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

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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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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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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