Letter | Published:

Embryonic epigenetic reprogramming by a pioneer transcription factor in plants

Nature volume 551, pages 124128 (02 November 2017) | Download Citation


Epigenetic modifications, including chromatin modifications and DNA methylation, have a central role in the regulation of gene expression in plants and animals. The transmission of epigenetic marks is crucial for certain genes to retain cell lineage-specific expression patterns and maintain cell fate1,2. However, the marks that have accumulated at regulatory loci during growth and development or in response to environmental stimuli need to be deleted in gametes or embryos, particularly in organisms such as plants that do not set aside a germ line, to ensure the proper development of offspring1,2. In Arabidopsis thaliana, prolonged exposure to cold temperatures (winter cold), in a process known as vernalization, triggers the mitotically stable epigenetic silencing of the potent floral repressor FLOWERING LOCUS C (FLC), and renders plants competent to flower in the spring; however, this silencing is reset during each generation3,4,5. Here we show that the seed-specific transcription factor LEAFY COTYLEDON1 (LEC1) promotes the initial establishment of an active chromatin state at FLC and activates its expression de novo in the pro-embryo, thus reversing the silenced state inherited from gametes. This active chromatin state is passed on from the pro-embryo to post-embryonic life, and leads to transmission of the embryonic memory of FLC activation to post-embryonic stages. Our findings reveal a mechanism for the reprogramming of embryonic chromatin states in plants, and provide insights into the epigenetic memory of embryonic active gene expression in post-embryonic phases, through which an embryonic factor acts to ‘control’ post-embryonic development processes that are distinct from embryogenesis in plants.

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We thank R. M. Amasino for providing the FLC::GUS plasmid and the seeds of FRI-Col, FRI flc-3 and FRI flc-2, I. E. Somssich for the pJawohl8-RNAi plasmid, and W. Yuan for technical assistance. This work was supported in part by the National Key Research and Development Program of China (2017YFA0503803), the Chinese Academy of Sciences (XDPB0404) and the Temasek Life Sciences Laboratory (Singapore).

Author information

Author notes

    • Xiaofeng Gu
    •  & Yizhong Wang

    Present addresses: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (X.G.); School of Life Sciences, Huazhong Normal University, 152 Luoyu Road, Wuhan, China (Y.W.).


  1. Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China

    • Zeng Tao
    • , Yizhong Wang
    •  & Yuehui He
  2. Department of Biological Sciences & Temasek Life Sciences Laboratory, National University of Singapore 117604, Singapore

    • Zeng Tao
    • , Lisha Shen
    • , Xiaofeng Gu
    • , Hao Yu
    •  & Yuehui He


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Y.H. conceived the project; Z.T. performed most of the experiments; L.S. performed and, together with H.Y., analysed the in situ experiments; X.G. and Y.W. participated in the ChIP experiments with anti-Flag and anti-H3K27me3; Z.T. conducted all statistical analyses; Z.T. and Y.H. analysed most of the data; Y.H., Z.T. and H.Y. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Yuehui He.

Reviewer Information Nature thanks R. Amasino and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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    Supplementary Figure

    This file contains the uncropped gels and blots for Extended Data Figs. 1b, 2d, and 8c, and the uncropped western blots for Extended Data Figs. 6a, 6c and 7d.

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