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Dynamic and spatial restriction of Polycomb activity by plant histone demethylases

Nature Plants volume 4, pages 681–689 (2018)Cite this article

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Abstract

Targeted changes in chromatin state at thousands of genes are central to eukaryotic development. RELATIVE OF EARLY FLOWERING 6 (REF6) is a Jumonji-type histone demethylase that counteracts Polycomb repressive complex 2 (PRC2)-mediated gene silencing in plants and was reported to select its binding sites in a direct, sequence-specific manner1,2,3. Here we show that REF6 and its two close paralogues determine spatial ‘boundaries’ of the repressive histone H3K27me3 mark in the genome and control the tissue-specific release from PRC2-mediated gene repression. Targeted mutagenesis revealed that these histone demethylases display pleiotropic, redundant functions in plant development, several of which depend on trans factor-mediated recruitment. Thus, Jumonji-type histone demethylases restrict repressive chromatin domains and contribute to tissue-specific gene activation via complementary targeting mechanisms.

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Fig. 1: Arabidopsis JMJ13 is a histone H3 lysine 27 demethylase and ELF6, REF6 and JMJ13 are essential developmental regulators in Arabidopsis.
Fig. 2: ELF6, REF6 and JMJ13 regulate Arabidopsis development via reduction of H3K27me3 level.
Fig. 3: Tissue-specific gene regulation by REF6.
Fig. 4: Mechanisms of REF6 target site recruitment.

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Acknowledgements

We thank X. Cao from Chinese Academy of Sciences, Beijing, China for kindly providing us with the ref6-1, ref6-3 and clf-28 mutants. We thank T. Ito from Temasek Life Sciences Laboratory (TLL), National University of Singapore for sending seeds of the jmj30-2 jmj32-1 double mutant. pREF6-REF6-GFP ref6-1 and pREF6-REF6∆ZnF-GFP ref6-1 are gifts from Y. Cui from Agriculture and Agri-Food Canada, London Research and Development Centre. The authors acknowledge the North German Supercomputing Alliance (HLRN) for providing HPC resources that contribute to the research results reported in this study. K.K. wishes to thank the Alexander von Humboldt foundation and the Federal Ministry of Education and Research for funding.

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Author notes

  1. Julia Engelhorn

    Present address: School of Life Sciences, University of Warwick, Coventry, UK

  2. These authors contributed equally: Wenhao Yan, Dijun Chen.

Authors and Affiliations

  1. Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany

    Wenhao Yan, Dijun Chen, Cezary Smaczniak & Kerstin Kaufmann

  2. LPCV, CNRS, CEA, INRA, Université Grenoble Alpes, Grenoble, France

    Julia Engelhorn & Cristel C. Carles

  3. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

    Haiyang Liu, Wenjing Yang & Dao-Xiu Zhou

  4. Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany

    Alexander Graf

  5. Institute Plant Science Paris-Saclay (IPS2), CNRS, INRA, Université Paris-sud 11, Université Paris-Saclay, Orsay, France

    Dao-Xiu Zhou

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Contributions

W.Y. conducted all the genetic studies, performed most of the experiments and interpreted the data. D.C. performed all bioinformatic analyses, interpreted the data and prepared the figures. C.S. analysed the protein complex isolation data. Mass spectrometry was performed by A.G. The enzyme activity assay was conducted by H.L., W.Yang; and D.-X.Z., K.K. and W.Y. conceived and initiated the project. K.K. wrote the manuscript with input from W.Y., D.C., J.E. and C.C.C.

Corresponding authors

Correspondence to Wenhao Yan or Kerstin Kaufmann.

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Supplementary information

Supplementary Information

Supplementary Text and Supplementary Figures 1–25.

Reporting Summary

Supplementary Data Set 1

Analysis of H3K27me3 ChIP-seq data in wild-type and elf6-3 ref6C jmj13G triple mutant.

Supplementary Data Set 2

Analysis of RNA-seq data in wild-type, ref6 single, elf6-3 ref6C double and elf6-3 ref6C jmj13G triple mutants.

Supplementary Data Set 3

Analysis of REF6 ChIP-seq data generated with or without DSG fixation.

Supplementary Data Set 4

GO analysis of tissue-specific REF6 targets.

Supplementary Data Set 5

Primers used in this study.

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Yan, W., Chen, D., Smaczniak, C. et al. Dynamic and spatial restriction of Polycomb activity by plant histone demethylases. Nature Plants 4, 681–689 (2018). https://doi.org/10.1038/s41477-018-0219-5

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