Arabidopsis REF6 is a histone H3 lysine 27 demethylase

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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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).

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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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The authors declare no competing financial interests.

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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