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Vernalization requires epigenetic silencing of FLC by histone methylation

Abstract

To ensure flowering in favourable conditions, many plants flower only after an extended period of cold, namely winter. In Arabidopsis, the acceleration of flowering by prolonged cold, a process called vernalization, involves downregulation of the protein FLC, which would otherwise prevent flowering1,2. This lowered FLC expression is maintained through subsequent development by the activity of VERNALIZATION (VRN) genes3,4. VRN1 encodes a DNA-binding protein4 whereas VRN2 encodes a homologue of one of the Polycomb group proteins, which maintain the silencing of genes during animal development3. Here we show that vernalization causes changes in histone methylation in discrete domains within the FLC locus, increasing dimethylation of lysines 9 and 27 on histone H3. Such modifications identify silenced chromatin states in Drosophila and human cells5,6,7. Dimethylation of H3 K27 was lost only in vrn2 mutants, but dimethylation of H3 K9 was absent from both vrn1 and vrn2, consistent with VRN1 functioning downstream of VRN2. The epigenetic memory of winter is thus mediated by a ‘histone code’ that specifies a silent chromatin state conserved between animals and plants.

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Figure 1: Histone modifications at FLC associated with vernalization.
Figure 2: Vernalization-induced changes in expression of an FLCGUS translational fusion.
Figure 3: The histone modifications associated with vernalization are dependent on the VRN genes.

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Acknowledgements

The authors thank J. Goodrich for excellent comments on the manuscript and J. Finnegan and R. Amasino for allowing us to cite their work as personal communications. This work was supported by a Core Strategic Grant to the John Innes Centre from the Biotechnology and Biological Sciences Research Council and a European Union Framework V grant to C.D.

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Correspondence to Caroline Dean.

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The authors declare that they have no competing financial interests.

Supplementary information

41586_2004_BFnature02269_MOESM1_ESM.jpg

Supplementary Figure 1: H3 dimethyl K4 and H3 dimethyl K9 histone modifications at FLC are associated with vernalization and are dependent on the VRN genes. (JPG 118 kb)

41586_2004_BFnature02269_MOESM2_ESM.jpg

Supplementary Figure 2: The H3 dimethyl K27 histone modification at FLC is associated with vernalization and is dependent on VRN2, but not VRN1. (JPG 114 kb)

Supplementary Figure 3: Primers used for ChIP analysis. (JPG 63 kb)

41586_2004_BFnature02269_MOESM4_ESM.jpg

Supplementary Figure 4: PCR analysis to show the amplification efficiency of all primer pairs used in the chromatin immunoprecipitation analysis. (JPG 79 kb)

Supplementary Figure Legends (DOC 20 kb)

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Bastow, R., Mylne, J., Lister, C. et al. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427, 164–167 (2004). https://doi.org/10.1038/nature02269

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