1290 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Pan, H., O'Brien, M.J., Wigglesworth, K., Eppig, J.J. & Schultz, R.M. Transcript profiling during mouse oocyte development and the effect of gonadotropin priming and development in vitro. Dev. Biol. 286, 493–506 (2005).

    Article  CAS  PubMed  Google Scholar 

  39. Faulkner, G.J. et al. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41, 563–571 (2009).

    Article  CAS  PubMed  Google Scholar 

  40. Arpanahi, A. et al. Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. Genome Res. 19, 1338–1349 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Gineitis, A.A., Zalenskaya, I.A., Yau, P.M., Bradbury, E.M. & Zalensky, A.O. Human sperm telomere-binding complex involves histone H2B and secures telomere membrane attachment. J. Cell Biol. 151, 1591–1598 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Chu, D.S. et al. Sperm chromatin proteomics identifies evolutionarily conserved fertility factors. Nature 443, 101–105 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Dorus, S. et al. Genomic and functional evolution of the Drosophila melanogaster sperm proteome. Nat. Genet. 38, 1440–1445 (2006).

    Article  CAS  PubMed  Google Scholar 

  45. Ooi, S.L. & Henikoff, S. Germline histone dynamics and epigenetics. Curr. Opin. Cell Biol. 19, 257–265 (2007).

    Article  CAS  PubMed  Google Scholar 

  46. van der Heijden, G.W. et al. Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote. Mech. Dev. 122, 1008–1022 (2005).

    Article  CAS  PubMed  Google Scholar 

  47. 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).

    Article  CAS  PubMed  Google Scholar 

  48. Minami, N., Suzuki, T. & Tsukamoto, S. Zygotic gene activation and maternal factors in mammals. J. Reprod. Dev. 53, 707–715 (2007).

    Article  CAS  PubMed  Google Scholar 

  49. Schuettengruber, B. & Cavalli, G. Recruitment of Polycomb group complexes and their role in the dynamic regulation of cell fate choice. Development 136, 3531–3542 (2009).

    Article  CAS  PubMed  Google Scholar 

  50. Bao, S. et al. Initiation of epigenetic reprogramming of the X chromosome in somatic nuclei transplanted to a mouse oocyte. EMBO Rep. 6, 748–754 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Kawahara, M. et al. High-frequency generation of viable mice from engineered bi-maternal embryos. Nat. Biotechnol. 25, 1045–1050 (2007).

    Article  CAS  PubMed  Google Scholar 

  52. Ng, R.K. & Gurdon, J.B. Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription. Nat. Cell Biol. 10, 102–109 (2008).

    Article  CAS  PubMed  Google Scholar 

  53. Katz, D.J., Edwards, T.M., Reinke, V. & Kelly, W.G.A. C. elegans LSD1 demethylase contributes to germline immortality by reprogramming epigenetic memory. Cell 137, 308–320 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. van der Heijden, G.W. et al. Parental origin of chromatin in human monopronuclear zygotes revealed by asymmetric histone methylation patterns, differs between IVF and ICSI. Mol. Reprod. Dev. 76, 101–108 (2009).

    Article  CAS  PubMed  Google Scholar 

  55. Ramos, L. et al. Incomplete nuclear transformation of human spermatozoa in oligo-astheno-teratospermia: characterization by indirect immunofluorescence of chromatin and thiol status. Hum. Reprod. 23, 259–270 (2008).

    Article  CAS  PubMed  Google Scholar 

  56. Chong, S. et al. Modifiers of epigenetic reprogramming show paternal effects in the mouse. Nat. Genet. 39, 614–622 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Lee, K., Haugen, H.S., Clegg, C.H. & Braun, R.E. Premature translation of protamine 1 mRNA causes precocious nuclear condensation and arrests spermatid differentiation in mice. Proc. Natl. Acad. Sci. USA 92, 12451–12455 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Dechat, T. et al. Detergent-salt resistance of LAP2α in interphase nuclei and phosphorylation-dependent association with chromosomes early in nuclear assembly implies functions in nuclear structure dynamics. EMBO J. 17, 4887–4902 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. O'Geen, H., Nicolet, C.M., Blahnik, K., Green, R. & Farnham, P.J. Comparison of sample preparation methods for ChIP-chip assays. Biotechniques 41, 577–580 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Umlauf, D., Goto, Y. & Feil, R. Site-specific analysis of histone methylation and acetylation. Methods Mol. Biol. 287, 99–120 (2004).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank T. Jenuwein (Max-Planck Institute of Immunobiology, Freiburg, Germany) and R. Foisner (Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria) for providing antisera. We are grateful to F. Zilbermann and the Friedrich Miescher Institute (FMI) animal facility for excellent technical assistance. We thank P. de Boer and R. Terranova for critical reading of the manuscript and all members of the Peters and Schübeler laboratories for discussions. U.B. and S.E. acknowledge the Boehringer Ingelheim Fonds for their PhD fellowships. M.H. was supported by the Swiss National Science Foundation and the Japan Society for the Promotion of Science. T.C.R. was supported by the Swiss Cancer Leagues. Research in the Peters laboratory is supported by the Novartis Research Foundation, the Swiss National Science Foundation, the European Network of Excellence “The Epigenome” and the EMBO YIP program.

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Author notes

  1. Urszula Brykczynska & Edward J Oakeley

    Present address: Present addresses: Department of Zoology and Animal Biology, University of Geneva, Sciences III, Geneva, Switzerland (U.B.) and Novartis Institutes for Biomedical Research, Basel, Switzerland (E.J.O.).,

Authors and Affiliations

  1. Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

    Urszula Brykczynska, Mizue Hisano, Serap Erkek, Edward J Oakeley, Tim C Roloff, Dirk Schübeler, Michael B Stadler & Antoine H F M Peters

  2. Department of Obstetrics and Gynaecology, Fertility Laboratory, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands

    Liliana Ramos

  3. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland

    Christian Beisel

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Contributions

U.B., M.H., S.E. and A.H.F.M.P. conceived and designed the experiments; U.B., M.H. and S.E. performed the experiments; L.R. provided purified samples of human spermatozoa; U.B., M.H., S.E., E.J.O., M.B.S. and A.H.F.M.P. analyzed the data; C.B. contributed to deep-sequencing; T.C.R. and D.S. provided advice on data analyses and the manuscript; U.B., S.E. and A.H.F.M.P. wrote the manuscript.

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Correspondence to Antoine H F M Peters.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8 and Supplementary Methods (PDF 2592 kb)

Supplementary Table 1

List of genes with modification states in human spermatozoa (XLS 3667 kb)

Supplementary Table 2

List of significantly over- and under-represented GO terms for Fig. 1d, 3d, 3e (XLS 842 kb)

Supplementary Table 3

Real-time PCR primer sequences (XLS 38 kb)

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Brykczynska, U., Hisano, M., Erkek, S. et al. Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nat Struct Mol Biol 17, 679–687 (2010). https://doi.org/10.1038/nsmb.1821

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