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Chromatin signature of embryonic pluripotency is established during genome activation


After fertilization the embryonic genome is inactive until transcription is initiated during the maternal–zygotic transition1,2,3. This transition coincides with the formation of pluripotent cells, which in mammals can be used to generate embryonic stem cells. To study the changes in chromatin structure that accompany pluripotency and genome activation, we mapped the genomic locations of histone H3 molecules bearing lysine trimethylation modifications before and after the maternal–zygotic transition in zebrafish. Histone H3 lysine 27 trimethylation (H3K27me3), which is repressive, and H3K4me3, which is activating, were not detected before the transition. After genome activation, more than 80% of genes were marked by H3K4me3, including many inactive developmental regulatory genes that were also marked by H3K27me3. Sequential chromatin immunoprecipitation demonstrated that the same promoter regions had both trimethylation marks. Such bivalent chromatin domains also exist in embryonic stem cells and are thought to poise genes for activation while keeping them repressed4,5,6,7,8. Furthermore, we found many inactive genes that were uniquely marked by H3K4me3. Despite this activating modification, these monovalent genes were neither expressed nor stably bound by RNA polymerase II. Inspection of published data sets revealed similar monovalent domains in embryonic stem cells. Moreover, H3K4me3 marks could form in the absence of both sequence-specific transcriptional activators and stable association of RNA polymerase II, as indicated by the analysis of an inducible transgene. These results indicate that bivalent and monovalent domains might poise embryonic genes for activation and that the chromatin profile associated with pluripotency is established during the maternal–zygotic transition.

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Figure 1: Large-scale changes in chromatin modifications during maternal–zygotic transition.
Figure 2: Bivalent chromatin domains in zebrafish embryos.
Figure 3: Many inactive genes are monovalently marked with H3K4me3.
Figure 4: H3K4me3 occupancy in the absence of a sequence-specific transcriptional activator.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

ChIP–chip data is available under GEO accession number GSE20023; custom designed array platform is under accession number GPL9970.


  1. Newport, J. & Kirschner, M. A major developmental transition in early Xenopus embryos: II. Control of the onset of transcription. Cell 30, 687–696 (1982)

    Google Scholar 

  2. Schier, A. F. The maternal-zygotic transition: death and birth of RNAs. Science 316, 406–407 (2007)

    Google Scholar 

  3. Tadros, W. & Lipshitz, H. D. The maternal-to-zygotic transition: a play in two acts. Development 136, 3033–3042 (2009)

    Google Scholar 

  4. Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)

    Google Scholar 

  5. Azuara, V. et al. Chromatin signatures of pluripotent cell lines. Nature Cell Biol. 8, 532–538 (2006)

    Google Scholar 

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

    Google Scholar 

  7. 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)

    Google Scholar 

  8. 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)

    Google Scholar 

  9. Schier, A. F. & Talbot, W. S. Molecular genetics of axis formation in zebrafish. Annu. Rev. Genet. 39, 561–613 (2005)

    Google Scholar 

  10. Schuettengruber, B., Chourrout, D., Vervoort, M., Leblanc, B. & Cavalli, G. Genome regulation by polycomb and trithorax proteins. Cell 128, 735–745 (2007)

    Google Scholar 

  11. Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707–719 (2007)

    Google Scholar 

  12. Rinn, J. L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311–1323 (2007)

    Google Scholar 

  13. Song, J. S. et al. Model-based analysis of two-color arrays (MA2C). Genome Biol. 8, R178 (2007)

    Google Scholar 

  14. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007)

    Google Scholar 

  15. Akkers, R. C. et al. A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Dev. Cell 17, 425–434 (2009)

    Google Scholar 

  16. Stock, J. K. et al. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nature Cell Biol. 9, 1428–1435 (2007)

    Google Scholar 

  17. Core, L. J. & Lis, J. T. Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791–1792 (2008)

    Google Scholar 

  18. Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88 (2007)

    Google Scholar 

  19. Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39, 1512–1516 (2007)

    Google Scholar 

  20. Muse, G. W. et al. RNA polymerase is poised for activation across the genome. Nature Genet. 39, 1507–1511 (2007)

    Google Scholar 

  21. Boettiger, A. N. & Levine, M. Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science 325, 471–473 (2009)

    Google Scholar 

  22. Dreijerink, K. M. et al. Menin links estrogen receptor activation to histone H3K4 trimethylation. Cancer Res. 66, 4929–4935 (2006)

    Google Scholar 

  23. Vermeulen, M. et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58–69 (2007)

    Google Scholar 

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

    Google Scholar 

  25. Sha, K. & Boyer, L. A. The chromatin signature of pluripotent cells. The Stem Cell Research Community, StemBook. 10.3824/stembook.1.45.1 〈〉 (2009)

  26. Yuzyuk, T., Fakhouri, T. H., Kiefer, J. & Mango, S. E. The polycomb complex protein mes-2/E(z) promotes the transition from developmental plasticity to differentiation in C. elegans embryos. Dev. Cell 16, 699–710 (2009)

    Google Scholar 

  27. Barski, A. et al. Chromatin poises miRNA- and protein-coding genes for expression. Genome Res. 19, 1742–1751 (2009)

    Google Scholar 

  28. Wardle, F. C. et al. Zebrafish promoter microarrays identify actively transcribed embryonic genes. Genome Biol. 7, R71 (2006)

    Google Scholar 

  29. 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)

    Google Scholar 

  30. Phatnani, H. P. & Greenleaf, A. L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20, 2922–2936 (2006)

    Google Scholar 

  31. Sagasti, A., Guido, M. R., Raible, D. W. & Schier, A. F. Repulsive interactions shape the morphologies and functional arrangement of zebrafish peripheral sensory arbors. Curr. Biol. 15, 804–814 (2005)

    Google Scholar 

  32. Link, V., Shevchenko, A. & Heisenberg, C. Proteomics of early zebrafish embryos. BMC Dev. Biol. 6, 1 (2006)

    Google Scholar 

  33. Shin, H., Liu, T., Manrai, A. K. & Liu, X. S. CEAS: Cis-regulatory Element Annotation System. Bioinformatics 25, 2605–2606 (2009)

    Google Scholar 

  34. Dennis, G. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, 3 (2003)

    Google Scholar 

  35. Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57 (2009)

    Google Scholar 

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We thank members of the Schier laboratory for help and advice; H. G. Shin, L. Taing and Z. J. Wu for computational analysis and discussions; N. Follmer and B. Lilley for technical advice; and J. Dubrulle, N. Francis, R. Losick, S. Mango, T. van Opijnen and W. Talbot for discussions and critical reading of the manuscript. This work was supported by NIH grants to X.S.L. (1R01 HG004069) and A.F.S. (5R01 GM56211), and by EMBO and HFSP (LT-00090/2007) fellowships to N.L.V.

Author Contributions N.L.V. and A.F.S. designed the study. N.L.V. performed the experiments. Y.Z. performed computational analysis. N.L.V., Y.Z., J.R., X.S.L. and A.F.S. designed and performed data analysis. I.G.W. provided technical support. F.I. provided RNA profiling data. A.R. provided analytical advice. N.L.V. and A.F.S. interpreted the data and wrote the paper with support from co-authors.

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Correspondence to X. Shirley Liu or Alexander F. Schier.

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Supplementary Information

This file contains Supplementary Discussions 1-5, Supplementary Figures S1-S9 with legends and Supplementary References. (PDF 1626 kb)

Supplementary Table 1

This file contains Supplementary Table 1, which includes the list of analyzed genes and their status for H3K4me3, H3K27me3, H3K36me3 and RNA polymerase II in zebrafish blastomeres. (XLS 110 kb)

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Vastenhouw, N., Zhang, Y., Woods, I. et al. Chromatin signature of embryonic pluripotency is established during genome activation. Nature 464, 922–926 (2010).

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