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Arabidopsis REF6 is a histone H3 lysine 27 demethylase

Nature Genetics volume 43, pages 715–719 (2011)Cite this article

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Abstract

Polycomb group (PcG)-mediated histone H3 lysine 27 trimethylation (H3K27me3) has a key role in gene repression and developmental regulation1,2,3,4. There is evidence that H3K27me3 is actively removed in plants5,6,7,8, but it is not known how this occurs. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), also known as Jumonji domain–containing protein 12 (JMJ12), specifically demethylates H3K27me3 and H3K27me2, whereas its metazoan counterparts, the KDM4 proteins, are H3K9 and H3K36 demethylases9,10. Plants overexpressing REF6 resembled mutants defective in H3K27me3-mediated gene silencing. Genetic interaction tests indicated that REF6 acts downstream of H3K27me3 methyltransferases. Mutations in REF6 caused ectopic and increased H3K27me3 level and decreased mRNA expression of hundreds of genes involved in regulating developmental patterning and responses to various stimuli. Our work shows that plants and metazoans use conserved mechanisms to regulate H3K27me3 dynamics but use distinct subfamilies of enzymes.

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Figure 1: REF6 is an H3K27me3/2 demethylase.
Figure 2: REF6ox plants show similar phenotypes to H3K27me3 silencing–deficient mutants.
Figure 3: Genetic interaction between H3K27me3 methyltransferases and REF6.
Figure 4: REF6 mutation causes H3K27me3 hypermethylation of several hundred endogenous genes.
Figure 5

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Gene Expression Omnibus

References

  1. Zhang, X. et al. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5, e129 (2007).

    Article  Google Scholar 

  2. Hennig, L. & Derkacheva, M. Diversity of Polycomb group complexes in plants: same rules, different players? Trends Genet. 25, 414–423 (2009).

    Article  CAS  Google Scholar 

  3. Pien, S. & Grossniklaus, U. Polycomb group and trithorax group proteins in Arabidopsis. Biochim. Biophys. Acta 1769, 375–382 (2007).

    Article  CAS  Google Scholar 

  4. Sawarkar, R. & Paro, R. Interpretation of developmental signaling at chromatin: the Polycomb perspective. Dev. Cell 19, 651–661 (2010).

    Article  CAS  Google Scholar 

  5. Schatlowski, N., Creasey, K., Goodrich, J. & Schubert, D. Keeping plants in shape: polycomb-group genes and histone methylation. Semin. Cell Dev. Biol. 19, 547–553 (2008).

    Article  CAS  Google Scholar 

  6. Finnegan, E.J. & Dennis, E.S. Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells. Curr. Biol. 17, 1978–1983 (2007).

    Article  CAS  Google Scholar 

  7. Kwon, C.S., Lee, D., Choi, G. & Chung, W.I. Histone occupancy-dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis. Plant J. 60, 112–121 (2009).

    Article  CAS  Google Scholar 

  8. Charron, J.B., He, H., Elling, A.A. & Deng, X.W. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21, 3732–3748 (2009).

    Article  CAS  Google Scholar 

  9. Lu, F. et al. Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J. Integr. Plant Biol. 50, 886–896 (2008).

    Article  CAS  Google Scholar 

  10. Agger, K., Christensen, J., Cloos, P.A. & Helin, K. The emerging functions of histone demethylases. Curr. Opin. Genet. Dev. 18, 159–168 (2008).

    Article  CAS  Google Scholar 

  11. Liu, C., Lu, F., Cui, X. & Cao, X. Histone methylation in higher plants. Annu. Rev. Plant Biol. 61, 395–420 (2010).

    Article  CAS  Google Scholar 

  12. Inagaki, S. et al. Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO J. 29, 3496–3506 (2010).

    Article  CAS  Google Scholar 

  13. Saze, H., Shiraishi, A., Miura, A. & Kakutani, T. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 319, 462–465 (2008).

    Article  CAS  Google Scholar 

  14. Lu, F., Cui, X., Zhang, S., Liu, C. & Cao, X. JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res. 20, 387–390 (2010).

    Article  Google Scholar 

  15. Searle, I.R., Pontes, O., Melnyk, C.W., Smith, L.M. & Baulcombe, D.C. JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev. 24, 986–991 (2010).

    Article  CAS  Google Scholar 

  16. Noh, B. et al. Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell 16, 2601–2613 (2004).

    Article  CAS  Google Scholar 

  17. Ko, J.H. et al. Growth habit determination by the balance of histone methylation activities in Arabidopsis. EMBO J. 29, 3208–3215 (2010).

    Article  CAS  Google Scholar 

  18. Lan, F., Nottke, A.C. & Shi, Y. Mechanisms involved in the regulation of histone lysine demethylases. Curr. Opin. Cell Biol. 20, 316–325 (2008).

    Article  CAS  Google Scholar 

  19. Zhang, X. et al. The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat. Struct. Mol. Biol. 14, 869–871 (2007).

    Article  CAS  Google Scholar 

  20. Turck, F. et al. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet. 3, e86 (2007).

    Article  Google Scholar 

  21. Larsson, A.S., Landberg, K. & Meeks-Wagner, D.R. The TERMINAL FLOWER2 (TFL2) gene controls the reproductive transition and meristem identity in Arabidopsis thaliana. Genetics 149, 597–605 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Gaudin, V. et al. Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 128, 4847–4858 (2001).

    CAS  PubMed  Google Scholar 

  23. Chanvivattana, Y. et al. Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 131, 5263–5276 (2004).

    Article  CAS  Google Scholar 

  24. Shen, W.-H. & Xu, L. Chromatin Remodeling in Stem Cell Maintenance in Arabidopsis thaliana. Mol. Plant 2, 600–609 (2009).

    Article  CAS  Google Scholar 

  25. Chen, D., Molitor, A., Liu, C. & Shen, W.H. The Arabidopsis PRC1-like ring-finger proteins are necessary for repression of embryonic traits during vegetative growth. Cell Res. 20, 1332–1344 (2010).

    Article  CAS  Google Scholar 

  26. Jiang, D., Wang, Y. & He, Y. Repression of FLOWERING LOCUS C and FLOWERING LOCUS T by the Arabidopsis Polycomb repressive complex 2 components. PLoS ONE 3, e3404 (2008).

    Article  Google Scholar 

  27. Goodrich, J. et al. A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 386, 44–51 (1997).

    Article  CAS  Google Scholar 

  28. Schubert, D. et al. Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27. EMBO J. 25, 4638–4649 (2006).

    Article  CAS  Google Scholar 

  29. Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).

    Article  CAS  Google Scholar 

  30. Nemhauser, J.L., Mockler, T.C. & Chory, J. Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol. 2, E258 (2004).

    Article  Google Scholar 

  31. Yu, X., Li, L., Guo, M., Chory, J. & Yin, Y. Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proc. Natl. Acad. Sci. USA 105, 7618–7623 (2008).

    Article  CAS  Google Scholar 

  32. Johnson, L. et al. Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res. 32, 6511–6518 (2004).

    Article  CAS  Google Scholar 

  33. Deng, X. et al. Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing. Proc. Natl. Acad. Sci. USA 107, 19114–19119 (2010).

    Article  CAS  Google Scholar 

  34. Doyle, M.R. & Amasino, R.M. A single amino acid change in the enhancer of zeste ortholog CURLY LEAF results in vernalization-independent, rapid flowering in Arabidopsis. Plant Physiol. 151, 1688–1697 (2009).

    Article  CAS  Google Scholar 

  35. Wang, D., Tyson, M.D., Jackson, S.S. & Yadegari, R. Partially redundant functions of two SET-domain polycomb-group proteins in controlling initiation of seed development in Arabidopsis. Proc. Natl. Acad. Sci. USA 103, 13244–13249 (2006).

    Article  CAS  Google Scholar 

  36. Earley, K.W. et al. Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 45, 616–629 (2006).

    Article  CAS  Google Scholar 

  37. English, J.J., Davenport, G.F., Elmayan, T., Vaucheret, H. & Baulcombe, D.C. Requirement of sense transcription for homology-dependent virus resistance and trans-inactivation. Plant J. 12, 597–603 (1997).

    CAS  Google Scholar 

  38. Zhang, Y. et al. SDIR1 is a RING finger E3 ligase that positively regulates stress-responsive abscisic acid signaling in Arabidopsis. Plant Cell 19, 1912–1929 (2007).

    Article  CAS  Google Scholar 

  39. Clough, S.J. & Bent, A.F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).

    Article  CAS  Google Scholar 

  40. Kotake, T., Takada, S., Nakahigashi, K., Ohto, M. & Goto, K. Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. Plant Cell Physiol. 44, 555–564 (2003).

    Article  CAS  Google Scholar 

  41. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

    Article  Google Scholar 

  42. Nicol, J.W., Helt, G.A., Blanchard, S.G. Jr., Raja, A. & Loraine, A.E. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730–2731 (2009).

    Article  CAS  Google Scholar 

  43. Zang, C. et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952–1958 (2009).

    Article  CAS  Google Scholar 

  44. Xu, H., Wei, C.L., Lin, F. & Sung, W.K. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 24, 2344–2349 (2008).

    Article  CAS  Google Scholar 

  45. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank our colleagues for comments and advice. We thank L. Gu for technical help in handling genomic datasets, Q. Zhu for technical help, the Arabidopsis Biological Resource Center for T-DNA insertion lines and I. Hanson for editing. This work was supported by the National Basic Research Program of China (grants 2009CB941500 and 2011CB915400 to X. Cao), and by the National Natural Science Foundation of China (grants 30930048 and 30921061 to X. Cao and 30971619 to X. Cui).

Author information

Author notes

  1. Falong Lu and Xia Cui: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Falong Lu, Xia Cui, Shuaibin Zhang & Xiaofeng Cao

  2. Graduate School of the Chinese Academy of Sciences, Beijing, China

    Falong Lu & Shuaibin Zhang

  3. Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,

    Thomas Jenuwein

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Contributions

F.L., X. Cui and X. Cao conceived and designed the study. F.L., X. Cui and S.Z. performed the experiments. T.J. contributed essential reagents and edited the manuscript. F.L., X. Cui and X. Cao analyzed data and wrote the paper.

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Correspondence to Xiaofeng Cao.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11 (PDF 2221 kb)

Supplementary Table 1

The list of genes marked by H3K27me3 in Col. (XLS 3189 kb)

Supplementary Table 2

Chromosomal regions in which H3K27me3 changed more than 3-fold in ref6-3. (XLS 425 kb)

Supplementary Table 3

Plain text format of enriched Gene Ontology (GO) terms. (XLS 112 kb)

Supplementary Table 4

List of genes for which transcription levels changed more than 20.6-fold with a q-value < 0.05 in ref6-3. (XLS 71 kb)

Supplementary Table 5

Sequences of primers used in this study. (XLS 50 kb)

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Lu, F., Cui, X., Zhang, S. et al. Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nat Genet 43, 715–719 (2011). https://doi.org/10.1038/ng.854

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