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Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis

Nature Plantsvolume 5pages424435 (2019) | Download Citation

Abstract

Some overwintering plants acquire competence to flower, after experiencing prolonged cold in winter, through a process termed vernalization. In the crucifer plant Arabidopsis thaliana, prolonged cold induces chromatin-mediated silencing of the potent floral repressor FLOWERING LOCUS C (FLC) by Polycomb proteins. This vernalized state is epigenetically maintained or ‘memorized’ in warm rendering plants competent to flower in spring, but is reset in the next generation. Here, we show that in early embryogenesis, two homologous B3 domain transcription factors LEAFY COTYLEDON 2 (LEC2) and FUSCA3 (FUS3) compete against two repressive B3-containing epigenome readers and Polycomb partners known as VAL1 and VAL2 for the cis-regulatory cold memory element (CME) of FLC to disrupt Polycomb silencing. Consistently, crystal structures of B3–CME complexes show that B3FUS3, B3LEC2 and B3VAL1 employ a nearly identical binding interface for CME. We further found that LEC2 and FUS3 recruit the scaffold protein FRIGIDA in association with active chromatin modifiers to establish an active chromatin state at FLC, which results in resetting of the silenced FLC to active and erasing the epigenetic parental memory of winter cold in early embryos. Following embryo development, LEC2 and FUS3 are developmentally silenced throughout post-embryonic stages, enabling VALs to bind to the CME again at seedling stages at which plants experience winter cold. Our findings illustrate how overwintering crucifer annuals or biennials in temperate climates employ a subfamily of B3 domain proteins to switch on, off and on again the expression of a key flowering gene in the embryo-to-plant-to-embryo cycle, and thus to synchronize growth and development with seasonal temperature changes in their life cycles.

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Data availability

The data that support the findings of this study are available within the paper and its Supplementary Information or from the corresponding authors on request. The coordinates and structure factors of the B3–CME complexes have been deposited in the RCSB Protein Data Bank with the accession codes: B3LEC2–DNACME: 6J9C; B3FUS3–DNACME: 6J9B; and B3VAL1–DNACME: 6J9A.

Additional information

Journal peer review information Nature Plants thanks Richard Amasino and other anonymous reviewer(s) for their contribution to the peer review of this work.

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

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Acknowledgements

We are very grateful to R. M. Amasino for providing the FRI-Col and FRIflc seeds. We thank T. Chen and Z. Gao for anti-CLF antibody validation and the staff members at the beamline BL19U1 of the National Center for Protein Sciences Shanghai (NCPSS) at the Shanghai Synchrotron Radiation Facility (SSRF) for data collection, the staff members at the Core Facility for Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS, for the help of the Octet-based in vitro binding assay. This work was supported in part by the National Key Research and Development Program of China (2016YFA0503200 to J.D. and 2017YFA0503803 to Y.H.), the National Natural Science Foundation of China (31830049 to Y.H. and 31622032 to J.D.) and the Chinese Academy of Sciences (XDB27030202 to Y.H.).

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Author notes

    • Zeng Tao

    Present address: College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China

  1. These authors contributed equally: Zeng Tao, Hongmiao Hu, Xiao Luo.

Affiliations

  1. Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China

    • Zeng Tao
    • , Hongmiao Hu
    • , Xiao Luo
    • , Bei Jia
    • , Jiamu Du
    •  & Yuehui He
  2. University of Chinese Academy of Sciences, Beijing, China

    • Hongmiao Hu
  3. Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China

    • Yuehui He

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Contributions

Y.H. and J.D. designed and supervised the research. H.H. and B.J. performed the structure-related analyses and the in vitro protein–DNA binding assays. Z.T. and X.L. conducted the other experiments. All authors took part in data analysis. Y.H. and J.D. wrote the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Jiamu Du or Yuehui He.

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https://doi.org/10.1038/s41477-019-0402-3