Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2

Nature Structural & Molecular Biology volume 25, pages 225–232 (2018)Cite this article

Subjects

Abstract

Polycomb repressive complex 2 (PRC2) catalyzes methylation on lysine 27 of histone H3 (H3K27) and is required for maintaining transcriptional patterns and cellular identity, but the specification and maintenance of genomic PRC2 binding and H3K27 methylation patterns remain incompletely understood. Epigenetic mechanisms have been proposed, wherein pre-existing H3K27 methylation directs recruitment and regulates the catalytic activity of PRC2 to support its own maintenance. Here we investigate whether such mechanisms are required for specifying H3K27 methylation patterns in mouse embryonic stem cells (mESCs). Through re-expression of PRC2 subunits in PRC2-knockout cells that have lost all H3K27 methylation, we demonstrate that methylation patterns can be accurately established de novo. We find that regional methylation kinetics correlate with original methylation patterns even in their absence, and specification of the genomic PRC2 binding pattern is retained and specifically dependent on the PRC2 core subunit SUZ12. Thus, the H3K27 methylation patterns in mESCs are not dependent on self-autonomous epigenetic inheritance.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Models of histone-methylation maintenance.
Fig. 2: Propagation-independent establishment of H3K27 methylation patterns.
Fig. 3: Regional de novo methylation kinetics.
Fig. 4: Suz12 binds CGIs independently of Eed, Ezh1, and Ezh2.
Fig. 5: Accurate H3K27 methylation and pluripotency established from Suz12-KO cells with methylation and PRC2 binding erased.
Fig. 6: An N-terminal Suz12 fragment is essential for CGI binding and correct H3K27 methylation patterns.

Similar content being viewed by others

References

  1. 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 

  2. Ferrari, K. J. et al. Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity. Mol. Cell 53, 49–62 (2014).

    Article  CAS  PubMed  Google Scholar 

  3. 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 

  4. Müller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197–208 (2002).

    Article  PubMed  Google Scholar 

  5. 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 

  6. Smits, A. H., Jansen, P. W., Poser, I., Hyman, A. A. & Vermeulen, M. Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics. Nucleic Acids Res. 41, e28 (2013).

    Article  CAS  PubMed  Google Scholar 

  7. Cao, R. & Zhang, Y. SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol. Cell 15, 57–67 (2004).

    Article  CAS  PubMed  Google Scholar 

  8. Pasini, D., Bracken, A. P., Jensen, M. R., Lazzerini Denchi, E. & Helin, K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J. 23, 4061–4071 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Montgomery, N. D. et al. The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation. Curr. Biol. 15, 942–947 (2005).

    Article  CAS  PubMed  Google Scholar 

  10. 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 

  11. Lewis, E. B. A gene complex controlling segmentation in Drosophila. Nature 276, 565–570 (1978).

    Article  CAS  PubMed  Google Scholar 

  12. Faust, C., Schumacher, A., Holdener, B. & Magnuson, T. The eed mutation disrupts anterior mesoderm production in mice. Development 121, 273–285 (1995).

    CAS  PubMed  Google Scholar 

  13. O’Carroll, D. et al. The polycomb-group gene Ezh2 is required for early mouse development. Mol. Cell. Biol. 21, 4330–4336 (2001).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Pengelly, A. R., Copur, Ö., Jäckle, H., Herzig, A. & Müller, J. A histone mutant reproduces the phenotype caused by loss of histone-modifying factor Polycomb. Science 339, 698–699 (2013).

    Article  CAS  PubMed  Google Scholar 

  15. Laugesen, A., Højfeldt, J. W. & Helin, K. Role of the Polycomb repressive complex 2 (PRC2) in transcriptional regulation and cancer. Cold Spring Harb. Perspect. Med. 6, a026575 (2016).

    Article  PubMed  Google Scholar 

  16. Peters, A. H. et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12, 1577–1589 (2003).

    Article  CAS  PubMed  Google Scholar 

  17. Jung, H. R., Pasini, D., Helin, K. & Jensen, O. N. Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36. Mol. Cell. Proteomics 9, 838–850 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Steiner, L. A., Schulz, V. P., Maksimova, Y., Wong, C. & Gallagher, P. G. Patterns of histone H3 lysine 27 monomethylation and erythroid cell type-specific gene expression. J. Biol. Chem. 286, 39457–39465 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mohammad, F. et al. EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas. Nat. Med. 23, 483–492 (2017).

    Article  CAS  PubMed  Google Scholar 

  20. Alabert, C. et al. Two distinct modes for propagation of histone PTMs across the cell cycle. Genes Dev. 29, 585–590 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Gaydos, L. J., Wang, W. & Strome, S. Gene repression. H3K27me and PRC2 transmit a memory of repression across generations and during development. Science 345, 1515–1518 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Laprell, F., Finkl, K. & Müller, J. Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA. Science 356, 85–88 (2017).

    Article  CAS  PubMed  Google Scholar 

  23. Coleman, R. T. & Struhl, G. Causal role for inheritance of H3K27me3 in maintaining the OFF state of a Drosophila HOX gene. Science 356, eaai8236 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  24. Ramachandran, S. & Henikoff, S. Replicating nucleosomes. Sci. Adv. 1, e1500587 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  25. 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 

  26. 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 

  27. Ptashne, M. Epigenetics: core misconcept. Proc. Natl Acad. Sci. USA 110, 7101–7103 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Henikoff, S. & Greally, J. M. Epigenetics, cellular memory and gene regulation. Curr. Biol. 26, R644–R648 (2016).

    Article  CAS  PubMed  Google Scholar 

  29. Chamberlain, S. J., Yee, D. & Magnuson, T. Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. Stem Cells 26, 1496–1505 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Pasini, D., Bracken, A. P., Hansen, J. B., Capillo, M. & Helin, K. The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol. Cell. Biol. 27, 3769–3779 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Schoeftner, S. et al. Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J. 25, 3110–3122 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Margueron, R. et al. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol. Cell 32, 503–518 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Riising, E. M. et al. Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. Mol. Cell 55, 347–360 (2014).

    Article  CAS  PubMed  Google Scholar 

  34. Knutson, S. K. et al. Durable tumor regression in genetically altered malignant rhabdoid tumors by inhibition of methyltransferase EZH2. Proc. Natl Acad. Sci. USA 110, 7922–7927 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Su, I. H. et al. Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nat. Immunol. 4, 124–131 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Rai, A. N. et al. Elements of the polycomb repressor SU(Z)12 needed for histone H3-K27 methylation, the interface with E(Z), and in vivo function. Mol. Cell. Biol. 33, 4844–4856 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Jiao, L. & Liu, X. Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2. Science 350, aac4383 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  38. Brooun, A. et al. Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance. Nat. Commun. 7, 11384 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Justin, N. et al. Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2. Nat. Commun. 7, 11316 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Blackledge, N. P. et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 157, 1445–1459 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Cooper, S. et al. Jarid2 binds mono-ubiquitylated H2A lysine 119 to mediate crosstalk between Polycomb complexes PRC1 and PRC2. Nat. Commun. 7, 13661 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Tavares, L. et al. RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. Cell 148, 664–678 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Gao, Z. et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol. Cell 45, 344–356 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Li, H. et al. Polycomb-like proteins link the PRC2 complex to CpG islands. Nature 549, 287–291 (2017).

    Article  CAS  PubMed  Google Scholar 

  45. Kloet, S. L. et al. The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation. Nat. Struct. Mol. Biol. 23, 682–690 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44, W3–W10 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    Article  CAS  PubMed  Google Scholar 

  49. Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

    Article  CAS  PubMed  Google Scholar 

  50. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  51. Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Lerdrup, M., Johansen, J. V., Agrawal-Singh, S. & Hansen, K. An interactive environment for agile analysis and visualization of ChIP-sequencing data. Nat. Struct. Mol. Biol. 23, 349–357 (2016).

    Article  CAS  PubMed  Google Scholar 

  54. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590–604 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank members of the Helin laboratory and A. Groth for advice and discussion, and J. Martin and the Transgenic Core Facility staff for assistance with morula injection experiments. H.D. was supported by a postdoctoral fellowship from the Danish Cancer Society. The work in the Helin laboratory was supported by grants to K.H. from The European Research Council (294666_DNAMET), the Seventh Framework Program of the European Union (4DCellFate), the Danish Cancer Society, the Danish National Research Foundation (DNRF82), the Danish Medical Research Council (DFF- 4183-00237), the Novo Nordisk Foundation (NNF16OC0023234), and The Lundbeck Foundation, and through a center grant from the Novo Nordisk Foundation (NNF17CC0027852)).

Author information

Author notes

  1. Andrey Tvardovskiy

    Present address: Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany

Authors and Affiliations

  1. Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Jonas W. Højfeldt, Anne Laugesen, Helene Damhofer, Lin Hedehus, Faizaan Mohammad & Kristian Helin

  2. The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Jonas W. Højfeldt, Anne Laugesen, Helene Damhofer, Lin Hedehus, Faizaan Mohammad & Kristian Helin

  3. Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Berthe M. Willumsen

  4. Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark

    Andrey Tvardovskiy & Ole N. Jensen

Authors
  1. Jonas W. Højfeldt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anne Laugesen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Berthe M. Willumsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Helene Damhofer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lin Hedehus
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Andrey Tvardovskiy
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Faizaan Mohammad
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ole N. Jensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Kristian Helin
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.W.H. and A.L. designed the study, performed the majority of experiments, performed data analysis and wrote the manuscript. K.H. designed the study, performed data analysis and wrote the manuscript. B.M.W. performed experiments regarding the generation of KO cell lines. H.D. performed experiments regarding the inhibitor study. L.H. and F.M. performed experiments regarding the blastocyst injection experiment. A.T. and O.N.J. performed and analyzed experiments critical for development of the project.

Corresponding author

Correspondence to Kristian Helin.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Integrated supplementary information

Supplementary Figure 1 Genetic erasure and restoration of H3K27 methylation patterns.

a, Western blots of extracts from PRC2-subunit knockout cell lines blotted for PRC2 subunits and H3K27 methylation. Experiment has been repeated at least three times with same result. Uncropped blot/gel images are shown in Supplementary Data Set 1. b, ChIP-seq signals generated with H3K27 methylation specific antibodies. The samples and the shown region is the same as Fig. 2b, but the ChIP-seq signals are here shown without spike-in normalization. Values on vertical axis correspond to reads per million mapped mouse reads. c, Heatmaps of sequence-depth normalized ChIP-seq data of H3K27 methylation in genic regions. Vertical axis contains all RefSeq genes > 250bp and horizontal axis is centered on genes represented by relative gene length. TSS: Transcription start site. Arrow ends at end of genes. d, Scatterplots comparing ChIP-seq signal within 5000 bp genomic regions between parental WT mESCs and Ezh1/Ezh2 dKO or EZH2 rescue cells. The entire mouse genome has been divided into 5000 bp regions and spike-in normalized signal quantified for each region. The quantified values are in units of reads per million Drosophila-mapped reads per 1000 bp.

Supplementary Figure 2 Gene deregulation and reversal in Ezh1/Ezh2-dKO and dKO + EZH2 cells.

a. MA plots of RNAseq data analyzed with DESeq2 for differential expression in either Ezh1/Ezh2 dKO (left) or dKO + EZH2 (right) relative to WT mESCs. Genes that are significantly upregulated (FDR < 0.05 and rlog2-fold change > 1) in Ezh1/Ezh2 dKO cells are colored red and significantly downregulated genes (FDR < 0.05, rlog2-fold change < -1) are colored blue. b. Plot of all genes that are differentially expressed in Ezh1/Ezh2 dKO cells together with their rlog2 fold expression changes (relative to WT mESCs) in Ezh1/Ezh2 dKO cells (red) and dKO + EZH2 cells (blue). The genes are ranked along horizontal axis according to the extent of deregulation in Ezh1/Ezh2 dKO cells.

Supplementary Figure 3 Effect of inhibitor treatment on mESC properties.

a. Schematic representation E14 and 7d cells, which have been treated with 10 µM Ezh2 inhibitor (EPZ6438) for 7 days. b. Outline of embroid body (EB) differentiation assay used to assess differentiation capacity. c. Quantification of beating clusters following EB differentiation. E14 or 7d cells were each differentiated in both absence or presence of inhibitor. Fractions in graph show number of beating clusters over total clusters observed. d. Proliferation curve for E14 and 7d cells. 7d cells were grown with continuous presence of inhibitor. At each time point, two individual wells are counted for each cell type. This experiment was repeated as a biological replicate 2 (not shown). e. Proliferation rate (doubling time) calculated from proliferation curve in panel d and from replicate experiment 2. Error bars represent 95% confidence interval based on linear regression of proliferation curves (6 duplicate data points per curve). f. Expression level of pluripotency genes. Circles show mean value of two technical replicates for each of three biological replicates. Wide black line marks represent the mean of the biological replicates, and error bars represent the s.e.m. g. Expression level of Hoxa10, which is upregulated in Ezh1/Ezh2 dKO vs WT mESCs, in E14 and 7d cells.

Supplementary Figure 4 Regional de novo methylation kinetics.

a. ChIP-seq tracks showing kinetics of re-methylation of all three states of H3K27 methylation as well as Suz12 binding in a representative genomic region following treatment with EZH2 inhibitor. ChIPseq signal is spike-in normalized (reads per million mapped Drosophila reads). b. Heatmaps of spike-in normalized ChIP-seq data of H3K27 methylation within random genomic regions. Vertical axis contains 50,000 random 5000 bp regions clustered (k-means clustering, k = 10) according to methylation state in E14 cells. The clusters are ordered according to highest methylation state in untreated cells. c, Biological replicate of experiment presented in Fig. 3c. ChIP-qPCR data probing kinetics of H3K27me3 (first row), H3K27me2 (second row), H3K27me1 (third row) and Suz12 (fourth row) at seven representative loci labeled (above graph) according to nearest gene and in approximate order of decreasing methylation rates (% of input/hr washout). Data values come from a single biological (n=1) experiment, with error bars depicting s.d. of technical duplicates.

Source data

Supplementary Figure 5 Accurate H3K27 methylation and restored pluripotency in SUZ12-rescue cells.

a, Heatmaps of sequence-depth normalized ChIP-seq data of H3K27 methylation in genic regions. Vertical axis contains all RefSeq genes > 250bp and horizontal axis is centered on genes represented by relative gene length. TSS: Transcription start site. Arrow ends at end of genes. b, Images of embryos derived from a morula injection experiment dissected at E13.5. In addition to embryos shown in Fig. 5c, three additional embryos were obtained from morulas injected with Suz12 KO cells and two additional embryos were obtained from injection of SUZ12-rescued cells (KO + SUZ12). Scale bar: 5 mm. c, Side-by-side comparison of embryos shown in Fig. 5b. Scale bar: 5 mm. d, Mouse embryonic fibroblasts (MEFs) and neural stem cells (NSCs) were derived from embryos shown in Fig. 5b and embryo #2 from Suz12 KO cells and SUZ12-rescued cells. These cells were analyzed by FACS to quantify the contribution of mCherry-positive cells.

Supplementary Figure 6 An N-terminal SUZ12 fragment is essential for CGI binding and correct H3K27 methylation patterns.

a, Heatmaps of sequence-depth normalized ChIP-seq data of H3K27 methylation in genic regions. Vertical axis contains all RefSeq genes > 250bp and horizontal axis is centered on genes represented by relative gene length. TSS: Transcription start site. Arrow ends at end of genes. b, Heatmaps of sequence-depth normalized ChIP-seq data of H3K27 methylation within random genomic regions. Vertical axis contains 50,000 random 5000 bp regions clustered (k-means clustering, k = 10) according to methylation state in E14 cells. Horizontal axis is 25,000 bp wide centered on regions used for clustering. The clusters are ordered according to highest methylation state in untreated cells. c, Heatmaps of sequence-depth normalized H3K27me1 ChIP-seq data clustered with H3K9me3 and H3K36me3. Regions in H3K27me1 positive clusters (8 and 9, 6670 regions) have been submitted to new clustering with published H3K9me3 and H3K36me3 data55 to yield clusters B1 to B6. Horizontal axis is 100,000 bp wide centered on regions (5000 bp) used for clustering.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Tables 1–5

Life Sciences Reporting Summary

Supplementary Dataset 1

Source Data

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Højfeldt, J.W., Laugesen, A., Willumsen, B.M. et al. Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. Nat Struct Mol Biol 25, 225–232 (2018). https://doi.org/10.1038/s41594-018-0036-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41594-018-0036-6

This article is cited by

Search

Advanced search

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